From 1b694069329b8703bac201b2dedef2cdb7b64f0e Mon Sep 17 00:00:00 2001
From: Daniel Himmelstein <daniel.himmelstein@gmail.com>
Date: Fri, 1 May 2020 12:46:56 -0400
Subject: [PATCH 01/50] USAGE: howto set citation style using pandoc defaults

merges https://github.com/manubot/rootstock/pull/338
closes https://github.com/manubot/rootstock/issues/334
---
 USAGE.md | 18 +++++++++++++++---
 1 file changed, 15 insertions(+), 3 deletions(-)

diff --git a/USAGE.md b/USAGE.md
index 4cf69ec..58f54d1 100644
--- a/USAGE.md
+++ b/USAGE.md
@@ -272,9 +272,21 @@ Modifying the manuscript formatting requires modifying the CSS in the file [`bui
 Common formatting changes, such as [font size](https://github.com/manubot/rootstock/issues/239) and [double spacing](https://github.com/manubot/rootstock/issues/244), can be found by searching the [Rootstock issues](https://github.com/manubot/rootstock/issues).
 Open a [new issue](https://github.com/manubot/rootstock/issues/new) if you have a new formatting question.
 
-Changing the citation style or which interactive HTML plugins are loaded requires editing the build script [`build/build.sh`](build/build.sh).
-The citation style is determined by the Citation Style Language file specified by `CSL_PATH`.
-It can be changed to use other existing styles as [described here](https://github.com/manubot/rootstock/issues/242#issuecomment-507688339).
+Changing the citation style or which interactive HTML plugins are loaded requires editing the options specified by Pandoc defaults files in [`build/pandoc-defaults`](build/pandoc-defaults).
+The citation style is determined by the Citation Style Language file specified in [`common.yaml`](build/pandoc-defaults/common.yaml):
+
+```yaml
+metadata:
+  csl: build/assets/style.csl
+```
+
+The value for `metadata.csl` can be a URL, allowing access to thousands of existing styles hosted by [Zotero](https://www.zotero.org/styles) or the [CSL GitHub](https://github.com/citation-style-language/styles).
+For example, the following options replace the Manubot citation style with the _PeerJ_ style:
+
+```yaml
+metadata:
+  csl: https://github.com/citation-style-language/styles/raw/906cd6d43d0c136190ecfbb12f6af0ca794e3c5b/peerj.csl
+```
 
 ## Spellchecking
 

From 92f0285a37636017e0a3e231bb64e414b8a0cfb5 Mon Sep 17 00:00:00 2001
From: Anthony Gitter <agitter@users.noreply.github.com>
Date: Tue, 5 May 2020 11:21:58 -0500
Subject: [PATCH 02/50] Fix spellcheck bug and track unique spelling errors

merges https://github.com/manubot/rootstock/pull/337
refs https://github.com/manubot/rootstock/issues/336

* Track unique spelling errors
Fixes a bug in how unique words were calculated.
Also stores the list of unique misspelled words in addition
to the locations of the misspelled words.

* Create separate spellcheck install script
* Add spellcheck to GitHub Actions workflow
* Search for expanded punctuation in misspelled words
---
 .appveyor.yml                  |  9 ++++++---
 .github/workflows/manubot.yaml |  7 +++++++
 .gitignore                     |  3 +++
 USAGE.md                       |  2 +-
 build/build.sh                 | 20 ++++++++++++++++++--
 ci/install-spellcheck.sh       | 12 ++++++++++++
 ci/install.sh                  |  7 +++----
 7 files changed, 50 insertions(+), 10 deletions(-)
 create mode 100755 ci/install-spellcheck.sh

diff --git a/.appveyor.yml b/.appveyor.yml
index bade8d0..d57e0cb 100644
--- a/.appveyor.yml
+++ b/.appveyor.yml
@@ -44,8 +44,11 @@ test_script:
   - |
       if [ "${SPELLCHECK:-}" = "true" ]; then
         SPELLING_ERRORS_FILENAME=spelling-errors-$APPVEYOR_BUILD_VERSION-${TRIGGERING_COMMIT:0:7}.txt
-        cp output/spelling-errors.txt $SPELLING_ERRORS_FILENAME;
+        cp output/spelling-errors.txt $SPELLING_ERRORS_FILENAME
         appveyor PushArtifact $SPELLING_ERRORS_FILENAME
+        SPELLING_ERROR_LOCATIONS_FILENAME=spelling-error-locations-$APPVEYOR_BUILD_VERSION-${TRIGGERING_COMMIT:0:7}.txt
+        cp output/spelling-error-locations.txt $SPELLING_ERROR_LOCATIONS_FILENAME
+        appveyor PushArtifact $SPELLING_ERROR_LOCATIONS_FILENAME
       fi
 
 build: off
@@ -59,8 +62,8 @@ on_success:
   - appveyor AddMessage "$JOB_MESSAGE is now complete."
   - |
       if [ "${SPELLCHECK:-}" = "true" ]; then
-        SPELLING_ERROR_COUNT=($(wc -l $SPELLING_ERRORS_FILENAME))
-        appveyor AddMessage " <details><summary>Found $SPELLING_ERROR_COUNT potential spelling error(s). Preview:</summary>$(cat $SPELLING_ERRORS_FILENAME)"
+        SPELLING_ERROR_COUNT=($(wc -l $SPELLING_ERROR_LOCATIONS_FILENAME))
+        appveyor AddMessage " <details><summary>Found $SPELLING_ERROR_COUNT potential spelling error(s). Preview:</summary>$(head -n 100 $SPELLING_ERROR_LOCATIONS_FILENAME)"
         appveyor AddMessage "... </details>"
       fi
 
diff --git a/.github/workflows/manubot.yaml b/.github/workflows/manubot.yaml
index 84c618d..42509c5 100644
--- a/.github/workflows/manubot.yaml
+++ b/.github/workflows/manubot.yaml
@@ -12,6 +12,7 @@ jobs:
     runs-on: ubuntu-latest
     env:
       GITHUB_PULL_REQUEST_SHA: ${{ github.event.pull_request.head.sha }}
+      SPELLCHECK: true
     steps:
       - name: Set Environment Variables
         run: |
@@ -38,6 +39,12 @@ jobs:
           environment-file: build/environment.yml
           auto-activate-base: false
           miniconda-version: 'latest'
+      - name: Install Spellcheck
+        shell: bash --login {0}
+        run: |
+          if [ "${SPELLCHECK:-}" = "true" ]; then
+            bash ci/install-spellcheck.sh
+          fi
       - name: Build Manuscript
         shell: bash --login {0}
         run: bash build/build.sh
diff --git a/.gitignore b/.gitignore
index ac39263..e57fe35 100644
--- a/.gitignore
+++ b/.gitignore
@@ -11,6 +11,9 @@ webpage/v
 # Manubot cache directory
 ci/cache
 
+# Pandoc filters downloaded during continuous integration setup
+build/assets/spellcheck.lua
+
 # Python
 __pycache__/
 *.pyc
diff --git a/USAGE.md b/USAGE.md
index 58f54d1..efec927 100644
--- a/USAGE.md
+++ b/USAGE.md
@@ -293,7 +293,7 @@ metadata:
 When the `SPELLCHECK` environment variable is `true`, the pandoc [spellcheck filter](https://github.com/pandoc/lua-filters/tree/master/spellcheck) is run.
 Potential spelling errors will be printed in the continuous integration log along with the files and line numbers in which they appeared.
 Words in `build/assets/custom-dictionary.txt` are ignored during spellchecking.
-Spellchecking is currently only supported for English language manuscripts and with Travis CI and AppVeyor continuous integration services.
+Spellchecking is currently only supported for English language manuscripts.
 
 ## Manubot feedback
 
diff --git a/build/build.sh b/build/build.sh
index 8cde86b..3c35bf4 100755
--- a/build/build.sh
+++ b/build/build.sh
@@ -85,12 +85,28 @@ fi
 # Spellcheck
 if [ "${SPELLCHECK:-}" = "true" ]; then
   export ASPELL_CONF="add-extra-dicts $(pwd)/build/assets/custom-dictionary.txt; ignore-case true"
+
+  # Identify and store spelling errors
+  pandoc --lua-filter build/assets/spellcheck.lua output/manuscript.md | sort -fu > output/spelling-errors.txt
+  echo >&2 "Potential spelling errors:"
+  cat output/spelling-errors.txt
+
+  # Add additional forms of punctuation that Pandoc converts so that the
+  # locations can be detected
+  # Create a new expanded spelling errors file so that the saved artifact
+  # contains only the original misspelled words
+  cp output/spelling-errors.txt output/expanded-spelling-errors.txt
+  grep "’" output/spelling-errors.txt | sed "s/’/'/g" >> output/expanded-spelling-errors.txt || true
+
+  # Find locations of spelling errors
   # Use "|| true" after grep because otherwise this step of the pipeline will
   # return exit code 1 if any of the markdown files do not contain a
   # misspelled word
-  pandoc --lua-filter spellcheck.lua output/manuscript.md | uniq | while read word; do grep -ion "\<$word\>" content/*.md; done | sort -h -t ":" -k 1b,1 -k2,2 > output/spelling-errors.txt || true
+  cat output/expanded-spelling-errors.txt | while read word; do grep -ion "\<$word\>" content/*.md; done | sort -h -t ":" -k 1b,1 -k2,2 > output/spelling-error-locations.txt || true
   echo >&2 "Filenames and line numbers with potential spelling errors:"
-  cat output/spelling-errors.txt
+  cat output/spelling-error-locations.txt
+
+  rm output/expanded-spelling-errors.txt
 fi
 
 echo >&2 "Build complete"
diff --git a/ci/install-spellcheck.sh b/ci/install-spellcheck.sh
new file mode 100755
index 0000000..6d5ac88
--- /dev/null
+++ b/ci/install-spellcheck.sh
@@ -0,0 +1,12 @@
+#!/usr/bin/env bash
+
+## install-spellcheck.sh: run during a CI build to install Pandoc spellcheck dependencies.
+
+# Set options for extra caution & debugging
+set -o errexit \
+    -o pipefail
+
+sudo apt-get update -y
+sudo apt-get install -y aspell aspell-en
+wget https://raw.githubusercontent.com/pandoc/lua-filters/13c3fa7e97206413609a48a82575cb43137e037f/spellcheck/spellcheck.lua
+mv spellcheck.lua build/assets/spellcheck.lua
diff --git a/ci/install.sh b/ci/install.sh
index 7d61b21..61928d7 100755
--- a/ci/install.sh
+++ b/ci/install.sh
@@ -1,6 +1,7 @@
 #!/usr/bin/env bash
 
-## install.sh: run during a Travis CI or AppVeyor build to install the conda environment.
+## install.sh: run during a Travis CI or AppVeyor build to install the conda environment
+## and the optional Pandoc spellcheck dependencies.
 
 # Set options for extra caution & debugging
 set -o errexit \
@@ -20,7 +21,5 @@ conda activate manubot
 
 # Install Spellcheck filter for Pandoc
 if [ "${SPELLCHECK:-}" = "true" ]; then
-  sudo apt-get update -y
-  sudo apt-get install -y aspell aspell-en
-  wget https://raw.githubusercontent.com/pandoc/lua-filters/1c553017ecc58914c22bf2372902dca4a456929b/spellcheck/spellcheck.lua
+  bash ci/install-spellcheck.sh
 fi

From 8b9b5ced2c7c963bf3ea5afb8f31f9a4a54ab697 Mon Sep 17 00:00:00 2001
From: Daniel Himmelstein <daniel.himmelstein@gmail.com>
Date: Thu, 7 May 2020 10:59:18 -0400
Subject: [PATCH 03/50]  move build/pandoc-defaults to build/pandoc/defaults
 (#340)

merges https://github.com/manubot/rootstock/pull/340

* Move build/pandoc-defaults to build/pandoc/defaults
Improves compatibility with Pandoc's directory naming
expectations in case when setting --data-dir=build/assets
in the future. Allows for other subdirectories like build/pandoc/filters

* set pandoc --data-dir

* update spellcheck filter to use build/pandoc/filters
---
 .gitignore                                    |  2 +-
 USAGE.md                                      |  4 +--
 build/README.md                               |  2 +-
 build/build.sh                                | 27 ++++++++++++-------
 .../defaults}/common.yaml                     |  0
 .../defaults}/docx.yaml                       |  0
 .../defaults}/html.yaml                       |  0
 .../defaults}/pdf-weasyprint.yaml             |  0
 ci/install-spellcheck.sh                      |  8 +++---
 9 files changed, 25 insertions(+), 18 deletions(-)
 rename build/{pandoc-defaults => pandoc/defaults}/common.yaml (100%)
 rename build/{pandoc-defaults => pandoc/defaults}/docx.yaml (100%)
 rename build/{pandoc-defaults => pandoc/defaults}/html.yaml (100%)
 rename build/{pandoc-defaults => pandoc/defaults}/pdf-weasyprint.yaml (100%)

diff --git a/.gitignore b/.gitignore
index e57fe35..e48c49e 100644
--- a/.gitignore
+++ b/.gitignore
@@ -12,7 +12,7 @@ webpage/v
 ci/cache
 
 # Pandoc filters downloaded during continuous integration setup
-build/assets/spellcheck.lua
+build/pandoc/filters/spellcheck.lua
 
 # Python
 __pycache__/
diff --git a/USAGE.md b/USAGE.md
index efec927..95f1b35 100644
--- a/USAGE.md
+++ b/USAGE.md
@@ -272,8 +272,8 @@ Modifying the manuscript formatting requires modifying the CSS in the file [`bui
 Common formatting changes, such as [font size](https://github.com/manubot/rootstock/issues/239) and [double spacing](https://github.com/manubot/rootstock/issues/244), can be found by searching the [Rootstock issues](https://github.com/manubot/rootstock/issues).
 Open a [new issue](https://github.com/manubot/rootstock/issues/new) if you have a new formatting question.
 
-Changing the citation style or which interactive HTML plugins are loaded requires editing the options specified by Pandoc defaults files in [`build/pandoc-defaults`](build/pandoc-defaults).
-The citation style is determined by the Citation Style Language file specified in [`common.yaml`](build/pandoc-defaults/common.yaml):
+Changing the citation style or which interactive HTML plugins are loaded requires editing the options specified by Pandoc defaults files in [`build/pandoc/defaults`](build/pandoc/defaults).
+The citation style is determined by the Citation Style Language file specified in [`common.yaml`](build/pandoc/defaults/common.yaml):
 
 ```yaml
 metadata:
diff --git a/build/README.md b/build/README.md
index 9516922..27bf76d 100644
--- a/build/README.md
+++ b/build/README.md
@@ -12,7 +12,7 @@ To export DOCX for all CI builds, set an environment variable (see docs for [Git
 Currently, equation numbers via `pandoc-eqnos` are not supported for DOCX output.
 
 Format conversion is done using [Pandoc](https://pandoc.org/MANUAL.html).
-`build.sh` calls `pandoc` commands using the options specified in [`pandoc-defaults`](pandoc-defaults).
+`build.sh` calls `pandoc` commands using the options specified in [`pandoc/defaults`](pandoc/defaults).
 Each file specifies a set of pandoc `--defaults` options for a given format.
 To change the options, either edit the YAML files directly or add additional `--defaults` files.
 
diff --git a/build/build.sh b/build/build.sh
index 3c35bf4..c3028c0 100755
--- a/build/build.sh
+++ b/build/build.sh
@@ -21,8 +21,8 @@ manubot process \
   --log-level=INFO
 
 # Pandoc's configuration is specified via files of option defaults
-# located in the PANDOC_DEFAULTS_DIR directory.
-PANDOC_DEFAULTS_DIR="${PANDOC_DEFAULTS_DIR:-build/pandoc-defaults}"
+# located in the $PANDOC_DATA_DIR/defaults directory.
+PANDOC_DATA_DIR="${PANDOC_DATA_DIR:-build/pandoc}"
 
 # Make output directory
 mkdir -p output
@@ -31,8 +31,9 @@ mkdir -p output
 # https://pandoc.org/MANUAL.html
 echo >&2 "Exporting HTML manuscript"
 pandoc --verbose \
-  --defaults="$PANDOC_DEFAULTS_DIR/common.yaml" \
-  --defaults="$PANDOC_DEFAULTS_DIR/html.yaml"
+  --data-dir="$PANDOC_DATA_DIR" \
+  --defaults=common.yaml \
+  --defaults=html.yaml
 
 # Return null if docker command is missing, otherwise return path to docker
 DOCKER_EXISTS="$(command -v docker || true)"
@@ -44,9 +45,10 @@ if [ "${BUILD_PDF:-}" != "false" ] && [ -z "$DOCKER_EXISTS" ]; then
   if [ -L images ]; then rm images; fi  # if images is a symlink, remove it
   ln -s content/images
   pandoc \
-    --defaults="$PANDOC_DEFAULTS_DIR/common.yaml" \
-    --defaults="$PANDOC_DEFAULTS_DIR/html.yaml" \
-    --defaults="$PANDOC_DEFAULTS_DIR/pdf-weasyprint.yaml"
+    --data-dir="$PANDOC_DATA_DIR" \
+    --defaults=common.yaml \
+    --defaults=html.yaml \
+    --defaults=pdf-weasyprint.yaml
   rm images
 fi
 
@@ -78,8 +80,9 @@ fi
 if [ "${BUILD_DOCX:-}" = "true" ]; then
   echo >&2 "Exporting Word Docx manuscript"
   pandoc --verbose \
-    --defaults="$PANDOC_DEFAULTS_DIR/common.yaml" \
-    --defaults="$PANDOC_DEFAULTS_DIR/docx.yaml"
+    --data-dir="$PANDOC_DATA_DIR" \
+    --defaults=common.yaml \
+    --defaults=docx.yaml
 fi
 
 # Spellcheck
@@ -87,7 +90,11 @@ if [ "${SPELLCHECK:-}" = "true" ]; then
   export ASPELL_CONF="add-extra-dicts $(pwd)/build/assets/custom-dictionary.txt; ignore-case true"
 
   # Identify and store spelling errors
-  pandoc --lua-filter build/assets/spellcheck.lua output/manuscript.md | sort -fu > output/spelling-errors.txt
+  pandoc \
+    --data-dir="$PANDOC_DATA_DIR" \
+    --lua-filter spellcheck.lua \
+    output/manuscript.md \
+    | sort -fu > output/spelling-errors.txt
   echo >&2 "Potential spelling errors:"
   cat output/spelling-errors.txt
 
diff --git a/build/pandoc-defaults/common.yaml b/build/pandoc/defaults/common.yaml
similarity index 100%
rename from build/pandoc-defaults/common.yaml
rename to build/pandoc/defaults/common.yaml
diff --git a/build/pandoc-defaults/docx.yaml b/build/pandoc/defaults/docx.yaml
similarity index 100%
rename from build/pandoc-defaults/docx.yaml
rename to build/pandoc/defaults/docx.yaml
diff --git a/build/pandoc-defaults/html.yaml b/build/pandoc/defaults/html.yaml
similarity index 100%
rename from build/pandoc-defaults/html.yaml
rename to build/pandoc/defaults/html.yaml
diff --git a/build/pandoc-defaults/pdf-weasyprint.yaml b/build/pandoc/defaults/pdf-weasyprint.yaml
similarity index 100%
rename from build/pandoc-defaults/pdf-weasyprint.yaml
rename to build/pandoc/defaults/pdf-weasyprint.yaml
diff --git a/ci/install-spellcheck.sh b/ci/install-spellcheck.sh
index 6d5ac88..e12661e 100755
--- a/ci/install-spellcheck.sh
+++ b/ci/install-spellcheck.sh
@@ -6,7 +6,7 @@
 set -o errexit \
     -o pipefail
 
-sudo apt-get update -y
-sudo apt-get install -y aspell aspell-en
-wget https://raw.githubusercontent.com/pandoc/lua-filters/13c3fa7e97206413609a48a82575cb43137e037f/spellcheck/spellcheck.lua
-mv spellcheck.lua build/assets/spellcheck.lua
+sudo apt-get update --yes
+sudo apt-get install --yes aspell aspell-en
+wget --directory-prefix=build/pandoc/filters \
+  https://github.com/pandoc/lua-filters/raw/13c3fa7e97206413609a48a82575cb43137e037f/spellcheck/spellcheck.lua

From b7462701ff85854a67d878db4af89d0268bb11d2 Mon Sep 17 00:00:00 2001
From: Daniel Himmelstein <daniel.himmelstein@gmail.com>
Date: Sun, 24 May 2020 19:42:56 -0400
Subject: [PATCH 04/50] Update manubot for more flexible citation processing

merges https://github.com/manubot/rootstock/pull/342

Includes major updates to how citations are processed by the pandoc-manubot-cite filter.
See the following commit messages for more information:

- https://github.com/manubot/manubot/commit/7055bcc6524fdf1ef97d838cf0158973e2061595
- https://github.com/manubot/manubot/commit/47b03e0c202e6a0561e6548ba08a4ad790f56eee

Removes requirement to prefix certain citekeys with raw: or tag:
Removes support for deprecated `content/citation-tags.tsv`.
Switches from tag to alias terminology for citation aliases.
closes https://github.com/manubot/manubot/issues/120

Removes pandas and jsonref dependencies, which are no longer needed.
---
 USAGE.md                | 84 ++++++++++++++++++++---------------------
 build/environment.yml   |  4 +-
 content/02.delete-me.md | 14 +++----
 3 files changed, 50 insertions(+), 52 deletions(-)

diff --git a/USAGE.md b/USAGE.md
index 95f1b35..06b7eaf 100644
--- a/USAGE.md
+++ b/USAGE.md
@@ -76,15 +76,15 @@ We recommend always specifying the width of SVG images (even if just `width="100
 
 ### Citations
 
-Manubot supports Pandoc [citations](https://pandoc.org/MANUAL.html#citations).
+Manubot supports [Pandoc citations](https://pandoc.org/MANUAL.html#citations), but with added support for citing persistent identifiers directly.
 Citations are processed in 3 stages:
 
 1. Pandoc parses the input Markdown to locate citation keys.
-2. The [`pandoc-manubot-cite`](https://github.com/manubot/manubot#pandoc-filter) filter automatically retreives the bibliographic metadata for citation keys.
-3. The [`pandoc-citeproc`](https://github.com/jgm/pandoc-citeproc/blob/master/man/pandoc-citeproc.1.md) filter renders in-text citations and generates styled references.
+2. The [`pandoc-manubot-cite` filter](https://github.com/manubot/manubot#pandoc-filter) automatically retrieves the bibliographic metadata for citation keys.
+3. The [`pandoc-citeproc` filter](https://github.com/jgm/pandoc-citeproc/blob/master/man/pandoc-citeproc.1.md) renders in-text citations and generates styled references.
 
-When using Manubot, citation keys should be formatted like `@source:identifier`,
-where `source` is one of the options described below.
+When citing persistent identifiers, citation keys should be formatted like `@prefix:accession`,
+where `prefix` is one of the options described below.
 When choosing which source to use for a citation, we recommend the following order:
 
 1. DOI (Digital Object Identifier), cite like `@doi:10.15363/thinklab.4`.
@@ -92,35 +92,38 @@ When choosing which source to use for a citation, we recommend the following ord
    shortDOIs begin with `10/` rather than `10.` and can also be cited.
    For example, Manubot will expand `@doi:10/993` to the DOI above.
    We suggest using shortDOIs to cite DOIs containing forbidden characters, such as `(` or `)`.
-2. PubMed Central ID, cite like `@pmcid:PMC4497619`.
-3. PubMed ID, cite like `@pmid:26158728`.
+2. PubMed Central ID, cite like `@pmc:PMC4497619`.
+3. PubMed ID, cite like `@pubmed:26158728`.
 4. _arXiv_ ID, cite like `@arxiv:1508.06576v2`.
 5. ISBN (International Standard Book Number), cite like `@isbn:9781339919881`.
-6. URL / webpage, cite like `@url:https://nyti.ms/1QUgAt1`.
+6. URL / webpage, cite like `@https://nyti.ms/1QUgAt1`.
    URL citations can be helpful if the above methods return incorrect metadata.
-   For example, `@doi:10.1038/ng.3834` [incorrectly handles](https://github.com/manubot/manubot/issues/158) the consortium name resulting in a blank author, while `@url:https://doi.org/10.1038/ng.3834` succeeds.
-   Similarly, `@url:https://doi.org/10.1101/142760` is a [workaround](https://github.com/manubot/manubot/issues/16) to set the journal name of bioRxiv preprints to _bioRxiv_.
+   For example, `@doi:10.1038/ng.3834` [incorrectly handles](https://github.com/manubot/manubot/issues/158) the consortium name resulting in a blank author, while `@https://doi.org/10.1038/ng.3834` succeeds.
+   Similarly, `@https://doi.org/10.1101/142760` is a [workaround](https://github.com/manubot/manubot/issues/16) to set the journal name of bioRxiv preprints to _bioRxiv_.
 7. Wikidata Items, cite like `@wikidata:Q50051684`.
-   Note that anyone can edit or add records on [Wikidata](https://www.wikidata.org), so users are encouraged to contribute metadata for hard-to-cite works to Wikidata as an alternative to using a `raw` citation.
-8. For references that do not have any of the persistent identifiers above, use a raw citation like `@raw:old-manuscript`.
-   Metadata for raw citations must be provided manually.
+   Note that anyone can edit or add records on [Wikidata](https://www.wikidata.org), so users are encouraged to contribute metadata for hard-to-cite works to Wikidata.
+8. Any other compact identifier supported by <https://identifiers.org>.
+   Manubot uses the Identifiers.org Resolution Service to support [hundreds](https://github.com/manubot/manubot/blob/7055bcc6524fdf1ef97d838cf0158973e2061595/manubot/cite/handlers.py#L122-L831 "Actual prefix support is determined by this manubot source code.") of [prefixes](https://registry.identifiers.org/registry "Identifiers.org prefix search").
+   For example, citing `@clinicaltrials:NCT04280705` will produce the same bibliographic metadata as `@https://identifiers.org/clinicaltrials:NCT04280705` or `@https://clinicaltrials.gov/ct2/show/NCT04280705`.
+9. For references that do not have any of the above persistent identifiers, the citation key does not need to include a prefix.
+   Citing `@old-manuscript` will work, but only if reference metadata is [provided manually](#reference-metadata).
 
 Cite multiple items at once like:
 
 ```md
-Here is a sentence with several citations [@doi:10.15363/thinklab.4; @pmid:26158728; @arxiv:1508.06576; @isbn:9780394603988].
+Here is a sentence with several citations [@doi:10.15363/thinklab.4; @pubmed:26158728; @arxiv:1508.06576; @isbn:9780394603988].
 ```
 
 Note that multiple citations must be semicolon separated.
 Be careful not to cite the same study using identifiers from multiple sources.
-For example, the following citations all refer to the same study, but will be treated as separate references: `[@doi:10.7717/peerj.705; @pmcid:PMC4304851; @pmid:25648772]`.
+For example, the following citations all refer to the same study, but will be treated as separate references: `[@doi:10.7717/peerj.705; @pmc:PMC4304851; @pubmed:25648772]`.
 
 Citation keys must adhere to the syntax described in the [Pandoc manual](https://pandoc.org/MANUAL.html#citations):
 
 > The citation key must begin with a letter, digit, or `_`, and may contain alphanumerics, `_`, and internal punctuation characters (`:.#$%&-+?<>~/`).
 
 To evaluate whether a citation key fully matches this syntax, try [this online regex](https://regex101.com/r/mXZyY2/latest).
-If the citation key is not valid, use the [citation tag](#citation-tag) workaround below.
+If the citation key is not valid, use the [citation aliases](#citation-aliases) workaround below.
 This is required for citation keys that contain forbidden characters such as `;` or `=` or end with a non-alphanumeric character such as `/`.
 <!-- See [jgm/pandoc#6026](https://github.com/jgm/pandoc/issues/6026) for progress on a more flexible Markdown citation key syntax. -->
 
@@ -134,66 +137,63 @@ pandoc:
   manubot-fail-on-errors: True
 ```
 
-#### Citation tags
+#### Citation aliases
 
-The system also supports citation tags, which map from one citation key (an alias) to another.
-Tags are recommended for the following applications:
+The system also supports citation aliases, which map from one citation key (the "alias" or "tag") to another.
+Aliases are recommended for the following applications:
 
-1. A citation's identifier contains forbidden characters, you must use a tag.
+1. A citation key contains forbidden characters.
 2. A single reference is cited many times.
-   Therefore, it might make sense to define a tag, so if the citation updates (e.g. a newer version becomes available), only a single change is required.
+   Therefore, it might make sense to define an alias, so if the citation updates (e.g. a newer version becomes available), only a single change is required.
 
-Tags can be defined using Markdown's [link reference syntax](https://spec.commonmark.org/0.29/#link-reference-definitions) as follows:
+Aliases can be defined using Markdown's [link reference syntax](https://spec.commonmark.org/0.29/#link-reference-definitions) as follows:
 
 ```markdown
-Citing a URL containing a `?` character [@tag:my-url].
-Citing a DOI containing parentheses [@doi:my-doi].
+Citing a URL containing a `?` character [@my-url].
+Citing a DOI containing parentheses [@my-doi].
 
-[@tag:my-url]: url:https://openreview.net/forum?id=HkwoSDPgg
-[@tag:my-doi]: doi:10.1016/S0022-2836(05)80360-2
+[@my-url]: https://openreview.net/forum?id=HkwoSDPgg
+[@my-doi]: doi:10.1016/S0022-2836(05)80360-2
 ```
 
 This syntax is also used by [`pandoc-url2cite`](https://github.com/phiresky/pandoc-url2cite).
 Make sure to place these link reference definitions in their own paragraphs.
 These paragraphs can be in any of the content Markdown files.
 
-Another method for defining tags is to define `pandoc.citekey-aliases` in `metadata.yaml`:
+Another method for defining aliases is to define `pandoc.citekey-aliases` in `metadata.yaml`:
 
 ```yaml
 pandoc:
   citekey-aliases:
-    tag:my-url: url:https://openreview.net/forum?id=HkwoSDPgg
-    tag:my-doi: doi:10.1016/S0022-2836(05)80360-2
+    my-url: https://openreview.net/forum?id=HkwoSDPgg
+    my-doi: doi:10.1016/S0022-2836(05)80360-2
 ```
 
-For backwards compatibility, tags can also be defined in `content/citation-tags.tsv`.
-If `citation-tags.tsv` defines the tag `study-x`, then this study can be cited like `@tag:study-x`.
-This method is deprecated.
-
 ## Reference metadata
 
 Manubot stores the bibliographic details for references (the set of all cited works) as CSL JSON ([Citation Style Language Items](http://citeproc-js.readthedocs.io/en/latest/csl-json/markup.html#csl-json-items)).
-For all citation sources besides `raw`, Manubot automatically generates CSL JSON.
+Manubot automatically generates CSL JSON for most persistent identifiers (as described in [Citations](#citations) above).
 In some cases, automatic metadata retrieval fails or provides incorrect or incomplete information.
-Errors are most common for `url` references.
+Errors are most common for references generated from scraping HTML metadata from websites.
+This occurs most frequently for `https`/`http`/`url` citations as well as identifiers.org prefixes without explicit support listed above.
 Therefore, Manubot supports user-provided metadata, which we refer to as "manual references".
 When a manual reference is provided, Manubot uses the supplied metadata and does not attempt to generate it.
 
 Manubot searches the `content` directory for files that match the glob pattern `manual-references*.*` and expects that these files contain manual references.
 [`content/manual-references.json`](content/manual-references.json) is the default file to specify custom CSL JSON metadata.
 Manual references are matched to citations using their "id" field.
-For example, to manually specify the metadata for the citation `@url:https://github.com/manubot/rootstock`, add a CSL JSON Item to `manual-references.json` that contains the following excerpt:
+For example, to manually specify the metadata for the citation `@https://github.com/manubot/rootstock`, add a CSL JSON Item to `manual-references.json` that contains the following excerpt:
 
 ```json
-"id": "url:https://github.com/manubot/rootstock",
+"id": "https://github.com/manubot/rootstock",
 ```
 
-The metadata for `raw` citations must be provided in a manual reference file (e.g. `manual-references.json`) or an error will occur.
-For example, to cite `@raw:private-message` in a manuscript, a corresponding CSL JSON Item is required, such as:
+The metadata for unhandled citations — any citation key that is a not a supported persistent ID — must be provided in a manual reference file (e.g. `manual-references.json`) or an error will occur.
+For example, to cite `@private-message` in a manuscript, a corresponding CSL JSON Item is required, such as:
 
 ```json
 {
-  "id": "raw:private-message",
+  "id": "private-message",
   "type": "personal_communication",
   "title": "Personal communication with Doctor X"
 }
@@ -204,10 +204,10 @@ For guidance on what CSL JSON should be like for different document types, refer
 
 Manubot offers some support for other bibliographic metadata formats besides CSL JSON, by delegating conversion to the `pandoc-citeproc --bib2json` [utility](https://github.com/jgm/pandoc-citeproc/blob/master/man/pandoc-citeproc.1.md#convert-mode).
 Formats are inferred from filename extensions.
-So, for example, to provide metadata for `@url:https://github.com/manubot/rootstock` in BibTeX format, create the file `content/manual-references.bib` and create an item whose definition starts with the excerpt:
+So, for example, to provide metadata for `@https://github.com/manubot/rootstock` in BibTeX format, create the file `content/manual-references.bib` and create an item whose definition starts with the excerpt:
 
 ```latex
-@misc{url:https://github.com/manubot/rootstock,
+@misc{https://github.com/manubot/rootstock,
 ```
 
 Processed reference metadata in CSL JSON format, either generated by Manubot or specified via manual references, is exported to `references.json`.
diff --git a/build/environment.yml b/build/environment.yml
index 84bc456..b156d6c 100644
--- a/build/environment.yml
+++ b/build/environment.yml
@@ -8,7 +8,6 @@ dependencies:
   - ghp-import=0.5.5
   - jinja2=2.11.2
   - jsonschema=3.2.0
-  - pandas=1.0.3
   - pandoc=2.9.2
   - pango=1.40.14
   - pip=20.0
@@ -20,8 +19,7 @@ dependencies:
   - yamllint=1.21.0
   - pip:
     - errorhandler==2.0.1
-    - git+https://github.com/manubot/manubot@890b76891f139a26d36cd9a4aa652f7e019501f8
-    - jsonref==0.2
+    - git+https://github.com/manubot/manubot@31968197d1ccd96a46bf092cdba4b575764bb954
     - opentimestamps-client==0.7.0
     - opentimestamps==0.4.1
     - pandoc-eqnos==2.1.1
diff --git a/content/02.delete-me.md b/content/02.delete-me.md
index 557caeb..8f2ed07 100644
--- a/content/02.delete-me.md
+++ b/content/02.delete-me.md
@@ -95,24 +95,24 @@ Bare URL link: <https://manubot.org>
 
 Citation by DOI [@doi:10.7554/eLife.32822].
 
-Citation by PubMed Central ID [@pmcid:PMC6103790].
+Citation by PubMed Central ID [@pmc:PMC6103790].
 
-Citation by PubMed ID [@pmid:30718888].
+Citation by PubMed ID [@pubmed:30718888].
 
 Citation by Wikidata ID [@wikidata:Q56458321].
 
 Citation by ISBN [@isbn:9780262517638].
 
-Citation by URL [@url:https://greenelab.github.io/meta-review/].
+Citation by URL [@https://greenelab.github.io/meta-review/].
 
-Citation by tag [@tag:deep-review].
+Citation by alias [@deep-review].
 
-Multiple citations can be put inside the same set of brackets [@doi:10.7554/eLife.32822; @tag:deep-review; @isbn:9780262517638].
-Manubot plugins provide easier, more convenient visualization of and navigation between citations [@doi:10.1371/journal.pcbi.1007128; @pmid:30718888; @pmcid:PMC6103790; @tag:deep-review].
+Multiple citations can be put inside the same set of brackets [@doi:10.7554/eLife.32822; @deep-review; @isbn:9780262517638].
+Manubot plugins provide easier, more convenient visualization of and navigation between citations [@doi:10.1371/journal.pcbi.1007128; @pubmed:30718888; @pmc:PMC6103790; @deep-review].
 
 Citation tags (i.e. aliases) can be defined in their own paragraphs using Markdown's reference link syntax:
 
-[@tag:deep-review]: doi:10.1098/rsif.2017.0387
+[@deep-review]: doi:10.1098/rsif.2017.0387
 
 ## Referencing figures, tables, equations
 

From d61267c8ff1d7bc16644f4e15b814c1b4ca2bd31 Mon Sep 17 00:00:00 2001
From: Vincent Rubinetti <vince.rubinetti@gmail.com>
Date: Fri, 5 Jun 2020 16:03:54 -0400
Subject: [PATCH 05/50] webpage: improve Hypothes.is plugin & CSS heading sizes

merges https://github.com/manubot/rootstock/pull/345

Enhancements related to Hypothes.is annotations plugin at build/plugins/hypothesis.html.
Adds button to load hypothesis plugin, rather than automatically loading it.
closes https://github.com/manubot/rootstock/issues/281

PDF build / print page view will no longer include annotations by default,
since hypothesis not loaded until activated.
closes https://github.com/manubot/rootstock/issues/280

Fix overlap of hypothesis sidebar and table of contents plugin on small screens.
closes https://github.com/manubot/rootstock/issues/306

Change default font sizes of h1 through h6 to be larger than base text size,
breaking with browser precedent
closes https://github.com/manubot/rootstock/issues/293
---
 build/plugins/hypothesis.html        | 95 +++++++++++++++++++++++++---
 build/plugins/table-of-contents.html |  7 +-
 build/themes/default.html            | 73 +++++++++++++++------
 content/02.delete-me.md              |  4 ++
 4 files changed, 147 insertions(+), 32 deletions(-)

diff --git a/build/plugins/hypothesis.html b/build/plugins/hypothesis.html
index b38888e..7bd1691 100644
--- a/build/plugins/hypothesis.html
+++ b/build/plugins/hypothesis.html
@@ -1,6 +1,16 @@
-<!-- annotations plugin configuration -->
+<!-- annotations plugin -->
 
 <script>
+    // /////////////////////////
+    // DESCRIPTION
+    // /////////////////////////
+
+    // This third-party plugin 'Hypothesis' allows public annotation of the
+    // manuscript.
+
+    // https://web.hypothes.is/
+
+    // plugin configuration
     window.hypothesisConfig = function() {
         return {
             branding: {
@@ -13,17 +23,82 @@
             }
         };
     };
-</script>
 
-<!-- annotations plugin -->
+    // hypothesis client script
+    const embed = 'https://hypothes.is/embed.js';
+    // hypothesis annotation count query url
+    const query = 'https://api.hypothes.is/api/search?limit=0&url='
 
-<script src='https://hypothes.is/embed.js'>
-    // /////////////////////////
-    // DESCRIPTION
-    // /////////////////////////
+    
+    // start script
+    function start() {
+        const button = makeButton();
+        document.body.insertBefore(button, document.body.firstChild);
+        insertCount(button);
+    }
 
-    // This third-party plugin 'Hypothesis' allows public annotation of the
-    // manuscript.
+    // make button
+    function makeButton() {
+        // create button
+        const button = document.createElement('button');
+        button.id = 'hypothesis_button';
+        button.innerHTML = document.querySelector('.icon_hypothesis').innerHTML;
+        button.title = 'Hypothesis annotations';
+        button.classList.add('icon_button');
 
-    // https://web.hypothes.is/
+        function onClick(event) {
+            onButtonClick(event, button);
+        }
+
+        // attach click listeners
+        button.addEventListener('click', onClick);
+
+        return button;
+    }
+
+    // insert annotations count
+    async function insertCount(button) {
+        // get annotation count from Hypothesis based on url
+        let count = '-';
+        try {
+            const canonical = document.querySelector('link[rel="canonical"]');
+            const location = window.location;
+            const url = encodeURIComponent((canonical || location).href);
+            const response = await fetch(query + url);
+            const json = await response.json();
+            count = json.total || '-';
+        } catch(error) {
+            console.log(error);
+        }
+        
+        // put count into button
+        const counter = document.createElement('span');
+        counter.id = 'hypothesis_count';
+        counter.innerHTML = count;
+        button.title = 'View ' + count + ' Hypothesis annotations';
+        button.append(counter);
+    }
+
+    // when button is clicked
+    function onButtonClick(event, button) {
+        const script = document.createElement('script');
+        script.src = embed;
+        document.body.append(script);
+        button.remove();
+    }
+
+    window.addEventListener('load', start);
 </script>
+
+<!-- hypothesis icon -->
+
+<template class="icon_hypothesis">
+    <!-- modified from: https://simpleicons.org/icons/hypothesis.svg / https://git.io/Jf1VB -->
+    <svg width="16" height="16" viewBox="0 0 24 24" tabindex="-1">
+        <path
+            fill="currentColor"
+            d="M3.43 0C2.5 0 1.72 .768 1.72 1.72V18.86C1.72 19.8 2.5 20.57 3.43 20.57H9.38L12 24L14.62 20.57H20.57C21.5 20.57 22.29 19.8 22.29 18.86V1.72C22.29 .77 21.5 0 20.57 0H3.43M5.14 3.43H7.72V9.43S8.58 7.72 10.28 7.72C12 7.72 13.74 8.57 13.74 11.24V17.14H11.16V12C11.16 10.61 10.28 10.07 9.43 10.29C8.57 10.5 7.72 11.41 7.72 13.29V17.14H5.14V3.43M18 13.72C18.95 13.72 19.72 14.5 19.72 15.42A1.71 1.71 0 0 1 18 17.13A1.71 1.71 0 0 1 16.29 15.42C16.29 14.5 17.05 13.71 18 13.71Z"
+            tabindex="-1"
+        ></path>
+    </svg>
+</template>
diff --git a/build/plugins/table-of-contents.html b/build/plugins/table-of-contents.html
index fc57f78..49d6e01 100644
--- a/build/plugins/table-of-contents.html
+++ b/build/plugins/table-of-contents.html
@@ -169,14 +169,13 @@
             // create toc button
             const button = document.createElement('button');
             button.id = 'toc_button';
-            button.innerHTML = document.querySelector(
-                '.icon_th_list'
-            ).innerHTML;
+            button.innerHTML = document.querySelector('.icon_th_list').innerHTML;
+            button.title = 'Table of Contents';
             button.classList.add('icon_button');
 
             // create header text
             const text = document.createElement('h3');
-            text.innerHTML = 'Table of Contents';
+            text.innerHTML = 'View Table of Contents';
 
             // create container for toc list
             const list = document.createElement('div');
diff --git a/build/themes/default.html b/build/themes/default.html
index 26675bd..cfff898 100644
--- a/build/themes/default.html
+++ b/build/themes/default.html
@@ -80,6 +80,26 @@
         border-bottom: solid 1px #bdbdbd;
     }
 
+    /* heading font sizes */
+    h1 {
+        font-size: 2em;
+    }
+    h2 {
+        font-size: 1.5em;
+    }
+    h3{
+        font-size: 1.35em;
+    }
+    h4 {
+        font-size: 1.25em;
+    }
+    h5 {
+        font-size: 1.15em;
+    }
+    h6 {
+        font-size: 1em;
+    }
+
     /* -------------------------------------------------- */
     /* manuscript header */
     /* -------------------------------------------------- */
@@ -513,22 +533,6 @@
             margin: 15px 0;
         }
 
-        /* heading 1 */
-        h1 {
-            font-size: 1.75em;
-        }
-
-        /* heading 2 */
-        h2 {
-            font-size: 1.25em;
-            margin-top: 0;
-        }
-
-        /* heading 3 */
-        h3 {
-            font-size: 1.10em;
-        }
-
         /* figures and tables */
         figure, table {
             font-size: 0.85em;
@@ -1182,10 +1186,39 @@
     /* hypothesis (annotations) plugin */
     /* -------------------------------------------------- */
 
+    /* hypothesis activation button */
+    #hypothesis_button {
+        box-sizing: border-box;
+        position: fixed;
+        top: 0;
+        right: 0;
+        width: 60px;
+        height: 60px;
+        background: #ffffff;
+        border-radius: 0;
+        border-left: solid 1px #bdbdbd;
+        border-bottom: solid 1px #bdbdbd;
+        box-shadow: 0 0 20px rgba(0, 0, 0, 0.05);
+        z-index: 2;
+    }
+
+    /* hypothesis button svg */
+    #hypothesis_button > svg {
+        position: relative;
+        top: -4px;
+    }
+
+    /* hypothesis annotation count */
+    #hypothesis_count {
+        position: absolute;
+        left: 0;
+        right: 0;
+        bottom: 5px;
+    }
+
     /* side panel */
     .annotator-frame {
         width: 280px !important;
-        z-index: 0 !important;
     }
 
     /* match highlight color to rest of theme */
@@ -1203,8 +1236,12 @@
         background: #f5f5f5 !important;
     }
 
-    /* always hide toolbar and tooltip on print */
+    /* always hide button, toolbar, and tooltip on print */
     @media only print {
+        #hypothesis_button {
+            display: none;
+        }
+
         .annotator-frame {
             display: none !important;
         }
diff --git a/content/02.delete-me.md b/content/02.delete-me.md
index 8f2ed07..78d9c7e 100644
--- a/content/02.delete-me.md
+++ b/content/02.delete-me.md
@@ -63,6 +63,10 @@ Document section headings:
 
 #### Heading 4
 
+##### Heading 5
+
+###### Heading 6
+
 ### A heading centered on its own printed page{.center .page_center}
 
 <!-- an arbitrary comment. visible in input, but not visible in output. -->

From adc7b8bca102594d8e7d46d93071c4018f0c6944 Mon Sep 17 00:00:00 2001
From: Sebastian Karcher <karcher@u.northwestern.edu>
Date: Thu, 11 Jun 2020 12:43:21 -0400
Subject: [PATCH 06/50] CSL: add space delimiter across the style

merges https://github.com/manubot/rootstock/pull/346
closes https://github.com/manubot/rootstock/issues/155
supersedes https://github.com/manubot/rootstock/pull/158
tested via https://github.com/manubot/manubot/pull/110
refs https://twitter.com/csl_styles/status/1270049414200074243

Add a space delimiter across the style.
Fixes some references where there is a missing space after the title,
when authors are missing.

Set second-field-align="flush"
This option is not supported by pandoc yet, but it more closely resembles
hanging-indent="true", which pandoc is currently using to layout the
bibliography.

Co-authored-by: Rintze M. Zelle <rintze.zelle@gmail.com>
---
 build/assets/style.csl | 44 ++++++++++++++++++++++--------------------
 1 file changed, 23 insertions(+), 21 deletions(-)

diff --git a/build/assets/style.csl b/build/assets/style.csl
index 84daaa1..942a043 100644
--- a/build/assets/style.csl
+++ b/build/assets/style.csl
@@ -1,4 +1,4 @@
-<?xml version="1.0" encoding="utf-8"?>
+<?xml version="1.0" encoding="utf-8"?>
 <style xmlns="http://purl.org/net/xbiblio/csl" class="in-text" version="1.0" demote-non-dropping-particle="never" default-locale="en-US">
   <!-- This style was edited with the Visual CSL Editor (http://editor.citationstyles.org/visualEditor/) -->
   <info>
@@ -47,29 +47,31 @@
       <text variable="citation-number"/>
     </layout>
   </citation>
-  <bibliography hanging-indent="true" second-field-align="margin">
+  <bibliography hanging-indent="true" second-field-align="flush">
     <layout>
       <text variable="citation-number" suffix=". "/>
-      <group>
-        <text variable="title" font-weight="bold"/>
-      </group>
-      <group display="block">
-        <text macro="author"/>
-      </group>
       <group delimiter=" ">
-        <text macro="venue" font-style="italic"/>
-        <date variable="issued" prefix="(" suffix=")">
-          <date-part name="year"/>
-          <date-part name="month" form="numeric-leading-zeros" prefix="-"/>
-          <date-part name="day" form="numeric-leading-zeros" prefix="-"/>
-        </date>
-        <text variable="URL"/>
-      </group>
-      <group display="block" delimiter=" · ">
-        <text variable="DOI" text-case="lowercase" prefix="DOI: "/>
-        <text variable="PMID" prefix="PMID: "/>
-        <text variable="PMCID" prefix="PMCID: "/>
-        <text variable="ISBN" prefix="ISBN: "/>
+        <group>
+          <text variable="title" font-weight="bold"/>
+        </group>
+        <group display="block">
+          <text macro="author"/>
+        </group>
+        <group delimiter=" ">
+          <text macro="venue" font-style="italic"/>
+          <date variable="issued" prefix="(" suffix=")">
+            <date-part name="year"/>
+            <date-part name="month" form="numeric-leading-zeros" prefix="-"/>
+            <date-part name="day" form="numeric-leading-zeros" prefix="-"/>
+          </date>
+          <text variable="URL"/>
+        </group>
+        <group display="block" delimiter=" · ">
+          <text variable="DOI" text-case="lowercase" prefix="DOI: "/>
+          <text variable="PMID" prefix="PMID: "/>
+          <text variable="PMCID" prefix="PMCID: "/>
+          <text variable="ISBN" prefix="ISBN: "/>
+        </group>
       </group>
     </layout>
   </bibliography>

From ce827c7789163dca33dfa3bd2df7aa828e57485d Mon Sep 17 00:00:00 2001
From: Vincent Rubinetti <vince.rubinetti@gmail.com>
Date: Fri, 26 Jun 2020 14:09:10 -0400
Subject: [PATCH 07/50] Improve themes for DOCX output

merges https://github.com/manubot/rootstock/pull/348
closes https://github.com/manubot/rootstock/issues/344

Update docx files that can be supplied to Pandoc via --reference-doc.

Recreate build/themes/default.docx from scratch (via a blank pandoc output).
Improves aesthetic and fixes issues like invisible table gridlines.

Add build/themes/nih-grant.docx that produces documents that adhere
to many of the National Institutes of Health (NIH) formatting requirements.
https://grants.nih.gov/grants/how-to-apply-application-guide/format-and-write/format-attachments.htm
---
 build/themes/default.docx   | Bin 15279 -> 17728 bytes
 build/themes/nih-grant.docx | Bin 0 -> 18126 bytes
 2 files changed, 0 insertions(+), 0 deletions(-)
 create mode 100644 build/themes/nih-grant.docx

diff --git a/build/themes/default.docx b/build/themes/default.docx
index a2a657a96c2eb80ab47aed9fc1245a656ca40d9b..ccc5b6e469a73a08c0d2fec9bd8bb09c6a0f0acb 100644
GIT binary patch
delta 13566
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zS$nGLS3Rp|S66jaSCwmb7$~};EI0%P2owkm2nYx%2&^R)qDKun4H)2CA2W*hqtvVD
z9)rw!tq=^y`L7`~S|x$*2C542*BE~9H-6xkNEBMc+=(x7Y>t=wnNq+R<Da9(h@_Tg
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b{;vf_PV&pAbOQjue!l!Z6@*Rjk6-@>wrb+W

literal 0
HcmV?d00001


From 45e5dad10636633a5f10df84d2a33e6b69fc6903 Mon Sep 17 00:00:00 2001
From: Anthony Gitter <agitter@users.noreply.github.com>
Date: Fri, 17 Jul 2020 11:15:22 -0500
Subject: [PATCH 08/50] Update figure usage

---
 USAGE.md | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/USAGE.md b/USAGE.md
index 06b7eaf..4323077 100644
--- a/USAGE.md
+++ b/USAGE.md
@@ -43,9 +43,11 @@ For easy creation of markdown tables, check out the [Tables Generator](https://w
 Figures can be included with the following markdown:
 
 ```md
+ 
 ![Caption for the example figure.](url_or_path_to_figure){#fig:example-id}
 ```
 
+The blank line before the figure is required.
 Support for figure numbering and citation is provided by [`pandoc-fignos`](https://github.com/tomduck/pandoc-fignos).
 This figure can be cited in the text using `@fig:example-id`.
 In context, a figure citation may look like: `Figure {@fig:example-id}B shows …`.

From 15db6237effc6edb2b8e675ea5cb8a17188d1e2c Mon Sep 17 00:00:00 2001
From: "C. Titus Brown" <titus@idyll.org>
Date: Wed, 30 Sep 2020 09:12:52 -0700
Subject: [PATCH 09/50] SETUP: wording tweaks (#366)

merges https://github.com/manubot/rootstock/pull/366

clarifies that
1. OWNER can be an organization!
2. no additional configuration is needed for github actions.
---
 SETUP.md | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/SETUP.md b/SETUP.md
index 2faa250..136376c 100644
--- a/SETUP.md
+++ b/SETUP.md
@@ -35,7 +35,7 @@ In general, assume that all commands in this setup are case-sensitive.
 **Edit the following commands with your manuscript's information:**
 
 ```sh
-# GitHub username (change from manubot)
+# GitHub username or organization name (change from manubot)
 OWNER=manubot
 # Repository name (change from rootstock)
 REPO=rootstock
@@ -115,7 +115,7 @@ git rm .appveyor.yml
 git rm ci/install.sh
 ```
 
-GitHub Actions is _usually_ able to deploy without any setup using the [`GITHUB_TOKEN`](https://help.github.com/en/actions/configuring-and-managing-workflows/authenticating-with-the-github_token) for authentication.
+GitHub Actions is _usually_ able to deploy without any additional setup using the [`GITHUB_TOKEN`](https://help.github.com/en/actions/configuring-and-managing-workflows/authenticating-with-the-github_token) for authentication.
 GitHub Pages deployment using `GITHUB_TOKEN` recently started working on GitHub without an official announcement.
 If it does not work for you after completing this setup, try reselecting "gh-pages branch" as the Source for GitHub Pages in the repository Settings.
 GitHub Pages should now trigger on the next commit.

From 73e377e70202afc919837f2deff39af2ceb40ebc Mon Sep 17 00:00:00 2001
From: Daniel Himmelstein <daniel.himmelstein@gmail.com>
Date: Sat, 3 Oct 2020 22:18:25 -0400
Subject: [PATCH 10/50] build.sh: skip docker if installed but not running

merges https://github.com/manubot/rootstock/pull/371
closes https://github.com/manubot/rootstock/issues/368

https://stackoverflow.com/a/55283209/4651668
https://stackoverflow.com/a/18035947/4651668
---
 build/build.sh | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/build/build.sh b/build/build.sh
index c3028c0..9d0b4e0 100755
--- a/build/build.sh
+++ b/build/build.sh
@@ -35,12 +35,12 @@ pandoc --verbose \
   --defaults=common.yaml \
   --defaults=html.yaml
 
-# Return null if docker command is missing, otherwise return path to docker
-DOCKER_EXISTS="$(command -v docker || true)"
+# Set DOCKER_RUNNING to a non-empty string if docker is running, otherwise null.
+DOCKER_RUNNING="$(docker info &> /dev/null && echo "yes" || true)"
 
 # Create PDF output (unless BUILD_PDF environment variable equals "false")
 # If Docker is not available, use WeasyPrint to create PDF
-if [ "${BUILD_PDF:-}" != "false" ] && [ -z "$DOCKER_EXISTS" ]; then
+if [ "${BUILD_PDF:-}" != "false" ] && [ -z "$DOCKER_RUNNING" ]; then
   echo >&2 "Exporting PDF manuscript using WeasyPrint"
   if [ -L images ]; then rm images; fi  # if images is a symlink, remove it
   ln -s content/images
@@ -53,7 +53,7 @@ if [ "${BUILD_PDF:-}" != "false" ] && [ -z "$DOCKER_EXISTS" ]; then
 fi
 
 # If Docker is available, use athenapdf to create PDF
-if [ "${BUILD_PDF:-}" != "false" ] && [ -n "$DOCKER_EXISTS" ]; then
+if [ "${BUILD_PDF:-}" != "false" ] && [ -n "$DOCKER_RUNNING" ]; then
   echo >&2 "Exporting PDF manuscript using Docker + Athena"
   if [ "${CI:-}" = "true" ]; then
     # Incease --delay for CI builds to ensure the webpage fully renders, even when the CI server is under high load.

From b92b960fcd0fb39c933375f84d5cfc365fc07ca0 Mon Sep 17 00:00:00 2001
From: Daniel Himmelstein <daniel.himmelstein@gmail.com>
Date: Tue, 6 Oct 2020 11:30:02 -0400
Subject: [PATCH 11/50] GitHub Actions: replace set-env with $GITHUB_ENV

merges https://github.com/manubot/rootstock/pull/374

From https://github.com/manubot/rootstock/runs/1212860980#step:2:10:

> Warning: The `set-env` command is deprecated and will be disabled soon.
> Please upgrade to using Environment Files.
> For more information see:
> https://github.blog/changelog/2020-10-01-github-actions-deprecating-set-env-and-add-path-commands/

https://docs.github.com/en/free-pro-team@latest/actions/reference/workflow-commands-for-github-actions#setting-an-environment-variable
---
 .github/workflows/manubot.yaml | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/.github/workflows/manubot.yaml b/.github/workflows/manubot.yaml
index 42509c5..0cabab3 100644
--- a/.github/workflows/manubot.yaml
+++ b/.github/workflows/manubot.yaml
@@ -17,8 +17,7 @@ jobs:
       - name: Set Environment Variables
         run: |
           TRIGGERING_SHA=${GITHUB_PULL_REQUEST_SHA:-$GITHUB_SHA}
-          TRIGGERING_SHA_7=${TRIGGERING_SHA::7}
-          echo "::set-env name=TRIGGERING_SHA_7::$TRIGGERING_SHA_7"
+          echo "TRIGGERING_SHA_7=${TRIGGERING_SHA::7}" >> $GITHUB_ENV
           echo "TRIGGERING_SHA: $TRIGGERING_SHA"
       - name: Checkout Repository
         uses: actions/checkout@v2

From 37a11499b204458dfb620970f103769289b31e1f Mon Sep 17 00:00:00 2001
From: Vincent Rubinetti <vince.rubinetti@gmail.com>
Date: Tue, 6 Oct 2020 19:49:27 -0400
Subject: [PATCH 12/50] website: TOC plugin new behavior & bug fix

merges https://github.com/manubot/rootstock/pull/372
closes https://github.com/manubot/rootstock/issues/369
---
 build/plugins/table-of-contents.html | 58 ++++++++++++++--------------
 1 file changed, 29 insertions(+), 29 deletions(-)

diff --git a/build/plugins/table-of-contents.html b/build/plugins/table-of-contents.html
index 49d6e01..e415945 100644
--- a/build/plugins/table-of-contents.html
+++ b/build/plugins/table-of-contents.html
@@ -1,5 +1,3 @@
-<!-- table of contents plugin -->
-
 <script>
     (function() {
         // /////////////////////////
@@ -22,10 +20,13 @@
             // which types of elements to add links for, in
             // "document.querySelector" format
             typesQuery: 'h1, h2, h3',
-            // whether default behavior is to be closed ('false'), open
-            // ('true'), or only open when screen wide enough to fit panel
-            // ('auto'). note: still always starts closed when page loads.
-            open: 'auto',
+            // whether toc starts open. use 'true' or 'false', or 'auto' to
+            // use 'true' behavior when screen wide enough and 'false' when not
+            startOpen: 'false',
+            // whether toc closes when clicking on toc link. use 'true' or
+            // 'false', or 'auto' to use 'false' behavior when screen wide
+            // enough and 'true' when not
+            clickClose: 'auto',
             // if list item is more than this many characters, text will be
             // truncated
             charLimit: '50',
@@ -50,13 +51,21 @@
             if (!panel)
                 return;
             makeEntries(panel);
+            // attach panel to document after making entries, so 'toc' heading
+            // in panel isn't included in toc
             document.body.insertBefore(panel, document.body.firstChild);
 
-            closePanel();
+            // initial panel state
+            if (
+                options.startOpen === 'true' ||
+                (options.startOpen === 'auto' && !isSmallScreen())
+            )
+                openPanel();
+            else
+                closePanel();
 
             // attach click, scroll, and hash change listeners to window
             window.addEventListener('click', onClick);
-            window.addEventListener('touchstart', onClick);
             window.addEventListener('scroll', onScroll);
             window.addEventListener('hashchange', onScroll);
             window.addEventListener('keyup', onKeyUp);
@@ -74,25 +83,10 @@
             return window.innerWidth < 816 + 260 * 2;
         }
 
-        // open/close panel based on option and screen size
-        function openOrClosePanel() {
-            if (
-                options.open === 'true' ||
-                (options.open === 'auto' && !isSmallScreen())
-            )
-                openPanel();
-            else
-                closePanel();
-        }
-
         // when mouse is clicked anywhere in window
         function onClick() {
-            const panel = document.getElementById('toc_panel');
-            if (!panel)
-                return;
-
-            if (panel.dataset.open === 'true')
-                openOrClosePanel();
+            if (isSmallScreen())
+                closePanel();
         }
 
         // when window is scrolled or hash changed
@@ -174,8 +168,8 @@
             button.classList.add('icon_button');
 
             // create header text
-            const text = document.createElement('h3');
-            text.innerHTML = 'View Table of Contents';
+            const text = document.createElement('h4');
+            text.innerHTML = 'Table of Contents';
 
             // create container for toc list
             const list = document.createElement('div');
@@ -252,8 +246,14 @@
         }
 
         // when link is clicked
-        function onLinkClick() {
-            openOrClosePanel();
+        function onLinkClick(event) {
+            if (
+                options.clickClose === 'true' ||
+                (options.clickClose === 'auto' && isSmallScreen())
+            )
+                closePanel();
+            else
+                openPanel();
         }
 
         // open panel if closed, close if opened

From 17492f1711e05278291d6b355125c990a1a068d6 Mon Sep 17 00:00:00 2001
From: Vincent Rubinetti <vince.rubinetti@gmail.com>
Date: Thu, 15 Oct 2020 22:46:15 -0400
Subject: [PATCH 13/50] HTML: inline-svg & d3 plugins

merges https://github.com/manubot/rootstock/pull/375
supersedes https://github.com/manubot/rootstock/pull/373

By default, these plugins are disabled. Enable in
`build/pandoc/defaults/html.yaml`.

Co-authored-by: Matthew Turk <matthewturk@gmail.com>
---
 build/pandoc/defaults/html.yaml |  3 ++
 build/plugins/d3.html           | 16 +++++++++
 build/plugins/inline-svg.html   | 62 +++++++++++++++++++++++++++++++++
 build/plugins/math.html         | 12 ++++---
 build/themes/default.html       | 11 +++---
 5 files changed, 96 insertions(+), 8 deletions(-)
 create mode 100644 build/plugins/d3.html
 create mode 100644 build/plugins/inline-svg.html

diff --git a/build/pandoc/defaults/html.yaml b/build/pandoc/defaults/html.yaml
index be2a423..956bbbc 100644
--- a/build/pandoc/defaults/html.yaml
+++ b/build/pandoc/defaults/html.yaml
@@ -2,8 +2,11 @@
 # Load on top of common defaults.
 to: html5
 output-file: output/manuscript.html
+# include-before-body:
+# - build/plugins/d3.html
 include-after-body:
 - build/themes/default.html
+# - build/plugins/inline-svg.html
 - build/plugins/anchors.html
 - build/plugins/accordion.html
 - build/plugins/tooltips.html
diff --git a/build/plugins/d3.html b/build/plugins/d3.html
new file mode 100644
index 0000000..48c16d8
--- /dev/null
+++ b/build/plugins/d3.html
@@ -0,0 +1,16 @@
+<!-- d3 plugin -->
+
+<script
+    src="https://cdnjs.cloudflare.com/ajax/libs/d3/6.2.0/d3.min.js"
+    integrity="sha512-C2RveGuPIWqkaLAluvoxyiaN1XYNe5ss11urhZWZYBUA9Ydgj+hfGKPcxCzTwut1/fmjEZR7Ac35f2aycT8Ogw=="
+    crossorigin="anonymous"
+>
+    // /////////////////////////
+    // DESCRIPTION
+    // /////////////////////////
+
+    // This third-party plugin 'D3' allows you to create complex, dynamic,
+    // interactive, data-driven visualizations in SVG.
+
+    // https://d3js.org/
+</script>
diff --git a/build/plugins/inline-svg.html b/build/plugins/inline-svg.html
new file mode 100644
index 0000000..be40242
--- /dev/null
+++ b/build/plugins/inline-svg.html
@@ -0,0 +1,62 @@
+<!-- inline svg plugin -->
+
+<script>
+  (function() {
+      // /////////////////////////
+      // DESCRIPTION
+      // /////////////////////////
+
+      // This Manubot plugin fetches the text source code of SVGs in <img> tags,
+      // and inserts it into the document in-place. This provides many
+      // advantages, such as being able to style SVGs globally from the CSS
+      // themes, and being able to make SVGs interactive with JavaScript and D3.
+      // If you have a script that expects SVGs to be inlined, wait for an
+      // "SVGLoaded" event before running it.
+
+      // Note: This requires the page to be served from a server to work
+      // See: https://stackoverflow.com/a/11063963/2180570
+      // Tip: Use the manubot commands to open the page in a local webserver
+      // See: https://github.com/manubot/rootstock#local-execution
+
+      // /////////////////////////
+      // SCRIPT
+      // /////////////////////////
+
+      // start script
+      async function start() {
+          // get all <img> tags that have "src" attributes that end with ".svg"
+          const imgs = document.querySelectorAll('img[src$=".svg"]');
+          const inlineSvgs = Array.from(imgs).map(inlineSvg);
+          await Promise.all(inlineSvgs);
+
+          // dispatch "inline finished" event
+          document.dispatchEvent(new Event('SVGLoaded'));
+      }
+
+      // take an svg <img> tag, fetch its source code, and replace it 
+      async function inlineSvg(img) {
+          try {
+              // fetch svg source code
+              const response = await fetch(img.src);
+              if (!response.ok) throw new Error('Couldn\'t get SVG source');
+              const source = await response.text();
+              if (!source.trim()) throw new Error('No SVG source');
+              // parse specifically as svg, create new (hidden) dom node
+              const svg = new DOMParser()
+                  .parseFromString(source, 'image/svg+xml')
+                  .querySelector('svg');
+              if (!svg) throw new Error('Couldn\'t parse SVG');
+              // transfer original img attributes into new svg
+              for (const { name, value } of img.attributes)
+                  svg.setAttribute(name, value);
+              // replace original image with new svg
+              img.outerHTML = svg.outerHTML;
+          } catch (error) {
+              console.log(error);
+          }
+      }
+
+      // start script when document is finished loading
+      window.addEventListener('load', start);
+  })();
+</script>
diff --git a/build/plugins/math.html b/build/plugins/math.html
index d7bc6ed..73f9bec 100644
--- a/build/plugins/math.html
+++ b/build/plugins/math.html
@@ -1,4 +1,4 @@
-<!-- math plugin configuration -->
+<!-- mathjax plugin configuration -->
 
 <script type="text/x-mathjax-config">
     MathJax.Hub.Config({
@@ -6,12 +6,16 @@
         "HTML-CSS": { linebreaks: { automatic: true } },
         "SVG": { linebreaks: { automatic: true } },
         "fast-preview": { disabled: true }
-    });
+  });
 </script>
 
-<!-- math plugin -->
+<!-- mathjax plugin -->
 
-<script src='https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML'>
+<script
+    src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-MML-AM_CHTML.js"
+    integrity="sha512-sRJwTwSmIAJfESgwGDn84X0s72u/n6qBjPShCGXi307x3ZFynu/u2A8652KZhmvjP0U0zeOFCxoMtj9imy9nOQ=="
+    crossorigin="anonymous"
+>
     // /////////////////////////
     // DESCRIPTION
     // /////////////////////////
diff --git a/build/themes/default.html b/build/themes/default.html
index cfff898..4022f31 100644
--- a/build/themes/default.html
+++ b/build/themes/default.html
@@ -216,7 +216,8 @@
     }
 
     /* figure image element */
-    figure img {
+    figure > img,
+    figure > svg {
         max-width: 100%;
         display: block;
         margin-left: auto;
@@ -224,7 +225,8 @@
     }
 
     /* figure auto-number */
-    img + figcaption > span:first-of-type {
+    img + figcaption > span:first-of-type,
+    svg + figcaption > span:first-of-type {
         font-weight: bold;
         margin-right: 5px;
     }
@@ -804,7 +806,8 @@
         }
 
         /* tooltip copy of <img> */
-        #tooltip_content > figure > img {
+        #tooltip_content > figure > img,
+        #tooltip_content > figure > svg {
             max-height: 260px;
         }
 
@@ -1055,7 +1058,7 @@
 
     @media only screen {
         /* regular <img> in document when hovered */
-        .lightbox_document_img:hover {
+        img.lightbox_document_img:hover {
             cursor: pointer;
         }
 

From e8b5c3455c47b02006527cada1e47b4ae0dd1439 Mon Sep 17 00:00:00 2001
From: Vincent Rubinetti <vince.rubinetti@gmail.com>
Date: Thu, 22 Oct 2020 15:03:43 -0400
Subject: [PATCH 14/50] fix mathjax loading error

merges https://github.com/manubot/rootstock/pull/378
closes https://github.com/manubot/rootstock/pull/377
refs https://github.com/manubot/rootstock/pull/375
---
 build/plugins/math.html | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/build/plugins/math.html b/build/plugins/math.html
index 73f9bec..f47b24d 100644
--- a/build/plugins/math.html
+++ b/build/plugins/math.html
@@ -12,8 +12,8 @@
 <!-- mathjax plugin -->
 
 <script
-    src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-MML-AM_CHTML.js"
-    integrity="sha512-sRJwTwSmIAJfESgwGDn84X0s72u/n6qBjPShCGXi307x3ZFynu/u2A8652KZhmvjP0U0zeOFCxoMtj9imy9nOQ=="
+    src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"
+    integrity="sha512-0doc9hKxR3PYwso42RD1p5ySZpzzuDiOwMrdCEh2WdJZCjcmFKc/wEnL+z8fBQrnHoiNWbo+3fiGkOYXBdQp4A=="
     crossorigin="anonymous"
 >
     // /////////////////////////

From b1d0de50ad091d3e6debcd9f7f8e4566733c75ee Mon Sep 17 00:00:00 2001
From: Daniel Himmelstein <daniel.himmelstein@gmail.com>
Date: Sun, 1 Nov 2020 09:32:00 -0500
Subject: [PATCH 15/50]  Upgrade environment on 2020-10-30

merges https://github.com/manubot/rootstock/pull/383

pandoc-eqnos upgrade addresses the following error:
UnboundLocalError: local variable 'ret' referenced before assignment
https://github.com/tomduck/pandoc-eqnos/issues/43

Hold back pandoc due to the lack of panflute support.

Switch commands in build/README.md to be relative to the repo root.
---
 build/README.md       | 12 +++++++-----
 build/environment.yml | 22 +++++++++++-----------
 2 files changed, 18 insertions(+), 16 deletions(-)

diff --git a/build/README.md b/build/README.md
index 27bf76d..f6087cf 100644
--- a/build/README.md
+++ b/build/README.md
@@ -20,30 +20,32 @@ To change the options, either edit the YAML files directly or add additional `--
 
 Note: currently, **Windows is not supported**.
 
-Install the [conda](https://conda.io) environment specified in [`environment.yml`](environment.yml) by running the following commands from this directory:
+Install the [conda](https://conda.io) environment specified in [`environment.yml`](environment.yml) by running the following commands
+(from the repository's root directory):
 
 ```sh
 # Install the environment
-conda env create --file environment.yml
+conda env create --file build/environment.yml
 ```
 
 If the `manubot` environment is already installed, but needs to be updated to reflect changes to `environment.yml`, use one of the following options:
 
 ```shell
 # option 1: update the existing environment.
-conda env update --file environment.yml
+conda env update --file build/environment.yml
 
 # option 2: remove and reinstall the manubot environment.
 # Slower than option 1, but guarantees a fresh environment.
 conda env remove --name manubot
-conda env create --file environment.yml
+conda env create --file build/environment.yml
 ```
 
 Activate with `conda activate manubot` (assumes `conda` version of [at least](https://github.com/conda/conda/blob/9d759d8edeb86569c25f6eb82053f09581013a2a/CHANGELOG.md#440-2017-12-20) 4.4).
 The environment should successfully install on both Linux and macOS.
 However, it will fail on Windows due to the [`pango`](https://anaconda.org/conda-forge/pango) dependency.
 
-Because the build process is dependent on having the appropriate version of the `manubot` Python package, it is necessary to use the version specified in `environment.yml`.
+Because the build process is dependent on having the appropriate version of the `manubot` Python package,
+it is necessary to use the version specified in `environment.yml`.
 The latest `manubot` release on PyPI may not be compatible with the latest version of this rootstock repository.
 
 ## Building PDFs
diff --git a/build/environment.yml b/build/environment.yml
index b156d6c..5eae4c9 100644
--- a/build/environment.yml
+++ b/build/environment.yml
@@ -10,22 +10,22 @@ dependencies:
   - jsonschema=3.2.0
   - pandoc=2.9.2
   - pango=1.40.14
-  - pip=20.0
-  - psutil=5.7.0
-  - python=3.7.6
+  - pip=20.2
+  - psutil=5.7.3
+  - python=3.7.8
   - pyyaml=5.3
-  - requests=2.23.0
-  - watchdog=0.10.2
-  - yamllint=1.21.0
+  - requests=2.24.0
+  - watchdog=0.10.3
+  - yamllint=1.25.0
   - pip:
     - errorhandler==2.0.1
-    - git+https://github.com/manubot/manubot@31968197d1ccd96a46bf092cdba4b575764bb954
+    - git+https://github.com/manubot/manubot@7c03b4a7d42506b3241e58cd5643a028443b9b9d
     - opentimestamps-client==0.7.0
     - opentimestamps==0.4.1
-    - pandoc-eqnos==2.1.1
-    - pandoc-fignos==2.2.0
-    - pandoc-tablenos==2.1.1
-    - pandoc-xnos==2.2.0
+    - pandoc-eqnos==2.3.0
+    - pandoc-fignos==2.3.1
+    - pandoc-tablenos==2.2.2
+    - pandoc-xnos==2.4.3
     - pybase62==0.4.3
     - pysha3==1.0.2
     - python-bitcoinlib==0.10.2

From aaefe9a4ffca65d1bbfccb6a3d7567b84888b5ef Mon Sep 17 00:00:00 2001
From: Daniel Himmelstein <daniel.himmelstein@gmail.com>
Date: Fri, 6 Nov 2020 13:18:22 -0500
Subject: [PATCH 16/50] Conda environment: pin additional manubot dependencies

merges https://github.com/manubot/rootstock/pull/385

Pin panflute dependency
We use panflute to build custom pandoc filters. Panflute versions
only work with specific versions of the Pandoc AST.
We need to pin pandoc/panflute to a version pair that is known to
work together.

Pin versions of additional explicit manubot dependencies, as of
https://github.com/manubot/manubot/blob/01d69f066eaf6554111e6bcf197f7ee1fcfb240b/setup.py#L65-L80

CI: use conda-incubator/setup-miniconda on GH actions
https://github.com/conda-incubator/setup-miniconda
appears to have replaced https://github.com/goanpeca/setup-miniconda.
The later is currently 31 commits behind.
---
 .github/workflows/manubot.yaml | 2 +-
 build/environment.yml          | 3 +++
 2 files changed, 4 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/manubot.yaml b/.github/workflows/manubot.yaml
index 0cabab3..3a3aeac 100644
--- a/.github/workflows/manubot.yaml
+++ b/.github/workflows/manubot.yaml
@@ -32,7 +32,7 @@ jobs:
           restore-keys: |
             ci-cache-refs/heads/master
       - name: Install Environment
-        uses: goanpeca/setup-miniconda@v1
+        uses: conda-incubator/setup-miniconda@v1
         with:
           activate-environment: manubot
           environment-file: build/environment.yml
diff --git a/build/environment.yml b/build/environment.yml
index 5eae4c9..df0319e 100644
--- a/build/environment.yml
+++ b/build/environment.yml
@@ -9,17 +9,20 @@ dependencies:
   - jinja2=2.11.2
   - jsonschema=3.2.0
   - pandoc=2.9.2
+  - panflute=1.12.5
   - pango=1.40.14
   - pip=20.2
   - psutil=5.7.3
   - python=3.7.8
   - pyyaml=5.3
   - requests=2.24.0
+  - toml=0.10.2
   - watchdog=0.10.3
   - yamllint=1.25.0
   - pip:
     - errorhandler==2.0.1
     - git+https://github.com/manubot/manubot@7c03b4a7d42506b3241e58cd5643a028443b9b9d
+    - isbnlib==3.10.3
     - opentimestamps-client==0.7.0
     - opentimestamps==0.4.1
     - pandoc-eqnos==2.3.0

From 97b294802ffcd39071b6e5b8ab59f60faf4be118 Mon Sep 17 00:00:00 2001
From: Daniel Himmelstein <daniel.himmelstein@gmail.com>
Date: Tue, 10 Nov 2020 07:51:35 -0500
Subject: [PATCH 17/50] CI: upgrade to conda-incubator/setup-miniconda@v2

merges https://github.com/manubot/rootstock/pull/389
closes https://github.com/manubot/rootstock/issues/388

> The `set-env` command is deprecated and will be disabled on
November 16th. Please upgrade to using Environment Files.
For more information see:
https://github.blog/changelog/2020-10-01-github-actions-deprecating-set-env-and-add-path-commands/
---
 .github/workflows/manubot.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/manubot.yaml b/.github/workflows/manubot.yaml
index 3a3aeac..9a2b89b 100644
--- a/.github/workflows/manubot.yaml
+++ b/.github/workflows/manubot.yaml
@@ -32,7 +32,7 @@ jobs:
           restore-keys: |
             ci-cache-refs/heads/master
       - name: Install Environment
-        uses: conda-incubator/setup-miniconda@v1
+        uses: conda-incubator/setup-miniconda@v2
         with:
           activate-environment: manubot
           environment-file: build/environment.yml

From 690aac113b4ee7dbb32a0af10a3d36c51a207025 Mon Sep 17 00:00:00 2001
From: Daniel Himmelstein <daniel.himmelstein@gmail.com>
Date: Thu, 10 Dec 2020 19:39:31 -0500
Subject: [PATCH 18/50] Switch default branch from master to main

merges https://github.com/manubot/rootstock/pull/399
closes https://github.com/manubot/rootstock/issues/349

Co-authored-by: Anthony Gitter <agitter@users.noreply.github.com>
---
 .appveyor.yml                  |  3 ++-
 .github/workflows/manubot.yaml | 20 +++++++++++++-------
 .travis.yml                    |  2 ++
 README.md                      |  4 ++--
 SETUP.md                       | 24 ++++++++++++++++++++----
 USAGE.md                       |  2 +-
 build/environment.yml          |  2 +-
 ci/README.md                   |  2 +-
 ci/deploy.sh                   |  3 ++-
 content/02.delete-me.md        |  2 +-
 output/README.md               |  4 ++--
 webpage/README.md              |  2 +-
 12 files changed, 48 insertions(+), 22 deletions(-)

diff --git a/.appveyor.yml b/.appveyor.yml
index d57e0cb..69d6e6c 100644
--- a/.appveyor.yml
+++ b/.appveyor.yml
@@ -8,10 +8,11 @@ skip_branch_with_pr: true
 # to only build commits from pull requests
 branches:
   only:
+    - main
     - master
 
 # Only run AppVeyor on commits that modify at least one of the following files
-# Delete these lines to run AppVeyor on all master branch commits
+# Delete these lines to run AppVeyor on all main/master branch commits
 only_commits:
   files:
     - .appveyor.yml
diff --git a/.github/workflows/manubot.yaml b/.github/workflows/manubot.yaml
index 9a2b89b..9a7d576 100644
--- a/.github/workflows/manubot.yaml
+++ b/.github/workflows/manubot.yaml
@@ -2,9 +2,11 @@ name: Manubot
 on:
   push:
     branches:
+      - main
       - master
   pull_request:
     branches:
+      - main
       - master
 jobs:
   manubot:
@@ -14,23 +16,27 @@ jobs:
       GITHUB_PULL_REQUEST_SHA: ${{ github.event.pull_request.head.sha }}
       SPELLCHECK: true
     steps:
-      - name: Set Environment Variables
-        run: |
-          TRIGGERING_SHA=${GITHUB_PULL_REQUEST_SHA:-$GITHUB_SHA}
-          echo "TRIGGERING_SHA_7=${TRIGGERING_SHA::7}" >> $GITHUB_ENV
-          echo "TRIGGERING_SHA: $TRIGGERING_SHA"
       - name: Checkout Repository
         uses: actions/checkout@v2
         with:
           # fetch entire commit history to support get_rootstock_commit
           fetch-depth: 0
+      - name: Set Environment Variables
+        run: |
+          TRIGGERING_SHA=${GITHUB_PULL_REQUEST_SHA:-$GITHUB_SHA}
+          echo "TRIGGERING_SHA_7=${TRIGGERING_SHA::7}" >> $GITHUB_ENV
+          echo "TRIGGERING_SHA: $TRIGGERING_SHA"
+          DEFAULT_BRANCH=$(git remote show origin | grep --perl-regexp --only-matching "(?<=HEAD branch: ).+")
+          echo "DEFAULT_BRANCH=${DEFAULT_BRANCH}" >> $GITHUB_ENV
+          echo "DEFAULT_BRANCH_REF=refs/heads/$DEFAULT_BRANCH" >> $GITHUB_ENV
+          echo "DEFAULT_BRANCH=$DEFAULT_BRANCH"
       - name: Cache
         uses: actions/cache@v1
         with:
           path: ci/cache
           key: ci-cache-${{ github.ref }}
           restore-keys: |
-            ci-cache-refs/heads/master
+            ci-cache-${{ env.DEFAULT_BRANCH_REF }}
       - name: Install Environment
         uses: conda-incubator/setup-miniconda@v2
         with:
@@ -53,7 +59,7 @@ jobs:
           name: manuscript-${{ github.run_id }}-${{ env.TRIGGERING_SHA_7 }}
           path: output
       - name: Deploy Manuscript
-        if: github.ref == 'refs/heads/master' && github.event_name == 'push' && !github.event.repository.fork
+        if: github.ref == env.DEFAULT_BRANCH_REF && github.event_name == 'push' && !github.event.repository.fork
         env:
           MANUBOT_ACCESS_TOKEN: ${{ secrets.GITHUB_TOKEN }}
           MANUBOT_SSH_PRIVATE_KEY: ${{ secrets.MANUBOT_SSH_PRIVATE_KEY }}
diff --git a/.travis.yml b/.travis.yml
index a842138..cf4cbb6 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -5,6 +5,7 @@ services:
   - docker
 branches:
   only:
+    - main
     - master
 env:
   - SPELLCHECK=true
@@ -20,5 +21,6 @@ deploy:
   script: bash ci/deploy.sh
   skip_cleanup: true
   on:
+    # branch kept as master since travis deployment is legacy.
     branch: master
     condition: $TRAVIS_EVENT_TYPE = "push" && (-v MANUBOT_SSH_PRIVATE_KEY || "${!encrypted_*}" != "")
diff --git a/README.md b/README.md
index d806e79..51fca30 100644
--- a/README.md
+++ b/README.md
@@ -5,7 +5,7 @@
 [![HTML Manuscript](https://img.shields.io/badge/manuscript-HTML-blue.svg)](https://manubot.github.io/rootstock/)
 [![PDF Manuscript](https://img.shields.io/badge/manuscript-PDF-blue.svg)](https://manubot.github.io/rootstock/manuscript.pdf)
 [![GitHub Actions Status](https://github.com/manubot/rootstock/workflows/Manubot/badge.svg)](https://github.com/manubot/rootstock/actions)
-[![Travis Build Status](https://travis-ci.com/manubot/rootstock.svg?branch=master)](https://travis-ci.com/manubot/rootstock)
+[![Travis Build Status](https://travis-ci.com/manubot/rootstock.svg?branch=main)](https://travis-ci.com/manubot/rootstock)
 <!-- usage note: delete CI badges above for services not used by your manuscript -->
 
 ## Manuscript description
@@ -79,7 +79,7 @@ Whenever a pull request is opened, CI (continuous integration) will test whether
 The build process aims to detect common errors, such as invalid citations.
 If your pull request build fails, see the CI logs for the cause of failure and revise your pull request accordingly.
 
-When a commit to the `master` branch occurs (for example, when a pull request is merged), CI builds the manuscript and writes the results to the [`gh-pages`](https://github.com/manubot/rootstock/tree/gh-pages) and [`output`](https://github.com/manubot/rootstock/tree/output) branches.
+When a commit to the `main` branch occurs (for example, when a pull request is merged), CI builds the manuscript and writes the results to the [`gh-pages`](https://github.com/manubot/rootstock/tree/gh-pages) and [`output`](https://github.com/manubot/rootstock/tree/output) branches.
 The `gh-pages` branch uses [GitHub Pages](https://pages.github.com/) to host the following URLs:
 
 + **HTML manuscript** at https://manubot.github.io/rootstock/
diff --git a/SETUP.md b/SETUP.md
index 136376c..fa83e0b 100644
--- a/SETUP.md
+++ b/SETUP.md
@@ -13,6 +13,7 @@
   * [README updates](#readme-updates)
   * [Finalize](#finalize)
 - [Merging upstream rootstock changes](#merging-upstream-rootstock-changes)
+  * [Default branch](#default-branch)
 
 _generated with [markdown-toc](https://ecotrust-canada.github.io/markdown-toc/)_
 
@@ -68,7 +69,7 @@ Do not initialize the repository, other than optionally adding a Description.
 Next, push your cloned manuscript:
 
 ```sh
-git push --set-upstream origin master
+git push --set-upstream origin main
 ```
 
 ## Continuous integration
@@ -263,7 +264,7 @@ If the changes look okay, commit and push:
 ```shell
 git add --update
 git commit --message "Brand repo to $OWNER/$REPO"
-git push origin master
+git push origin main
 ```
 
 You should be good to go now.
@@ -290,7 +291,7 @@ Second, pull the new commits from rootstock, but do not automerge:
 git config remote.rootstock.url || git remote add rootstock https://github.com/manubot/rootstock.git
 
 # pull the new commits from rootstock
-git pull --no-ff --no-rebase --no-commit rootstock master
+git pull --no-ff --no-rebase --no-commit rootstock main
 ```
 
 If all goes well, there won't be any conflicts.
@@ -302,7 +303,7 @@ You may notice changes that affect how items in `content` are processed.
 If so, you should edit and stage `content` files as needed.
 When there are no longer any unstaged changes, then do `git commit`.
 
-If updating `master` via a pull request, proceed to push the commit to GitHub and open a pull request.
+If updating your default branch (i.e. `main` or `master`) via a pull request, proceed to push the commit to GitHub and open a pull request.
 Once the pull request is ready to merge, use GitHub's "Create a merge commit" option rather than "Squash and merge" or "Rebase and merge" to preserve the rootstock commit hashes.
 
 The environment for local builds does not automatically update when [`build/environment.yml`](build/environment.yml) changes.
@@ -312,3 +313,18 @@ To update your local conda `manubot` environment with new changes, run:
 # update a local conda environment
 conda env update --file build/environment.yml
 ```
+
+## Default branch
+
+On 2020-10-01, GitHub [changed](https://github.blog/changelog/2020-10-01-the-default-branch-for-newly-created-repositories-is-now-main/) the default branch name for new repositories from `master` to `main`.
+More information on GitHub's migration is available at [github/renaming](https://github.com/github/renaming).
+
+On 2020-12-10, Manubot [updated](https://github.com/manubot/rootstock/pull/399) the Rootstock default branch to `main`.
+For existing manuscripts, the default branch will remain `master`,
+unless manually switched to `main`.
+Rootstock has been configured to run continuous integration on both `main` and `master`,
+so existing manuscripts can, but are not required, to switch their default branch to `main`.
+
+Upgrading to the latest Rootstock will change several READMEs links to `main`.
+For manuscripts that do not plan to switch their default branch,
+do not include these changes in the upgrade merge commit.
diff --git a/USAGE.md b/USAGE.md
index 4323077..a7e446b 100644
--- a/USAGE.md
+++ b/USAGE.md
@@ -13,7 +13,7 @@ For basic formatting, check out the [CommonMark Help](https://commonmark.org/hel
 In addition, Manubot supports an extended version of markdown, tailored for scholarly writing, which includes [Pandoc's Markdown](https://pandoc.org/MANUAL.html#pandocs-markdown) and the extensions discussed below.
 
 The `content/02.delete-me.md` file in the Rootstock repository shows many of the elements and formatting options supported by Manubot.
-See the [raw markdown](https://gitlab.com/manubot/rootstock/blob/master/content/02.delete-me.md#L) in this file and compare it to the [rendered manuscript](https://manubot.github.io/rootstock/).
+See the [raw markdown](https://gitlab.com/manubot/rootstock/blob/main/content/02.delete-me.md#L) in this file and compare it to the [rendered manuscript](https://manubot.github.io/rootstock/).
 
 Within a paragraph in markdown, single newlines are interpreted as whitespace (same as a space).
 A paragraph's source does not need to contain newlines.
diff --git a/build/environment.yml b/build/environment.yml
index df0319e..f81dfc8 100644
--- a/build/environment.yml
+++ b/build/environment.yml
@@ -21,7 +21,7 @@ dependencies:
   - yamllint=1.25.0
   - pip:
     - errorhandler==2.0.1
-    - git+https://github.com/manubot/manubot@7c03b4a7d42506b3241e58cd5643a028443b9b9d
+    - git+https://github.com/manubot/manubot@55c5e1e526261ebadd2aefed2c2757792d8d2ebf
     - isbnlib==3.10.3
     - opentimestamps-client==0.7.0
     - opentimestamps==0.4.1
diff --git a/ci/README.md b/ci/README.md
index db6ccca..3e89fc2 100644
--- a/ci/README.md
+++ b/ci/README.md
@@ -1,7 +1,7 @@
 # Continuous integration tools
 
 This directory contains tools and files for continuous integration (CI).
-Specifically, [`deploy.sh`](deploy.sh) runs on successful `master` branch builds that are not pull requests.
+Specifically, [`deploy.sh`](deploy.sh) runs on successful `main` branch builds that are not pull requests.
 The contents of `../webpage` are committed to the `gh-pages` branch.
 The contents of `../output` are committed to the `output` branch.
 
diff --git a/ci/deploy.sh b/ci/deploy.sh
index ed3d8a8..3c6d44d 100755
--- a/ci/deploy.sh
+++ b/ci/deploy.sh
@@ -12,7 +12,8 @@ REPO_SLUG=${TRAVIS_REPO_SLUG:-$GITHUB_REPOSITORY}
 COMMIT=${TRAVIS_COMMIT:-$GITHUB_SHA}
 CI_BUILD_WEB_URL=${CI_BUILD_WEB_URL:-$TRAVIS_BUILD_WEB_URL}
 CI_JOB_WEB_URL=${CI_JOB_WEB_URL:-$TRAVIS_JOB_WEB_URL}
-BRANCH=${TRAVIS_BRANCH:-master}
+BRANCH=${TRAVIS_BRANCH:-$DEFAULT_BRANCH}
+BRANCH=${BRANCH:-main}
 
 # Add commit hash to the README
 OWNER_NAME="$(dirname "$REPO_SLUG")"
diff --git a/content/02.delete-me.md b/content/02.delete-me.md
index 78d9c7e..c2b1fd0 100644
--- a/content/02.delete-me.md
+++ b/content/02.delete-me.md
@@ -186,7 +186,7 @@ Loaded from a specific (hashed) version of the image on GitHub.
 **A vector `.svg` image loaded from GitHub.**
 The parameter `sanitize=true` is necessary to properly load SVGs hosted via GitHub URLs.
 White background specified to serve as a backdrop for transparent sections of the image.
-](https://raw.githubusercontent.com/manubot/resources/master/test/vector.svg?sanitize=true "Vector image"){#fig:vector-image height=2.5in .white}
+](https://raw.githubusercontent.com/manubot/resources/main/test/vector.svg?sanitize=true "Vector image"){#fig:vector-image height=2.5in .white}
 
 ## Tables
 
diff --git a/output/README.md b/output/README.md
index fbdc3a6..12d8f51 100644
--- a/output/README.md
+++ b/output/README.md
@@ -1,8 +1,8 @@
 # Generated citation / reference files
 
 The `output` branch contains files automatically generated by the manuscript build process.
-It consists of the contents of the `output` directory of the `master` branch.
-These files are not tracked in `master`, but instead written to the `output` branch by continuous integration builds.
+It consists of the contents of the `output` directory of the `main` branch.
+These files are not tracked in `main`, but instead written to the `output` branch by continuous integration builds.
 
 ## Files
 
diff --git a/webpage/README.md b/webpage/README.md
index 9e22c56..739f497 100644
--- a/webpage/README.md
+++ b/webpage/README.md
@@ -6,7 +6,7 @@ To redirect to the permalink for the latest manuscript version at anytime, use t
 
 ## Files
 
-This directory contains the following files, which are mostly ignored on the `master` branch:
+This directory contains the following files, which are mostly ignored on the `main` branch:
 
 + [`index.html`](index.html) is an HTML manuscript.
 + [`manuscript.pdf`](manuscript.pdf) is a PDF manuscript.

From 2191d929a12a233347ee79c673b8f2971c10e6dd Mon Sep 17 00:00:00 2001
From: Daniel Himmelstein <daniel.himmelstein@gmail.com>
Date: Sun, 27 Dec 2020 18:12:42 -0500
Subject: [PATCH 19/50] enable citekey prefix inference

merges https://github.com/manubot/rootstock/pull/404
refs https://github.com/manubot/manubot/issues/123
---
 USAGE.md              | 15 ++++++++++++++-
 build/environment.yml |  2 +-
 2 files changed, 15 insertions(+), 2 deletions(-)

diff --git a/USAGE.md b/USAGE.md
index a7e446b..5bd004a 100644
--- a/USAGE.md
+++ b/USAGE.md
@@ -110,6 +110,19 @@ When choosing which source to use for a citation, we recommend the following ord
 9. For references that do not have any of the above persistent identifiers, the citation key does not need to include a prefix.
    Citing `@old-manuscript` will work, but only if reference metadata is [provided manually](#reference-metadata).
 
+Manubot is able to infer certain prefixes,
+such some citations can be formatted like `@accession` (without a prefix).
+Examples includes DOIs like `@10.15363/thinklab.4` or `@10/993`,
+PMC / PubMed identifiers like `@PMC4497619` or `@26158728`,
+arXiv identifier like `@1508.06576v2`,
+and Wikidata identifiers like `@Q50051684`.
+To disable citekey prefix inference, add the following to `metadata.yaml`:
+
+```yaml
+pandoc:
+  manubot-infer-citekey-prefixes: false
+```
+
 Cite multiple items at once like:
 
 ```md
@@ -136,7 +149,7 @@ By default, `pandoc-manubot-cite` does not fail upon invalid citations, although
 
 ```yaml
 pandoc:
-  manubot-fail-on-errors: True
+  manubot-fail-on-errors: true
 ```
 
 #### Citation aliases
diff --git a/build/environment.yml b/build/environment.yml
index f81dfc8..abee7fb 100644
--- a/build/environment.yml
+++ b/build/environment.yml
@@ -21,7 +21,7 @@ dependencies:
   - yamllint=1.25.0
   - pip:
     - errorhandler==2.0.1
-    - git+https://github.com/manubot/manubot@55c5e1e526261ebadd2aefed2c2757792d8d2ebf
+    - git+https://github.com/manubot/manubot@553090a16ac24a9fdc3f8df241a91b790c140865
     - isbnlib==3.10.3
     - opentimestamps-client==0.7.0
     - opentimestamps==0.4.1

From 87c11957cf69b73ebed5518f7928b99adb1dc5d6 Mon Sep 17 00:00:00 2001
From: Vincent Rubinetti <vince.rubinetti@gmail.com>
Date: Fri, 5 Feb 2021 12:43:51 -0500
Subject: [PATCH 20/50] Webpage: refactor plugins & add scite plugin

merges https://github.com/manubot/rootstock/pull/409

* moves repeated and shared/generic functions to separate "core" plugin
* reorganizes html.yaml config into first and third party plugins
* removes functionality to set plugin options from url
* reformats plugins with Prettier (eg 4 space tabs to 2 space)
* removes anonymizer wrapper. Just make <script> tag into module to keep scope local
  and avoid function name conflicts. this reduces the indent of the whole script by one level.
* moves plugin specific CSS to plugins themselves
* adds scite plugin (uncomment to enable)
---
 build/pandoc/defaults/html.yaml      |   24 +-
 build/plugins/accordion.html         |  405 ++----
 build/plugins/analytics.html         |    8 +-
 build/plugins/anchors.html           |  259 ++--
 build/plugins/attributes.html        |  212 ++-
 build/plugins/core.html              |  129 ++
 build/plugins/d3.html                |   24 +-
 build/plugins/hypothesis.html        |  234 ++--
 build/plugins/inline-svg.html        |  113 +-
 build/plugins/jump-to-first.html     |  362 ++----
 build/plugins/lightbox.html          | 1254 +++++++++---------
 build/plugins/link-highlight.html    |  339 +++--
 build/plugins/math.html              |   27 -
 build/plugins/mathjax.html           |   53 +
 build/plugins/scite.html             |   61 +
 build/plugins/table-of-contents.html |  707 +++++-----
 build/plugins/tooltips.html          | 1099 +++++++---------
 build/themes/default.html            | 1803 +++++++++-----------------
 18 files changed, 3212 insertions(+), 3901 deletions(-)
 create mode 100644 build/plugins/core.html
 delete mode 100644 build/plugins/math.html
 create mode 100644 build/plugins/mathjax.html
 create mode 100644 build/plugins/scite.html

diff --git a/build/pandoc/defaults/html.yaml b/build/pandoc/defaults/html.yaml
index 956bbbc..50d2981 100644
--- a/build/pandoc/defaults/html.yaml
+++ b/build/pandoc/defaults/html.yaml
@@ -3,22 +3,28 @@
 to: html5
 output-file: output/manuscript.html
 # include-before-body:
-# - build/plugins/d3.html
+### third-party plugins
+#- build/plugins/d3.html
 include-after-body:
+### theme
 - build/themes/default.html
-# - build/plugins/inline-svg.html
-- build/plugins/anchors.html
+### first-party plugins
+- build/plugins/core.html # needed for all first-party plugins
 - build/plugins/accordion.html
-- build/plugins/tooltips.html
+- build/plugins/anchors.html
+- build/plugins/attributes.html
+#- build/plugins/inline-svg.html
 - build/plugins/jump-to-first.html
+- build/plugins/lightbox.html
 - build/plugins/link-highlight.html
 - build/plugins/table-of-contents.html
-- build/plugins/lightbox.html
-- build/plugins/attributes.html
-- build/plugins/math.html
-- build/plugins/hypothesis.html
+- build/plugins/tooltips.html
+### third-party plugins
 - build/plugins/analytics.html
+- build/plugins/hypothesis.html
+- build/plugins/mathjax.html
+#- build/plugins/scite.html
 variables:
-  math: ''
+  math: ""
 html-math-method:
   method: mathjax
diff --git a/build/plugins/accordion.html b/build/plugins/accordion.html
index eaddd54..98ba165 100644
--- a/build/plugins/accordion.html
+++ b/build/plugins/accordion.html
@@ -1,272 +1,145 @@
-<!-- accordion plugin -->
-
-<script>
-    (function() {
-        // /////////////////////////
-        // DESCRIPTION
-        // /////////////////////////
-
-        // This Manubot plugin allows sections of content under <h2> headings
-        // to be collapsible.
-
-        // /////////////////////////
-        // OPTIONS
-        // /////////////////////////
-
-        // plugin name prefix for url parameters
-        const pluginName = 'accordion';
-
-        // default plugin options
-        const options = {
-            // whether to always start expanded ('false'), always start
-            // collapsed ('true'), or start collapsed when screen small ('auto')
-            startCollapsed: 'auto',
-            // whether plugin is on or not
-            enabled: 'true'
-        };
-
-        // change options above, or override with url parameter, eg:
-        // 'manuscript.html?pluginName-enabled=false'
-
-        // /////////////////////////
-        // SCRIPT
-        // /////////////////////////
-
-        // start script
-        function start() {
-            // run through each <h2> heading
-            const headings = document.querySelectorAll('h2');
-            for (const heading of headings) {
-                addArrow(heading);
-
-                // start expanded/collapsed based on option
-                if (
-                    options.startCollapsed === 'true' ||
-                    (options.startCollapsed === 'auto' && isSmallScreen())
-                )
-                    collapseHeading(heading);
-                else
-                    expandHeading(heading);
-            }
-
-            // attach hash change listener to window
-            window.addEventListener('hashchange', onHashChange);
-        }
-
-        // when hash (eg manuscript.html#introduction) changes
-        function onHashChange() {
-            const target = getHashTarget();
-            if (target)
-                goToElement(target);
-        }
-
-        // add arrow to heading
-        function addArrow(heading) {
-            // add arrow button
-            const arrow = document.createElement('button');
-            arrow.innerHTML = document.querySelector(
-                '.icon_angle_down'
-            ).innerHTML;
-            arrow.classList.add('icon_button', 'accordion_arrow');
-            heading.insertBefore(arrow, heading.firstChild);
-
-            // attach click listener to heading and button
-            heading.addEventListener('click', onHeadingClick);
-            arrow.addEventListener('click', onArrowClick);
-        }
-
-        // determine if on mobile-like device with small screen
-        function isSmallScreen() {
-            return Math.min(window.innerWidth, window.innerHeight) < 480;
-        }
-
-        // scroll to and focus element
-        function goToElement(element, offset) {
-            // expand accordion section if collapsed
-            expandElement(element);
-            const y =
-                getRectInView(element).top -
-                getRectInView(document.documentElement).top -
-                (offset || 0);
-            // trigger any function listening for "onscroll" event
-            window.dispatchEvent(new Event('scroll'));
-            window.scrollTo(0, y);
-            document.activeElement.blur();
-            element.focus();
-        }
-
-        // get element that is target of hash
-        function getHashTarget(link) {
-            const hash = link ? link.hash : window.location.hash;
-            const id = hash.slice(1);
-            let target = document.querySelector('[id="' + id + '"]');
-            if (!target)
-                return;
-
-            // if figure or table, modify target to get expected element
-            if (id.indexOf('fig:') === 0)
-                target = target.querySelector('figure');
-            if (id.indexOf('tbl:') === 0)
-                target = target.querySelector('table');
-
-            return target;
-        }
-
-        // when <h2> heading is clicked
-        function onHeadingClick(event) {
-            // only collapse if <h2> itself is target of click (eg, user did
-            // not click on anchor within <h2>)
-            if (event.target === this)
-                toggleCollapse(this);
-        }
-
-        // when arrow button is clicked
-        function onArrowClick() {
-            toggleCollapse(this.parentNode);
-        }
-
-        // collapse section if expanded, expand if collapsed
-        function toggleCollapse(heading) {
-            if (heading.dataset.collapsed === 'false')
-                collapseHeading(heading);
-            else
-                expandHeading(heading);
-        }
-
-        // elements to exclude from collapse, such as table of contents panel,
-        // hypothesis panel, etc
-        const exclude = '#toc_panel, div.annotator-frame, #lightbox_overlay';
-
-        // collapse section
-        function collapseHeading(heading) {
-            heading.setAttribute('data-collapsed', 'true');
-            const children = getChildren(heading);
-            for (const child of children)
-                child.setAttribute('data-collapsed', 'true');
-        }
-
-        // expand section
-        function expandHeading(heading) {
-            heading.setAttribute('data-collapsed', 'false');
-            const children = getChildren(heading);
-            for (const child of children)
-                child.setAttribute('data-collapsed', 'false');
-        }
-
-        // get list of elements between this <h2> and next <h2> or <h1>
-        // ("children" of the <h2> section)
-        function getChildren(heading) {
-            return nextUntil(heading, 'h2, h1', exclude);
-        }
-
-        // get position/dimensions of element or viewport
-        function getRectInView(element) {
-            let rect = {};
-            rect.left = 0;
-            rect.top = 0;
-            rect.right = document.documentElement.clientWidth;
-            rect.bottom = document.documentElement.clientHeight;
-            let style = {};
-
-            if (element instanceof HTMLElement) {
-                rect = element.getBoundingClientRect();
-                style = window.getComputedStyle(element);
-            }
-
-            const margin = {};
-            margin.left = parseFloat(style.marginLeftWidth) || 0;
-            margin.top = parseFloat(style.marginTopWidth) || 0;
-            margin.right = parseFloat(style.marginRightWidth) || 0;
-            margin.bottom = parseFloat(style.marginBottomWidth) || 0;
-
-            const border = {};
-            border.left = parseFloat(style.borderLeftWidth) || 0;
-            border.top = parseFloat(style.borderTopWidth) || 0;
-            border.right = parseFloat(style.borderRightWidth) || 0;
-            border.bottom = parseFloat(style.borderBottomWidth) || 0;
-
-            const newRect = {};
-            newRect.left = rect.left + margin.left + border.left;
-            newRect.top = rect.top + margin.top + border.top;
-            newRect.right = rect.right + margin.right + border.right;
-            newRect.bottom = rect.bottom + margin.bottom + border.bottom;
-            newRect.width = newRect.right - newRect.left;
-            newRect.height = newRect.bottom - newRect.top;
-
-            return newRect;
-        }
-
-        // get list of elements after a start element up to element matching
-        // query
-        function nextUntil(element, query, exclude) {
-            const elements = [];
-            while (element = element.nextElementSibling, element) {
-                if (element.matches(query))
-                    break;
-                if (!element.matches(exclude))
-                    elements.push(element);
-            }
-            return elements;
-        }
-
-        // get closest element before specified element that matches query
-        function firstBefore(element, query) {
-            while (
-                element &&
-                element !== document.body &&
-                !element.matches(query)
-            )
-                element = element.previousElementSibling || element.parentNode;
-
-            return element;
-        }
-
-        // check if element is part of collapsed heading
-        function isCollapsed(element) {
-            while (element && element !== document.body) {
-                if (element.dataset.collapsed === 'true')
-                    return true;
-                element = element.parentNode;
-            }
-            return false;
-        }
-
-        // expand heading containing element if necesary
-        function expandElement(element) {
-            if (isCollapsed(element)) {
-                const heading = firstBefore(element, 'h2');
-                if (heading)
-                    heading.click();
-            }
-        }
-
-        // load options from url parameters
-        function loadOptions() {
-            const url = window.location.search;
-            const params = new URLSearchParams(url);
-            for (const optionName of Object.keys(options)) {
-                const paramName = pluginName + '-' + optionName;
-                const param = params.get(paramName);
-                if (param !== '' && param !== null)
-                    options[optionName] = param;
-            }
-        }
-        loadOptions();
-
-        // start script when document is finished loading
-        if (options.enabled === 'true')
-            window.addEventListener('load', start);
-    })();
+<!--
+  Accordion Plugin
+
+  Allows sections of content under h2 headings to be collapsible.
+-->
+
+<script type="module">
+  // whether to always start expanded ('false'), always start collapsed
+  // ('true'), or start collapsed when screen small ('auto')
+  const startCollapsed = "auto";
+
+  // start script
+  function start() {
+    // run through each <h2> heading
+    const headings = document.querySelectorAll("h2");
+    for (const heading of headings) {
+      addArrow(heading);
+
+      // start expanded/collapsed based on option
+      if (
+        startCollapsed === "true" ||
+        (startCollapsed === "auto" && isSmallScreen())
+      )
+        collapseHeading(heading);
+      else expandElement(heading);
+    }
+
+    // attach hash change listener to window
+    window.addEventListener("hashchange", onHashChange);
+  }
+
+  // when hash (eg manuscript.html#introduction) changes
+  function onHashChange() {
+    const target = getHashTarget();
+    if (target) goToElement(target);
+  }
+
+  // add arrow to heading
+  function addArrow(heading) {
+    // add arrow button
+    const arrow = document.createElement("button");
+    arrow.innerHTML = document.querySelector(".icon_angle_down").innerHTML;
+    arrow.classList.add("icon_button", "accordion_arrow");
+    heading.insertBefore(arrow, heading.firstChild);
+
+    // attach click listener to heading and button
+    heading.addEventListener("click", onHeadingClick);
+    arrow.addEventListener("click", onArrowClick);
+  }
+
+  // determine if on mobile-like device with small screen
+  function isSmallScreen() {
+    return Math.min(window.innerWidth, window.innerHeight) < 480;
+  }
+
+  // when <h2> heading is clicked
+  function onHeadingClick(event) {
+    // only collapse if <h2> itself is target of click (eg, user did
+    // not click on anchor within <h2>)
+    if (event.target === this) toggleCollapse(this);
+  }
+
+  // when arrow button is clicked
+  function onArrowClick() {
+    toggleCollapse(this.parentNode);
+  }
+
+  // collapse section if expanded, expand if collapsed
+  function toggleCollapse(heading) {
+    if (heading.dataset.collapsed === "false") collapseHeading(heading);
+    else expandElement(heading);
+  }
+
+  // elements to exclude from collapse, such as table of contents panel,
+  // hypothesis panel, etc
+  const exclude = "#toc_panel, div.annotator-frame, #lightbox_overlay";
+
+  // collapse section
+  function collapseHeading(heading) {
+    heading.setAttribute("data-collapsed", "true");
+    const children = getChildren(heading);
+    for (const child of children) child.setAttribute("data-collapsed", "true");
+  }
+
+  // expand section
+  function expandElement(heading) {
+    heading.setAttribute("data-collapsed", "false");
+    const children = getChildren(heading);
+    for (const child of children) child.setAttribute("data-collapsed", "false");
+  }
+
+  // get list of elements between this <h2> and next <h2> or <h1>
+  // ("children" of the <h2> section)
+  function getChildren(heading) {
+    return nextUntil(heading, "h2, h1", exclude);
+  }
+
+  // start script when document is finished loading
+  window.addEventListener("load", start);
 </script>
 
 <!-- angle down icon -->
 
 <template class="icon_angle_down">
-    <!-- modified from: https://fontawesome.com/icons/angle-down -->
-    <svg width="16" height="16" viewBox="0 0 448 512">
-        <path
-            fill="currentColor"
-            d="M207.029 381.476L12.686 187.132c-9.373-9.373-9.373-24.569 0-33.941l22.667-22.667c9.357-9.357 24.522-9.375 33.901-.04L224 284.505l154.745-154.021c9.379-9.335 24.544-9.317 33.901.04l22.667 22.667c9.373 9.373 9.373 24.569 0 33.941L240.971 381.476c-9.373 9.372-24.569 9.372-33.942 0z"
-        ></path>
-    </svg>
+  <!-- modified from: https://fontawesome.com/icons/angle-down -->
+  <svg width="16" height="16" viewBox="0 0 448 512">
+    <path
+      fill="currentColor"
+      d="M207.029 381.476L12.686 187.132c-9.373-9.373-9.373-24.569 0-33.941l22.667-22.667c9.357-9.357 24.522-9.375 33.901-.04L224 284.505l154.745-154.021c9.379-9.335 24.544-9.317 33.901.04l22.667 22.667c9.373 9.373 9.373 24.569 0 33.941L240.971 381.476c-9.373 9.372-24.569 9.372-33.942 0z"
+    ></path>
+  </svg>
 </template>
+
+<style>
+  @media only screen {
+    /* accordion arrow button */
+    .accordion_arrow {
+      margin-right: 10px;
+    }
+
+    /* arrow icon when <h2> data-collapsed attribute true */
+    h2[data-collapsed="true"] > .accordion_arrow > svg {
+      transform: rotate(-90deg);
+    }
+
+    /* all elements (except <h2>'s) when data-collapsed attribute true */
+    *:not(h2)[data-collapsed="true"] {
+      display: none;
+    }
+
+    /* accordion arrow button when hovered and <h2>'s when hovered */
+    .accordion_arrow:hover,
+    h2[data-collapsed="true"]:hover,
+    h2[data-collapsed="false"]:hover {
+      cursor: pointer;
+    }
+  }
+
+  /* always hide accordion arrow button on print */
+  @media only print {
+    .accordion_arrow {
+      display: none;
+    }
+  }
+</style>
diff --git a/build/plugins/analytics.html b/build/plugins/analytics.html
index 0e641a1..cbab532 100644
--- a/build/plugins/analytics.html
+++ b/build/plugins/analytics.html
@@ -1,3 +1,5 @@
-<!-- analytics plugin -->
-
-<!-- copy and paste code from Google Analytics or similar service here -->
+<!--
+  Analytics Plugin (third-party) 
+  
+  Copy and paste code from Google Analytics or similar service here.
+-->
diff --git a/build/plugins/anchors.html b/build/plugins/anchors.html
index 4f2e6ba..68f1225 100644
--- a/build/plugins/anchors.html
+++ b/build/plugins/anchors.html
@@ -1,144 +1,127 @@
-<!-- anchors plugin -->
-
-<script>
-    (function() {
-        // /////////////////////////
-        // DESCRIPTION
-        // /////////////////////////
-
-        // This Manubot plugin adds an anchor next to each of a certain type
-        // of element that provides a human-readable url to that specific
-        // item/position in the document (eg "manuscript.html#abstract"). It
-        // also makes it such that scrolling out of view of a target removes
-        // its identifier from the url.
-
-        // /////////////////////////
-        // OPTIONS
-        // /////////////////////////
-
-        // plugin name prefix for url parameters
-        const pluginName = 'anchors';
-
-        // default plugin options
-        const options = {
-            // which types of elements to add anchors next to, in
-            // "document.querySelector" format
-            typesQuery: 'h1, h2, h3, [id^="fig:"], [id^="tbl:"], [id^="eq:"]',
-            // whether plugin is on or not
-            enabled: 'true'
-        };
-
-        // change options above, or override with url parameter, eg:
-        // 'manuscript.html?pluginName-enabled=false'
-
-        // /////////////////////////
-        // SCRIPT
-        // /////////////////////////
-
-        // start script
-        function start() {
-            // add anchor to each element of specified types
-            const elements = document.querySelectorAll(options.typesQuery);
-            for (const element of elements)
-                addAnchor(element);
-
-            // attach scroll listener to window
-            window.addEventListener('scroll', onScroll);
-        }
-
-        // when window is scrolled
-        function onScroll() {
-            // if url has hash and user has scrolled out of view of hash
-            // target, remove hash from url
-            const tolerance = 100;
-            const target = getHashTarget();
-            if (target) {
-                if (
-                    target.getBoundingClientRect().top >
-                        window.innerHeight + tolerance ||
-                    target.getBoundingClientRect().bottom < 0 - tolerance
-                )
-                    history.pushState(null, null, ' ');
-            }
-        }
-
-        // add anchor to element
-        function addAnchor(element) {
-            let addTo; // element to add anchor button to
-
-            // if figure or table, modify withId and addTo to get expected
-            // elements
-            if (element.id.indexOf('fig:') === 0) {
-                addTo = element.querySelector('figcaption');
-            } else if (element.id.indexOf('tbl:') === 0) {
-                addTo = element.querySelector('caption');
-            } else if (element.id.indexOf('eq:') === 0) {
-                addTo = element.querySelector('.eqnos-number');
-            }
-
-            addTo = addTo || element;
-            const id = element.id || null;
-
-            // do not add anchor if element doesn't have assigned id.
-            // id is generated by pandoc and is assumed to be unique and
-            // human-readable
-            if (!id)
-                return;
-
-            // create anchor button
-            const anchor = document.createElement('a');
-            anchor.innerHTML = document.querySelector('.icon_link').innerHTML;
-            anchor.title = 'Link to this part of the document';
-            anchor.classList.add('icon_button', 'anchor');
-            anchor.dataset.ignore = 'true';
-            anchor.href = '#' + id;
-            addTo.appendChild(anchor);
-        }
-
-        // get element that is target of link or url hash
-        function getHashTarget() {
-            const hash = window.location.hash;
-            const id = hash.slice(1);
-            let target = document.querySelector('[id="' + id + '"]');
-            if (!target)
-                return;
-
-            // if figure or table, modify target to get expected element
-            if (id.indexOf('fig:') === 0)
-                target = target.querySelector('figure');
-            if (id.indexOf('tbl:') === 0)
-                target = target.querySelector('table');
-
-            return target;
-        }
-
-        // load options from url parameters
-        function loadOptions() {
-            const url = window.location.search;
-            const params = new URLSearchParams(url);
-            for (const optionName of Object.keys(options)) {
-                const paramName = pluginName + '-' + optionName;
-                const param = params.get(paramName);
-                if (param !== '' && param !== null)
-                    options[optionName] = param;
-            }
-        }
-        loadOptions();
-
-        // start script when document is finished loading
-        if (options.enabled === 'true')
-            window.addEventListener('load', start);
-    })();
+<!--
+  Anchors Plugin
+
+  Adds an anchor next to each of a certain type of element that provides a
+  human-readable url to that specific item/position in the document (e.g.
+  "manuscript.html#abstract"). It also makes it such that scrolling out of view
+  of a target removes its identifier from the url.
+-->
+
+<script type="module">
+  // which types of elements to add anchors next to, in "document.querySelector"
+  // format
+  const typesQuery = 'h1, h2, h3, [id^="fig:"], [id^="tbl:"], [id^="eq:"]';
+
+  // start script
+  function start() {
+    // add anchor to each element of specified types
+    const elements = document.querySelectorAll(typesQuery);
+    for (const element of elements) addAnchor(element);
+
+    // attach scroll listener to window
+    window.addEventListener("scroll", onScroll);
+  }
+
+  // when window is scrolled
+  function onScroll() {
+    // if url has hash and user has scrolled out of view of hash
+    // target, remove hash from url
+    const tolerance = 100;
+    const target = getHashTarget();
+    if (target) {
+      if (
+        target.getBoundingClientRect().top > window.innerHeight + tolerance ||
+        target.getBoundingClientRect().bottom < 0 - tolerance
+      )
+        history.pushState(null, null, " ");
+    }
+  }
+
+  // add anchor to element
+  function addAnchor(element) {
+    let addTo; // element to add anchor button to
+
+    // if figure or table, modify withId and addTo to get expected
+    // elements
+    if (element.id.indexOf("fig:") === 0) {
+      addTo = element.querySelector("figcaption");
+    } else if (element.id.indexOf("tbl:") === 0) {
+      addTo = element.querySelector("caption");
+    } else if (element.id.indexOf("eq:") === 0) {
+      addTo = element.querySelector(".eqnos-number");
+    }
+
+    addTo = addTo || element;
+    const id = element.id || null;
+
+    // do not add anchor if element doesn't have assigned id.
+    // id is generated by pandoc and is assumed to be unique and
+    // human-readable
+    if (!id) return;
+
+    // create anchor button
+    const anchor = document.createElement("a");
+    anchor.innerHTML = document.querySelector(".icon_link").innerHTML;
+    anchor.title = "Link to this part of the document";
+    anchor.classList.add("icon_button", "anchor");
+    anchor.dataset.ignore = "true";
+    anchor.href = "#" + id;
+    addTo.appendChild(anchor);
+  }
+
+  // start script when document is finished loading
+  window.addEventListener("load", start);
 </script>
 
 <!-- link icon -->
 
 <template class="icon_link">
-    <!-- modified from: https://fontawesome.com/icons/link -->
-    <svg width="16" height="16" viewBox="0 0 512 512">
-        <path
-            fill="currentColor"
-            d="M326.612 185.391c59.747 59.809 58.927 155.698.36 214.59-.11.12-.24.25-.36.37l-67.2 67.2c-59.27 59.27-155.699 59.262-214.96 0-59.27-59.26-59.27-155.7 0-214.96l37.106-37.106c9.84-9.84 26.786-3.3 27.294 10.606.648 17.722 3.826 35.527 9.69 52.721 1.986 5.822.567 12.262-3.783 16.612l-13.087 13.087c-28.026 28.026-28.905 73.66-1.155 101.96 28.024 28.579 74.086 28.749 102.325.51l67.2-67.19c28.191-28.191 28.073-73.757 0-101.83-3.701-3.694-7.429-6.564-10.341-8.569a16.037 16.037 0 0 1-6.947-12.606c-.396-10.567 3.348-21.456 11.698-29.806l21.054-21.055c5.521-5.521 14.182-6.199 20.584-1.731a152.482 152.482 0 0 1 20.522 17.197zM467.547 44.449c-59.261-59.262-155.69-59.27-214.96 0l-67.2 67.2c-.12.12-.25.25-.36.37-58.566 58.892-59.387 154.781.36 214.59a152.454 152.454 0 0 0 20.521 17.196c6.402 4.468 15.064 3.789 20.584-1.731l21.054-21.055c8.35-8.35 12.094-19.239 11.698-29.806a16.037 16.037 0 0 0-6.947-12.606c-2.912-2.005-6.64-4.875-10.341-8.569-28.073-28.073-28.191-73.639 0-101.83l67.2-67.19c28.239-28.239 74.3-28.069 102.325.51 27.75 28.3 26.872 73.934-1.155 101.96l-13.087 13.087c-4.35 4.35-5.769 10.79-3.783 16.612 5.864 17.194 9.042 34.999 9.69 52.721.509 13.906 17.454 20.446 27.294 10.606l37.106-37.106c59.271-59.259 59.271-155.699.001-214.959z"
-        ></path>
-    </svg>
+  <!-- modified from: https://fontawesome.com/icons/link -->
+  <svg width="16" height="16" viewBox="0 0 512 512">
+    <path
+      fill="currentColor"
+      d="M326.612 185.391c59.747 59.809 58.927 155.698.36 214.59-.11.12-.24.25-.36.37l-67.2 67.2c-59.27 59.27-155.699 59.262-214.96 0-59.27-59.26-59.27-155.7 0-214.96l37.106-37.106c9.84-9.84 26.786-3.3 27.294 10.606.648 17.722 3.826 35.527 9.69 52.721 1.986 5.822.567 12.262-3.783 16.612l-13.087 13.087c-28.026 28.026-28.905 73.66-1.155 101.96 28.024 28.579 74.086 28.749 102.325.51l67.2-67.19c28.191-28.191 28.073-73.757 0-101.83-3.701-3.694-7.429-6.564-10.341-8.569a16.037 16.037 0 0 1-6.947-12.606c-.396-10.567 3.348-21.456 11.698-29.806l21.054-21.055c5.521-5.521 14.182-6.199 20.584-1.731a152.482 152.482 0 0 1 20.522 17.197zM467.547 44.449c-59.261-59.262-155.69-59.27-214.96 0l-67.2 67.2c-.12.12-.25.25-.36.37-58.566 58.892-59.387 154.781.36 214.59a152.454 152.454 0 0 0 20.521 17.196c6.402 4.468 15.064 3.789 20.584-1.731l21.054-21.055c8.35-8.35 12.094-19.239 11.698-29.806a16.037 16.037 0 0 0-6.947-12.606c-2.912-2.005-6.64-4.875-10.341-8.569-28.073-28.073-28.191-73.639 0-101.83l67.2-67.19c28.239-28.239 74.3-28.069 102.325.51 27.75 28.3 26.872 73.934-1.155 101.96l-13.087 13.087c-4.35 4.35-5.769 10.79-3.783 16.612 5.864 17.194 9.042 34.999 9.69 52.721.509 13.906 17.454 20.446 27.294 10.606l37.106-37.106c59.271-59.259 59.271-155.699.001-214.959z"
+    ></path>
+  </svg>
 </template>
+
+<style>
+  @media only screen {
+    /* anchor button */
+    .anchor {
+      opacity: 0;
+      margin-left: 5px;
+    }
+
+    /* anchor buttons within <h2>'s */
+    h2 .anchor {
+      margin-left: 10px;
+    }
+
+    /* anchor buttons when hovered/focused and anything containing an anchor button when hovered */
+    *:hover > .anchor,
+    .anchor:hover,
+    .anchor:focus {
+      opacity: 1;
+    }
+
+    /* anchor button when hovered */
+    .anchor:hover {
+      cursor: pointer;
+    }
+  }
+
+  /* always show anchor button on devices with no mouse/hover ability */
+  @media (hover: none) {
+    .anchor {
+      opacity: 1;
+    }
+  }
+
+  /* always hide anchor button on print */
+  @media only print {
+    .anchor {
+      display: none;
+    }
+  }
+</style>
diff --git a/build/plugins/attributes.html b/build/plugins/attributes.html
index b968198..7009782 100644
--- a/build/plugins/attributes.html
+++ b/build/plugins/attributes.html
@@ -1,130 +1,84 @@
-<!-- attributes plugin -->
-
-<script>
-    (function() {
-        // /////////////////////////
-        // DESCRIPTION
-        // /////////////////////////
-
-        // This Manubot plugin allows arbitrary HTML attributes to be attached
-        // to (almost) any element. Place an HTML comment inside or next to the
-        // desired element in the format <!-- $attribute="value" -->
-
-        // /////////////////////////
-        // OPTIONS
-        // /////////////////////////
-
-        // plugin name prefix for url parameters
-        const pluginName = 'attributes';
-
-        // default plugin options
-        const options = {
-            // whether plugin is on or not
-            enabled: 'true'
-        };
-
-        // change options above, or override with url parameter, eg:
-        // 'manuscript.html?pluginName-enabled=false'
-
-        // /////////////////////////
-        // SCRIPT
-        // /////////////////////////
-
-        // start script
-        function start() {
-            // get list of comments in document
-            const comments = findComments();
-
-            for(const comment of comments)
-                if (comment.parentElement)
-                    addAttributes(
-                        comment.parentElement,
-                        comment.nodeValue.trim()
-                    );
-        }
-
-        // add html attributes to specified element based on string of 
-        // html attributes and values
-        function addAttributes(element, text) {
-            // regex's for finding attribute/value pairs in the format of
-            // attribute="value" or attribute='value
-            const regex2 = /\$([a-zA-Z\-]+)?=\"(.+?)\"/;
-            const regex1 = /\$([a-zA-Z\-]+)?=\'(.+?)\'/;
-
-            // loop through attribute/value pairs
-            let match;
-            while(match = text.match(regex2) || text.match(regex1)) {
-                // get attribute and value from regex capture groups
-                let attribute = match[1];
-                let value = match[2];
-
-                // remove from string
-                text = text.substring(match.index + match[0].length);
-
-                if (!attribute || !value)
-                    break;
-
-                // set attribute of parent element
-                try {
-                    element.setAttribute(attribute, value);
-                } catch(error) {
-                    console.log(error);
-                }
-
-                // special case for colspan
-                if (attribute === 'colspan')
-                    removeTableCells(element, value);
-            }
-        }
-
-        // get list of comment elements in document
-        function findComments() {
-            const comments = [];
-
-            // iterate over comment nodes in document
-            function acceptNode(node) {
-                return NodeFilter.FILTER_ACCEPT;
-            }
-            const iterator = document.createNodeIterator(
-                document.body,
-                NodeFilter.SHOW_COMMENT,
-                acceptNode
-            );
-            let node;
-            while(node = iterator.nextNode())
-                comments.push(node);
-
-            return comments;
-        }
-
-        // remove certain number of cells after specified cell
-        function removeTableCells(cell, number) {
-            number = parseInt(number);
-            if (!number)
-                return;
-
-            // remove elements
-            for(; number > 1; number--) {
-                if (cell.nextElementSibling)
-                    cell.nextElementSibling.remove();
-            }
-        }
-
-        // load options from url parameters
-        function loadOptions() {
-            const url = window.location.search;
-            const params = new URLSearchParams(url);
-            for (const optionName of Object.keys(options)) {
-                const paramName = pluginName + '-' + optionName;
-                const param = params.get(paramName);
-                if (param !== '' && param !== null)
-                    options[optionName] = param;
-            }
-        }
-        loadOptions();
-
-        // start script when document is finished loading
-        if (options.enabled === 'true')
-            window.addEventListener('load', start);
-    })();
+<!-- 
+    Attributes Plugin
+
+    Allows arbitrary HTML attributes to be attached to (almost) any element.
+    Place an HTML comment inside or next to the desired element with the content:
+    $attribute="value"
+-->
+
+<script type="module">
+  // start script
+  function start() {
+    // get list of comments in document
+    const comments = findComments();
+
+    for (const comment of comments)
+      if (comment.parentElement)
+        addAttributes(comment.parentElement, comment.nodeValue.trim());
+  }
+
+  // add html attributes to specified element based on string of
+  // html attributes and values
+  function addAttributes(element, text) {
+    // regex's for finding attribute/value pairs in the format of
+    // attribute="value" or attribute='value
+    const regex2 = /\$([a-zA-Z\-]+)?=\"(.+?)\"/;
+    const regex1 = /\$([a-zA-Z\-]+)?=\'(.+?)\'/;
+
+    // loop through attribute/value pairs
+    let match;
+    while ((match = text.match(regex2) || text.match(regex1))) {
+      // get attribute and value from regex capture groups
+      let attribute = match[1];
+      let value = match[2];
+
+      // remove from string
+      text = text.substring(match.index + match[0].length);
+
+      if (!attribute || !value) break;
+
+      // set attribute of parent element
+      try {
+        element.setAttribute(attribute, value);
+      } catch (error) {
+        console.log(error);
+      }
+
+      // special case for colspan
+      if (attribute === "colspan") removeTableCells(element, value);
+    }
+  }
+
+  // get list of comment elements in document
+  function findComments() {
+    const comments = [];
+
+    // iterate over comment nodes in document
+    function acceptNode(node) {
+      return NodeFilter.FILTER_ACCEPT;
+    }
+    const iterator = document.createNodeIterator(
+      document.body,
+      NodeFilter.SHOW_COMMENT,
+      acceptNode
+    );
+    let node;
+    while ((node = iterator.nextNode())) comments.push(node);
+
+    return comments;
+  }
+
+  // remove certain number of cells after specified cell
+  function removeTableCells(cell, number) {
+    number = parseInt(number);
+    if (!number) return;
+
+    // remove elements
+    for (; number > 1; number--) {
+      if (cell.nextElementSibling) cell.nextElementSibling.remove();
+    }
+  }
+
+  // start script when document is finished loading
+  window.addEventListener("load", start);
 </script>
diff --git a/build/plugins/core.html b/build/plugins/core.html
new file mode 100644
index 0000000..4c680a4
--- /dev/null
+++ b/build/plugins/core.html
@@ -0,0 +1,129 @@
+<!-- 
+    Plugin Core
+
+    Functions needed for and shared across all first-party plugins.
+-->
+
+<script>
+  // get element that is target of hash (from link element or url)
+  function getHashTarget(link) {
+    const hash = link ? link.hash : window.location.hash;
+    const id = hash.slice(1);
+    let target = document.querySelector(`[id="${id}"]`);
+    if (!target) return;
+
+    // if figure or table, modify target to get expected element
+    if (id.indexOf("fig:") === 0) target = target.querySelector("figure");
+    if (id.indexOf("tbl:") === 0) target = target.querySelector("table");
+
+    return target;
+  }
+
+  // get position/dimensions of element or viewport
+  function getRectInView(element) {
+    let rect = {};
+    rect.left = 0;
+    rect.top = 0;
+    rect.right = document.documentElement.clientWidth;
+    rect.bottom = document.documentElement.clientHeight;
+    let style = {};
+
+    if (element instanceof HTMLElement) {
+      rect = element.getBoundingClientRect();
+      style = window.getComputedStyle(element);
+    }
+
+    const margin = {};
+    margin.left = parseFloat(style.marginLeftWidth) || 0;
+    margin.top = parseFloat(style.marginTopWidth) || 0;
+    margin.right = parseFloat(style.marginRightWidth) || 0;
+    margin.bottom = parseFloat(style.marginBottomWidth) || 0;
+
+    const border = {};
+    border.left = parseFloat(style.borderLeftWidth) || 0;
+    border.top = parseFloat(style.borderTopWidth) || 0;
+    border.right = parseFloat(style.borderRightWidth) || 0;
+    border.bottom = parseFloat(style.borderBottomWidth) || 0;
+
+    const newRect = {};
+    newRect.left = rect.left + margin.left + border.left;
+    newRect.top = rect.top + margin.top + border.top;
+    newRect.right = rect.right + margin.right + border.right;
+    newRect.bottom = rect.bottom + margin.bottom + border.bottom;
+    newRect.width = newRect.right - newRect.left;
+    newRect.height = newRect.bottom - newRect.top;
+
+    return newRect;
+  }
+
+  // get position of element relative to page
+  function getRectInPage(element) {
+    const rect = getRectInView(element);
+    const body = getRectInView(document.body);
+
+    const newRect = {};
+    newRect.left = rect.left - body.left;
+    newRect.top = rect.top - body.top;
+    newRect.right = rect.right - body.left;
+    newRect.bottom = rect.bottom - body.top;
+    newRect.width = rect.width;
+    newRect.height = rect.height;
+
+    return newRect;
+  }
+
+  // get closest element before specified element that matches query
+  function firstBefore(element, query) {
+    while (element && element !== document.body && !element.matches(query))
+      element = element.previousElementSibling || element.parentNode;
+
+    return element;
+  }
+
+  // check if element is part of collapsed heading
+  function isCollapsed(element) {
+    while (element && element !== document.body) {
+      if (element.dataset.collapsed === "true") return true;
+      element = element.parentNode;
+    }
+    return false;
+  }
+
+  // expand any collapsed parent containers of element if necessary
+  function expandElement(element) {
+    if (isCollapsed(element)) {
+      // accordion plugin
+      const heading = firstBefore(element, "h2");
+      if (heading) heading.click();
+      // details/summary HTML element
+      const summary = firstBefore(element, "summary");
+      if (summary) summary.click();
+    }
+  }
+
+  // scroll to and focus element
+  function goToElement(element, offset) {
+    // expand accordion section if collapsed
+    expandElement(element);
+    const y =
+      getRectInView(element).top -
+      getRectInView(document.documentElement).top -
+      (offset || 0);
+
+    // trigger any function listening for "onscroll" event
+    window.dispatchEvent(new Event("scroll"));
+    window.scrollTo(0, y);
+    document.activeElement.blur();
+    element.focus();
+  }
+
+  // get list of elements after a start element up to element matching query
+  function nextUntil(element, query, exclude) {
+    const elements = [];
+    while (((element = element.nextElementSibling), element)) {
+      if (element.matches(query)) break;
+      if (!element.matches(exclude)) elements.push(element);
+    }
+    return elements;
+  }
+</script>
diff --git a/build/plugins/d3.html b/build/plugins/d3.html
index 48c16d8..d04226e 100644
--- a/build/plugins/d3.html
+++ b/build/plugins/d3.html
@@ -1,16 +1,12 @@
-<!-- d3 plugin -->
+<!--
+  D3 Plugin (third-party) 
+  
+  Allows you to create complex, dynamic,interactive, data-driven visualizations
+  in SVG. See https://d3js.org/.
+-->
 
 <script
-    src="https://cdnjs.cloudflare.com/ajax/libs/d3/6.2.0/d3.min.js"
-    integrity="sha512-C2RveGuPIWqkaLAluvoxyiaN1XYNe5ss11urhZWZYBUA9Ydgj+hfGKPcxCzTwut1/fmjEZR7Ac35f2aycT8Ogw=="
-    crossorigin="anonymous"
->
-    // /////////////////////////
-    // DESCRIPTION
-    // /////////////////////////
-
-    // This third-party plugin 'D3' allows you to create complex, dynamic,
-    // interactive, data-driven visualizations in SVG.
-
-    // https://d3js.org/
-</script>
+  src="https://cdnjs.cloudflare.com/ajax/libs/d3/6.2.0/d3.min.js"
+  integrity="sha512-C2RveGuPIWqkaLAluvoxyiaN1XYNe5ss11urhZWZYBUA9Ydgj+hfGKPcxCzTwut1/fmjEZR7Ac35f2aycT8Ogw=="
+  crossorigin="anonymous"
+></script>
diff --git a/build/plugins/hypothesis.html b/build/plugins/hypothesis.html
index 7bd1691..1986d36 100644
--- a/build/plugins/hypothesis.html
+++ b/build/plugins/hypothesis.html
@@ -1,104 +1,166 @@
-<!-- annotations plugin -->
+<!-- 
+  Annotations Plugin
+
+  Allows public annotation of the  manuscript. See https://web.hypothes.is/.
+-->
 
 <script>
-    // /////////////////////////
-    // DESCRIPTION
-    // /////////////////////////
-
-    // This third-party plugin 'Hypothesis' allows public annotation of the
-    // manuscript.
-
-    // https://web.hypothes.is/
-
-    // plugin configuration
-    window.hypothesisConfig = function() {
-        return {
-            branding: {
-                accentColor: '#2196f3',
-                appBackgroundColor: '#f8f8f8',
-                ctaBackgroundColor: '#f8f8f8',
-                ctaTextColor: '#000000',
-                selectionFontFamily: 'Open Sans, Helvetica, sans serif',
-                annotationFontFamily: 'Open Sans, Helvetica, sans serif'
-            }
-        };
+  // configuration
+  window.hypothesisConfig = function () {
+    return {
+      branding: {
+        accentColor: "#2196f3",
+        appBackgroundColor: "#f8f8f8",
+        ctaBackgroundColor: "#f8f8f8",
+        ctaTextColor: "#000000",
+        selectionFontFamily: "Open Sans, Helvetica, sans serif",
+        annotationFontFamily: "Open Sans, Helvetica, sans serif",
+      },
     };
+  };
 
-    // hypothesis client script
-    const embed = 'https://hypothes.is/embed.js';
-    // hypothesis annotation count query url
-    const query = 'https://api.hypothes.is/api/search?limit=0&url='
-
-    
-    // start script
-    function start() {
-        const button = makeButton();
-        document.body.insertBefore(button, document.body.firstChild);
-        insertCount(button);
-    }
-
-    // make button
-    function makeButton() {
-        // create button
-        const button = document.createElement('button');
-        button.id = 'hypothesis_button';
-        button.innerHTML = document.querySelector('.icon_hypothesis').innerHTML;
-        button.title = 'Hypothesis annotations';
-        button.classList.add('icon_button');
+  // hypothesis client script
+  const embed = "https://hypothes.is/embed.js";
+  // hypothesis annotation count query url
+  const query = "https://api.hypothes.is/api/search?limit=0&url=";
 
-        function onClick(event) {
-            onButtonClick(event, button);
-        }
+  // start script
+  function start() {
+    const button = makeButton();
+    document.body.insertBefore(button, document.body.firstChild);
+    insertCount(button);
+  }
 
-        // attach click listeners
-        button.addEventListener('click', onClick);
+  // make button
+  function makeButton() {
+    // create button
+    const button = document.createElement("button");
+    button.id = "hypothesis_button";
+    button.innerHTML = document.querySelector(".icon_hypothesis").innerHTML;
+    button.title = "Hypothesis annotations";
+    button.classList.add("icon_button");
 
-        return button;
+    function onClick(event) {
+      onButtonClick(event, button);
     }
 
-    // insert annotations count
-    async function insertCount(button) {
-        // get annotation count from Hypothesis based on url
-        let count = '-';
-        try {
-            const canonical = document.querySelector('link[rel="canonical"]');
-            const location = window.location;
-            const url = encodeURIComponent((canonical || location).href);
-            const response = await fetch(query + url);
-            const json = await response.json();
-            count = json.total || '-';
-        } catch(error) {
-            console.log(error);
-        }
-        
-        // put count into button
-        const counter = document.createElement('span');
-        counter.id = 'hypothesis_count';
-        counter.innerHTML = count;
-        button.title = 'View ' + count + ' Hypothesis annotations';
-        button.append(counter);
-    }
+    // attach click listeners
+    button.addEventListener("click", onClick);
+
+    return button;
+  }
 
-    // when button is clicked
-    function onButtonClick(event, button) {
-        const script = document.createElement('script');
-        script.src = embed;
-        document.body.append(script);
-        button.remove();
+  // insert annotations count
+  async function insertCount(button) {
+    // get annotation count from Hypothesis based on url
+    let count = "-";
+    try {
+      const canonical = document.querySelector('link[rel="canonical"]');
+      const location = window.location;
+      const url = encodeURIComponent((canonical || location).href);
+      const response = await fetch(query + url);
+      const json = await response.json();
+      count = json.total || "-";
+    } catch (error) {
+      console.log(error);
     }
 
-    window.addEventListener('load', start);
+    // put count into button
+    const counter = document.createElement("span");
+    counter.id = "hypothesis_count";
+    counter.innerHTML = count;
+    button.title = "View " + count + " Hypothesis annotations";
+    button.append(counter);
+  }
+
+  // when button is clicked
+  function onButtonClick(event, button) {
+    const script = document.createElement("script");
+    script.src = embed;
+    document.body.append(script);
+    button.remove();
+  }
+
+  // start script when document is finished loading
+  window.addEventListener("load", start);
 </script>
 
 <!-- hypothesis icon -->
 
 <template class="icon_hypothesis">
-    <!-- modified from: https://simpleicons.org/icons/hypothesis.svg / https://git.io/Jf1VB -->
-    <svg width="16" height="16" viewBox="0 0 24 24" tabindex="-1">
-        <path
-            fill="currentColor"
-            d="M3.43 0C2.5 0 1.72 .768 1.72 1.72V18.86C1.72 19.8 2.5 20.57 3.43 20.57H9.38L12 24L14.62 20.57H20.57C21.5 20.57 22.29 19.8 22.29 18.86V1.72C22.29 .77 21.5 0 20.57 0H3.43M5.14 3.43H7.72V9.43S8.58 7.72 10.28 7.72C12 7.72 13.74 8.57 13.74 11.24V17.14H11.16V12C11.16 10.61 10.28 10.07 9.43 10.29C8.57 10.5 7.72 11.41 7.72 13.29V17.14H5.14V3.43M18 13.72C18.95 13.72 19.72 14.5 19.72 15.42A1.71 1.71 0 0 1 18 17.13A1.71 1.71 0 0 1 16.29 15.42C16.29 14.5 17.05 13.71 18 13.71Z"
-            tabindex="-1"
-        ></path>
-    </svg>
+  <!-- modified from: https://simpleicons.org/icons/hypothesis.svg / https://git.io/Jf1VB -->
+  <svg width="16" height="16" viewBox="0 0 24 24" tabindex="-1">
+    <path
+      fill="currentColor"
+      d="M3.43 0C2.5 0 1.72 .768 1.72 1.72V18.86C1.72 19.8 2.5 20.57 3.43 20.57H9.38L12 24L14.62 20.57H20.57C21.5 20.57 22.29 19.8 22.29 18.86V1.72C22.29 .77 21.5 0 20.57 0H3.43M5.14 3.43H7.72V9.43S8.58 7.72 10.28 7.72C12 7.72 13.74 8.57 13.74 11.24V17.14H11.16V12C11.16 10.61 10.28 10.07 9.43 10.29C8.57 10.5 7.72 11.41 7.72 13.29V17.14H5.14V3.43M18 13.72C18.95 13.72 19.72 14.5 19.72 15.42A1.71 1.71 0 0 1 18 17.13A1.71 1.71 0 0 1 16.29 15.42C16.29 14.5 17.05 13.71 18 13.71Z"
+      tabindex="-1"
+    ></path>
+  </svg>
 </template>
+
+<style>
+  /* hypothesis activation button */
+  #hypothesis_button {
+    box-sizing: border-box;
+    position: fixed;
+    top: 0;
+    right: 0;
+    width: 60px;
+    height: 60px;
+    background: #ffffff;
+    border-radius: 0;
+    border-left: solid 1px #bdbdbd;
+    border-bottom: solid 1px #bdbdbd;
+    box-shadow: 0 0 20px rgba(0, 0, 0, 0.05);
+    z-index: 2;
+  }
+
+  /* hypothesis button svg */
+  #hypothesis_button > svg {
+    position: relative;
+    top: -4px;
+  }
+
+  /* hypothesis annotation count */
+  #hypothesis_count {
+    position: absolute;
+    left: 0;
+    right: 0;
+    bottom: 5px;
+  }
+
+  /* side panel */
+  .annotator-frame {
+    width: 280px !important;
+  }
+
+  /* match highlight color to rest of theme */
+  .annotator-highlights-always-on .annotator-hl {
+    background-color: #ffeb3b !important;
+  }
+
+  /* match focused color to rest of theme */
+  .annotator-hl.annotator-hl-focused {
+    background-color: #ff8a65 !important;
+  }
+
+  /* match bucket bar color to rest of theme */
+  .annotator-bucket-bar {
+    background: #f5f5f5 !important;
+  }
+
+  /* always hide button, toolbar, and tooltip on print */
+  @media only print {
+    #hypothesis_button {
+      display: none;
+    }
+
+    .annotator-frame {
+      display: none !important;
+    }
+
+    hypothesis-adder {
+      display: none !important;
+    }
+  }
+</style>
diff --git a/build/plugins/inline-svg.html b/build/plugins/inline-svg.html
index be40242..619a3a1 100644
--- a/build/plugins/inline-svg.html
+++ b/build/plugins/inline-svg.html
@@ -1,62 +1,53 @@
-<!-- inline svg plugin -->
-
-<script>
-  (function() {
-      // /////////////////////////
-      // DESCRIPTION
-      // /////////////////////////
-
-      // This Manubot plugin fetches the text source code of SVGs in <img> tags,
-      // and inserts it into the document in-place. This provides many
-      // advantages, such as being able to style SVGs globally from the CSS
-      // themes, and being able to make SVGs interactive with JavaScript and D3.
-      // If you have a script that expects SVGs to be inlined, wait for an
-      // "SVGLoaded" event before running it.
-
-      // Note: This requires the page to be served from a server to work
-      // See: https://stackoverflow.com/a/11063963/2180570
-      // Tip: Use the manubot commands to open the page in a local webserver
-      // See: https://github.com/manubot/rootstock#local-execution
-
-      // /////////////////////////
-      // SCRIPT
-      // /////////////////////////
-
-      // start script
-      async function start() {
-          // get all <img> tags that have "src" attributes that end with ".svg"
-          const imgs = document.querySelectorAll('img[src$=".svg"]');
-          const inlineSvgs = Array.from(imgs).map(inlineSvg);
-          await Promise.all(inlineSvgs);
-
-          // dispatch "inline finished" event
-          document.dispatchEvent(new Event('SVGLoaded'));
-      }
-
-      // take an svg <img> tag, fetch its source code, and replace it 
-      async function inlineSvg(img) {
-          try {
-              // fetch svg source code
-              const response = await fetch(img.src);
-              if (!response.ok) throw new Error('Couldn\'t get SVG source');
-              const source = await response.text();
-              if (!source.trim()) throw new Error('No SVG source');
-              // parse specifically as svg, create new (hidden) dom node
-              const svg = new DOMParser()
-                  .parseFromString(source, 'image/svg+xml')
-                  .querySelector('svg');
-              if (!svg) throw new Error('Couldn\'t parse SVG');
-              // transfer original img attributes into new svg
-              for (const { name, value } of img.attributes)
-                  svg.setAttribute(name, value);
-              // replace original image with new svg
-              img.outerHTML = svg.outerHTML;
-          } catch (error) {
-              console.log(error);
-          }
-      }
-
-      // start script when document is finished loading
-      window.addEventListener('load', start);
-  })();
+<!--
+  Inline Svg Plugin
+
+  Fetches the text source code of SVGs in <img> tags, and inserts it into the
+  document in-place. This provides many advantages, such as being able to style
+  SVGs globally from the CSS themes, and being able to make SVGs interactive
+  with JavaScript and D3. If you have a script that expects SVGs to be inlined,
+  wait for an "SVGLoaded" event before running it.
+
+  Note: This requires the page to be served from a server to work
+  See: https://stackoverflow.com/a/11063963/2180570
+  Tip: Use the manubot commands to open the page in a local webserver
+  See: https://github.com/manubot/rootstock#local-execution
+-->
+
+<script type="module">
+  // start script
+  async function start() {
+    // get all <img> tags that have "src" attributes that end with ".svg"
+    const imgs = document.querySelectorAll('img[src$=".svg"]');
+    const inlineSvgs = Array.from(imgs).map(inlineSvg);
+    await Promise.all(inlineSvgs);
+
+    // dispatch "inline finished" event
+    document.dispatchEvent(new Event("SVGLoaded"));
+  }
+
+  // take an svg <img> tag, fetch its source code, and replace it
+  async function inlineSvg(img) {
+    try {
+      // fetch svg source code
+      const response = await fetch(img.src);
+      if (!response.ok) throw new Error("Couldn't get SVG source");
+      const source = await response.text();
+      if (!source.trim()) throw new Error("No SVG source");
+      // parse specifically as svg, create new (hidden) dom node
+      const svg = new DOMParser()
+        .parseFromString(source, "image/svg+xml")
+        .querySelector("svg");
+      if (!svg) throw new Error("Couldn't parse SVG");
+      // transfer original img attributes into new svg
+      for (const { name, value } of img.attributes)
+        svg.setAttribute(name, value);
+      // replace original image with new svg
+      img.outerHTML = svg.outerHTML;
+    } catch (error) {
+      console.log(error);
+    }
+  }
+
+  // start script when document is finished loading
+  window.addEventListener("load", start);
 </script>
diff --git a/build/plugins/jump-to-first.html b/build/plugins/jump-to-first.html
index e8a8088..d205093 100644
--- a/build/plugins/jump-to-first.html
+++ b/build/plugins/jump-to-first.html
@@ -1,272 +1,102 @@
-<!-- jump to first plugin -->
-
-<script>
-    (function() {
-        // /////////////////////////
-        // DESCRIPTION
-        // /////////////////////////
-
-        // This Manubot plugin adds a button next to each reference entry,
-        // figure, and table that jumps the page to the first occurrence of a
-        // link to that item in the manuscript.
-
-        // /////////////////////////
-        // OPTIONS
-        // /////////////////////////
-
-        // plugin name prefix for url parameters
-        const pluginName = 'jumpToFirst';
-
-        // default plugin options
-        const options = {
-            // whether to add buttons next to reference entries
-            references: 'true',
-            // whether to add buttons next to figures
-            figures: 'true',
-            // whether to add buttons next to tables
-            tables: 'true',
-            // whether plugin is on or not
-            enabled: 'true'
-        };
-
-        // change options above, or override with url parameter, eg:
-        // 'manuscript.html?pluginName-enabled=false'
-
-        // /////////////////////////
-        // SCRIPT
-        // /////////////////////////
-
-        // start script
-        function start() {
-            if (options.references !== 'false')
-                makeReferenceButtons();
-            if (options.figures !== 'false')
-                makeFigureButtons();
-            if (options.tables !== 'false')
-                makeTableButtons();
-        }
-
-        // when jump button clicked
-        function onButtonClick() {
-            const first = getFirstOccurrence(this.dataset.id);
-            if (!first)
-                return;
-
-            // update url hash so navigating "back" in history will return
-            // user to jump button
-            window.location.hash = this.dataset.id;
-            // scroll to link
-            window.setTimeout(function() {
-                goToElement(first, window.innerHeight * 0.5);
-            }, 0);
-        }
-
-        // get first occurence of link to item in document
-        function getFirstOccurrence(id) {
-            let query = 'a';
-            query += '[href="#' + id + '"]';
-            // exclude buttons, anchor links, toc links, etc
-            query +=
-                ':not(.button):not(.icon_button):not(.anchor):not(.toc_link)';
-            return document.querySelector(query);
-        }
-
-        // add button next to each reference entry
-        function makeReferenceButtons() {
-            const references = document.querySelectorAll('div[id^="ref-"]');
-            for (const reference of references) {
-                // get reference id and element to add button to
-                const id = reference.id;
-                const container = reference.firstElementChild;
-                const first = getFirstOccurrence(id);
-
-                // if can't find link to reference, ignore
-                if (!first)
-                    continue;
-
-                // make jump button
-                let button = document.createElement('button');
-                button.classList.add('icon_button', 'jump_arrow');
-                button.title =
-                    'Jump to the first occurence of this reference in the document';
-                button.innerHTML = document.querySelector(
-                    '.icon_angle_double_up'
-                ).innerHTML;
-                button.dataset.id = id;
-                button.dataset.ignore = 'true';
-                container.innerHTML = button.outerHTML + container.innerHTML;
-                button = container.firstElementChild;
-                button.addEventListener('click', onButtonClick);
-            }
-        }
-
-        // add button next to each figure
-        function makeFigureButtons() {
-            const figures = document.querySelectorAll('[id^="fig:"]');
-            for (const figure of figures) {
-                // get figure id and element to add button to
-                const id = figure.id;
-                const container = figure.querySelector('figcaption') || figure;
-                const first = getFirstOccurrence(id);
-
-                // if can't find link to figure, ignore
-                if (!first)
-                    continue;
-
-                // make jump button
-                const button = document.createElement('button');
-                button.classList.add('icon_button', 'jump_arrow');
-                button.title =
-                    'Jump to the first occurence of this figure in the document';
-                button.innerHTML = document.querySelector(
-                    '.icon_angle_double_up'
-                ).innerHTML;
-                button.dataset.id = id;
-                button.dataset.ignore = 'true';
-                container.insertBefore(button, container.firstElementChild);
-                button.addEventListener('click', onButtonClick);
-            }
-        }
-
-        // add button next to each figure
-        function makeTableButtons() {
-            const tables = document.querySelectorAll('[id^="tbl:"]');
-            for (const table of tables) {
-                // get ref id and element to add button to
-                const id = table.id;
-                const container = table.querySelector('caption') || table;
-                const first = getFirstOccurrence(id);
-
-                // if can't find link to table, ignore
-                if (!first)
-                    continue;
-
-                // make jump button
-                const button = document.createElement('button');
-                button.classList.add('icon_button', 'jump_arrow');
-                button.title =
-                    'Jump to the first occurence of this table in the document';
-                button.innerHTML = document.querySelector(
-                    '.icon_angle_double_up'
-                ).innerHTML;
-                button.dataset.id = id;
-                button.dataset.ignore = 'true';
-                container.insertBefore(button, container.firstElementChild);
-                button.addEventListener('click', onButtonClick);
-            }
-        }
-
-        // scroll to and focus element
-        function goToElement(element, offset) {
-            // expand accordion section if collapsed
-            expandElement(element);
-            const y =
-                getRectInView(element).top -
-                getRectInView(document.documentElement).top -
-                (offset || 0);
-            // trigger any function listening for "onscroll" event
-            window.dispatchEvent(new Event('scroll'));
-            window.scrollTo(0, y);
-            document.activeElement.blur();
-            element.focus();
-        }
-
-        // get position/dimensions of element or viewport
-        function getRectInView(element) {
-            let rect = {};
-            rect.left = 0;
-            rect.top = 0;
-            rect.right = document.documentElement.clientWidth;
-            rect.bottom = document.documentElement.clientHeight;
-            let style = {};
-
-            if (element instanceof HTMLElement) {
-                rect = element.getBoundingClientRect();
-                style = window.getComputedStyle(element);
-            }
-
-            const margin = {};
-            margin.left = parseFloat(style.marginLeftWidth) || 0;
-            margin.top = parseFloat(style.marginTopWidth) || 0;
-            margin.right = parseFloat(style.marginRightWidth) || 0;
-            margin.bottom = parseFloat(style.marginBottomWidth) || 0;
-
-            const border = {};
-            border.left = parseFloat(style.borderLeftWidth) || 0;
-            border.top = parseFloat(style.borderTopWidth) || 0;
-            border.right = parseFloat(style.borderRightWidth) || 0;
-            border.bottom = parseFloat(style.borderBottomWidth) || 0;
-
-            const newRect = {};
-            newRect.left = rect.left + margin.left + border.left;
-            newRect.top = rect.top + margin.top + border.top;
-            newRect.right = rect.right + margin.right + border.right;
-            newRect.bottom = rect.bottom + margin.bottom + border.bottom;
-            newRect.width = newRect.right - newRect.left;
-            newRect.height = newRect.bottom - newRect.top;
-
-            return newRect;
-        }
-
-        // get closest element before specified element that matches query
-        function firstBefore(element, query) {
-            while (
-                element &&
-                element !== document.body &&
-                !element.matches(query)
-            )
-                element = element.previousElementSibling || element.parentNode;
-
-            return element;
-        }
-
-        // check if element is part of collapsed heading
-        function isCollapsed(element) {
-            while (element && element !== document.body) {
-                if (element.dataset.collapsed === 'true')
-                    return true;
-                element = element.parentNode;
-            }
-            return false;
-        }
-
-        // (for interaction with accordion plugin)
-        // expand heading containing element if necesary
-        function expandElement(element) {
-            if (isCollapsed(element)) {
-                const heading = firstBefore(element, 'h2');
-                if (heading)
-                    heading.click();
-            }
-        }
-
-        // load options from url parameters
-        function loadOptions() {
-            const url = window.location.search;
-            const params = new URLSearchParams(url);
-            for (const optionName of Object.keys(options)) {
-                const paramName = pluginName + '-' + optionName;
-                const param = params.get(paramName);
-                if (param !== '' && param !== null)
-                    options[optionName] = param;
-            }
-        }
-        loadOptions();
-
-        // start script when document is finished loading
-        if (options.enabled === 'true')
-            window.addEventListener('load', start);
-    })();
+<!--
+  Jump to First Plugin
+
+  Adds a button next to each reference entry, figure, and table that jumps the
+  page to the first occurrence of a link to that item in the manuscript.
+-->
+
+<script type="module">
+  // whether to add buttons next to reference entries
+  const references = "true";
+  // whether to add buttons next to figures
+  const figures = "true";
+  // whether to add buttons next to tables
+  const tables = "true";
+
+  // start script
+  function start() {
+    if (references !== "false") makeButtons("ref-", "p", "reference");
+    if (figures !== "false") makeButtons("fig:", "figcaption", "figure");
+    if (tables !== "false") makeButtons("tbl:", "caption", "table");
+  }
+
+  // when jump button clicked
+  function onButtonClick() {
+    const first = getFirstOccurrence(this.dataset.id);
+    if (!first) return;
+
+    // update url hash so navigating "back" in history will return user to button
+    window.location.hash = this.dataset.id;
+    // scroll to link
+    const timeout = function () {
+      goToElement(first, window.innerHeight * 0.5);
+    };
+    window.setTimeout(timeout, 0);
+  }
+
+  // get first occurrence of link to item in document
+  function getFirstOccurrence(id) {
+    let query = "a";
+    query += '[href="#' + id + '"]';
+    // exclude buttons, anchor links, toc links, etc
+    query += ":not(.button):not(.icon_button):not(.anchor):not(.toc_link)";
+    return document.querySelector(query);
+  }
+
+  // add button next to each reference entry, figure, or table
+  function makeButtons(query, containerQuery, subject) {
+    const elements = document.querySelectorAll(`[id^="${query}"`);
+    for (const element of elements) {
+      const id = element.id;
+      const buttonContainer = element.querySelector(containerQuery);
+      const first = getFirstOccurrence(id);
+
+      // if can't find link to reference or place to put button, ignore
+      if (!first || !buttonContainer) continue;
+
+      // make jump button
+      let button = document.createElement("button");
+      button.classList.add("icon_button", "jump_arrow");
+      button.title = `Jump to the first occurrence of this ${subject} in the document`;
+      const icon = document.querySelector(".icon_angle_double_up");
+      button.innerHTML = icon.innerHTML;
+      button.dataset.id = id;
+      button.dataset.ignore = "true";
+      button.addEventListener("click", onButtonClick);
+      buttonContainer.prepend(button);
+    }
+  }
+
+  // start script when document is finished loading
+  window.addEventListener("load", start);
 </script>
 
 <!-- angle double up icon -->
 
 <template class="icon_angle_double_up">
-    <!-- modified from: https://fontawesome.com/icons/angle-double-up -->
-    <svg width="16" height="16" viewBox="0 0 320 512">
-        <path
-            fill="currentColor"
-            d="M177 255.7l136 136c9.4 9.4 9.4 24.6 0 33.9l-22.6 22.6c-9.4 9.4-24.6 9.4-33.9 0L160 351.9l-96.4 96.4c-9.4 9.4-24.6 9.4-33.9 0L7 425.7c-9.4-9.4-9.4-24.6 0-33.9l136-136c9.4-9.5 24.6-9.5 34-.1zm-34-192L7 199.7c-9.4 9.4-9.4 24.6 0 33.9l22.6 22.6c9.4 9.4 24.6 9.4 33.9 0l96.4-96.4 96.4 96.4c9.4 9.4 24.6 9.4 33.9 0l22.6-22.6c9.4-9.4 9.4-24.6 0-33.9l-136-136c-9.2-9.4-24.4-9.4-33.8 0z"
-        ></path>
-    </svg>
+  <!-- modified from: https://fontawesome.com/icons/angle-double-up -->
+  <svg width="16" height="16" viewBox="0 0 320 512">
+    <path
+      fill="currentColor"
+      d="M177 255.7l136 136c9.4 9.4 9.4 24.6 0 33.9l-22.6 22.6c-9.4 9.4-24.6 9.4-33.9 0L160 351.9l-96.4 96.4c-9.4 9.4-24.6 9.4-33.9 0L7 425.7c-9.4-9.4-9.4-24.6 0-33.9l136-136c9.4-9.5 24.6-9.5 34-.1zm-34-192L7 199.7c-9.4 9.4-9.4 24.6 0 33.9l22.6 22.6c9.4 9.4 24.6 9.4 33.9 0l96.4-96.4 96.4 96.4c9.4 9.4 24.6 9.4 33.9 0l22.6-22.6c9.4-9.4 9.4-24.6 0-33.9l-136-136c-9.2-9.4-24.4-9.4-33.8 0z"
+    ></path>
+  </svg>
 </template>
+
+<style>
+  @media only screen {
+    /* jump button */
+    .jump_arrow {
+      position: relative;
+      top: 0.125em;
+      margin-right: 5px;
+    }
+  }
+
+  /* always hide jump button on print */
+  @media only print {
+    .jump_arrow {
+      display: none;
+    }
+  }
+</style>
diff --git a/build/plugins/lightbox.html b/build/plugins/lightbox.html
index 6b9f2ae..1fbdf77 100644
--- a/build/plugins/lightbox.html
+++ b/build/plugins/lightbox.html
@@ -1,620 +1,660 @@
-<!-- lightbox plugin -->
-
-<script>
-    (function() {
-        // /////////////////////////
-        // DESCRIPTION
-        // /////////////////////////
-
-        // This Manubot plugin makes it such that when a user clicks on an
-        // image, the image fills the screen and the user can pan/drag/zoom
-        // the image and navigate between other images in the document.
-
-        // /////////////////////////
-        // OPTIONS
-        // /////////////////////////
-
-        // plugin name prefix for url parameters
-        const pluginName = 'lightbox';
-
-        // default plugin options
-        const options = {
-            // list of possible zoom/scale factors
-            zoomSteps:
-                '0.1, 0.25, 0.333333, 0.5, 0.666666, 0.75, 1,' +
-                '1.25, 1.5, 1.75, 2, 2.5, 3, 3.5, 4, 5, 6, 7, 8',
-            // whether to fit image to view ('fit'), display at 100% and shrink
-            // if necessary ('shrink'), or always display at 100% ('100')
-            defaultZoom: 'fit',
-            // whether to zoom in/out toward center of view ('true') or mouse
-            // ('false')
-            centerZoom: 'false',
-            // whether plugin is on or not
-            enabled: 'true'
-        };
-
-        // change options above, or override with url parameter, eg:
-        // 'manuscript.html?pluginName-enabled=false'
-
-        // /////////////////////////
-        // SCRIPT
-        // /////////////////////////
-
-        // start script
-        function start() {
-            // run through each <img> element
-            const imgs = document.querySelectorAll('figure > img');
-            let count = 1;
-            for (const img of imgs) {
-                img.classList.add('lightbox_document_img');
-                img.dataset.number = count;
-                img.dataset.total = imgs.length;
-                img.addEventListener('click', openLightbox);
-                count++;
-            }
-
-            // attach mouse and key listeners to window
-            window.addEventListener('mousemove', onWindowMouseMove);
-            window.addEventListener('keyup', onKeyUp);
+<!-- 
+    Lightbox Plugin
+
+    Makes it such that when a user clicks on an image, the image fills the
+    screen and the user can pan/drag/zoom the image and navigate between other
+    images in the document.
+-->
+
+<script type="module">
+  // list of possible zoom/scale factors
+  const zooms =
+    "0.1, 0.25, 0.333333, 0.5, 0.666666, 0.75, 1, 1.25, 1.5, 1.75, 2, 2.5, 3, 3.5, 4, 5, 6, 7, 8";
+  // whether to fit image to view ('fit'), display at 100% and shrink if
+  // necessary ('shrink'), or always display at 100% ('100')
+  const defaultZoom = "fit";
+  // whether to zoom in/out toward center of view ('true') or mouse ('false')
+  const centerZoom = "false";
+
+  // start script
+  function start() {
+    // run through each <img> element
+    const imgs = document.querySelectorAll("figure > img");
+    let count = 1;
+    for (const img of imgs) {
+      img.classList.add("lightbox_document_img");
+      img.dataset.number = count;
+      img.dataset.total = imgs.length;
+      img.addEventListener("click", openLightbox);
+      count++;
+    }
+
+    // attach mouse and key listeners to window
+    window.addEventListener("mousemove", onWindowMouseMove);
+    window.addEventListener("keyup", onKeyUp);
+  }
+
+  // when mouse is moved anywhere in window
+  function onWindowMouseMove(event) {
+    window.mouseX = event.clientX;
+    window.mouseY = event.clientY;
+  }
+
+  // when key pressed
+  function onKeyUp(event) {
+    if (!event || !event.key) return;
+
+    switch (event.key) {
+      // trigger click of prev button
+      case "ArrowLeft":
+        const prevButton = document.getElementById("lightbox_prev_button");
+        if (prevButton) prevButton.click();
+        break;
+      // trigger click of next button
+      case "ArrowRight":
+        const nextButton = document.getElementById("lightbox_next_button");
+        if (nextButton) nextButton.click();
+        break;
+      // close on esc
+      case "Escape":
+        closeLightbox();
+        break;
+    }
+  }
+
+  // open lightbox
+  function openLightbox() {
+    const lightbox = makeLightbox(this);
+    if (!lightbox) return;
+
+    blurBody(lightbox);
+    document.body.appendChild(lightbox);
+  }
+
+  // make lightbox
+  function makeLightbox(img) {
+    // delete lightbox if it exists, start fresh
+    closeLightbox();
+
+    // create screen overlay containing lightbox
+    const overlay = document.createElement("div");
+    overlay.id = "lightbox_overlay";
+
+    // create image info boxes
+    const numberInfo = document.createElement("div");
+    const zoomInfo = document.createElement("div");
+    numberInfo.id = "lightbox_number_info";
+    zoomInfo.id = "lightbox_zoom_info";
+
+    // create container for image
+    const imageContainer = document.createElement("div");
+    imageContainer.id = "lightbox_image_container";
+    const lightboxImg = makeLightboxImg(
+      img,
+      imageContainer,
+      numberInfo,
+      zoomInfo
+    );
+    imageContainer.appendChild(lightboxImg);
+
+    // create bottom container for caption and navigation buttons
+    const bottomContainer = document.createElement("div");
+    bottomContainer.id = "lightbox_bottom_container";
+    const caption = makeCaption(img);
+    const prevButton = makePrevButton(img);
+    const nextButton = makeNextButton(img);
+    bottomContainer.appendChild(prevButton);
+    bottomContainer.appendChild(caption);
+    bottomContainer.appendChild(nextButton);
+
+    // attach top middle and bottom to overlay
+    overlay.appendChild(numberInfo);
+    overlay.appendChild(zoomInfo);
+    overlay.appendChild(imageContainer);
+    overlay.appendChild(bottomContainer);
+
+    return overlay;
+  }
+
+  // make <img> object that is intuitively draggable and zoomable
+  function makeLightboxImg(sourceImg, container, numberInfoBox, zoomInfoBox) {
+    // create copy of source <img>
+    const img = sourceImg.cloneNode(true);
+    img.classList.remove("lightbox_document_img");
+    img.removeAttribute("id");
+    img.removeAttribute("width");
+    img.removeAttribute("height");
+    img.style.position = "unset";
+    img.style.margin = "0";
+    img.style.padding = "0";
+    img.style.width = "";
+    img.style.height = "";
+    img.style.minWidth = "";
+    img.style.minHeight = "";
+    img.style.maxWidth = "";
+    img.style.maxHeight = "";
+    img.id = "lightbox_img";
+
+    // build sorted list of zoomSteps
+    const zoomSteps = zooms.split(/[^0-9.]/).map((step) => parseFloat(step));
+    zoomSteps.sort((a, b) => a - b);
+
+    // <img> object property variables
+    let zoom = 1;
+    let translateX = 0;
+    let translateY = 0;
+    let clickMouseX = undefined;
+    let clickMouseY = undefined;
+    let clickTranslateX = undefined;
+    let clickTranslateY = undefined;
+
+    updateNumberInfo();
+
+    // update image numbers displayed in info box
+    function updateNumberInfo() {
+      numberInfoBox.innerHTML =
+        sourceImg.dataset.number + " of " + sourceImg.dataset.total;
+    }
+
+    // update zoom displayed in info box
+    function updateZoomInfo() {
+      let zoomInfo = zoom * 100;
+      if (!Number.isInteger(zoomInfo)) zoomInfo = zoomInfo.toFixed(2);
+      zoomInfoBox.innerHTML = zoomInfo + "%";
+    }
+
+    // move to closest zoom step above current zoom
+    const zoomIn = function () {
+      for (const zoomStep of zoomSteps) {
+        if (zoomStep > zoom) {
+          zoom = zoomStep;
+          break;
         }
-
-        // when mouse is moved anywhere in window
-        function onWindowMouseMove(event) {
-            window.mouseX = event.clientX;
-            window.mouseY = event.clientY;
-        }
-
-        // when key pressed
-        function onKeyUp(event) {
-            if (!event || !event.key)
-                return;
-
-            switch (event.key) {
-                // trigger click of prev button
-                case 'ArrowLeft':
-                    const prevButton = document.getElementById(
-                        'lightbox_prev_button'
-                    );
-                    if (prevButton)
-                        prevButton.click();
-                    break;
-                // trigger click of next button
-                case 'ArrowRight':
-                    const nextButton = document.getElementById(
-                        'lightbox_next_button'
-                    );
-                    if (nextButton)
-                        nextButton.click();
-                    break;
-                // close on esc
-                case 'Escape':
-                    closeLightbox();
-                    break;
-            }
-        }
-
-        // open lightbox
-        function openLightbox() {
-            const lightbox = makeLightbox(this);
-            if (!lightbox)
-                return;
-
-            blurBody(lightbox);
-            document.body.appendChild(lightbox);
-        }
-
-        // make lightbox
-        function makeLightbox(img) {
-            // delete lightbox if it exists, start fresh
-            closeLightbox();
-
-            // create screen overlay containing lightbox
-            const overlay = document.createElement('div');
-            overlay.id = 'lightbox_overlay';
-
-            // create image info boxes
-            const numberInfo = document.createElement('div');
-            const zoomInfo = document.createElement('div');
-            numberInfo.id = 'lightbox_number_info';
-            zoomInfo.id = 'lightbox_zoom_info';
-
-            // create container for image
-            const imageContainer = document.createElement('div');
-            imageContainer.id = 'lightbox_image_container';
-            const lightboxImg = makeLightboxImg(
-                img,
-                imageContainer,
-                numberInfo,
-                zoomInfo
-            );
-            imageContainer.appendChild(lightboxImg);
-
-            // create bottom container for caption and navigation buttons
-            const bottomContainer = document.createElement('div');
-            bottomContainer.id = 'lightbox_bottom_container';
-            const caption = makeCaption(img);
-            const prevButton = makePrevButton(img);
-            const nextButton = makeNextButton(img);
-            bottomContainer.appendChild(prevButton);
-            bottomContainer.appendChild(caption);
-            bottomContainer.appendChild(nextButton);
-
-            // attach top middle and bottom to overlay
-            overlay.appendChild(numberInfo);
-            overlay.appendChild(zoomInfo);
-            overlay.appendChild(imageContainer);
-            overlay.appendChild(bottomContainer);
-
-            return overlay;
-        }
-
-        // make <img> object that is intuitively draggable and zoomable
-        function makeLightboxImg(
-            sourceImg,
-            container,
-            numberInfoBox,
-            zoomInfoBox
-        ) {
-            // create copy of source <img>
-            const img = sourceImg.cloneNode(true);
-            img.classList.remove('lightbox_document_img');
-            img.removeAttribute('id');
-            img.removeAttribute('width');
-            img.removeAttribute('height');
-            img.style.position = 'unset';
-            img.style.margin = '0';
-            img.style.padding = '0';
-            img.style.width = '';
-            img.style.height = '';
-            img.style.minWidth = '';
-            img.style.minHeight = '';
-            img.style.maxWidth = '';
-            img.style.maxHeight = '';
-            img.id = 'lightbox_img';
-
-            // build sorted list of unique zoomSteps, always including a 100%
-            let zoomSteps = [];
-            const optionsZooms = options.zoomSteps.split(/[^0-9.]/);
-            for (const optionZoom of optionsZooms) {
-                const newZoom = parseFloat(optionZoom);
-                if (newZoom && !zoomSteps.includes(newZoom))
-                    zoomSteps.push(newZoom);
-            }
-            if (!zoomSteps.includes(1))
-                zoomSteps.push(1);
-            zoomSteps = zoomSteps.sort(function sortNumber(a, b) {
-                return a - b;
-            });
-
-            // <img> object property variables
-            let zoom = 1;
-            let translateX = 0;
-            let translateY = 0;
-            let clickMouseX = undefined;
-            let clickMouseY = undefined;
-            let clickTranslateX = undefined;
-            let clickTranslateY = undefined;
-
-            updateNumberInfo();
-
-            // update image numbers displayed in info box
-            function updateNumberInfo() {
-                numberInfoBox.innerHTML =
-                    sourceImg.dataset.number + ' of ' + sourceImg.dataset.total;
-            }
-
-            // update zoom displayed in info box
-            function updateZoomInfo() {
-                let zoomInfo = zoom * 100;
-                if (!Number.isInteger(zoomInfo))
-                    zoomInfo = zoomInfo.toFixed(2);
-                zoomInfoBox.innerHTML = zoomInfo + '%';
-            }
-
-            // move to closest zoom step above current zoom
-            const zoomIn = function() {
-                for (const zoomStep of zoomSteps) {
-                    if (zoomStep > zoom) {
-                        zoom = zoomStep;
-                        break;
-                    }
-                }
-                updateTransform();
-            };
-
-            // move to closest zoom step above current zoom
-            const zoomOut = function() {
-                zoomSteps.reverse();
-                for (const zoomStep of zoomSteps) {
-                    if (zoomStep < zoom) {
-                        zoom = zoomStep;
-                        break;
-                    }
-                }
-                zoomSteps.reverse();
-
-                updateTransform();
-            };
-
-            // update display of <img> based on scale/translate properties
-            const updateTransform = function() {
-                // set transform
-                img.style.transform =
-                    'translate(' +
-                    (translateX || 0) +
-                    'px,' +
-                    (translateY || 0) +
-                    'px) scale(' +
-                    (zoom || 1) +
-                    ')';
-
-                // get new width/height after scale
-                const rect = img.getBoundingClientRect();
-                // limit translate
-                translateX = Math.max(translateX, -rect.width / 2);
-                translateX = Math.min(translateX, rect.width / 2);
-                translateY = Math.max(translateY, -rect.height / 2);
-                translateY = Math.min(translateY, rect.height / 2);
-
-                // set transform
-                img.style.transform =
-                    'translate(' +
-                    (translateX || 0) +
-                    'px,' +
-                    (translateY || 0) +
-                    'px) scale(' +
-                    (zoom || 1) +
-                    ')';
-
-                updateZoomInfo();
-            };
-
-            // fit <img> to container
-            const fit = function() {
-                // no x/y offset, 100% zoom by default
-                translateX = 0;
-                translateY = 0;
-                zoom = 1;
-
-                // widths of <img> and container
-                const imgWidth = img.naturalWidth;
-                const imgHeight = img.naturalHeight;
-                const containerWidth = parseFloat(
-                    window.getComputedStyle(container).width
-                );
-                const containerHeight = parseFloat(
-                    window.getComputedStyle(container).height
-                );
-
-                // how much zooming is needed to fit <img> to container
-                const xRatio = imgWidth / containerWidth;
-                const yRatio = imgHeight / containerHeight;
-                const maxRatio = Math.max(xRatio, yRatio);
-                const newZoom = 1 / maxRatio;
-
-                // fit <img> to container according to option
-                if (options.defaultZoom === 'shrink') {
-                    if (maxRatio > 1)
-                        zoom = newZoom;
-                } else if (options.defaultZoom === 'fit')
-                    zoom = newZoom;
-
-                updateTransform();
-            };
-
-            // when mouse wheel is rolled anywhere in container
-            const onContainerWheel = function(event) {
-                if (!event)
-                    return;
-
-                // let ctrl + mouse wheel to zoom behave as normal
-                if (event.ctrlKey)
-                    return;
-
-                // prevent normal scroll behavior
-                event.preventDefault();
-                event.stopPropagation();
-
-                // point around which to scale img
-                const viewRect = container.getBoundingClientRect();
-                const viewX = (viewRect.left + viewRect.right) / 2;
-                const viewY = (viewRect.top + viewRect.bottom) / 2;
-                const originX = options.centerZoom === 'true' ? viewX : mouseX;
-                const originY = options.centerZoom === 'true' ? viewY : mouseY;
-
-                // get point on image under origin
-                const oldRect = img.getBoundingClientRect();
-                const oldPercentX = (originX - oldRect.left) / oldRect.width;
-                const oldPercentY = (originY - oldRect.top) / oldRect.height;
-
-                // increment/decrement zoom
-                if (event.deltaY < 0)
-                    zoomIn();
-                if (event.deltaY > 0)
-                    zoomOut();
-
-                // get offset between previous image point and origin
-                const newRect = img.getBoundingClientRect();
-                const offsetX =
-                    originX - (newRect.left + newRect.width * oldPercentX);
-                const offsetY =
-                    originY - (newRect.top + newRect.height * oldPercentY);
-
-                // translate image to keep image point under origin
-                translateX += offsetX;
-                translateY += offsetY;
-
-                // perform translate
-                updateTransform();
-            };
-
-            // when container is clicked
-            function onContainerClick(event) {
-                // if container itself is target of click, and not other
-                // element above it
-                if (event.target === this)
-                    closeLightbox();
-            }
-
-            // when mouse button is pressed on image
-            const onImageMouseDown = function(event) {
-                // store original mouse position relative to image
-                clickMouseX = window.mouseX;
-                clickMouseY = window.mouseY;
-                clickTranslateX = translateX;
-                clickTranslateY = translateY;
-                event.stopPropagation();
-                event.preventDefault();
-            };
-
-            // when mouse button is released anywhere in window
-            const onWindowMouseUp = function(event) {
-                // reset original mouse position
-                clickMouseX = undefined;
-                clickMouseY = undefined;
-                clickTranslateX = undefined;
-                clickTranslateY = undefined;
-
-                // remove global listener if lightbox removed from document
-                if (!document.body.contains(container))
-                    window.removeEventListener('mouseup', onWindowMouseUp);
-            };
-
-            // when mouse is moved anywhere in window
-            const onWindowMouseMove = function(event) {
-                if (
-                    clickMouseX === undefined ||
-                    clickMouseY === undefined ||
-                    clickTranslateX === undefined ||
-                    clickTranslateY === undefined
-                )
-                    return;
-
-                // offset image based on original and current mouse position
-                translateX = clickTranslateX + window.mouseX - clickMouseX;
-                translateY = clickTranslateY + window.mouseY - clickMouseY;
-                updateTransform();
-                event.preventDefault();
-
-                // remove global listener if lightbox removed from document
-                if (!document.body.contains(container))
-                    window.removeEventListener('mousemove', onWindowMouseMove);
-            };
-
-            // when window is resized
-            const onWindowResize = function(event) {
-                fit();
-
-                // remove global listener if lightbox removed from document
-                if (!document.body.contains(container))
-                    window.removeEventListener('resize', onWindowResize);
-            };
-
-            // attach the necessary event listeners
-            img.addEventListener('dblclick', fit);
-            img.addEventListener('mousedown', onImageMouseDown);
-            container.addEventListener('wheel', onContainerWheel);
-            container.addEventListener('mousedown', onContainerClick);
-            container.addEventListener('touchstart', onContainerClick);
-            window.addEventListener('mouseup', onWindowMouseUp);
-            window.addEventListener('mousemove', onWindowMouseMove);
-            window.addEventListener('resize', onWindowResize);
-
-            // run fit() after lightbox atttached to document and <img> Loaded
-            // so needed container and img dimensions available
-            img.addEventListener('load', fit);
-
-            return img;
+      }
+      updateTransform();
+    };
+
+    // move to closest zoom step above current zoom
+    const zoomOut = function () {
+      zoomSteps.reverse();
+      for (const zoomStep of zoomSteps) {
+        if (zoomStep < zoom) {
+          zoom = zoomStep;
+          break;
         }
-
-        // make caption
-        function makeCaption(img) {
-            const caption = document.createElement('div');
-            caption.id = 'lightbox_caption';
-            const captionSource = img.nextElementSibling;
-            if (captionSource.tagName.toLowerCase() === 'figcaption') {
-                const captionCopy = makeCopy(captionSource);
-                caption.innerHTML = captionCopy.innerHTML;
-            }
-
-            caption.addEventListener('touchstart', function(event) {
-                event.stopPropagation();
-            });
-
-            return caption;
-        }
-
-        // make carbon copy of html dom element
-        function makeCopy(source) {
-            const sourceCopy = source.cloneNode(true);
-
-            // delete elements marked with ignore (eg anchor and jump buttons)
-            const deleteFromCopy = sourceCopy.querySelectorAll(
-                '[data-ignore="true"]'
-            );
-            for (const element of deleteFromCopy)
-                element.remove();
-
-            // delete certain element attributes
-            const attributes = [
-                'id',
-                'data-collapsed',
-                'data-selected',
-                'data-highlighted',
-                'data-glow'
-            ];
-            for (const attribute of attributes) {
-                sourceCopy.removeAttribute(attribute);
-                const elements = sourceCopy.querySelectorAll(
-                    '[' + attribute + ']'
-                );
-                for (const element of elements)
-                    element.removeAttribute(attribute);
-            }
-
-            return sourceCopy;
-        }
-
-        // make button to jump to previous image in document
-        function makePrevButton(img) {
-            const prevButton = document.createElement('button');
-            prevButton.id = 'lightbox_prev_button';
-            prevButton.title = 'Jump to the previous image in the document [←]';
-            prevButton.classList.add('icon_button', 'lightbox_button');
-            prevButton.innerHTML = document.querySelector(
-                '.icon_caret_left'
-            ).innerHTML;
-
-            // attach click listeners to button
-            prevButton.addEventListener('click', function() {
-                getPrevImg(img).click();
-            });
-
-            return prevButton;
-        }
-
-        // make button to jump to next image in document
-        function makeNextButton(img) {
-            const nextButton = document.createElement('button');
-            nextButton.id = 'lightbox_next_button';
-            nextButton.title = 'Jump to the next image in the document [→]';
-            nextButton.classList.add('icon_button', 'lightbox_button');
-            nextButton.innerHTML = document.querySelector(
-                '.icon_caret_right'
-            ).innerHTML;
-
-            // attach click listeners to button
-            nextButton.addEventListener('click', function() {
-                getNextImg(img).click();
-            });
-
-            return nextButton;
-        }
-
-        // get previous image in document
-        function getPrevImg(img) {
-            const imgs = document.querySelectorAll('.lightbox_document_img');
-
-            // find index of provided img
-            let index;
-            for (index = 0; index < imgs.length; index++) {
-                if (imgs[index] === img)
-                    break;
-            }
-
-
-            // wrap index to other side if < 1
-            if (index - 1 >= 0)
-                index--;
-            else
-                index = imgs.length - 1;
-            return imgs[index];
-        }
-
-        // get next image in document
-        function getNextImg(img) {
-            const imgs = document.querySelectorAll('.lightbox_document_img');
-
-            // find index of provided img
-            let index;
-            for (index = 0; index < imgs.length; index++) {
-                if (imgs[index] === img)
-                    break;
-            }
-
-
-            // wrap index to other side if > total
-            if (index + 1 <= imgs.length - 1)
-                index++;
-            else
-                index = 0;
-            return imgs[index];
-        }
-
-        // close lightbox
-        function closeLightbox() {
-            focusBody();
-
-            const lightbox = document.getElementById('lightbox_overlay');
-            if (lightbox)
-                lightbox.remove();
-        }
-
-        // make all elements behind lightbox non-focusable
-        function blurBody(overlay) {
-            const all = document.querySelectorAll('*');
-            for (const element of all)
-                element.tabIndex = -1;
-            document.body.classList.add('body_no_scroll');
-        }
-
-        // make all elements focusable again
-        function focusBody() {
-            const all = document.querySelectorAll('*');
-            for (const element of all)
-                element.removeAttribute('tabIndex');
-            document.body.classList.remove('body_no_scroll');
-        }
-
-        // load options from url parameters
-        function loadOptions() {
-            const url = window.location.search;
-            const params = new URLSearchParams(url);
-            for (const optionName of Object.keys(options)) {
-                const paramName = pluginName + '-' + optionName;
-                const param = params.get(paramName);
-                if (param !== '' && param !== null)
-                    options[optionName] = param;
-            }
-        }
-        loadOptions();
-
-        // start script when document is finished loading
-        if (options.enabled === 'true')
-            window.addEventListener('load', start);
-    })();
+      }
+      zoomSteps.reverse();
+
+      updateTransform();
+    };
+
+    // update display of <img> based on scale/translate properties
+    const updateTransform = function () {
+      // set transform
+      img.style.transform =
+        "translate(" +
+        (translateX || 0) +
+        "px," +
+        (translateY || 0) +
+        "px) scale(" +
+        (zoom || 1) +
+        ")";
+
+      // get new width/height after scale
+      const rect = img.getBoundingClientRect();
+      // limit translate
+      translateX = Math.max(translateX, -rect.width / 2);
+      translateX = Math.min(translateX, rect.width / 2);
+      translateY = Math.max(translateY, -rect.height / 2);
+      translateY = Math.min(translateY, rect.height / 2);
+
+      // set transform
+      img.style.transform =
+        "translate(" +
+        (translateX || 0) +
+        "px," +
+        (translateY || 0) +
+        "px) scale(" +
+        (zoom || 1) +
+        ")";
+
+      updateZoomInfo();
+    };
+
+    // fit <img> to container
+    const fit = function () {
+      // no x/y offset, 100% zoom by default
+      translateX = 0;
+      translateY = 0;
+      zoom = 1;
+
+      // widths of <img> and container
+      const imgWidth = img.naturalWidth;
+      const imgHeight = img.naturalHeight;
+      const containerWidth = parseFloat(
+        window.getComputedStyle(container).width
+      );
+      const containerHeight = parseFloat(
+        window.getComputedStyle(container).height
+      );
+
+      // how much zooming is needed to fit <img> to container
+      const xRatio = imgWidth / containerWidth;
+      const yRatio = imgHeight / containerHeight;
+      const maxRatio = Math.max(xRatio, yRatio);
+      const newZoom = 1 / maxRatio;
+
+      // fit <img> to container according to option
+      if (defaultZoom === "shrink") {
+        if (maxRatio > 1) zoom = newZoom;
+      } else if (defaultZoom === "fit") zoom = newZoom;
+
+      updateTransform();
+    };
+
+    // when mouse wheel is rolled anywhere in container
+    const onContainerWheel = function (event) {
+      if (!event) return;
+
+      // let ctrl + mouse wheel to zoom behave as normal
+      if (event.ctrlKey) return;
+
+      // prevent normal scroll behavior
+      event.preventDefault();
+      event.stopPropagation();
+
+      // point around which to scale img
+      const viewRect = container.getBoundingClientRect();
+      const viewX = (viewRect.left + viewRect.right) / 2;
+      const viewY = (viewRect.top + viewRect.bottom) / 2;
+      const originX = centerZoom === "true" ? viewX : mouseX;
+      const originY = centerZoom === "true" ? viewY : mouseY;
+
+      // get point on image under origin
+      const oldRect = img.getBoundingClientRect();
+      const oldPercentX = (originX - oldRect.left) / oldRect.width;
+      const oldPercentY = (originY - oldRect.top) / oldRect.height;
+
+      // increment/decrement zoom
+      if (event.deltaY < 0) zoomIn();
+      if (event.deltaY > 0) zoomOut();
+
+      // get offset between previous image point and origin
+      const newRect = img.getBoundingClientRect();
+      const offsetX = originX - (newRect.left + newRect.width * oldPercentX);
+      const offsetY = originY - (newRect.top + newRect.height * oldPercentY);
+
+      // translate image to keep image point under origin
+      translateX += offsetX;
+      translateY += offsetY;
+
+      // perform translate
+      updateTransform();
+    };
+
+    // when container is clicked
+    function onContainerClick(event) {
+      // if container itself is target of click, and not other
+      // element above it
+      if (event.target === this) closeLightbox();
+    }
+
+    // when mouse button is pressed on image
+    const onImageMouseDown = function (event) {
+      // store original mouse position relative to image
+      clickMouseX = window.mouseX;
+      clickMouseY = window.mouseY;
+      clickTranslateX = translateX;
+      clickTranslateY = translateY;
+      event.stopPropagation();
+      event.preventDefault();
+    };
+
+    // when mouse button is released anywhere in window
+    const onWindowMouseUp = function (event) {
+      // reset original mouse position
+      clickMouseX = undefined;
+      clickMouseY = undefined;
+      clickTranslateX = undefined;
+      clickTranslateY = undefined;
+
+      // remove global listener if lightbox removed from document
+      if (!document.body.contains(container))
+        window.removeEventListener("mouseup", onWindowMouseUp);
+    };
+
+    // when mouse is moved anywhere in window
+    const onWindowMouseMove = function (event) {
+      if (
+        clickMouseX === undefined ||
+        clickMouseY === undefined ||
+        clickTranslateX === undefined ||
+        clickTranslateY === undefined
+      )
+        return;
+
+      // offset image based on original and current mouse position
+      translateX = clickTranslateX + window.mouseX - clickMouseX;
+      translateY = clickTranslateY + window.mouseY - clickMouseY;
+      updateTransform();
+      event.preventDefault();
+
+      // remove global listener if lightbox removed from document
+      if (!document.body.contains(container))
+        window.removeEventListener("mousemove", onWindowMouseMove);
+    };
+
+    // when window is resized
+    const onWindowResize = function (event) {
+      fit();
+
+      // remove global listener if lightbox removed from document
+      if (!document.body.contains(container))
+        window.removeEventListener("resize", onWindowResize);
+    };
+
+    // attach the necessary event listeners
+    img.addEventListener("dblclick", fit);
+    img.addEventListener("mousedown", onImageMouseDown);
+    container.addEventListener("wheel", onContainerWheel);
+    container.addEventListener("mousedown", onContainerClick);
+    container.addEventListener("touchstart", onContainerClick);
+    window.addEventListener("mouseup", onWindowMouseUp);
+    window.addEventListener("mousemove", onWindowMouseMove);
+    window.addEventListener("resize", onWindowResize);
+
+    // run fit() after lightbox atttached to document and <img> Loaded
+    // so needed container and img dimensions available
+    img.addEventListener("load", fit);
+
+    return img;
+  }
+
+  // make caption
+  function makeCaption(img) {
+    const caption = document.createElement("div");
+    caption.id = "lightbox_caption";
+    const captionSource = img.nextElementSibling;
+    if (captionSource.tagName.toLowerCase() === "figcaption") {
+      const captionCopy = makeCopy(captionSource);
+      caption.innerHTML = captionCopy.innerHTML;
+    }
+
+    caption.addEventListener("touchstart", function (event) {
+      event.stopPropagation();
+    });
+
+    return caption;
+  }
+
+  // make carbon copy of html dom element
+  function makeCopy(source) {
+    const sourceCopy = source.cloneNode(true);
+
+    // delete elements marked with ignore (eg anchor and jump buttons)
+    const deleteFromCopy = sourceCopy.querySelectorAll('[data-ignore="true"]');
+    for (const element of deleteFromCopy) element.remove();
+
+    // delete certain element attributes
+    const attributes = [
+      "id",
+      "data-collapsed",
+      "data-selected",
+      "data-highlighted",
+      "data-glow",
+    ];
+    for (const attribute of attributes) {
+      sourceCopy.removeAttribute(attribute);
+      const elements = sourceCopy.querySelectorAll("[" + attribute + "]");
+      for (const element of elements) element.removeAttribute(attribute);
+    }
+
+    return sourceCopy;
+  }
+
+  // make button to jump to previous image in document
+  function makePrevButton(img) {
+    const prevButton = document.createElement("button");
+    prevButton.id = "lightbox_prev_button";
+    prevButton.title = "Jump to the previous image in the document [←]";
+    prevButton.classList.add("icon_button", "lightbox_button");
+    prevButton.innerHTML = document.querySelector(".icon_caret_left").innerHTML;
+
+    // attach click listeners to button
+    prevButton.addEventListener("click", function () {
+      getPrevImg(img).click();
+    });
+
+    return prevButton;
+  }
+
+  // make button to jump to next image in document
+  function makeNextButton(img) {
+    const nextButton = document.createElement("button");
+    nextButton.id = "lightbox_next_button";
+    nextButton.title = "Jump to the next image in the document [→]";
+    nextButton.classList.add("icon_button", "lightbox_button");
+    nextButton.innerHTML = document.querySelector(
+      ".icon_caret_right"
+    ).innerHTML;
+
+    // attach click listeners to button
+    nextButton.addEventListener("click", function () {
+      getNextImg(img).click();
+    });
+
+    return nextButton;
+  }
+
+  // get previous image in document
+  function getPrevImg(img) {
+    const imgs = document.querySelectorAll(".lightbox_document_img");
+
+    // find index of provided img
+    let index;
+    for (index = 0; index < imgs.length; index++) {
+      if (imgs[index] === img) break;
+    }
+
+    // wrap index to other side if < 1
+    if (index - 1 >= 0) index--;
+    else index = imgs.length - 1;
+    return imgs[index];
+  }
+
+  // get next image in document
+  function getNextImg(img) {
+    const imgs = document.querySelectorAll(".lightbox_document_img");
+
+    // find index of provided img
+    let index;
+    for (index = 0; index < imgs.length; index++) {
+      if (imgs[index] === img) break;
+    }
+
+    // wrap index to other side if > total
+    if (index + 1 <= imgs.length - 1) index++;
+    else index = 0;
+    return imgs[index];
+  }
+
+  // close lightbox
+  function closeLightbox() {
+    focusBody();
+
+    const lightbox = document.getElementById("lightbox_overlay");
+    if (lightbox) lightbox.remove();
+  }
+
+  // make all elements behind lightbox non-focusable
+  function blurBody(overlay) {
+    const all = document.querySelectorAll("*");
+    for (const element of all) element.tabIndex = -1;
+    document.body.classList.add("body_no_scroll");
+  }
+
+  // make all elements focusable again
+  function focusBody() {
+    const all = document.querySelectorAll("*");
+    for (const element of all) element.removeAttribute("tabIndex");
+    document.body.classList.remove("body_no_scroll");
+  }
+
+  // start script when document is finished loading
+  window.addEventListener("load", start);
 </script>
 
 <!-- caret left icon -->
 
 <template class="icon_caret_left">
-    <!-- modified from: https://fontawesome.com/icons/caret-left -->
-    <svg width="16" height="16" viewBox="0 0 192 512">
-        <path
-            fill="currentColor"
-            d="M192 127.338v257.324c0 17.818-21.543 26.741-34.142 14.142L29.196 270.142c-7.81-7.81-7.81-20.474 0-28.284l128.662-128.662c12.599-12.6 34.142-3.676 34.142 14.142z"
-        ></path>
-    </svg>
+  <!-- modified from: https://fontawesome.com/icons/caret-left -->
+  <svg width="16" height="16" viewBox="0 0 192 512">
+    <path
+      fill="currentColor"
+      d="M192 127.338v257.324c0 17.818-21.543 26.741-34.142 14.142L29.196 270.142c-7.81-7.81-7.81-20.474 0-28.284l128.662-128.662c12.599-12.6 34.142-3.676 34.142 14.142z"
+    ></path>
+  </svg>
 </template>
 
 <!-- caret right icon -->
 
 <template class="icon_caret_right">
-    <!-- modified from: https://fontawesome.com/icons/caret-right -->
-    <svg width="16" height="16" viewBox="0 0 192 512">
-        <path
-            fill="currentColor"
-            d="M0 384.662V127.338c0-17.818 21.543-26.741 34.142-14.142l128.662 128.662c7.81 7.81 7.81 20.474 0 28.284L34.142 398.804C21.543 411.404 0 402.48 0 384.662z"
-        ></path>
-    </svg>
+  <!-- modified from: https://fontawesome.com/icons/caret-right -->
+  <svg width="16" height="16" viewBox="0 0 192 512">
+    <path
+      fill="currentColor"
+      d="M0 384.662V127.338c0-17.818 21.543-26.741 34.142-14.142l128.662 128.662c7.81 7.81 7.81 20.474 0 28.284L34.142 398.804C21.543 411.404 0 402.48 0 384.662z"
+    ></path>
+  </svg>
 </template>
+
+<style>
+  @media only screen {
+    /* regular <img> in document when hovered */
+    img.lightbox_document_img:hover {
+      cursor: pointer;
+    }
+
+    .body_no_scroll {
+      overflow: hidden !important;
+    }
+
+    /* screen overlay */
+    #lightbox_overlay {
+      display: flex;
+      flex-direction: column;
+      position: fixed;
+      left: 0;
+      top: 0;
+      right: 0;
+      bottom: 0;
+      background: rgba(0, 0, 0, 0.75);
+      z-index: 3;
+    }
+
+    /* middle area containing lightbox image */
+    #lightbox_image_container {
+      flex-grow: 1;
+      display: flex;
+      justify-content: center;
+      align-items: center;
+      overflow: hidden;
+      position: relative;
+      padding: 20px;
+    }
+
+    /* bottom area containing caption */
+    #lightbox_bottom_container {
+      display: flex;
+      justify-content: center;
+      align-items: center;
+      height: 100px;
+      min-height: 100px;
+      max-height: 100px;
+      background: rgba(0, 0, 0, 0.5);
+    }
+
+    /* image number info text box */
+    #lightbox_number_info {
+      position: absolute;
+      color: #ffffff;
+      font-weight: 600;
+      left: 2px;
+      top: 0;
+      z-index: 4;
+    }
+
+    /* zoom info text box */
+    #lightbox_zoom_info {
+      position: absolute;
+      color: #ffffff;
+      font-weight: 600;
+      right: 2px;
+      top: 0;
+      z-index: 4;
+    }
+
+    /* copy of image caption */
+    #lightbox_caption {
+      box-sizing: border-box;
+      display: inline-block;
+      width: 100%;
+      max-height: 100%;
+      padding: 10px 0;
+      text-align: center;
+      overflow-y: auto;
+      color: #ffffff;
+    }
+
+    /* navigation previous/next button */
+    .lightbox_button {
+      width: 100px;
+      height: 100%;
+      min-width: 100px;
+      min-height: 100%;
+      color: #ffffff;
+    }
+
+    /* navigation previous/next button when hovered */
+    .lightbox_button:hover {
+      background: none !important;
+    }
+
+    /* navigation button icon */
+    .lightbox_button > svg {
+      height: 25px;
+    }
+
+    /* figure auto-number */
+    #lightbox_caption > span:first-of-type {
+      font-weight: bold;
+      margin-right: 5px;
+    }
+
+    /* lightbox image when hovered */
+    #lightbox_img:hover {
+      cursor: grab;
+    }
+
+    /* lightbox image when grabbed */
+    #lightbox_img:active {
+      cursor: grabbing;
+    }
+  }
+
+  /* when on screen < 480px wide */
+  @media only screen and (max-width: 480px) {
+    /* make navigation buttons skinnier on small screens to make more room for caption text */
+    .lightbox_button {
+      width: 50px;
+      min-width: 50px;
+    }
+  }
+
+  /* always hide lightbox on print */
+  @media only print {
+    #lightbox_overlay {
+      display: none;
+    }
+  }
+</style>
diff --git a/build/plugins/link-highlight.html b/build/plugins/link-highlight.html
index 4462f50..04263a8 100644
--- a/build/plugins/link-highlight.html
+++ b/build/plugins/link-highlight.html
@@ -1,184 +1,157 @@
-<!-- link highlight plugin -->
-
-<script>
-    (function() {
-        // /////////////////////////
-        // DESCRIPTION
-        // /////////////////////////
-
-        // This Manubot plugin makes it such that when a user hovers or
-        // focuses a link, other links that have the same target will be
-        // highlighted. It also makes it such that when clicking a link, the
-        // target of the link (eg reference, figure, table) is briefly
-        // highlighted.
-
-        // /////////////////////////
-        // OPTIONS
-        // /////////////////////////
-
-        // plugin name prefix for url parameters
-        const pluginName = 'linkHighlight';
-
-        // default plugin options
-        const options = {
-            // whether to also highlight links that go to external urls
-            externalLinks: 'false',
-            // whether user must click off to unhighlight instead of just
-            // un-hovering
-            clickUnhighlight: 'false',
-            // whether to also highlight links that are unique
-            highlightUnique: 'true',
-            // whether plugin is on or not
-            enabled: 'true'
-        };
-
-        // change options above, or override with url parameter, eg:
-        // 'manuscript.html?pluginName-enabled=false'
-
-        // /////////////////////////
-        // SCRIPT
-        // /////////////////////////
-
-        // start script
-        function start() {
-            const links = getLinks();
-            for (const link of links) {
-                // attach mouse and focus listeners to link
-                link.addEventListener('mouseenter', onLinkFocus);
-                link.addEventListener('focus', onLinkFocus);
-                link.addEventListener('mouseleave', onLinkUnhover);
-            }
-
-            // attach click and hash change listeners to window
-            window.addEventListener('click', onClick);
-            window.addEventListener('touchstart', onClick);
-            window.addEventListener('hashchange', onHashChange);
-
-            // run hash change on window load in case user has navigated
-            // directly to hash
-            onHashChange();
-        }
-
-        // when link is focused (tabbed to) or hovered
-        function onLinkFocus() {
-            highlight(this);
-        }
-
-        // when link is unhovered
-        function onLinkUnhover() {
-            if (options.clickUnhighlight !== 'true')
-                unhighlightAll();
-        }
-
-        // when the mouse is clicked anywhere in window
-        function onClick(event) {
-            unhighlightAll();
-        }
-
-        // when hash (eg manuscript.html#introduction) changes
-        function onHashChange() {
-            const target = getHashTarget();
-            if (target)
-                glowElement(target);
-        }
-
-        // get element that is target of link or url hash
-        function getHashTarget(link) {
-            const hash = link ? link.hash : window.location.hash;
-            const id = hash.slice(1);
-            let target = document.querySelector('[id="' + id + '"]');
-            if (!target)
-                return;
-
-            return target;
-        }
-
-        // start glow sequence on an element
-        function glowElement(element) {
-            const startGlow = function() {
-                onGlowEnd();
-                element.dataset.glow = 'true';
-                element.addEventListener('animationend', onGlowEnd);
-            };
-            const onGlowEnd = function() {
-                element.removeAttribute('data-glow');
-                element.removeEventListener('animationend', onGlowEnd);
-            };
-            startGlow();
-        }
-
-        // highlight link and all others with same target
-        function highlight(link) {
-            // force unhighlight all to start fresh
-            unhighlightAll();
-
-            // get links with same target
-            if (!link)
-                return;
-            const sameLinks = getSameLinks(link);
-
-            // if link unique and option is off, exit and don't highlight
-            if (sameLinks.length <= 1 && options.highlightUnique !== 'true')
-                return;
-
-            // highlight all same links, and "select" (special highlight) this
-            // one
-            for (const sameLink of sameLinks) {
-                if (sameLink === link)
-                    sameLink.setAttribute('data-selected', 'true');
-                else
-                    sameLink.setAttribute('data-highlighted', 'true');
-            }
-        }
-
-        // unhighlight all links
-        function unhighlightAll() {
-            const links = getLinks();
-            for (const link of links) {
-                link.setAttribute('data-selected', 'false');
-                link.setAttribute('data-highlighted', 'false');
-            }
-        }
-
-        // get links with same target
-        function getSameLinks(link) {
-            const results = [];
-            const links = getLinks();
-            for (const otherLink of links) {
-                if (
-                    otherLink.getAttribute('href') === link.getAttribute('href')
-                )
-                    results.push(otherLink);
-            }
-            return results;
-        }
-
-        // get all links of types we wish to handle
-        function getLinks() {
-            let query = 'a';
-            if (options.externalLinks !== 'true')
-                query += '[href^="#"]';
-            // exclude buttons, anchor links, toc links, etc
-            query +=
-                ':not(.button):not(.icon_button):not(.anchor):not(.toc_link)';
-            return document.querySelectorAll(query);
-        }
-
-        // load options from url parameters
-        function loadOptions() {
-            const url = window.location.search;
-            const params = new URLSearchParams(url);
-            for (const optionName of Object.keys(options)) {
-                const paramName = pluginName + '-' + optionName;
-                const param = params.get(paramName);
-                if (param !== '' && param !== null)
-                    options[optionName] = param;
-            }
-        }
-        loadOptions();
-
-        // start script when document is finished loading
-        if (options.enabled === 'true')
-            window.addEventListener('load', start);
-    })();
+<!-- 
+  Link Highlight Plugin
+
+  Makes it such that when a user hovers or focuses a link, other links that have
+  the same target will be highlighted. It also makes it such that when clicking
+  a link, the target of the link (eg reference, figure, table) is briefly
+  highlighted.
+-->
+
+<script type="module">
+  // whether to also highlight links that go to external urls
+  const externalLinks = "false";
+  // whether user must click off to unhighlight instead of just
+  // un-hovering
+  const clickUnhighlight = "false";
+  // whether to also highlight links that are unique
+  const highlightUnique = "true";
+
+  // start script
+  function start() {
+    const links = getLinks();
+    for (const link of links) {
+      // attach mouse and focus listeners to link
+      link.addEventListener("mouseenter", onLinkFocus);
+      link.addEventListener("focus", onLinkFocus);
+      link.addEventListener("mouseleave", onLinkUnhover);
+    }
+
+    // attach click and hash change listeners to window
+    window.addEventListener("click", onClick);
+    window.addEventListener("touchstart", onClick);
+    window.addEventListener("hashchange", onHashChange);
+
+    // run hash change on window load in case user has navigated
+    // directly to hash
+    onHashChange();
+  }
+
+  // when link is focused (tabbed to) or hovered
+  function onLinkFocus() {
+    highlight(this);
+  }
+
+  // when link is unhovered
+  function onLinkUnhover() {
+    if (clickUnhighlight !== "true") unhighlightAll();
+  }
+
+  // when the mouse is clicked anywhere in window
+  function onClick(event) {
+    unhighlightAll();
+  }
+
+  // when hash (eg manuscript.html#introduction) changes
+  function onHashChange() {
+    const target = getHashTarget();
+    if (target) glowElement(target);
+  }
+
+  // start glow sequence on an element
+  function glowElement(element) {
+    const startGlow = function () {
+      onGlowEnd();
+      element.dataset.glow = "true";
+      element.addEventListener("animationend", onGlowEnd);
+    };
+    const onGlowEnd = function () {
+      element.removeAttribute("data-glow");
+      element.removeEventListener("animationend", onGlowEnd);
+    };
+    startGlow();
+  }
+
+  // highlight link and all others with same target
+  function highlight(link) {
+    // force unhighlight all to start fresh
+    unhighlightAll();
+
+    // get links with same target
+    if (!link) return;
+    const sameLinks = getSameLinks(link);
+
+    // if link unique and option is off, exit and don't highlight
+    if (sameLinks.length <= 1 && highlightUnique !== "true") return;
+
+    // highlight all same links, and "select" (special highlight) this
+    // one
+    for (const sameLink of sameLinks) {
+      if (sameLink === link) sameLink.setAttribute("data-selected", "true");
+      else sameLink.setAttribute("data-highlighted", "true");
+    }
+  }
+
+  // unhighlight all links
+  function unhighlightAll() {
+    const links = getLinks();
+    for (const link of links) {
+      link.setAttribute("data-selected", "false");
+      link.setAttribute("data-highlighted", "false");
+    }
+  }
+
+  // get links with same target
+  function getSameLinks(link) {
+    const results = [];
+    const links = getLinks();
+    for (const otherLink of links) {
+      if (otherLink.getAttribute("href") === link.getAttribute("href"))
+        results.push(otherLink);
+    }
+    return results;
+  }
+
+  // get all links of types we wish to handle
+  function getLinks() {
+    let query = "a";
+    if (externalLinks !== "true") query += '[href^="#"]';
+    // exclude buttons, anchor links, toc links, etc
+    query += ":not(.button):not(.icon_button):not(.anchor):not(.toc_link)";
+    return document.querySelectorAll(query);
+  }
+
+  // start script when document is finished loading
+  window.addEventListener("load", start);
 </script>
+
+<style>
+  @media only screen {
+    /* anything with data-highlighted attribute true */
+    [data-highlighted="true"] {
+      background: #ffeb3b;
+    }
+
+    /* anything with data-selected attribute true */
+    [data-selected="true"] {
+      background: #ff8a65 !important;
+    }
+
+    /* animation definition for glow */
+    @keyframes highlight_glow {
+      0% {
+        background: none;
+      }
+      10% {
+        background: #bbdefb;
+      }
+      100% {
+        background: none;
+      }
+    }
+
+    /* anything with data-glow attribute true */
+    [data-glow="true"] {
+      animation: highlight_glow 2s;
+    }
+  }
+</style>
diff --git a/build/plugins/math.html b/build/plugins/math.html
deleted file mode 100644
index f47b24d..0000000
--- a/build/plugins/math.html
+++ /dev/null
@@ -1,27 +0,0 @@
-<!-- mathjax plugin configuration -->
-
-<script type="text/x-mathjax-config">
-    MathJax.Hub.Config({
-        "CommonHTML": { linebreaks: { automatic: true } },
-        "HTML-CSS": { linebreaks: { automatic: true } },
-        "SVG": { linebreaks: { automatic: true } },
-        "fast-preview": { disabled: true }
-  });
-</script>
-
-<!-- mathjax plugin -->
-
-<script
-    src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"
-    integrity="sha512-0doc9hKxR3PYwso42RD1p5ySZpzzuDiOwMrdCEh2WdJZCjcmFKc/wEnL+z8fBQrnHoiNWbo+3fiGkOYXBdQp4A=="
-    crossorigin="anonymous"
->
-    // /////////////////////////
-    // DESCRIPTION
-    // /////////////////////////
-
-    // This third-party plugin 'MathJax' allows the proper rendering of
-    // math/equations written in LaTeX.
-
-    // https://www.mathjax.org/
-</script>
diff --git a/build/plugins/mathjax.html b/build/plugins/mathjax.html
new file mode 100644
index 0000000..14ba331
--- /dev/null
+++ b/build/plugins/mathjax.html
@@ -0,0 +1,53 @@
+<!-- 
+  Mathjax Plugin (third-party) 
+
+  Allows the proper rendering of math/equations written in LaTeX.
+  See https://www.mathjax.org/.
+-->
+
+<script type="text/x-mathjax-config">
+  // configuration
+  MathJax.Hub.Config({
+    "CommonHTML": { linebreaks: { automatic: true } },
+    "HTML-CSS": { linebreaks: { automatic: true } },
+    "SVG": { linebreaks: { automatic: true } },
+    "fast-preview": { disabled: true }
+  });
+</script>
+
+<script
+  src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"
+  integrity="sha512-0doc9hKxR3PYwso42RD1p5ySZpzzuDiOwMrdCEh2WdJZCjcmFKc/wEnL+z8fBQrnHoiNWbo+3fiGkOYXBdQp4A=="
+  crossorigin="anonymous"
+></script>
+
+<style>
+  /* mathjax containers */
+  .math.display > span:not(.MathJax_Preview) {
+    /* turn inline element (no dimensions) into block (allows fixed width and thus scrolling) */
+    display: flex !important;
+    overflow-x: auto !important;
+    overflow-y: hidden !important;
+    justify-content: center;
+    align-items: center;
+    margin: 0 !important;
+  }
+
+  /* right click menu */
+  .MathJax_Menu {
+    border-radius: 5px !important;
+    border: solid 1px #bdbdbd !important;
+    box-shadow: none !important;
+  }
+
+  /* equation auto-number */
+  span[id^="eq:"] > span.math.display + span {
+    font-weight: 600;
+  }
+
+  /* equation */
+  span[id^="eq:"] > span.math.display > span {
+    /* nudge to make room for equation auto-number and anchor */
+    margin-right: 60px !important;
+  }
+</style>
diff --git a/build/plugins/scite.html b/build/plugins/scite.html
new file mode 100644
index 0000000..d01fe51
--- /dev/null
+++ b/build/plugins/scite.html
@@ -0,0 +1,61 @@
+<!-- 
+  Scite Plugin (third party)
+
+  Adds a Scite badge next to each citation in the references section.
+  See https://scite.ai/.
+-->
+
+<link
+  rel="stylesheet"
+  type="text/css"
+  href="https://cdn.scite.ai/badge/scite-badge-latest.min.css"
+/>
+<script
+  async
+  type="application/javascript"
+  src="https://cdn.scite.ai/badge/scite-badge-latest.min.js"
+></script>
+
+<script>
+  // start script
+  function start() {
+    // get citation elements
+    const query = ".references div[id*='ref-']";
+    const elements = document.querySelectorAll(query);
+    for (const element of elements) addBadge(element);
+
+    // attach scroll listener to window
+    window.addEventListener("scroll", onScroll);
+  }
+
+  // add badge in citation element
+  function addBadge(element) {
+    // get citation text
+    const text = element.innerText;
+    // find doi string, eg "DOI: xxxxx/xxxxx"
+    const match = text.match(/DOI:\s+(\S*)/) || {};
+    const doi = match[1];
+    if (!doi) return;
+    // create cite badge and put after citation
+    const badge = document.createElement("div");
+    badge.innerHTML = "Loading Scite badge...";
+    badge.classList.add("scite-badge");
+    badge.setAttribute("data-doi", doi);
+    badge.setAttribute("data-layout", "horizontal");
+    badge.setAttribute("data-show-zero", "true");
+    element.append(badge);
+    // modify preceding citation <p> element
+    const p = element.querySelector("p");
+    if (p) p.style.marginBottom = "0";
+  }
+
+  // start script when document is finished loading
+  window.addEventListener("load", start);
+</script>
+
+<style>
+  .scite-badge {
+    text-indent: 0;
+    margin-top: 10px;
+  }
+</style>
diff --git a/build/plugins/table-of-contents.html b/build/plugins/table-of-contents.html
index e415945..ea24c97 100644
--- a/build/plugins/table-of-contents.html
+++ b/build/plugins/table-of-contents.html
@@ -1,315 +1,404 @@
-<script>
-    (function() {
-        // /////////////////////////
-        // DESCRIPTION
-        // /////////////////////////
-
-        // This Manubot plugin provides a "table of contents" (toc) panel on
-        // the side of the document that allows the user to conveniently
-        // navigate between sections of the document.
-
-        // /////////////////////////
-        // OPTIONS
-        // /////////////////////////
-
-        // plugin name prefix for url parameters
-        const pluginName = 'tableOfContents';
-
-        // default plugin options
-        const options = {
-            // which types of elements to add links for, in
-            // "document.querySelector" format
-            typesQuery: 'h1, h2, h3',
-            // whether toc starts open. use 'true' or 'false', or 'auto' to
-            // use 'true' behavior when screen wide enough and 'false' when not
-            startOpen: 'false',
-            // whether toc closes when clicking on toc link. use 'true' or
-            // 'false', or 'auto' to use 'false' behavior when screen wide
-            // enough and 'true' when not
-            clickClose: 'auto',
-            // if list item is more than this many characters, text will be
-            // truncated
-            charLimit: '50',
-            // whether or not to show bullets next to each toc item
-            bullets: 'false',
-            // whether plugin is on or not
-            enabled: 'true'
-        };
-
-        // change options above, or override with url parameter, eg:
-        // 'manuscript.html?pluginName-enabled=false'
-
-        // /////////////////////////
-        // SCRIPT
-        // /////////////////////////
-
-        // start script
-        function start() {
-            // make toc panel and populate with entries (links to document
-            // sections)
-            const panel = makePanel();
-            if (!panel)
-                return;
-            makeEntries(panel);
-            // attach panel to document after making entries, so 'toc' heading
-            // in panel isn't included in toc
-            document.body.insertBefore(panel, document.body.firstChild);
-
-            // initial panel state
-            if (
-                options.startOpen === 'true' ||
-                (options.startOpen === 'auto' && !isSmallScreen())
-            )
-                openPanel();
-            else
-                closePanel();
-
-            // attach click, scroll, and hash change listeners to window
-            window.addEventListener('click', onClick);
-            window.addEventListener('scroll', onScroll);
-            window.addEventListener('hashchange', onScroll);
-            window.addEventListener('keyup', onKeyUp);
-            onScroll();
-
-            // add class to push document body down out of way of toc button
-            document.body.classList.add('toc_body_nudge');
-        }
-
-        // determine if screen wide enough to fit toc panel
-        function isSmallScreen() {
-            // in default theme:
-            // 816px = 8.5in = width of "page" (<body>) element
-            // 260px = min width of toc panel (*2 for both sides of <body>)
-            return window.innerWidth < 816 + 260 * 2;
-        }
-
-        // when mouse is clicked anywhere in window
-        function onClick() {
-            if (isSmallScreen())
-                closePanel();
-        }
-
-        // when window is scrolled or hash changed
-        function onScroll() {
-            highlightViewed();
-        }
-
-        // when key pressed
-        function onKeyUp(event) {
-            if (!event || !event.key)
-                return;
-
-            // close on esc
-            if (event.key === 'Escape')
-                closePanel();
-        }
-
-        // find entry of currently viewed document section in toc and highlight
-        function highlightViewed() {
-            const firstId = getFirstInView(options.typesQuery);
-
-            // get toc entries (links), unhighlight all, then highlight viewed
-            const list = document.getElementById('toc_list');
-            if (!firstId || !list)
-                return;
-            const links = list.querySelectorAll('a');
-            for (const link of links)
-                link.dataset.viewing = 'false';
-            const link = list.querySelector('a[href="#' + firstId + '"]');
-            if (!link)
-                return;
-            link.dataset.viewing = 'true';
-        }
-
-        // get first or previous toc listed element in top half of view
-        function getFirstInView(query) {
-            // get all elements matching query and with id
-            const elements = document.querySelectorAll(query);
-            const elementsWithIds = [];
-            for (const element of elements) {
-                if (element.id)
-                    elementsWithIds.push(element);
-            }
-
-
-            // get first or previous element in top half of view
-            for (let i = 0; i < elementsWithIds.length; i++) {
-                const element = elementsWithIds[i];
-                const prevElement = elementsWithIds[Math.max(0, i - 1)];
-                if (element.getBoundingClientRect().top >= 0) {
-                    if (
-                        element.getBoundingClientRect().top <
-                        window.innerHeight / 2
-                    )
-                        return element.id;
-                    else
-                        return prevElement.id;
-                }
-            }
-        }
-
-        // make panel
-        function makePanel() {
-            // create panel
-            const panel = document.createElement('div');
-            panel.id = 'toc_panel';
-            if (options.bullets === 'true')
-                panel.dataset.bullets = 'true';
-
-            // create header
-            const header = document.createElement('div');
-            header.id = 'toc_header';
-
-            // create toc button
-            const button = document.createElement('button');
-            button.id = 'toc_button';
-            button.innerHTML = document.querySelector('.icon_th_list').innerHTML;
-            button.title = 'Table of Contents';
-            button.classList.add('icon_button');
-
-            // create header text
-            const text = document.createElement('h4');
-            text.innerHTML = 'Table of Contents';
-
-            // create container for toc list
-            const list = document.createElement('div');
-            list.id = 'toc_list';
-
-            // attach click listeners
-            panel.addEventListener('click', onPanelClick);
-            header.addEventListener('click', onHeaderClick);
-            button.addEventListener('click', onButtonClick);
-
-            // attach elements
-            header.appendChild(button);
-            header.appendChild(text);
-            panel.appendChild(header);
-            panel.appendChild(list);
-
-            return panel;
-        }
-
-        // create toc entries (links) to each element of the specified types
-        function makeEntries(panel) {
-            const elements = document.querySelectorAll(options.typesQuery);
-            for (const element of elements) {
-                // do not add link if element doesn't have assigned id
-                if (!element.id)
-                    continue;
-
-                // create link/list item
-                const link = document.createElement('a');
-                link.classList.add('toc_link');
-                switch (element.tagName.toLowerCase()) {
-                    case 'h1':
-                        link.dataset.level = '1';
-                        break;
-                    case 'h2':
-                        link.dataset.level = '2';
-                        break;
-                    case 'h3':
-                        link.dataset.level = '3';
-                        break;
-                    case 'h4':
-                        link.dataset.level = '4';
-                        break;
-                }
-                link.title = element.innerText;
-                let text = element.innerText;
-                if (text.length > options.charLimit)
-                    text = text.slice(0, options.charLimit) + '...';
-                link.innerHTML = text;
-                link.href = '#' + element.id;
-                link.addEventListener('click', onLinkClick);
-
-                // attach link
-                panel.querySelector('#toc_list').appendChild(link);
-            }
-        }
-
-        // when panel is clicked
-        function onPanelClick(event) {
-            // stop click from propagating to window/document and closing panel
-            event.stopPropagation();
-        }
-
-        // when header itself is clicked
-        function onHeaderClick(event) {
-            togglePanel();
-        }
-
-        // when button is clicked
-        function onButtonClick(event) {
-            togglePanel();
-            // stop header underneath button from also being clicked
-            event.stopPropagation();
-        }
-
-        // when link is clicked
-        function onLinkClick(event) {
-            if (
-                options.clickClose === 'true' ||
-                (options.clickClose === 'auto' && isSmallScreen())
-            )
-                closePanel();
-            else
-                openPanel();
-        }
-
-        // open panel if closed, close if opened
-        function togglePanel() {
-            const panel = document.getElementById('toc_panel');
-            if (!panel)
-                return;
-
-            if (panel.dataset.open === 'true')
-                closePanel();
-            else
-                openPanel();
-        }
-
-        // open panel
-        function openPanel() {
-            const panel = document.getElementById('toc_panel');
-            if (panel)
-                panel.dataset.open = 'true';
-        }
-
-        // close panel
-        function closePanel() {
-            const panel = document.getElementById('toc_panel');
-            if (panel)
-                panel.dataset.open = 'false';
-        }
-
-        // load options from url parameters
-        function loadOptions() {
-            const url = window.location.search;
-            const params = new URLSearchParams(url);
-            for (const optionName of Object.keys(options)) {
-                const paramName = pluginName + '-' + optionName;
-                const param = params.get(paramName);
-                if (param !== '' && param !== null)
-                    options[optionName] = param;
-            }
-        }
-        loadOptions();
-
-        // start script when document is finished loading
-        if (options.enabled === 'true')
-            window.addEventListener('load', start);
-    })();
+<!--
+  Table of Contents Plugin
+
+  Provides a "table of contents" (toc) panel on the side of the document that
+  allows the user to conveniently navigate between sections of the document.
+-->
+
+<script type="module">
+  // which types of elements to add links for, in "document.querySelector" format
+  const typesQuery = "h1, h2, h3";
+  // whether toc starts open. use 'true' or 'false', or 'auto' to
+  // use 'true' behavior when screen wide enough and 'false' when not
+  const startOpen = "false";
+  // whether toc closes when clicking on toc link. use 'true' or
+  // 'false', or 'auto' to use 'false' behavior when screen wide
+  // enough and 'true' when not
+  const clickClose = "auto";
+  // if list item is more than this many characters, text will be
+  // truncated
+  const charLimit = "50";
+  // whether or not to show bullets next to each toc item
+  const bullets = "false";
+
+  // start script
+  function start() {
+    // make toc panel and populate with entries (links to document
+    // sections)
+    const panel = makePanel();
+    if (!panel) return;
+    makeEntries(panel);
+    // attach panel to document after making entries, so 'toc' heading
+    // in panel isn't included in toc
+    document.body.insertBefore(panel, document.body.firstChild);
+
+    // initial panel state
+    if (startOpen === "true" || (startOpen === "auto" && !isSmallScreen()))
+      openPanel();
+    else closePanel();
+
+    // attach click, scroll, and hash change listeners to window
+    window.addEventListener("click", onClick);
+    window.addEventListener("scroll", onScroll);
+    window.addEventListener("hashchange", onScroll);
+    window.addEventListener("keyup", onKeyUp);
+    onScroll();
+
+    // add class to push document body down out of way of toc button
+    document.body.classList.add("toc_body_nudge");
+  }
+
+  // determine if screen wide enough to fit toc panel
+  function isSmallScreen() {
+    // in default theme:
+    // 816px = 8.5in = width of "page" (<body>) element
+    // 260px = min width of toc panel (*2 for both sides of <body>)
+    return window.innerWidth < 816 + 260 * 2;
+  }
+
+  // when mouse is clicked anywhere in window
+  function onClick() {
+    if (isSmallScreen()) closePanel();
+  }
+
+  // when window is scrolled or hash changed
+  function onScroll() {
+    highlightViewed();
+  }
+
+  // when key pressed
+  function onKeyUp(event) {
+    if (!event || !event.key) return;
+
+    // close on esc
+    if (event.key === "Escape") closePanel();
+  }
+
+  // find entry of currently viewed document section in toc and highlight
+  function highlightViewed() {
+    const firstId = getFirstInView(typesQuery);
+
+    // get toc entries (links), unhighlight all, then highlight viewed
+    const list = document.getElementById("toc_list");
+    if (!firstId || !list) return;
+    const links = list.querySelectorAll("a");
+    for (const link of links) link.dataset.viewing = "false";
+    const link = list.querySelector('a[href="#' + firstId + '"]');
+    if (!link) return;
+    link.dataset.viewing = "true";
+  }
+
+  // get first or previous toc listed element in top half of view
+  function getFirstInView(query) {
+    // get all elements matching query and with id
+    const elements = document.querySelectorAll(query);
+    const elementsWithIds = [];
+    for (const element of elements) {
+      if (element.id) elementsWithIds.push(element);
+    }
+
+    // get first or previous element in top half of view
+    for (let i = 0; i < elementsWithIds.length; i++) {
+      const element = elementsWithIds[i];
+      const prevElement = elementsWithIds[Math.max(0, i - 1)];
+      if (element.getBoundingClientRect().top >= 0) {
+        if (element.getBoundingClientRect().top < window.innerHeight / 2)
+          return element.id;
+        else return prevElement.id;
+      }
+    }
+  }
+
+  // make panel
+  function makePanel() {
+    // create panel
+    const panel = document.createElement("div");
+    panel.id = "toc_panel";
+    if (bullets === "true") panel.dataset.bullets = "true";
+
+    // create header
+    const header = document.createElement("div");
+    header.id = "toc_header";
+
+    // create toc button
+    const button = document.createElement("button");
+    button.id = "toc_button";
+    button.innerHTML = document.querySelector(".icon_th_list").innerHTML;
+    button.title = "Table of Contents";
+    button.classList.add("icon_button");
+
+    // create header text
+    const text = document.createElement("h4");
+    text.innerHTML = "Table of Contents";
+
+    // create container for toc list
+    const list = document.createElement("div");
+    list.id = "toc_list";
+
+    // attach click listeners
+    panel.addEventListener("click", onPanelClick);
+    header.addEventListener("click", onHeaderClick);
+    button.addEventListener("click", onButtonClick);
+
+    // attach elements
+    header.appendChild(button);
+    header.appendChild(text);
+    panel.appendChild(header);
+    panel.appendChild(list);
+
+    return panel;
+  }
+
+  // create toc entries (links) to each element of the specified types
+  function makeEntries(panel) {
+    const elements = document.querySelectorAll(typesQuery);
+    for (const element of elements) {
+      // do not add link if element doesn't have assigned id
+      if (!element.id) continue;
+
+      // create link/list item
+      const link = document.createElement("a");
+      link.classList.add("toc_link");
+      switch (element.tagName.toLowerCase()) {
+        case "h1":
+          link.dataset.level = "1";
+          break;
+        case "h2":
+          link.dataset.level = "2";
+          break;
+        case "h3":
+          link.dataset.level = "3";
+          break;
+        case "h4":
+          link.dataset.level = "4";
+          break;
+      }
+      link.title = element.innerText;
+      let text = element.innerText;
+      if (text.length > charLimit) text = text.slice(0, charLimit) + "...";
+      link.innerHTML = text;
+      link.href = "#" + element.id;
+      link.addEventListener("click", onLinkClick);
+
+      // attach link
+      panel.querySelector("#toc_list").appendChild(link);
+    }
+  }
+
+  // when panel is clicked
+  function onPanelClick(event) {
+    // stop click from propagating to window/document and closing panel
+    event.stopPropagation();
+  }
+
+  // when header itself is clicked
+  function onHeaderClick(event) {
+    togglePanel();
+  }
+
+  // when button is clicked
+  function onButtonClick(event) {
+    togglePanel();
+    // stop header underneath button from also being clicked
+    event.stopPropagation();
+  }
+
+  // when link is clicked
+  function onLinkClick(event) {
+    if (clickClose === "true" || (clickClose === "auto" && isSmallScreen()))
+      closePanel();
+    else openPanel();
+  }
+
+  // open panel if closed, close if opened
+  function togglePanel() {
+    const panel = document.getElementById("toc_panel");
+    if (!panel) return;
+
+    if (panel.dataset.open === "true") closePanel();
+    else openPanel();
+  }
+
+  // open panel
+  function openPanel() {
+    const panel = document.getElementById("toc_panel");
+    if (panel) panel.dataset.open = "true";
+  }
+
+  // close panel
+  function closePanel() {
+    const panel = document.getElementById("toc_panel");
+    if (panel) panel.dataset.open = "false";
+  }
+
+  // start script when document is finished loading
+  window.addEventListener("load", start);
 </script>
 
 <!-- th list icon -->
 
 <template class="icon_th_list">
-    <!-- modified from: https://fontawesome.com/icons/th-list -->
-    <svg width="16" height="16" viewBox="0 0 512 512" tabindex="-1">
-        <path
-            fill="currentColor"
-            d="M96 96c0 26.51-21.49 48-48 48S0 122.51 0 96s21.49-48 48-48 48 21.49 48 48zM48 208c-26.51 0-48 21.49-48 48s21.49 48 48 48 48-21.49 48-48-21.49-48-48-48zm0 160c-26.51 0-48 21.49-48 48s21.49 48 48 48 48-21.49 48-48-21.49-48-48-48zm96-236h352c8.837 0 16-7.163 16-16V76c0-8.837-7.163-16-16-16H144c-8.837 0-16 7.163-16 16v40c0 8.837 7.163 16 16 16zm0 160h352c8.837 0 16-7.163 16-16v-40c0-8.837-7.163-16-16-16H144c-8.837 0-16 7.163-16 16v40c0 8.837 7.163 16 16 16zm0 160h352c8.837 0 16-7.163 16-16v-40c0-8.837-7.163-16-16-16H144c-8.837 0-16 7.163-16 16v40c0 8.837 7.163 16 16 16z"
-            tabindex="-1"
-        ></path>
-    </svg>
+  <!-- modified from: https://fontawesome.com/icons/th-list -->
+  <svg width="16" height="16" viewBox="0 0 512 512" tabindex="-1">
+    <path
+      fill="currentColor"
+      d="M96 96c0 26.51-21.49 48-48 48S0 122.51 0 96s21.49-48 48-48 48 21.49 48 48zM48 208c-26.51 0-48 21.49-48 48s21.49 48 48 48 48-21.49 48-48-21.49-48-48-48zm0 160c-26.51 0-48 21.49-48 48s21.49 48 48 48 48-21.49 48-48-21.49-48-48-48zm96-236h352c8.837 0 16-7.163 16-16V76c0-8.837-7.163-16-16-16H144c-8.837 0-16 7.163-16 16v40c0 8.837 7.163 16 16 16zm0 160h352c8.837 0 16-7.163 16-16v-40c0-8.837-7.163-16-16-16H144c-8.837 0-16 7.163-16 16v40c0 8.837 7.163 16 16 16zm0 160h352c8.837 0 16-7.163 16-16v-40c0-8.837-7.163-16-16-16H144c-8.837 0-16 7.163-16 16v40c0 8.837 7.163 16 16 16z"
+      tabindex="-1"
+    ></path>
+  </svg>
 </template>
+
+<style>
+  @media only screen {
+    /* toc panel */
+    #toc_panel {
+      box-sizing: border-box;
+      position: fixed;
+      top: 0;
+      left: 0;
+      background: #ffffff;
+      box-shadow: 0 0 20px rgba(0, 0, 0, 0.05);
+      z-index: 2;
+    }
+
+    /* toc panel when closed */
+    #toc_panel[data-open="false"] {
+      min-width: 60px;
+      width: 60px;
+      height: 60px;
+      border-right: solid 1px #bdbdbd;
+      border-bottom: solid 1px #bdbdbd;
+    }
+
+    /* toc panel when open */
+    #toc_panel[data-open="true"] {
+      min-width: 260px;
+      max-width: 480px;
+      /* keep panel edge consistent distance away from "page" edge */
+      width: calc(((100vw - 8.5in) / 2) - 30px - 40px);
+      bottom: 0;
+      border-right: solid 1px #bdbdbd;
+    }
+
+    /* toc panel header */
+    #toc_header {
+      box-sizing: border-box;
+      display: flex;
+      flex-direction: row;
+      align-items: center;
+      height: 60px;
+      margin: 0;
+      padding: 20px;
+    }
+
+    /* toc panel header when hovered */
+    #toc_header:hover {
+      cursor: pointer;
+    }
+
+    /* toc panel header when panel open */
+    #toc_panel[data-open="true"] > #toc_header {
+      border-bottom: solid 1px #bdbdbd;
+    }
+
+    /* toc open/close header button */
+    #toc_button {
+      margin-right: 20px;
+    }
+
+    /* hide toc list and header text when closed */
+    #toc_panel[data-open="false"] > #toc_header > *:not(#toc_button),
+    #toc_panel[data-open="false"] > #toc_list {
+      display: none;
+    }
+
+    /* toc list of entries */
+    #toc_list {
+      box-sizing: border-box;
+      width: 100%;
+      padding: 20px;
+      position: absolute;
+      top: calc(60px + 1px);
+      bottom: 0;
+      overflow: auto;
+    }
+
+    /* toc entry, link to section in document */
+    .toc_link {
+      display: block;
+      padding: 5px;
+      position: relative;
+      font-weight: 600;
+      text-decoration: none;
+    }
+
+    /* toc entry when hovered or when "viewed" */
+    .toc_link:hover,
+    .toc_link[data-viewing="true"] {
+      background: #f5f5f5;
+    }
+
+    /* toc entry, level 1 indentation */
+    .toc_link[data-level="1"] {
+      margin-left: 0;
+    }
+
+    /* toc entry, level 2 indentation */
+    .toc_link[data-level="2"] {
+      margin-left: 20px;
+    }
+
+    /* toc entry, level 3 indentation */
+    .toc_link[data-level="3"] {
+      margin-left: 40px;
+    }
+
+    /* toc entry, level 4 indentation */
+    .toc_link[data-level="4"] {
+      margin-left: 60px;
+    }
+
+    /* toc entry bullets */
+    #toc_panel[data-bullets="true"] .toc_link[data-level]:before {
+      position: absolute;
+      left: -15px;
+      top: -1px;
+      font-size: 1.5em;
+    }
+
+    /* toc entry, level 2 bullet */
+    #toc_panel[data-bullets="true"] .toc_link[data-level="2"]:before {
+      content: "\2022";
+    }
+
+    /* toc entry, level 3 bullet */
+    #toc_panel[data-bullets="true"] .toc_link[data-level="3"]:before {
+      content: "\25AB";
+    }
+
+    /* toc entry, level 4 bullet */
+    #toc_panel[data-bullets="true"] .toc_link[data-level="4"]:before {
+      content: "-";
+    }
+  }
+
+  /* when on screen < 8.5in wide */
+  @media only screen and (max-width: 8.5in) {
+    /* push <body> ("page") element down to make room for toc icon */
+    .toc_body_nudge {
+      padding-top: 60px;
+    }
+
+    /* toc icon when panel closed and not hovered */
+    #toc_panel[data-open="false"]:not(:hover) {
+      background: rgba(255, 255, 255, 0.75);
+    }
+  }
+
+  /* always hide toc panel on print */
+  @media only print {
+    #toc_panel {
+      display: none;
+    }
+  }
+</style>
diff --git a/build/plugins/tooltips.html b/build/plugins/tooltips.html
index f9cbc60..b6fc505 100644
--- a/build/plugins/tooltips.html
+++ b/build/plugins/tooltips.html
@@ -1,614 +1,507 @@
-<!-- tooltips plugin -->
-
-<script>
-    (function() {
-        // /////////////////////////
-        // DESCRIPTION
-        // /////////////////////////
-
-        // This Manubot plugin makes it such that when the user hovers or
-        // focuses a link to a citation or figure, a tooltip appears with a
-        // preview of the reference content, along with arrows to navigate
-        // between instances of the same reference in the document.
-
-        // /////////////////////////
-        // OPTIONS
-        // /////////////////////////
-
-        // plugin name prefix for url parameters
-        const pluginName = 'tooltips';
-
-        // default plugin options
-        const options = {
-            // whether user must click off to close tooltip instead of just
-            // un-hovering
-            clickClose: 'false',
-            // delay (in ms) between opening and closing tooltip
-            delay: '100',
-            // whether plugin is on or not
-            enabled: 'true'
-        };
-
-        // change options above, or override with url parameter, eg:
-        // 'manuscript.html?pluginName-enabled=false'
-
-        // /////////////////////////
-        // SCRIPT
-        // /////////////////////////
-
-        // start script
-        function start() {
-            const links = getLinks();
-            for (const link of links) {
-                // attach hover and focus listeners to link
-                link.addEventListener('mouseover', onLinkHover);
-                link.addEventListener('mouseleave', onLinkUnhover);
-                link.addEventListener('focus', onLinkFocus);
-                link.addEventListener('touchend', onLinkTouch);
-            }
-
-            // attach mouse, key, and resize listeners to window
-            window.addEventListener('mousedown', onClick);
-            window.addEventListener('touchstart', onClick);
-            window.addEventListener('keyup', onKeyUp);
-            window.addEventListener('resize', onResize);
-        }
-
-        // when link is hovered
-        function onLinkHover() {
-            // function to open tooltip
-            const delayOpenTooltip = function() {
-                openTooltip(this);
-            }.bind(this);
-
-            // run open function after delay
-            this.openTooltipTimer = window.setTimeout(
-                delayOpenTooltip,
-                options.delay
-            );
-        }
-
-        // when mouse leaves link
-        function onLinkUnhover() {
-            // cancel opening tooltip
-            window.clearTimeout(this.openTooltipTimer);
-
-            // don't close on unhover if option specifies
-            if (options.clickClose === 'true')
-                return;
-
-            // function to close tooltip
-            const delayCloseTooltip = function() {
-                // if tooltip open and if mouse isn't over tooltip, close
-                const tooltip = document.getElementById('tooltip');
-                if (tooltip && !tooltip.matches(':hover'))
-                    closeTooltip();
-            };
-
-            // run close function after delay
-            this.closeTooltipTimer = window.setTimeout(
-                delayCloseTooltip,
-                options.delay
-            );
-        }
-
-        // when link is focused (tabbed to)
-        function onLinkFocus(event) {
-            openTooltip(this);
-        }
-
-        // when link is touched on touch screen
-        function onLinkTouch(event) {
-            // attempt to force hover state on first tap always, and trigger
-            // regular link click (and navigation) on second tap
-            if (event.target === document.activeElement)
-                event.target.click();
-            else {
-                document.activeElement.blur();
-                event.target.focus();
-            }
-            if (event.cancelable)
-                event.preventDefault();
-            event.stopPropagation();
-            return false;
-        }
-
-        // when mouse is clicked anywhere in window
-        function onClick(event) {
-            closeTooltip();
-        }
-
-        // when key pressed
-        function onKeyUp(event) {
-            if (!event || !event.key)
-                return;
-
-            switch (event.key) {
-                // trigger click of prev button
-                case 'ArrowLeft':
-                    const prevButton = document.getElementById(
-                        'tooltip_prev_button'
-                    );
-                    if (prevButton)
-                        prevButton.click();
-                    break;
-                // trigger click of next button
-                case 'ArrowRight':
-                    const nextButton = document.getElementById(
-                        'tooltip_next_button'
-                    );
-                    if (nextButton)
-                        nextButton.click();
-                    break;
-                // close on esc
-                case 'Escape':
-                    closeTooltip();
-                    break;
-            }
-        }
-
-        // when window is resized or zoomed
-        function onResize() {
-            closeTooltip();
-        }
-
-        // get all links of types we wish to handle
-        function getLinks() {
-            const queries = [];
-            // exclude buttons, anchor links, toc links, etc
-            const exclude =
-                ':not(.button):not(.icon_button):not(.anchor):not(.toc_link)';
-            queries.push('a[href^="#ref-"]' + exclude); // citation links
-            queries.push('a[href^="#fig:"]' + exclude); // figure links
-            const query = queries.join(', ');
-            return document.querySelectorAll(query);
-        }
-
-        // get links with same target, get index of link in set, get total
-        // same links
-        function getSameLinks(link) {
-            const sameLinks = [];
-            const links = getLinks();
-            for (const otherLink of links) {
-                if (
-                    otherLink.getAttribute('href') === link.getAttribute('href')
-                )
-                    sameLinks.push(otherLink);
-            }
-
-            return {
-                elements: sameLinks,
-                index: sameLinks.indexOf(link),
-                total: sameLinks.length
-            };
-        }
-
-        // open tooltip
-        function openTooltip(link) {
-            // delete tooltip if it exists, start fresh
-            closeTooltip();
-
-            // make tooltip element
-            const tooltip = makeTooltip(link);
-
-            // if source couldn't be found and tooltip not made, exit
-            if (!tooltip)
-                return;
-
-            // make navbar elements
-            const navBar = makeNavBar(link);
-            if (navBar)
-                tooltip.firstElementChild.appendChild(navBar);
-
-            // attach tooltip to page
-            document.body.appendChild(tooltip);
-
-            // position tooltip
-            const position = function() {
-                positionTooltip(link);
-            };
-            position();
-
-            // if tooltip contains images, position again after they've loaded
-            const imgs = tooltip.querySelectorAll('img');
-            for (const img of imgs)
-                img.addEventListener('load', position);
-        }
-
-        // close (delete) tooltip
-        function closeTooltip() {
-            const tooltip = document.getElementById('tooltip');
-            if (tooltip)
-                tooltip.remove();
-        }
-
-        // make tooltip
-        function makeTooltip(link) {
-            // get target element that link points to
-            const source = getSource(link);
-
-            // if source can't be found, exit
-            if (!source)
-                return;
-
-            // create new tooltip
-            const tooltip = document.createElement('div');
-            tooltip.id = 'tooltip';
-            const tooltipContent = document.createElement('div');
-            tooltipContent.id = 'tooltip_content';
-            tooltip.appendChild(tooltipContent);
-
-            // make copy of source node and put in tooltip
-            const sourceCopy = makeCopy(source);
-            tooltipContent.appendChild(sourceCopy);
-
-            // attach mouse event listeners
-            tooltip.addEventListener('click', onTooltipClick);
-            tooltip.addEventListener('mousedown', onTooltipClick);
-            tooltip.addEventListener('touchstart', onTooltipClick);
-            tooltip.addEventListener('mouseleave', onTooltipUnhover);
-
-            // (for interaction with lightbox plugin)
-            // transfer click on tooltip copied img to original img
-            const sourceImg = source.querySelector('img');
-            const sourceCopyImg = sourceCopy.querySelector('img');
-            if (sourceImg && sourceCopyImg) {
-                const clickImg = function() {
-                    sourceImg.click();
-                    closeTooltip();
-                };
-                sourceCopyImg.addEventListener('click', clickImg);
-            }
-
-            return tooltip;
-        }
-
-        // make carbon copy of html dom element
-        function makeCopy(source) {
-            const sourceCopy = source.cloneNode(true);
-
-            // delete elements marked with ignore (eg anchor and jump buttons)
-            const deleteFromCopy = sourceCopy.querySelectorAll(
-                '[data-ignore="true"]'
-            );
-            for (const element of deleteFromCopy)
-                element.remove();
-
-            // delete certain element attributes
-            const attributes = [
-                'id',
-                'data-collapsed',
-                'data-selected',
-                'data-highlighted',
-                'data-glow'
-            ];
-            for (const attribute of attributes) {
-                sourceCopy.removeAttribute(attribute);
-                const elements = sourceCopy.querySelectorAll(
-                    '[' + attribute + ']'
-                );
-                for (const element of elements)
-                    element.removeAttribute(attribute);
-            }
-
-            return sourceCopy;
-        }
-
-        // when tooltip is clicked
-        function onTooltipClick(event) {
-            // when user clicks on tooltip, stop click from transferring
-            // outside of tooltip (eg, click off to close tooltip, or eg click
-            // off to unhighlight same refs)
-            event.stopPropagation();
-        }
-
-        // when tooltip is unhovered
-        function onTooltipUnhover(event) {
-            if (options.clickClose === 'true')
-                return;
-
-            // make sure new mouse/touch/focus no longer over tooltip or any
-            // element within it
-            const tooltip = document.getElementById('tooltip');
-            if (!tooltip)
-                return;
-            if (this.contains(event.relatedTarget))
-                return;
-
-            closeTooltip();
-        }
-
-        // make nav bar to go betwen prev/next instances of same reference
-        function makeNavBar(link) {
-            // find other links to the same source
-            const sameLinks = getSameLinks(link);
-
-            // don't show nav bar when singular reference
-            if (sameLinks.total <= 1)
-                return;
-
-            // find prev/next links with same target
-            const prevLink = getPrevLink(link, sameLinks);
-            const nextLink = getNextLink(link, sameLinks);
-
-            // create nav bar
-            const navBar = document.createElement('div');
-            navBar.id = 'tooltip_nav_bar';
-            const text = sameLinks.index + 1 + ' of ' + sameLinks.total;
-
-            // create nav bar prev/next buttons
-            const prevButton = document.createElement('button');
-            const nextButton = document.createElement('button');
-            prevButton.id = 'tooltip_prev_button';
-            nextButton.id = 'tooltip_next_button';
-            prevButton.title =
-                'Jump to the previous occurence of this item in the document [←]';
-            nextButton.title =
-                'Jump to the next occurence of this item in the document [→]';
-            prevButton.classList.add('icon_button');
-            nextButton.classList.add('icon_button');
-            prevButton.innerHTML = document.querySelector(
-                '.icon_caret_left'
-            ).innerHTML;
-            nextButton.innerHTML = document.querySelector(
-                '.icon_caret_right'
-            ).innerHTML;
-            navBar.appendChild(prevButton);
-            navBar.appendChild(document.createTextNode(text));
-            navBar.appendChild(nextButton);
-
-            // attach click listeners to buttons
-            prevButton.addEventListener('click', function() {
-                onPrevNextClick(link, prevLink);
-            });
-            nextButton.addEventListener('click', function() {
-                onPrevNextClick(link, nextLink);
-            });
-
-            return navBar;
-        }
-
-        // get previous link with same target
-        function getPrevLink(link, sameLinks) {
-            if (!sameLinks)
-                sameLinks = getSameLinks(link);
-            // wrap index to other side if < 1
-            let index;
-            if (sameLinks.index - 1 >= 0)
-                index = sameLinks.index - 1;
-            else
-                index = sameLinks.total - 1;
-            return sameLinks.elements[index];
-        }
-
-        // get next link with same target
-        function getNextLink(link, sameLinks) {
-            if (!sameLinks)
-                sameLinks = getSameLinks(link);
-            // wrap index to other side if > total
-            let index;
-            if (sameLinks.index + 1 <= sameLinks.total - 1)
-                index = sameLinks.index + 1;
-            else
-                index = 0;
-            return sameLinks.elements[index];
-        }
-
-        // get element that is target of link or url hash
-        function getSource(link) {
-            const hash = link ? link.hash : window.location.hash;
-            const id = hash.slice(1);
-            let target = document.querySelector('[id="' + id + '"]');
-            if (!target)
-                return;
-
-            // if ref or figure, modify target to get expected element
-            if (id.indexOf('ref-') === 0)
-                target = target.querySelector('p');
-            else if (id.indexOf('fig:') === 0)
-                target = target.querySelector('figure');
-
-            return target;
-        }
-
-        // when prev/next arrow button is clicked
-        function onPrevNextClick(link, prevNextLink) {
-            if (link && prevNextLink)
-                goToElement(prevNextLink, window.innerHeight * 0.5);
-        }
-
-        // scroll to and focus element
-        function goToElement(element, offset) {
-            // expand accordion section if collapsed
-            expandElement(element);
-            const y =
-                getRectInView(element).top -
-                getRectInView(document.documentElement).top -
-                (offset || 0);
-            // trigger any function listening for "onscroll" event
-            window.dispatchEvent(new Event('scroll'));
-            window.scrollTo(0, y);
-            document.activeElement.blur();
-            element.focus();
-        }
-
-        // determine position to place tooltip based on link position in
-        // viewport and tooltip size
-        function positionTooltip(link, left, top) {
-            const tooltipElement = document.getElementById('tooltip');
-            if (!tooltipElement)
-                return;
-
-            // get convenient vars for position/dimensions of
-            // link/tooltip/page/view
-            link = getRectInPage(link);
-            const tooltip = getRectInPage(tooltipElement);
-            const view = getRectInPage();
-
-            // horizontal positioning
-            if (left)
-                // use explicit value
-                left = left;
-            else if (link.left + tooltip.width < view.right)
-                // fit tooltip to right of link
-                left = link.left;
-            else if (link.right - tooltip.width > view.left)
-                // fit tooltip to left of link
-                left = link.right - tooltip.width;
-            // center tooltip in view
-            else
-                left = (view.right - view.left) / 2 - tooltip.width / 2;
-
-            // vertical positioning
-            if (top)
-                // use explicit value
-                top = top;
-            else if (link.top - tooltip.height > view.top)
-                // fit tooltip above link
-                top = link.top - tooltip.height;
-            else if (link.bottom + tooltip.height < view.bottom)
-                // fit tooltip below link
-                top = link.bottom;
-            else {
-                // center tooltip in view
-                top = view.top + view.height / 2 - tooltip.height / 2;
-                // nudge off of link to left/right if possible
-                if (link.right + tooltip.width < view.right)
-                    left = link.right;
-                else if (link.left - tooltip.width > view.left)
-                    left = link.left - tooltip.width;
-            }
-
-            tooltipElement.style.left = left + 'px';
-            tooltipElement.style.top = top + 'px';
-        }
-
-        // get position/dimensions of element or viewport
-        function getRectInView(element) {
-            let rect = {};
-            rect.left = 0;
-            rect.top = 0;
-            rect.right = document.documentElement.clientWidth;
-            rect.bottom = document.documentElement.clientHeight;
-            let style = {};
-
-            if (element instanceof HTMLElement) {
-                rect = element.getBoundingClientRect();
-                style = window.getComputedStyle(element);
-            }
-
-            const margin = {};
-            margin.left = parseFloat(style.marginLeftWidth) || 0;
-            margin.top = parseFloat(style.marginTopWidth) || 0;
-            margin.right = parseFloat(style.marginRightWidth) || 0;
-            margin.bottom = parseFloat(style.marginBottomWidth) || 0;
-
-            const border = {};
-            border.left = parseFloat(style.borderLeftWidth) || 0;
-            border.top = parseFloat(style.borderTopWidth) || 0;
-            border.right = parseFloat(style.borderRightWidth) || 0;
-            border.bottom = parseFloat(style.borderBottomWidth) || 0;
-
-            const newRect = {};
-            newRect.left = rect.left + margin.left + border.left;
-            newRect.top = rect.top + margin.top + border.top;
-            newRect.right = rect.right + margin.right + border.right;
-            newRect.bottom = rect.bottom + margin.bottom + border.bottom;
-            newRect.width = newRect.right - newRect.left;
-            newRect.height = newRect.bottom - newRect.top;
-
-            return newRect;
-        }
-
-        // get position of element relative to page
-        function getRectInPage(element) {
-            const rect = getRectInView(element);
-            const body = getRectInView(document.body);
-
-            const newRect = {};
-            newRect.left = rect.left - body.left;
-            newRect.top = rect.top - body.top;
-            newRect.right = rect.right - body.left;
-            newRect.bottom = rect.bottom - body.top;
-            newRect.width = rect.width;
-            newRect.height = rect.height;
-
-            return newRect;
-        }
-
-        // (for interaction with accordion plugin)
-        // get closest element before specified element that matches query
-        function firstBefore(element, query) {
-            while (
-                element &&
-                element !== document.body &&
-                !element.matches(query)
-            )
-                element = element.previousElementSibling || element.parentNode;
-
-            return element;
-        }
-
-        // (for interaction with accordion plugin)
-        // check if element is part of collapsed heading
-        function isCollapsed(element) {
-            while (element && element !== document.body) {
-                if (element.dataset.collapsed === 'true')
-                    return true;
-                element = element.parentNode;
-            }
-            return false;
-        }
-
-        // (for interaction with accordion plugin)
-        // expand heading containing element if necesary
-        function expandElement(element) {
-            if (isCollapsed(element)) {
-                const heading = firstBefore(element, 'h2');
-                if (heading)
-                    heading.click();
-            }
-        }
-
-        // load options from url parameters
-        function loadOptions() {
-            const url = window.location.search;
-            const params = new URLSearchParams(url);
-            for (const optionName of Object.keys(options)) {
-                const paramName = pluginName + '-' + optionName;
-                const param = params.get(paramName);
-                if (param !== '' && param !== null)
-                    options[optionName] = param;
-            }
-        }
-        loadOptions();
-
-        // start script when document is finished loading
-        if (options.enabled === 'true')
-            window.addEventListener('load', start);
-    })();
+<!-- 
+  Tooltips Plugin
+
+  Makes it such that when the user hovers or focuses a link to a citation or
+  figure, a tooltip appears with a preview of the reference content, along with
+  arrows to navigate between instances of the same reference in the document.
+-->
+
+<script type="module">
+  // whether user must click off to close tooltip instead of just un-hovering
+  const clickClose = "false";
+  // delay (in ms) between opening and closing tooltip
+  const delay = "100";
+
+  // start script
+  function start() {
+    const links = getLinks();
+    for (const link of links) {
+      // attach hover and focus listeners to link
+      link.addEventListener("mouseover", onLinkHover);
+      link.addEventListener("mouseleave", onLinkUnhover);
+      link.addEventListener("focus", onLinkFocus);
+      link.addEventListener("touchend", onLinkTouch);
+    }
+
+    // attach mouse, key, and resize listeners to window
+    window.addEventListener("mousedown", onClick);
+    window.addEventListener("touchstart", onClick);
+    window.addEventListener("keyup", onKeyUp);
+    window.addEventListener("resize", onResize);
+  }
+
+  // when link is hovered
+  function onLinkHover() {
+    // function to open tooltip
+    const delayOpenTooltip = function () {
+      openTooltip(this);
+    }.bind(this);
+
+    // run open function after delay
+    this.openTooltipTimer = window.setTimeout(delayOpenTooltip, delay);
+  }
+
+  // when mouse leaves link
+  function onLinkUnhover() {
+    // cancel opening tooltip
+    window.clearTimeout(this.openTooltipTimer);
+
+    // don't close on unhover if option specifies
+    if (clickClose === "true") return;
+
+    // function to close tooltip
+    const delayCloseTooltip = function () {
+      // if tooltip open and if mouse isn't over tooltip, close
+      const tooltip = document.getElementById("tooltip");
+      if (tooltip && !tooltip.matches(":hover")) closeTooltip();
+    };
+
+    // run close function after delay
+    this.closeTooltipTimer = window.setTimeout(delayCloseTooltip, delay);
+  }
+
+  // when link is focused (tabbed to)
+  function onLinkFocus(event) {
+    openTooltip(this);
+  }
+
+  // when link is touched on touch screen
+  function onLinkTouch(event) {
+    // attempt to force hover state on first tap always, and trigger
+    // regular link click (and navigation) on second tap
+    if (event.target === document.activeElement) event.target.click();
+    else {
+      document.activeElement.blur();
+      event.target.focus();
+    }
+    if (event.cancelable) event.preventDefault();
+    event.stopPropagation();
+    return false;
+  }
+
+  // when mouse is clicked anywhere in window
+  function onClick(event) {
+    closeTooltip();
+  }
+
+  // when key pressed
+  function onKeyUp(event) {
+    if (!event || !event.key) return;
+
+    switch (event.key) {
+      // trigger click of prev button
+      case "ArrowLeft":
+        const prevButton = document.getElementById("tooltip_prev_button");
+        if (prevButton) prevButton.click();
+        break;
+      // trigger click of next button
+      case "ArrowRight":
+        const nextButton = document.getElementById("tooltip_next_button");
+        if (nextButton) nextButton.click();
+        break;
+      // close on esc
+      case "Escape":
+        closeTooltip();
+        break;
+    }
+  }
+
+  // when window is resized or zoomed
+  function onResize() {
+    closeTooltip();
+  }
+
+  // get all links of types we wish to handle
+  function getLinks() {
+    const queries = [];
+    // exclude buttons, anchor links, toc links, etc
+    const exclude =
+      ":not(.button):not(.icon_button):not(.anchor):not(.toc_link)";
+    queries.push('a[href^="#ref-"]' + exclude); // citation links
+    queries.push('a[href^="#fig:"]' + exclude); // figure links
+    const query = queries.join(", ");
+    return document.querySelectorAll(query);
+  }
+
+  // get links with same target, get index of link in set, get total
+  // same links
+  function getSameLinks(link) {
+    const sameLinks = [];
+    const links = getLinks();
+    for (const otherLink of links) {
+      if (otherLink.getAttribute("href") === link.getAttribute("href"))
+        sameLinks.push(otherLink);
+    }
+
+    return {
+      elements: sameLinks,
+      index: sameLinks.indexOf(link),
+      total: sameLinks.length,
+    };
+  }
+
+  // open tooltip
+  function openTooltip(link) {
+    // delete tooltip if it exists, start fresh
+    closeTooltip();
+
+    // make tooltip element
+    const tooltip = makeTooltip(link);
+
+    // if source couldn't be found and tooltip not made, exit
+    if (!tooltip) return;
+
+    // make navbar elements
+    const navBar = makeNavBar(link);
+    if (navBar) tooltip.firstElementChild.appendChild(navBar);
+
+    // attach tooltip to page
+    document.body.appendChild(tooltip);
+
+    // position tooltip
+    const position = function () {
+      positionTooltip(link);
+    };
+    position();
+
+    // if tooltip contains images, position again after they've loaded
+    const imgs = tooltip.querySelectorAll("img");
+    for (const img of imgs) img.addEventListener("load", position);
+  }
+
+  // close (delete) tooltip
+  function closeTooltip() {
+    const tooltip = document.getElementById("tooltip");
+    if (tooltip) tooltip.remove();
+  }
+
+  // make tooltip
+  function makeTooltip(link) {
+    // get target element that link points to
+    const source = getSource(link);
+
+    // if source can't be found, exit
+    if (!source) return;
+
+    // create new tooltip
+    const tooltip = document.createElement("div");
+    tooltip.id = "tooltip";
+    const tooltipContent = document.createElement("div");
+    tooltipContent.id = "tooltip_content";
+    tooltip.appendChild(tooltipContent);
+
+    // make copy of source node and put in tooltip
+    const sourceCopy = makeCopy(source);
+    tooltipContent.appendChild(sourceCopy);
+
+    // attach mouse event listeners
+    tooltip.addEventListener("click", onTooltipClick);
+    tooltip.addEventListener("mousedown", onTooltipClick);
+    tooltip.addEventListener("touchstart", onTooltipClick);
+    tooltip.addEventListener("mouseleave", onTooltipUnhover);
+
+    // (for interaction with lightbox plugin)
+    // transfer click on tooltip copied img to original img
+    const sourceImg = source.querySelector("img");
+    const sourceCopyImg = sourceCopy.querySelector("img");
+    if (sourceImg && sourceCopyImg) {
+      const clickImg = function () {
+        sourceImg.click();
+        closeTooltip();
+      };
+      sourceCopyImg.addEventListener("click", clickImg);
+    }
+
+    return tooltip;
+  }
+
+  // make carbon copy of html dom element
+  function makeCopy(source) {
+    const sourceCopy = source.cloneNode(true);
+
+    // delete elements marked with ignore (eg anchor and jump buttons)
+    const deleteFromCopy = sourceCopy.querySelectorAll('[data-ignore="true"]');
+    for (const element of deleteFromCopy) element.remove();
+
+    // delete certain element attributes
+    const attributes = [
+      "id",
+      "data-collapsed",
+      "data-selected",
+      "data-highlighted",
+      "data-glow",
+    ];
+    for (const attribute of attributes) {
+      sourceCopy.removeAttribute(attribute);
+      const elements = sourceCopy.querySelectorAll("[" + attribute + "]");
+      for (const element of elements) element.removeAttribute(attribute);
+    }
+
+    return sourceCopy;
+  }
+
+  // when tooltip is clicked
+  function onTooltipClick(event) {
+    // when user clicks on tooltip, stop click from transferring
+    // outside of tooltip (eg, click off to close tooltip, or eg click
+    // off to unhighlight same refs)
+    event.stopPropagation();
+  }
+
+  // when tooltip is unhovered
+  function onTooltipUnhover(event) {
+    if (clickClose === "true") return;
+
+    // make sure new mouse/touch/focus no longer over tooltip or any
+    // element within it
+    const tooltip = document.getElementById("tooltip");
+    if (!tooltip) return;
+    if (this.contains(event.relatedTarget)) return;
+
+    closeTooltip();
+  }
+
+  // make nav bar to go betwen prev/next instances of same reference
+  function makeNavBar(link) {
+    // find other links to the same source
+    const sameLinks = getSameLinks(link);
+
+    // don't show nav bar when singular reference
+    if (sameLinks.total <= 1) return;
+
+    // find prev/next links with same target
+    const prevLink = getPrevLink(link, sameLinks);
+    const nextLink = getNextLink(link, sameLinks);
+
+    // create nav bar
+    const navBar = document.createElement("div");
+    navBar.id = "tooltip_nav_bar";
+    const text = sameLinks.index + 1 + " of " + sameLinks.total;
+
+    // create nav bar prev/next buttons
+    const prevButton = document.createElement("button");
+    const nextButton = document.createElement("button");
+    prevButton.id = "tooltip_prev_button";
+    nextButton.id = "tooltip_next_button";
+    prevButton.title =
+      "Jump to the previous occurence of this item in the document [←]";
+    nextButton.title =
+      "Jump to the next occurence of this item in the document [→]";
+    prevButton.classList.add("icon_button");
+    nextButton.classList.add("icon_button");
+    prevButton.innerHTML = document.querySelector(".icon_caret_left").innerHTML;
+    nextButton.innerHTML = document.querySelector(
+      ".icon_caret_right"
+    ).innerHTML;
+    navBar.appendChild(prevButton);
+    navBar.appendChild(document.createTextNode(text));
+    navBar.appendChild(nextButton);
+
+    // attach click listeners to buttons
+    prevButton.addEventListener("click", function () {
+      onPrevNextClick(link, prevLink);
+    });
+    nextButton.addEventListener("click", function () {
+      onPrevNextClick(link, nextLink);
+    });
+
+    return navBar;
+  }
+
+  // get previous link with same target
+  function getPrevLink(link, sameLinks) {
+    if (!sameLinks) sameLinks = getSameLinks(link);
+    // wrap index to other side if < 1
+    let index;
+    if (sameLinks.index - 1 >= 0) index = sameLinks.index - 1;
+    else index = sameLinks.total - 1;
+    return sameLinks.elements[index];
+  }
+
+  // get next link with same target
+  function getNextLink(link, sameLinks) {
+    if (!sameLinks) sameLinks = getSameLinks(link);
+    // wrap index to other side if > total
+    let index;
+    if (sameLinks.index + 1 <= sameLinks.total - 1) index = sameLinks.index + 1;
+    else index = 0;
+    return sameLinks.elements[index];
+  }
+
+  // get element that is target of link or url hash
+  function getSource(link) {
+    const hash = link ? link.hash : window.location.hash;
+    const id = hash.slice(1);
+    let target = document.querySelector('[id="' + id + '"]');
+    if (!target) return;
+
+    // if ref or figure, modify target to get expected element
+    if (id.indexOf("ref-") === 0) target = target.querySelector("p");
+    else if (id.indexOf("fig:") === 0) target = target.querySelector("figure");
+
+    return target;
+  }
+
+  // when prev/next arrow button is clicked
+  function onPrevNextClick(link, prevNextLink) {
+    if (link && prevNextLink)
+      goToElement(prevNextLink, window.innerHeight * 0.5);
+  }
+
+  // scroll to and focus element
+  function goToElement(element, offset) {
+    // expand accordion section if collapsed
+    expandElement(element);
+    const y =
+      getRectInView(element).top -
+      getRectInView(document.documentElement).top -
+      (offset || 0);
+    // trigger any function listening for "onscroll" event
+    window.dispatchEvent(new Event("scroll"));
+    window.scrollTo(0, y);
+    document.activeElement.blur();
+    element.focus();
+  }
+
+  // determine position to place tooltip based on link position in
+  // viewport and tooltip size
+  function positionTooltip(link, left, top) {
+    const tooltipElement = document.getElementById("tooltip");
+    if (!tooltipElement) return;
+
+    // get convenient vars for position/dimensions of
+    // link/tooltip/page/view
+    link = getRectInPage(link);
+    const tooltip = getRectInPage(tooltipElement);
+    const view = getRectInPage();
+
+    // horizontal positioning
+    if (left)
+      // use explicit value
+      left = left;
+    else if (link.left + tooltip.width < view.right)
+      // fit tooltip to right of link
+      left = link.left;
+    else if (link.right - tooltip.width > view.left)
+      // fit tooltip to left of link
+      left = link.right - tooltip.width;
+    // center tooltip in view
+    else left = (view.right - view.left) / 2 - tooltip.width / 2;
+
+    // vertical positioning
+    if (top)
+      // use explicit value
+      top = top;
+    else if (link.top - tooltip.height > view.top)
+      // fit tooltip above link
+      top = link.top - tooltip.height;
+    else if (link.bottom + tooltip.height < view.bottom)
+      // fit tooltip below link
+      top = link.bottom;
+    else {
+      // center tooltip in view
+      top = view.top + view.height / 2 - tooltip.height / 2;
+      // nudge off of link to left/right if possible
+      if (link.right + tooltip.width < view.right) left = link.right;
+      else if (link.left - tooltip.width > view.left)
+        left = link.left - tooltip.width;
+    }
+
+    tooltipElement.style.left = left + "px";
+    tooltipElement.style.top = top + "px";
+  }
+
+  // start script when document is finished loading
+  window.addEventListener("load", start);
 </script>
 
 <!-- caret left icon -->
 
 <template class="icon_caret_left">
-    <!-- modified from: https://fontawesome.com/icons/caret-left -->
-    <svg width="16" height="16" viewBox="0 0 192 512">
-        <path
-            fill="currentColor"
-            d="M192 127.338v257.324c0 17.818-21.543 26.741-34.142 14.142L29.196 270.142c-7.81-7.81-7.81-20.474 0-28.284l128.662-128.662c12.599-12.6 34.142-3.676 34.142 14.142z"
-        ></path>
-    </svg>
+  <!-- modified from: https://fontawesome.com/icons/caret-left -->
+  <svg width="16" height="16" viewBox="0 0 192 512">
+    <path
+      fill="currentColor"
+      d="M192 127.338v257.324c0 17.818-21.543 26.741-34.142 14.142L29.196 270.142c-7.81-7.81-7.81-20.474 0-28.284l128.662-128.662c12.599-12.6 34.142-3.676 34.142 14.142z"
+    ></path>
+  </svg>
 </template>
 
 <!-- caret right icon -->
 
 <template class="icon_caret_right">
-    <!-- modified from: https://fontawesome.com/icons/caret-right -->
-    <svg width="16" height="16" viewBox="0 0 192 512">
-        <path
-            fill="currentColor"
-            d="M0 384.662V127.338c0-17.818 21.543-26.741 34.142-14.142l128.662 128.662c7.81 7.81 7.81 20.474 0 28.284L34.142 398.804C21.543 411.404 0 402.48 0 384.662z"
-        ></path>
-    </svg>
+  <!-- modified from: https://fontawesome.com/icons/caret-right -->
+  <svg width="16" height="16" viewBox="0 0 192 512">
+    <path
+      fill="currentColor"
+      d="M0 384.662V127.338c0-17.818 21.543-26.741 34.142-14.142l128.662 128.662c7.81 7.81 7.81 20.474 0 28.284L34.142 398.804C21.543 411.404 0 402.48 0 384.662z"
+    ></path>
+  </svg>
 </template>
+
+<style>
+  @media only screen {
+    /* tooltip container */
+    #tooltip {
+      position: absolute;
+      width: 50%;
+      min-width: 240px;
+      max-width: 75%;
+      z-index: 1;
+    }
+
+    /* tooltip content */
+    #tooltip_content {
+      margin-bottom: 5px;
+      padding: 20px;
+      border-radius: 5px;
+      border: solid 1px #bdbdbd;
+      box-shadow: 0 0 20px rgba(0, 0, 0, 0.05);
+      background: #ffffff;
+      overflow-wrap: break-word;
+    }
+
+    /* tooltip copy of paragraphs and figures */
+    #tooltip_content > p,
+    #tooltip_content > figure {
+      margin: 0;
+      max-height: 320px;
+      overflow-y: auto;
+    }
+
+    /* tooltip copy of <img> */
+    #tooltip_content > figure > img,
+    #tooltip_content > figure > svg {
+      max-height: 260px;
+    }
+
+    /* navigation bar */
+    #tooltip_nav_bar {
+      margin-top: 10px;
+      text-align: center;
+    }
+
+    /* navigation bar previous/next buton */
+    #tooltip_nav_bar > .icon_button {
+      position: relative;
+      top: 3px;
+    }
+
+    /* navigation bar previous button */
+    #tooltip_nav_bar > .icon_button:first-of-type {
+      margin-right: 5px;
+    }
+
+    /* navigation bar next button */
+    #tooltip_nav_bar > .icon_button:last-of-type {
+      margin-left: 5px;
+    }
+  }
+
+  /* always hide tooltip on print */
+  @media only print {
+    #tooltip {
+      display: none;
+    }
+  }
+</style>
diff --git a/build/themes/default.html b/build/themes/default.html
index 4022f31..2396cc4 100644
--- a/build/themes/default.html
+++ b/build/themes/default.html
@@ -1,60 +1,525 @@
 <!-- default theme -->
 
 <style>
-    /* import google fonts */
-    @import url("https://fonts.googleapis.com/css?family=Open+Sans:400,600,700");
-    @import url("https://fonts.googleapis.com/css?family=Source+Code+Pro");
-
-    /* -------------------------------------------------- */
-    /* global */
-    /* -------------------------------------------------- */
-
-    /* all elements */
-    * {
-        /* force sans-serif font unless specified otherwise */
-        font-family: "Open Sans", "Helvetica", sans-serif;
-
-        /* prevent text inflation on some mobile browsers */
-        -webkit-text-size-adjust: none !important;
-        -moz-text-size-adjust: none !important;
-        -o-text-size-adjust: none !important;
-        text-size-adjust: none !important;
+  /* import google fonts */
+  @import url("https://fonts.googleapis.com/css?family=Open+Sans:400,600,700");
+  @import url("https://fonts.googleapis.com/css?family=Source+Code+Pro");
+
+  /* -------------------------------------------------- */
+  /* global */
+  /* -------------------------------------------------- */
+
+  /* all elements */
+  * {
+    /* force sans-serif font unless specified otherwise */
+    font-family: "Open Sans", "Helvetica", sans-serif;
+
+    /* prevent text inflation on some mobile browsers */
+    -webkit-text-size-adjust: none !important;
+    -moz-text-size-adjust: none !important;
+    -o-text-size-adjust: none !important;
+    text-size-adjust: none !important;
+  }
+
+  @media only screen {
+    /* "page" element */
+    body {
+      position: relative;
+      box-sizing: border-box;
+      font-size: 12pt;
+      line-height: 1.5;
+      max-width: 8.5in;
+      margin: 20px auto;
+      padding: 40px;
+      border-radius: 5px;
+      border: solid 1px #bdbdbd;
+      box-shadow: 0 0 20px rgba(0, 0, 0, 0.05);
+      background: #ffffff;
+    }
+  }
+
+  /* when on screen < 8.5in wide */
+  @media only screen and (max-width: 8.5in) {
+    /* "page" element */
+    body {
+      padding: 20px;
+      margin: 0;
+      border-radius: 0;
+      border: none;
+      box-shadow: 0 0 20px rgba(0, 0, 0, 0.05) inset;
+      background: none;
+    }
+  }
+
+  /* -------------------------------------------------- */
+  /* headings */
+  /* -------------------------------------------------- */
+
+  /* all headings */
+  h1,
+  h2,
+  h3,
+  h4,
+  h5,
+  h6 {
+    margin: 20px 0;
+    padding: 0;
+    font-weight: bold;
+  }
+
+  /* biggest heading */
+  h1 {
+    margin: 40px 0;
+    text-align: center;
+  }
+
+  /* second biggest heading */
+  h2 {
+    margin-top: 30px;
+    padding-bottom: 5px;
+    border-bottom: solid 1px #bdbdbd;
+  }
+
+  /* heading font sizes */
+  h1 {
+    font-size: 2em;
+  }
+  h2 {
+    font-size: 1.5em;
+  }
+  h3 {
+    font-size: 1.35em;
+  }
+  h4 {
+    font-size: 1.25em;
+  }
+  h5 {
+    font-size: 1.15em;
+  }
+  h6 {
+    font-size: 1em;
+  }
+
+  /* -------------------------------------------------- */
+  /* manuscript header */
+  /* -------------------------------------------------- */
+
+  /* manuscript title */
+  header > h1 {
+    margin: 0;
+  }
+
+  /* manuscript title caption text (ie "automatically generated on") */
+  header + p {
+    text-align: center;
+    margin-top: 10px;
+  }
+
+  /* -------------------------------------------------- */
+  /* text elements */
+  /* -------------------------------------------------- */
+
+  /* links */
+  a {
+    color: #2196f3;
+    overflow-wrap: break-word;
+  }
+
+  /* superscripts and subscripts */
+  sub,
+  sup {
+    /* prevent from affecting line height */
+    line-height: 0;
+  }
+
+  /* unordered and ordered lists*/
+  ul,
+  ol {
+    padding-left: 20px;
+  }
+
+  /* class for styling text semibold */
+  .semibold {
+    font-weight: 600;
+  }
+
+  /* class for styling elements horizontally left aligned */
+  .left {
+    display: block;
+    text-align: left;
+    margin-left: auto;
+    margin-right: 0;
+    justify-content: left;
+  }
+
+  /* class for styling elements horizontally centered */
+  .center {
+    display: block;
+    text-align: center;
+    margin-left: auto;
+    margin-right: auto;
+    justify-content: center;
+  }
+
+  /* class for styling elements horizontally right aligned */
+  .right {
+    display: block;
+    text-align: right;
+    margin-left: 0;
+    margin-right: auto;
+    justify-content: right;
+  }
+
+  /* -------------------------------------------------- */
+  /* section elements */
+  /* -------------------------------------------------- */
+
+  /* horizontal divider line */
+  hr {
+    border: none;
+    height: 1px;
+    background: #bdbdbd;
+  }
+
+  /* paragraphs, horizontal dividers, figures, tables, code */
+  p,
+  hr,
+  figure,
+  table,
+  pre {
+    /* treat all as "paragraphs", with consistent vertical margins */
+    margin-top: 20px;
+    margin-bottom: 20px;
+  }
+
+  /* -------------------------------------------------- */
+  /* figures */
+  /* -------------------------------------------------- */
+
+  /* figure */
+  figure {
+    max-width: 100%;
+    margin-left: auto;
+    margin-right: auto;
+  }
+
+  /* figure caption */
+  figcaption {
+    padding: 0;
+    padding-top: 10px;
+  }
+
+  /* figure image element */
+  figure > img,
+  figure > svg {
+    max-width: 100%;
+    display: block;
+    margin-left: auto;
+    margin-right: auto;
+  }
+
+  /* figure auto-number */
+  img + figcaption > span:first-of-type,
+  svg + figcaption > span:first-of-type {
+    font-weight: bold;
+    margin-right: 5px;
+  }
+
+  /* -------------------------------------------------- */
+  /* tables */
+  /* -------------------------------------------------- */
+
+  /* table */
+  table {
+    border-collapse: collapse;
+    border-spacing: 0;
+    width: 100%;
+    margin-left: auto;
+    margin-right: auto;
+  }
+
+  /* table cells */
+  th,
+  td {
+    border: solid 1px #bdbdbd;
+    padding: 10px;
+    /* squash table if too wide for page by forcing line breaks */
+    overflow-wrap: break-word;
+    word-break: break-word;
+  }
+
+  /* header row and even rows */
+  th,
+  tr:nth-child(2n) {
+    background-color: #fafafa;
+  }
+
+  /* odd rows */
+  tr:nth-child(2n + 1) {
+    background-color: #ffffff;
+  }
+
+  /* table caption */
+  caption {
+    text-align: left;
+    padding: 0;
+    padding-bottom: 10px;
+  }
+
+  /* table auto-number */
+  table > caption > span:first-of-type,
+  div.table_wrapper > table > caption > span:first-of-type {
+    font-weight: bold;
+    margin-right: 5px;
+  }
+
+  /* -------------------------------------------------- */
+  /* code */
+  /* -------------------------------------------------- */
+
+  /* multi-line code block */
+  pre {
+    padding: 10px;
+    background-color: #eeeeee;
+    color: #000000;
+    border-radius: 5px;
+    break-inside: avoid;
+    text-align: left;
+  }
+
+  /* inline code, ie code within normal text */
+  :not(pre) > code {
+    padding: 0 4px;
+    background-color: #eeeeee;
+    color: #000000;
+    border-radius: 5px;
+  }
+
+  /* code text */
+  /* apply all children, to reach syntax highlighting sub-elements */
+  code,
+  code * {
+    /* force monospace font */
+    font-family: "Source Code Pro", "Courier New", monospace;
+  }
+
+  /* -------------------------------------------------- */
+  /* quotes */
+  /* -------------------------------------------------- */
+
+  /* quoted text */
+  blockquote {
+    margin: 0;
+    padding: 0;
+    border-left: 4px solid #bdbdbd;
+    padding-left: 16px;
+    break-inside: avoid;
+  }
+
+  /* -------------------------------------------------- */
+  /* banners */
+  /* -------------------------------------------------- */
+
+  /* info banners */
+  .banner {
+    box-sizing: border-box;
+    display: block;
+    position: relative;
+    width: 100%;
+    margin-top: 20px;
+    margin-bottom: 20px;
+    padding: 20px;
+    text-align: center;
+  }
+
+  /* paragraph in banner */
+  .banner > p {
+    margin: 0;
+  }
+
+  /* -------------------------------------------------- */
+  /* highlight colors */
+  /* -------------------------------------------------- */
+
+  .white {
+    background: #ffffff;
+  }
+  .lightgrey {
+    background: #eeeeee;
+  }
+  .grey {
+    background: #757575;
+  }
+  .darkgrey {
+    background: #424242;
+  }
+  .black {
+    background: #000000;
+  }
+  .lightred {
+    background: #ffcdd2;
+  }
+  .lightyellow {
+    background: #ffecb3;
+  }
+  .lightgreen {
+    background: #dcedc8;
+  }
+  .lightblue {
+    background: #e3f2fd;
+  }
+  .lightpurple {
+    background: #f3e5f5;
+  }
+  .red {
+    background: #f44336;
+  }
+  .orange {
+    background: #ff9800;
+  }
+  .yellow {
+    background: #ffeb3b;
+  }
+  .green {
+    background: #4caf50;
+  }
+  .blue {
+    background: #2196f3;
+  }
+  .purple {
+    background: #9c27b0;
+  }
+  .white,
+  .lightgrey,
+  .lightred,
+  .lightyellow,
+  .lightgreen,
+  .lightblue,
+  .lightpurple,
+  .orange,
+  .yellow,
+  .white a,
+  .lightgrey a,
+  .lightred a,
+  .lightyellow a,
+  .lightgreen a,
+  .lightblue a,
+  .lightpurple a,
+  .orange a,
+  .yellow a {
+    color: #000000;
+  }
+  .grey,
+  .darkgrey,
+  .black,
+  .red,
+  .green,
+  .blue,
+  .purple,
+  .grey a,
+  .darkgrey a,
+  .black a,
+  .red a,
+  .green a,
+  .blue a,
+  .purple a {
+    color: #ffffff;
+  }
+
+  /* -------------------------------------------------- */
+  /* buttons */
+  /* -------------------------------------------------- */
+
+  /* class for styling links like buttons */
+  .button {
+    display: inline-flex;
+    justify-content: center;
+    align-items: center;
+    margin: 5px;
+    padding: 10px 20px;
+    font-size: 0.75em;
+    font-weight: 600;
+    text-transform: uppercase;
+    text-decoration: none;
+    letter-spacing: 1px;
+    background: none;
+    color: #2196f3;
+    border: solid 1px #bdbdbd;
+    border-radius: 5px;
+  }
+
+  /* buttons when hovered */
+  .button:hover:not([disabled]),
+  .icon_button:hover:not([disabled]) {
+    cursor: pointer;
+    background: #f5f5f5;
+  }
+
+  /* buttons when disabled */
+  .button[disabled],
+  .icon_button[disabled] {
+    opacity: 0.35;
+    pointer-events: none;
+  }
+
+  /* class for styling buttons containg only single icon */
+  .icon_button {
+    display: inline-flex;
+    justify-content: center;
+    align-items: center;
+    text-decoration: none;
+    margin: 0;
+    padding: 0;
+    background: none;
+    border-radius: 5px;
+    border: none;
+    width: 20px;
+    height: 20px;
+    min-width: 20px;
+    min-height: 20px;
+  }
+
+  /* icon button inner svg image */
+  .icon_button > svg {
+    height: 16px;
+  }
+
+  /* -------------------------------------------------- */
+  /* icons */
+  /* -------------------------------------------------- */
+
+  /* class for styling icons inline with text */
+  .inline_icon {
+    height: 1em;
+    position: relative;
+    top: 0.125em;
+  }
+
+  /* -------------------------------------------------- */
+  /* print control */
+  /* -------------------------------------------------- */
+
+  @media print {
+    @page {
+      /* suggested printing margin */
+      margin: 0.5in;
+    }
+
+    /* document and "page" elements */
+    html,
+    body {
+      margin: 0;
+      padding: 0;
+      width: 100%;
+      height: 100%;
+    }
+
+    /* "page" element */
+    body {
+      font-size: 11pt !important;
+      line-height: 1.35;
     }
 
-    @media only screen {
-        /* "page" element */
-        body {
-            position: relative;
-            box-sizing: border-box;
-            font-size: 12pt;
-            line-height: 1.5;
-            max-width: 8.5in;
-            margin: 20px auto;
-            padding: 40px;
-            border-radius: 5px;
-            border: solid 1px #bdbdbd;
-            box-shadow: 0 0 20px rgba(0, 0, 0, 0.05);
-            background: #ffffff;
-        }
-    }
-
-    /* when on screen < 8.5in wide */
-    @media only screen and (max-width: 8.5in) {
-        /* "page" element */
-        body {
-            padding: 20px;
-            margin: 0;
-            border-radius: 0;
-            border: none;
-            box-shadow: 0 0 20px rgba(0, 0, 0, 0.05) inset;
-            background: none;
-        }
-    }
-
-    /* -------------------------------------------------- */
-    /* headings */
-    /* -------------------------------------------------- */
-
     /* all headings */
     h1,
     h2,
@@ -62,1195 +527,133 @@
     h4,
     h5,
     h6 {
-        margin: 20px 0;
-        padding: 0;
-        font-weight: bold;
-    }
-
-    /* biggest heading */
-    h1 {
-        margin: 40px 0;
-        text-align: center;
-    }
-
-    /* second biggest heading */
-    h2 {
-        margin-top: 30px;
-        padding-bottom: 5px;
-        border-bottom: solid 1px #bdbdbd;
-    }
-
-    /* heading font sizes */
-    h1 {
-        font-size: 2em;
-    }
-    h2 {
-        font-size: 1.5em;
-    }
-    h3{
-        font-size: 1.35em;
-    }
-    h4 {
-        font-size: 1.25em;
-    }
-    h5 {
-        font-size: 1.15em;
-    }
-    h6 {
-        font-size: 1em;
-    }
-
-    /* -------------------------------------------------- */
-    /* manuscript header */
-    /* -------------------------------------------------- */
-
-    /* manuscript title */
-    header > h1 {
-        margin: 0;
-    }
-
-    /* manuscript title caption text (ie "automatically generated on") */
-    header + p {
-        text-align: center;
-        margin-top: 10px;
-    }
-
-    /* -------------------------------------------------- */
-    /* text elements */
-    /* -------------------------------------------------- */
-
-    /* links */
-    a {
-        color: #2196f3;
-        overflow-wrap: break-word;
-    }
-
-    /* normal links (not empty, not button link, not syntax highlighting link) */
-    a:not(:empty):not(.button):not(.sourceLine) {
-        padding-left: 1px;
-        padding-right: 1px;
-    }
-
-    /* superscripts and subscripts */
-    sub,
-    sup {
-        /* prevent from affecting line height */
-        line-height: 0;
-    }
-
-    /* unordered and ordered lists*/
-    ul,
-    ol {
-        padding-left: 20px;
-    }
-
-    /* class for styling text semibold */
-    .semibold {
-        font-weight: 600;
-    }
-
-    /* class for styling elements horizontally left aligned */
-    .left {
-        display: block;
-        text-align: left;
-        margin-left: auto;
-        margin-right: 0;
-        justify-content: left;
-    }
-
-    /* class for styling elements horizontally centered */
-    .center {
-        display: block;
-        text-align: center;
-        margin-left: auto;
-        margin-right: auto;
-        justify-content: center;
-    }
-
-    /* class for styling elements horizontally right aligned */
-    .right {
-        display: block;
-        text-align: right;
-        margin-left: 0;
-        margin-right: auto;
-        justify-content: right;
+      margin: 15px 0;
     }
 
-    /* -------------------------------------------------- */
-    /* section elements */
-    /* -------------------------------------------------- */
-
-    /* horizontal divider line */
-    hr {
-        border: none;
-        height: 1px;
-        background: #bdbdbd;
-    }
-
-    /* paragraphs, horizontal dividers, figures, tables, code */
-    p,
-    hr,
+    /* figures and tables */
     figure,
-    table,
-    pre {
-        /* treat all as "paragraphs", with consistent vertical margins */
-        margin-top: 20px;
-        margin-bottom: 20px;
-    }
-
-    /* -------------------------------------------------- */
-    /* figures */
-    /* -------------------------------------------------- */
-
-    /* figure */
-    figure {
-        max-width: 100%;
-        margin-left: auto;
-        margin-right: auto;
-    }
-
-    /* figure caption */
-    figcaption {
-        padding: 0;
-        padding-top: 10px;
-    }
-
-    /* figure image element */
-    figure > img,
-    figure > svg {
-        max-width: 100%;
-        display: block;
-        margin-left: auto;
-        margin-right: auto;
-    }
-
-    /* figure auto-number */
-    img + figcaption > span:first-of-type,
-    svg + figcaption > span:first-of-type {
-        font-weight: bold;
-        margin-right: 5px;
-    }
-
-    /* -------------------------------------------------- */
-    /* tables */
-    /* -------------------------------------------------- */
-
-    /* table */
     table {
-        border-collapse: collapse;
-        border-spacing: 0;
-        width: 100%;
-        margin-left: auto;
-        margin-right: auto;
+      font-size: 0.85em;
     }
 
     /* table cells */
     th,
     td {
-        border: solid 1px #bdbdbd;
-        padding: 10px;
-        /* squash table if too wide for page by forcing line breaks */
-        overflow-wrap: break-word;
-        word-break: break-word;
-    }
-
-    /* header row and even rows */
-    th,
-    tr:nth-child(2n) {
-        background-color: #fafafa;
-    }
-
-    /* odd rows */
-    tr:nth-child(2n + 1) {
-        background-color: #ffffff;
+      padding: 5px;
     }
 
-    /* table caption */
-    caption {
-        text-align: left;
-        padding: 0;
-        padding-bottom: 10px;
+    /* shrink font awesome icons */
+    i.fas,
+    i.fab,
+    i.far,
+    i.fal {
+      transform: scale(0.85);
     }
 
-    /* table auto-number */
-    table > caption > span:first-of-type,
-    div.table_wrapper > table > caption > span:first-of-type {
-        font-weight: bold;
-        margin-right: 5px;
-    }
-
-    /* -------------------------------------------------- */
-    /* code */
-    /* -------------------------------------------------- */
-
-    /* multi-line code block */
-    pre {
-        padding: 10px;
-        background-color: #eeeeee;
-        color: #000000;
-        border-radius: 5px;
-        break-inside: avoid;
-        text-align: left;
-    }
-
-    /* inline code, ie code within normal text */
-    :not(pre) > code {
-        padding: 0 4px;
-        background-color: #eeeeee;
-        color: #000000;
-        border-radius: 5px;
-    }
-
-    /* code text */
-    /* apply all children, to reach syntax highlighting sub-elements */
-    code,
-    code * {
-        /* force monospace font */
-        font-family: "Source Code Pro", "Courier New", monospace;
-    }
-
-    /* -------------------------------------------------- */
-    /* quotes */
-    /* -------------------------------------------------- */
-
-    /* quoted text */
-    blockquote {
-        margin: 0;
-        padding: 0;
-        border-left: 4px solid #bdbdbd;
-        padding-left: 16px;
-        break-inside: avoid;
-    }
-
-    /* -------------------------------------------------- */
-    /* banners */
-    /* -------------------------------------------------- */
-
-    /* info banners */
+    /* decrease banner margins */
     .banner {
-        box-sizing: border-box;
-        display: block;
-        position: relative;
-        width: 100%;
-        margin-top: 20px;
-        margin-bottom: 20px;
-        padding: 20px;
-        text-align: center;
+      margin-top: 15px;
+      margin-bottom: 15px;
+      padding: 15px;
     }
 
-    /* paragraph in banner */
-    .banner > p {
-        margin: 0;
+    /* class for centering an element vertically on its own page */
+    .page_center {
+      margin: auto;
+      width: 100%;
+      height: 100%;
+      display: flex;
+      align-items: center;
+      vertical-align: middle;
+      break-before: page;
+      break-after: page;
     }
 
-    /* -------------------------------------------------- */
-    /* highlight colors */
-    /* -------------------------------------------------- */
-
-    .white {
-        background: #ffffff;
-    }
-    .lightgrey {
-        background: #eeeeee;
-    }
-    .grey {
-        background: #757575;
-    }
-    .darkgrey {
-        background: #424242;
-    }
-    .black {
-        background: #000000;
-    }
-    .lightred {
-        background: #ffcdd2;
-    }
-    .lightyellow {
-        background: #ffecb3;
-    }
-    .lightgreen {
-        background: #dcedc8;
-    }
-    .lightblue {
-        background: #e3f2fd;
-    }
-    .lightpurple {
-        background: #f3e5f5;
-    }
-    .red {
-        background: #f44336;
-    }
-    .orange {
-        background: #ff9800;
-    }
-    .yellow {
-        background: #ffeb3b;
-    }
-    .green {
-        background: #4caf50;
-    }
-    .blue {
-        background: #2196f3;
-    }
-    .purple {
-        background: #9c27b0;
-    }
-    .white,
-    .lightgrey,
-    .lightred,
-    .lightyellow,
-    .lightgreen,
-    .lightblue,
-    .lightpurple,
-    .orange,
-    .yellow,
-    .white a,
-    .lightgrey a,
-    .lightred a,
-    .lightyellow a,
-    .lightgreen a,
-    .lightblue a,
-    .lightpurple a,
-    .orange a,
-    .yellow a {
-        color: #000000;
-    }
-    .grey,
-    .darkgrey,
-    .black,
-    .red,
-    .green,
-    .blue,
-    .purple,
-    .grey a,
-    .darkgrey a,
-    .black a,
-    .red a,
-    .green a,
-    .blue a,
-    .purple a {
-        color: #ffffff;
+    /* always insert a page break before the element */
+    .page_break_before {
+      break-before: page;
     }
 
-    /* -------------------------------------------------- */
-    /* buttons */
-    /* -------------------------------------------------- */
-
-    /* class for styling links like buttons */
-    .button {
-        display: inline-flex;
-        justify-content: center;
-        align-items: center;
-        margin: 5px;
-        padding: 10px 20px;
-        font-size: 0.75em;
-        font-weight: 600;
-        text-transform: uppercase;
-        text-decoration: none;
-        letter-spacing: 1px;
-        background: none;
-        color: #2196f3;
-        border: solid 1px #bdbdbd;
-        border-radius: 5px;
+    /* always insert a page break after the element */
+    .page_break_after {
+      break-after: page;
     }
 
-    /* buttons when hovered */
-    .button:hover:not([disabled]),
-    .icon_button:hover:not([disabled]) {
-        cursor: pointer;
-        background: #f5f5f5;
+    /* avoid page break before the element */
+    .page_break_before_avoid {
+      break-before: avoid;
     }
 
-    /* buttons when disabled */
-    .button[disabled],
-    .icon_button[disabled] {
-        opacity: 0.35;
-        pointer-events: none;
+    /* avoid page break after the element */
+    .page_break_after_avoid {
+      break-after: avoid;
     }
 
-    /* class for styling buttons containg only single icon */
-    .icon_button {
-        display: inline-flex;
-        justify-content: center;
-        align-items: center;
-        text-decoration: none;
-        margin: 0;
-        padding: 0;
-        background: none;
-        border-radius: 5px;
-        border: none;
-        width: 20px;
-        height: 20px;
-        min-width: 20px;
-        min-height: 20px;
+    /* avoid page break inside the element */
+    .page_break_inside_avoid {
+      break-inside: avoid;
     }
+  }
 
-    /* icon button inner svg image */
-    .icon_button > svg {
-        height: 16px;
-    }
-
-    /* -------------------------------------------------- */
-    /* icons */
-    /* -------------------------------------------------- */
+  /* -------------------------------------------------- */
+  /* override pandoc css quirks */
+  /* -------------------------------------------------- */
 
-    /* class for styling icons inline with text */
-    .inline_icon {
-        height: 1em;
-        position: relative;
-        top: 0.125em;
-    }
-
-    /* -------------------------------------------------- */
-    /* print control */
-    /* -------------------------------------------------- */
-
-    @media print {
-        @page {
-            /* suggested printing margin */
-            margin: 0.5in;
-        }
-
-        /* document and "page" elements */
-        html, body {
-            margin: 0;
-            padding: 0;
-            width: 100%;
-            height: 100%;
-        }
-
-        /* "page" element */
-        body {
-            font-size: 11pt !important;
-            line-height: 1.35;
-        }
-
-        /* all headings */
-        h1,
-        h2,
-        h3,
-        h4,
-        h5,
-        h6 {
-            margin: 15px 0;
-        }
-
-        /* figures and tables */
-        figure, table {
-            font-size: 0.85em;
-        }
-
-        /* table cells */
-        th,
-        td {
-            padding: 5px;
-        }
-
-        /* shrink font awesome icons */
-        i.fas,
-        i.fab,
-        i.far,
-        i.fal {
-            transform: scale(0.85);
-        }
-
-        /* decrease banner margins */
-        .banner {
-            margin-top: 15px;
-            margin-bottom: 15px;
-            padding: 15px;
-        }
-
-        /* class for centering an element vertically on its own page */
-        .page_center {
-            margin: auto;
-            width: 100%;
-            height: 100%;
-            display: flex;
-            align-items: center;
-            vertical-align: middle;
-            break-before: page;
-            break-after: page;
-        }
-
-        /* always insert a page break before the element */
-        .page_break_before {
-            break-before: page;
-        }
-
-        /* always insert a page break after the element */
-        .page_break_after {
-            break-after: page;
-        }
-
-        /* avoid page break before the element */
-        .page_break_before_avoid {
-            break-before: avoid;
-        }
-
-        /* avoid page break after the element */
-        .page_break_after_avoid {
-            break-after: avoid;
-        }
-
-        /* avoid page break inside the element */
-        .page_break_inside_avoid {
-            break-inside: avoid;
-        }
-    }
+  .sourceCode {
+    /* prevent unsightly overflow in wide code blocks */
+    overflow: auto !important;
+  }
 
-    /* -------------------------------------------------- */
-    /* override pandoc css quirks */
-    /* -------------------------------------------------- */
+  div.sourceCode {
+    /* prevent background fill on top-most code block  container */
+    background: none !important;
+  }
 
-    .sourceCode {
-        /* prevent unsightly overflow in wide code blocks */
-        overflow: auto !important;
-    }
+  .sourceCode * {
+    /* force consistent line spacing */
+    line-height: 1.5 !important;
+  }
 
-    div.sourceCode {
-        /* prevent background fill on top-most code block  container */
-        background: none !important;
-    }
+  div.sourceCode {
+    /* style code block margins same as <pre> element */
+    margin-top: 20px;
+    margin-bottom: 20px;
+  }
 
-    .sourceCode * {
-        /* force consistent line spacing */
-        line-height: 1.5 !important;
-    }
+  /* -------------------------------------------------- */
+  /* tablenos */
+  /* -------------------------------------------------- */
 
-    div.sourceCode {
-        /* style code block margins same as <pre> element */
-        margin-top: 20px;
-        margin-bottom: 20px;
-    }
+  /* tablenos wrapper */
+  .tablenos {
+    /* show scrollbar on tables if necessary to prevent overflow */
+    width: 100%;
+    margin: 20px 0;
+  }
 
-    /* -------------------------------------------------- */
-    /* tablenos */
-    /* -------------------------------------------------- */
+  .tablenos > table {
+    /* move margins from table to table_wrapper to allow margin collapsing */
+    margin: 0;
+  }
 
+  @media only screen {
     /* tablenos wrapper */
     .tablenos {
-        /* show scrollbar on tables if necessary to prevent overflow */
-        width: 100%;
-        margin: 20px 0;
-    }
-
-    .tablenos > table {
-        /* move margins from table to table_wrapper to allow margin collapsing */
-        margin: 0;
-    }
-
-    @media only screen {
-        /* tablenos wrapper */
-        .tablenos {
-            /* show scrollbar on tables if necessary to prevent overflow */
-            overflow-x: auto !important;
-        }
-
-        .tablenos th,
-        .tablenos td {
-            overflow-wrap: unset !important;
-            word-break: unset !important;
-        }
-
-        /* table in wrapper */
-        .tablenos table,
-        .tablenos table * {
-            /* don't break table words */
-            overflow-wrap: normal !important;
-        }
-    }
-
-    /* -------------------------------------------------- */
-    /* mathjax */
-    /* -------------------------------------------------- */
-
-    /* mathjax containers */
-    .math.display > span:not(.MathJax_Preview) {
-        /* turn inline element (no dimensions) into block (allows fixed width and thus scrolling) */
-        display: flex !important;
-        overflow-x: auto !important;
-        overflow-y: hidden !important;
-        justify-content: center;
-        align-items: center;
-        margin: 0 !important;
-    }
-
-    /* right click menu */
-    .MathJax_Menu {
-        border-radius: 5px !important;
-        border: solid 1px #bdbdbd !important;
-        box-shadow: none !important;
-    }
-
-    /* equation auto-number */
-    span[id^="eq:"] > span.math.display + span {
-        font-weight: 600;
-    }
-
-    /* equation */
-    span[id^="eq:"] > span.math.display > span {
-        /* nudge to make room for equation auto-number and anchor */
-        margin-right: 60px !important;
-    }
-
-    /* -------------------------------------------------- */
-    /* anchors plugin */
-    /* -------------------------------------------------- */
-
-    @media only screen {
-        /* anchor button */
-        .anchor {
-            opacity: 0;
-            margin-left: 5px;
-        }
-
-        /* anchor buttons within <h2>'s */
-        h2 .anchor {
-            margin-left: 10px;
-        }
-
-        /* anchor buttons when hovered/focused and anything containing an anchor button when hovered */
-        *:hover > .anchor,
-        .anchor:hover,
-        .anchor:focus {
-            opacity: 1;
-        }
-
-        /* anchor button when hovered */
-        .anchor:hover {
-            cursor: pointer;
-        }
-    }
-
-    /* always show anchor button on devices with no mouse/hover ability */
-    @media (hover: none) {
-        .anchor {
-            opacity: 1;
-        }
-    }
-
-    /* always hide anchor button on print */
-    @media only print {
-        .anchor {
-            display: none;
-        }
-    }
-
-    /* -------------------------------------------------- */
-    /* accordion plugin */
-    /* -------------------------------------------------- */
-
-    @media only screen {
-        /* accordion arrow button */
-        .accordion_arrow {
-            margin-right: 10px;
-        }
-
-        /* arrow icon when <h2> data-collapsed attribute true */
-        h2[data-collapsed="true"] > .accordion_arrow > svg {
-            transform: rotate(-90deg);
-        }
-
-        /* all elements (except <h2>'s) when data-collapsed attribute true */
-        *:not(h2)[data-collapsed="true"] {
-            display: none;
-        }
-
-        /* accordion arrow button when hovered and <h2>'s when hovered */
-        .accordion_arrow:hover,
-        h2[data-collapsed="true"]:hover,
-        h2[data-collapsed="false"]:hover {
-            cursor: pointer;
-        }
+      /* show scrollbar on tables if necessary to prevent overflow */
+      overflow-x: auto !important;
     }
 
-    /* always hide accordion arrow button on print */
-    @media only print {
-        .accordion_arrow {
-            display: none;
-        }
+    .tablenos th,
+    .tablenos td {
+      overflow-wrap: unset !important;
+      word-break: unset !important;
     }
 
-    /* -------------------------------------------------- */
-    /* tooltips plugin */
-    /* -------------------------------------------------- */
-
-    @media only screen {
-        /* tooltip container */
-        #tooltip {
-            position: absolute;
-            width: 50%;
-            min-width: 240px;
-            max-width: 75%;
-            z-index: 1;
-        }
-
-        /* tooltip content */
-        #tooltip_content {
-            margin-bottom: 5px;
-            padding: 20px;
-            border-radius: 5px;
-            border: solid 1px #bdbdbd;
-            box-shadow: 0 0 20px rgba(0, 0, 0, 0.05);
-            background: #ffffff;
-            overflow-wrap: break-word;
-        }
-
-        /* tooltip copy of paragraphs and figures */
-        #tooltip_content > p,
-        #tooltip_content > figure {
-            margin: 0;
-            max-height: 320px;
-            overflow-y: auto;
-        }
-
-        /* tooltip copy of <img> */
-        #tooltip_content > figure > img,
-        #tooltip_content > figure > svg {
-            max-height: 260px;
-        }
-
-        /* navigation bar */
-        #tooltip_nav_bar {
-            margin-top: 10px;
-            text-align: center;
-        }
-
-        /* navigation bar previous/next buton */
-        #tooltip_nav_bar > .icon_button {
-            position: relative;
-            top: 3px;
-        }
-
-        /* navigation bar previous button */
-        #tooltip_nav_bar > .icon_button:first-of-type {
-            margin-right: 5px;
-        }
-
-        /* navigation bar next button */
-        #tooltip_nav_bar > .icon_button:last-of-type {
-            margin-left: 5px;
-        }
-    }
-
-    /* always hide tooltip on print */
-    @media only print {
-        #tooltip {
-            display: none;
-        }
-    }
-
-    /* -------------------------------------------------- */
-    /* jump to first plugin */
-    /* -------------------------------------------------- */
-
-    @media only screen {
-        /* jump button */
-        .jump_arrow {
-            position: relative;
-            top: 0.125em;
-            margin-right: 5px;
-        }
-    }
-
-    /* always hide jump button on print */
-    @media only print {
-        .jump_arrow {
-            display: none;
-        }
-    }
-
-    /* -------------------------------------------------- */
-    /* link highlight plugin */
-    /* -------------------------------------------------- */
-
-    @media only screen {
-        /* anything with data-highlighted attribute true */
-        [data-highlighted="true"] {
-            background: #ffeb3b;
-        }
-
-        /* anything with data-selected attribute true */
-        [data-selected="true"] {
-            background: #ff8a65 !important;
-        }
-
-        /* animation definition for glow */
-        @keyframes highlight_glow {
-            0% {
-                background: none;
-            }
-            10% {
-                background: #bbdefb;
-            }
-            100% {
-                background: none;
-            }
-        }
-
-        /* anything with data-glow attribute true */
-        [data-glow="true"] {
-            animation: highlight_glow 2s;
-        }
-    }
-
-    /* -------------------------------------------------- */
-    /* table of contents plugin */
-    /* -------------------------------------------------- */
-
-    @media only screen {
-        /* toc panel */
-        #toc_panel {
-            box-sizing: border-box;
-            position: fixed;
-            top: 0;
-            left: 0;
-            background: #ffffff;
-            box-shadow: 0 0 20px rgba(0, 0, 0, 0.05);
-            z-index: 2;
-        }
-
-        /* toc panel when closed */
-        #toc_panel[data-open="false"] {
-            min-width: 60px;
-            width: 60px;
-            height: 60px;
-            border-right: solid 1px #bdbdbd;
-            border-bottom: solid 1px #bdbdbd;
-        }
-
-        /* toc panel when open */
-        #toc_panel[data-open="true"] {
-            min-width: 260px;
-            max-width: 480px;
-            /* keep panel edge consistent distance away from "page" edge */
-            width: calc(((100vw - 8.5in) / 2) - 30px - 40px);
-            bottom: 0;
-            border-right: solid 1px #bdbdbd;
-        }
-
-        /* toc panel header */
-        #toc_header {
-            box-sizing: border-box;
-            display: flex;
-            flex-direction: row;
-            align-items: center;
-            height: 60px;
-            margin: 0;
-            padding: 20px;
-        }
-
-        /* toc panel header when hovered */
-        #toc_header:hover {
-            cursor: pointer;
-        }
-
-        /* toc panel header when panel open */
-        #toc_panel[data-open="true"] > #toc_header {
-            border-bottom: solid 1px #bdbdbd;
-        }
-
-        /* toc open/close header button */
-        #toc_button {
-            margin-right: 20px;
-        }
-
-        /* hide toc list and header text when closed */
-        #toc_panel[data-open="false"] > #toc_header > *:not(#toc_button),
-        #toc_panel[data-open="false"] > #toc_list {
-            display: none;
-        }
-
-        /* toc list of entries */
-        #toc_list {
-            box-sizing: border-box;
-            width: 100%;
-            padding: 20px;
-            position: absolute;
-            top: calc(60px + 1px);
-            bottom: 0;
-            overflow: auto;
-        }
-
-        /* toc entry, link to section in document */
-        .toc_link {
-            display: block;
-            padding: 5px;
-            position: relative;
-            font-weight: 600;
-            text-decoration: none;
-        }
-
-        /* toc entry when hovered or when "viewed" */
-        .toc_link:hover,
-        .toc_link[data-viewing="true"] {
-            background: #f5f5f5;
-        }
-
-        /* toc entry, level 1 indentation */
-        .toc_link[data-level="1"] {
-            margin-left: 0;
-        }
-
-        /* toc entry, level 2 indentation */
-        .toc_link[data-level="2"] {
-            margin-left: 20px;
-        }
-
-        /* toc entry, level 3 indentation */
-        .toc_link[data-level="3"] {
-            margin-left: 40px;
-        }
-
-        /* toc entry, level 4 indentation */
-        .toc_link[data-level="4"] {
-            margin-left: 60px;
-        }
-
-        /* toc entry bullets */
-        #toc_panel[data-bullets="true"] .toc_link[data-level]:before {
-            position: absolute;
-            left: -15px;
-            top: -1px;
-            font-size: 1.5em;
-        }
-
-        /* toc entry, level 2 bullet */
-        #toc_panel[data-bullets="true"] .toc_link[data-level="2"]:before {
-            content: "\2022";
-        }
-
-        /* toc entry, level 3 bullet */
-        #toc_panel[data-bullets="true"] .toc_link[data-level="3"]:before {
-            content: "\25AB";
-        }
-
-        /* toc entry, level 4 bullet */
-        #toc_panel[data-bullets="true"] .toc_link[data-level="4"]:before {
-            content: "-";
-        }
-    }
-
-    /* when on screen < 8.5in wide */
-    @media only screen and (max-width: 8.5in) {
-        /* push <body> ("page") element down to make room for toc icon */
-        .toc_body_nudge {
-            padding-top: 60px;
-        }
-
-        /* toc icon when panel closed and not hovered */
-        #toc_panel[data-open="false"]:not(:hover) {
-            background: rgba(255, 255, 255, 0.75);
-        }
-    }
-
-    /* always hide toc panel on print */
-    @media only print {
-        #toc_panel {
-            display: none;
-        }
-    }
-
-    /* -------------------------------------------------- */
-    /* lightbox plugin */
-    /* -------------------------------------------------- */
-
-    @media only screen {
-        /* regular <img> in document when hovered */
-        img.lightbox_document_img:hover {
-            cursor: pointer;
-        }
-
-        .body_no_scroll {
-            overflow: hidden !important;
-        }
-
-        /* screen overlay */
-        #lightbox_overlay {
-            display: flex;
-            flex-direction: column;
-            position: fixed;
-            left: 0;
-            top: 0;
-            right: 0;
-            bottom: 0;
-            background: rgba(0, 0, 0, 0.75);
-            z-index: 3;
-        }
-
-        /* middle area containing lightbox image */
-        #lightbox_image_container {
-            flex-grow: 1;
-            display: flex;
-            justify-content: center;
-            align-items: center;
-            overflow: hidden;
-            position: relative;
-            padding: 20px;
-        }
-
-        /* bottom area containing caption */
-        #lightbox_bottom_container {
-            display: flex;
-            justify-content: center;
-            align-items: center;
-            height: 100px;
-            min-height: 100px;
-            max-height: 100px;
-            background: rgba(0, 0, 0, 0.5);
-        }
-
-        /* image number info text box */
-        #lightbox_number_info {
-            position: absolute;
-            color: #ffffff;
-            font-weight: 600;
-            left: 2px;
-            top: 0;
-            z-index: 4;
-        }
-
-        /* zoom info text box */
-        #lightbox_zoom_info {
-            position: absolute;
-            color: #ffffff;
-            font-weight: 600;
-            right: 2px;
-            top: 0;
-            z-index: 4;
-        }
-
-        /* copy of image caption */
-        #lightbox_caption {
-            box-sizing: border-box;
-            display: inline-block;
-            width: 100%;
-            max-height: 100%;
-            padding: 10px 0;
-            text-align: center;
-            overflow-y: auto;
-            color: #ffffff;
-        }
-
-        /* navigation previous/next button */
-        .lightbox_button {
-            width: 100px;
-            height: 100%;
-            min-width: 100px;
-            min-height: 100%;
-            color: #ffffff;
-        }
-
-        /* navigation previous/next button when hovered */
-        .lightbox_button:hover {
-            background: none !important;
-        }
-
-        /* navigation button icon */
-        .lightbox_button > svg {
-            height: 25px;
-        }
-
-        /* figure auto-number */
-        #lightbox_caption > span:first-of-type {
-            font-weight: bold;
-            margin-right: 5px;
-        }
-
-        /* lightbox image when hovered */
-        #lightbox_img:hover {
-            cursor: grab;
-        }
-
-        /* lightbox image when grabbed */
-        #lightbox_img:active {
-            cursor: grabbing;
-        }
-    }
-
-    /* when on screen < 480px wide */
-    @media only screen and (max-width: 480px) {
-        /* make navigation buttons skinnier on small screens to make more room for caption text */
-        .lightbox_button {
-            width: 50px;
-            min-width: 50px;
-        }
-    }
-
-    /* always hide lightbox on print */
-    @media only print {
-        #lightbox_overlay {
-            display: none;
-        }
-    }
-
-    /* -------------------------------------------------- */
-    /* hypothesis (annotations) plugin */
-    /* -------------------------------------------------- */
-
-    /* hypothesis activation button */
-    #hypothesis_button {
-        box-sizing: border-box;
-        position: fixed;
-        top: 0;
-        right: 0;
-        width: 60px;
-        height: 60px;
-        background: #ffffff;
-        border-radius: 0;
-        border-left: solid 1px #bdbdbd;
-        border-bottom: solid 1px #bdbdbd;
-        box-shadow: 0 0 20px rgba(0, 0, 0, 0.05);
-        z-index: 2;
-    }
-
-    /* hypothesis button svg */
-    #hypothesis_button > svg {
-        position: relative;
-        top: -4px;
-    }
-
-    /* hypothesis annotation count */
-    #hypothesis_count {
-        position: absolute;
-        left: 0;
-        right: 0;
-        bottom: 5px;
-    }
-
-    /* side panel */
-    .annotator-frame {
-        width: 280px !important;
-    }
-
-    /* match highlight color to rest of theme */
-    .annotator-highlights-always-on .annotator-hl {
-        background-color: #ffeb3b !important;
-    }
-
-    /* match focused color to rest of theme */
-    .annotator-hl.annotator-hl-focused {
-        background-color: #ff8a65 !important;
-    }
-
-    /* match bucket bar color to rest of theme */
-    .annotator-bucket-bar {
-        background: #f5f5f5 !important;
-    }
-
-    /* always hide button, toolbar, and tooltip on print */
-    @media only print {
-        #hypothesis_button {
-            display: none;
-        }
-
-        .annotator-frame {
-            display: none !important;
-        }
-
-        hypothesis-adder {
-            display: none !important;
-        }
+    /* table in wrapper */
+    .tablenos table,
+    .tablenos table * {
+      /* don't break table words */
+      overflow-wrap: normal !important;
     }
+  }
 </style>

From 52ab9dc8bba4d0c6cee348fa9d7b0b764a89ffcf Mon Sep 17 00:00:00 2001
From: Vincent Rubinetti <vince.rubinetti@gmail.com>
Date: Fri, 12 Feb 2021 10:49:07 -0500
Subject: [PATCH 21/50] Update scite plugin

merges https://github.com/manubot/rootstock/pull/415
---
 build/plugins/scite.html | 17 +++++++++--------
 1 file changed, 9 insertions(+), 8 deletions(-)

diff --git a/build/plugins/scite.html b/build/plugins/scite.html
index d01fe51..4d62049 100644
--- a/build/plugins/scite.html
+++ b/build/plugins/scite.html
@@ -5,11 +5,6 @@
   See https://scite.ai/.
 -->
 
-<link
-  rel="stylesheet"
-  type="text/css"
-  href="https://cdn.scite.ai/badge/scite-badge-latest.min.css"
-/>
 <script
   async
   type="application/javascript"
@@ -19,13 +14,13 @@
 <script>
   // start script
   function start() {
+    // if printing, exit and don't run badges
+    if (window.matchMedia("print").matches) return;
+
     // get citation elements
     const query = ".references div[id*='ref-']";
     const elements = document.querySelectorAll(query);
     for (const element of elements) addBadge(element);
-
-    // attach scroll listener to window
-    window.addEventListener("scroll", onScroll);
   }
 
   // add badge in citation element
@@ -58,4 +53,10 @@
     text-indent: 0;
     margin-top: 10px;
   }
+
+  @media print {
+    .scite-badge {
+      display: none;
+    }
+  }
 </style>

From f09ce13278540620afe5a67840ef23284d4d83f9 Mon Sep 17 00:00:00 2001
From: nfry321 <58332182+nfry321@users.noreply.github.com>
Date: Sun, 21 Mar 2021 12:55:32 +0000
Subject: [PATCH 22/50] setup.bash: interactive script to guide setup

merges https://github.com/manubot/rootstock/pull/417
closes https://github.com/manubot/rootstock/issues/401
---
 SETUP.md   |  30 ++++++-
 setup.bash | 230 +++++++++++++++++++++++++++++++++++++++++++++++++++++
 2 files changed, 258 insertions(+), 2 deletions(-)
 create mode 100755 setup.bash

diff --git a/SETUP.md b/SETUP.md
index fa83e0b..cacd6a7 100644
--- a/SETUP.md
+++ b/SETUP.md
@@ -1,7 +1,8 @@
 # Table of contents
 
 - [Creating a new manuscript](#creating-a-new-manuscript)
-  * [Configuration](#configuration)
+  * [Using setup script](#using-setup-script)
+  * [Manual configuration](#manual-configuration)
   * [Create repository](#create-repository)
   * [Continuous integration](#continuous-integration)
     + [GitHub Actions](#github-actions)
@@ -27,8 +28,33 @@ These steps should be performed in a command-line shell (terminal), starting in
 Setup is supported on Linux, macOS, and Windows.
 Windows setup requires [Git Bash](https://gitforwindows.org/) or [Windows Subsystem for Linux](https://docs.microsoft.com/en-us/windows/wsl/faq).
 
-## Configuration
+## Using setup script
+Creating a new manuscript using GitHub actions, the recommended default CI service (see below), can be achieved easily using the [setup script](https://github.com/manubot/rootstock/blob/main/setup.bash).
+This simply runs the steps detailed below in the manual configuration.
 
+Use the command below to copy `setup.bash` and run it.
+You can check the code that will be executed [here](https://github.com/manubot/rootstock/blob/main/setup.bash).
+
+````sh
+bash <( curl --location https://github.com/manubot/rootstock/raw/main/setup.bash )
+````
+The script will then take you through the process of cloning the rootstock repo, make the changes required to use GitHub actions, edit the README to point to your repo and commit the changes.
+Your new manuscript repo is then ready for you to start adding your own content.
+
+This script does not not create the remote repo for you, so you will be prompted to manually create an empty GitHub repository at <https://github.com/new>.
+Do not initialize the repository, other than optionally adding a description.
+
+### CLI
+There is also a command line interface for users who want to create manuscripts at scale and in an automated way.
+See the help for details.
+
+````sh
+bash setup.bash --help
+````
+
+## Manual configuration
+
+If you do not wish to use the above setup script to configure your new manuscript repository, you can instead execute the steps manually.
 First, you must configure two environment variables (`OWNER` and `REPO`).
 These variables specify the GitHub repository for the manuscript (i.e. `https://github.com/OWNER/REPO`).
 Make sure that the case of `OWNER` matches how your username is displayed on GitHub.
diff --git a/setup.bash b/setup.bash
new file mode 100755
index 0000000..3d45a08
--- /dev/null
+++ b/setup.bash
@@ -0,0 +1,230 @@
+#!/bin/bash
+# Setup Manubot
+# Based on https://github.com/manubot/rootstock/blob/main/SETUP.md
+# This is designed to be run from the bash terminal
+
+# Stop on first error.
+set -e
+
+usage() {
+echo "Usage: $0 [--owner text] [--repo text] [--yes]"
+echo "Guides the user through the creation of a new Manubot repository for their manuscript."
+echo
+echo "If no options are supplied a fully interactive process is used."
+echo "OWNER and REPO refer to the details of your manuscript repo location:"
+echo "i.e. https://github.com/OWNER/REPO."
+echo
+echo "Options:"
+echo "  -o --owner   GitHub user or organisation name."
+echo "  -r --repo    Name of the repository for your new manuscript."
+echo "  -y --yes     Non-interactive mode. Continue script without asking for confirmation that the repo exists."
+echo "  -s --ssh     Use SSH to authenticate GitHub account. HTTPS is used by default."
+echo "               Option only effective if --yes is also set, otherwise answer given in user interaction takes precedence."
+echo "  -h --help    Display usage information."
+1>&2; exit 1; }
+
+# Check if to continue
+check(){
+while true
+do
+ echo "Once you have created your repo press enter to continue setup,"
+ read -r -p "or type exit to quit now: " input
+
+ case $input in
+   "")
+     echo
+     echo "Continuing Setup..."
+     echo
+     break
+     ;;
+  [eE][xX][iI][tT])
+     exit 1
+     ;;
+  *)
+     echo
+     echo "Invalid input, try again..."
+     echo
+     ;;
+ esac
+done
+}
+
+# Option strings
+SHORT=o:r:hys
+LONG=owner:,repo:,help,yes,ssh
+
+YES=0  # continue when prompted
+AUTH=0 # used https or ssh auth
+
+# read the options
+OPTS=$(getopt --options $SHORT --long $LONG --name "$0" -- "$@")
+
+if [ $? != 0 ] ; then echo "Failed to parse options...exiting." >&2 ; exit 1 ; fi
+
+eval set -- "$OPTS"
+
+# extract options and their arguments into variables.
+while true ; do
+  case "$1" in
+    -o | --owner )
+      shift;
+      OWNER=$1
+      shift
+      ;;
+    -r | --repo )
+      REPO="$2"
+      shift 2
+      ;;
+    -y | --yes )
+      YES=1
+      shift
+      ;;
+    -s | --ssh )
+      AUTH=1;
+      shift
+      ;;
+    -- )
+      shift
+      break
+      ;;
+    -h | --help )
+      shift
+      usage
+      exit 1
+      ;;
+    *)
+      echo "Internal error!"
+      exit 1
+      ;;
+  esac
+done
+
+if [ -z "${OWNER}" ] || [ -z "${REPO}" ]; then
+  echo "This script will take you through the setup process for Manubot."
+  echo "First, we need to specify where to create the GitHub repo for your manuscript."
+  echo
+  echo "The URL will take this format: https://github.com/OWNER/REPO."
+  echo "OWNER is your username or organisation"
+  echo "REPO is the name of your repository"
+  echo
+  read -r -p "Type in the OWNER now:" input
+  OWNER=$input
+  read -r -p "Type in the REPO now:" input
+  REPO=$input
+fi
+
+# If using interactive mode, check remote repo exists.
+if [[ "$YES" == '0' ]]; then
+  while true
+  do
+   echo
+   read -r -p "Have you manually created https://github.com/${OWNER}/${REPO}? [y/n] " input
+
+   case $input in
+     [yY][eE][sS]|[yY])
+
+       echo
+       echo "Continuing Setup..."
+       echo
+       break
+       ;;
+    [nN][oO]|[nN])
+       echo
+       echo "Go to https://github.com/new and create https://github.com/${OWNER}/${REPO}"
+       echo "Note: the new repo must be completely empty or the script will fail."
+       echo
+       check
+       break
+       ;;
+    *)
+       echo
+       echo "Invalid input, try again..."
+       echo
+       ;;
+   esac
+  done
+else
+  echo "Setting up https://github.com/${OWNER}/${REPO}"
+fi
+
+# Clone manubot/rootstock
+echo
+echo "Cloning Rootstock..."
+echo
+git clone --single-branch https://github.com/manubot/rootstock.git ${REPO}
+cd ${REPO}
+
+echo
+echo "Setup tracking of remote..."
+
+# Configure remotes
+git remote add rootstock https://github.com/manubot/rootstock.git
+
+# Check auth method
+if [[ "$YES" == '0' ]]; then
+  while true
+  do
+   echo
+   read -r -p "Would you like to use SSH to authenticate your GitHub account? [y/n] " input
+
+   case $input in
+     [yY][eE][sS]|[yY])
+       AUTH=1
+       break
+       ;;
+    [nN][oO]|[nN])
+       AUTH=0
+       break
+       ;;
+    *)
+       echo
+       echo "Invalid input, try again..."
+       echo
+       ;;
+   esac
+  done
+fi
+
+case $AUTH in
+  0)
+  echo
+  echo "Seting origin URL using its https web address"
+  echo
+  git remote set-url origin https://github.com/${OWNER}/${REPO}.git
+  ;;
+  1)
+  echo
+  echo "Seting origin URL using SSH"
+  echo
+  git remote set-url origin git@github.com:$OWNER/$REPO.git
+  ;;
+esac
+
+git push --set-upstream origin main
+
+# To use GitHub Actions only:
+echo "Setup for GitHub Actions ONLY..."
+# remove Travis CI config
+git rm .travis.yml
+# remove AppVeyor config
+git rm .appveyor.yml
+# remove ci/install.sh if using neither Travis CI nor AppVeyor
+git rm ci/install.sh
+
+# Update README
+echo "Updating README..."
+# Perform substitutions
+sed "s/manubot\/rootstock/${OWNER}\/${REPO}/g" README.md > tmp && mv -f tmp README.md
+sed "s/manubot\.github\.io\/rootstock/${OWNER}\.github\.io\/${REPO}/g" README.md > tmp && mv -f tmp README.md
+
+echo "Committing rebrand..."
+git add --update
+git commit --message "Brand repo to $OWNER/$REPO"
+git push origin main
+echo
+echo "Setup complete"
+echo
+echo "The new repo has been created at $(pwd)"
+echo
+echo "A good first step is to modify content/metadata.yaml with the relevant information for your manuscript."
+echo

From 99776841cd694c1c612060114ecc0f3e5f686e5f Mon Sep 17 00:00:00 2001
From: Tiago Lubiana <tiago.lubiana.alves@usp.br>
Date: Sat, 15 May 2021 17:23:42 -0300
Subject: [PATCH 23/50] Add "gh repo create" to SETUP.md

merges https://github.com/manubot/rootstock/pull/419
closes https://github.com/manubot/rootstock/issues/418

Co-authored-by: Daniel Himmelstein <daniel.himmelstein@gmail.com>
Co-authored-by: Anthony Gitter <agitter@users.noreply.github.com>
---
 SETUP.md | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/SETUP.md b/SETUP.md
index cacd6a7..33ccbf2 100644
--- a/SETUP.md
+++ b/SETUP.md
@@ -89,7 +89,8 @@ git remote set-url origin https://github.com/$OWNER/$REPO.git
 git remote set-url origin git@github.com:$OWNER/$REPO.git
 ```
 
-Next, you must manually create an empty GitHub repository at <https://github.com/new>.
+Then create an empty repository on GitHub. 
+You can do this at <https://github.com/new> or via the [GitHub command line interface](https://github.com/cli/cli) (if installed) with `gh repo create`.
 Make sure to use the same "Owner" and "Repository name" specified above.
 Do not initialize the repository, other than optionally adding a Description.
 Next, push your cloned manuscript:

From 95bf5b230344996762e383bb37c0198b18d9c38e Mon Sep 17 00:00:00 2001
From: Daniel Himmelstein <daniel.himmelstein@gmail.com>
Date: Sat, 29 May 2021 17:30:35 -0400
Subject: [PATCH 24/50] BUILD_LATEX for basic LaTeX manuscript

merges https://github.com/manubot/rootstock/pull/384
refs https://github.com/manubot/rootstock/issues/249
---
 build/build.sh                   | 9 +++++++++
 build/pandoc/defaults/latex.yaml | 4 ++++
 2 files changed, 13 insertions(+)
 create mode 100644 build/pandoc/defaults/latex.yaml

diff --git a/build/build.sh b/build/build.sh
index 9d0b4e0..5cebfc5 100755
--- a/build/build.sh
+++ b/build/build.sh
@@ -85,6 +85,15 @@ if [ "${BUILD_DOCX:-}" = "true" ]; then
     --defaults=docx.yaml
 fi
 
+# Create LaTeX output (if BUILD_LATEX environment variable equals "true")
+if [ "${BUILD_LATEX:-}" = "true" ]; then
+  echo >&2 "Exporting LaTeX manuscript"
+  pandoc \
+    --data-dir="$PANDOC_DATA_DIR" \
+    --defaults=common.yaml \
+    --defaults=latex.yaml
+fi
+
 # Spellcheck
 if [ "${SPELLCHECK:-}" = "true" ]; then
   export ASPELL_CONF="add-extra-dicts $(pwd)/build/assets/custom-dictionary.txt; ignore-case true"
diff --git a/build/pandoc/defaults/latex.yaml b/build/pandoc/defaults/latex.yaml
new file mode 100644
index 0000000..481302d
--- /dev/null
+++ b/build/pandoc/defaults/latex.yaml
@@ -0,0 +1,4 @@
+# Pandoc --defaults for LaTeX output.
+# Load on top of common defaults.
+to: latex
+output-file: output/manuscript.tex

From defe787b0ad8a21a745cc82c3117770896caaf8b Mon Sep 17 00:00:00 2001
From: Vincent Rubinetti <vince.rubinetti@gmail.com>
Date: Thu, 10 Jun 2021 19:18:11 -0400
Subject: [PATCH 25/50] Pandoc 2.14: update HTML plugins, CSL style, citekey
 syntax

merges https://github.com/manubot/rootstock/pull/427

Co-authored-by: Daniel Himmelstein <daniel.himmelstein@gmail.com>
Co-authored-by: Anthony Gitter <agitter@users.noreply.github.com>
---
 USAGE.md                          | 25 +++++++++++++++++--------
 build/assets/style.csl            |  2 +-
 build/environment.yml             | 16 ++++++++--------
 build/pandoc/defaults/common.yaml |  2 +-
 build/pandoc/defaults/html.yaml   |  1 +
 build/plugins/anchors.html        |  3 ++-
 build/plugins/jump-to-first.html  | 10 ++++++----
 build/plugins/tooltips.html       |  8 ++++----
 build/themes/default.html         | 13 ++++++++++---
 content/02.delete-me.md           |  2 +-
 10 files changed, 51 insertions(+), 31 deletions(-)

diff --git a/USAGE.md b/USAGE.md
index 5bd004a..0b2ee47 100644
--- a/USAGE.md
+++ b/USAGE.md
@@ -133,14 +133,23 @@ Note that multiple citations must be semicolon separated.
 Be careful not to cite the same study using identifiers from multiple sources.
 For example, the following citations all refer to the same study, but will be treated as separate references: `[@doi:10.7717/peerj.705; @pmc:PMC4304851; @pubmed:25648772]`.
 
-Citation keys must adhere to the syntax described in the [Pandoc manual](https://pandoc.org/MANUAL.html#citations):
-
-> The citation key must begin with a letter, digit, or `_`, and may contain alphanumerics, `_`, and internal punctuation characters (`:.#$%&-+?<>~/`).
-
-To evaluate whether a citation key fully matches this syntax, try [this online regex](https://regex101.com/r/mXZyY2/latest).
-If the citation key is not valid, use the [citation aliases](#citation-aliases) workaround below.
-This is required for citation keys that contain forbidden characters such as `;` or `=` or end with a non-alphanumeric character such as `/`.
-<!-- See [jgm/pandoc#6026](https://github.com/jgm/pandoc/issues/6026) for progress on a more flexible Markdown citation key syntax. -->
+The citation key syntax is described in the [Pandoc manual](https://pandoc.org/MANUAL.html#citation-syntax):
+
+> Unless a citation key start with a letter, digit, or `_`,
+> and contains only alphanumerics and internal punctuation characters (`:.#$%&-+?<>~/`),
+> it must be surrounded by curly braces,
+> which are not considered part of the key.
+> In `@Foo_bar.baz.`, the key is `Foo_bar.baz`.
+> The final period is not *internal* punctuation,
+> so it is not included in the key.
+> In `@{Foo_bar.baz.}`, the key is `Foo_bar.baz.`, including the final period.
+> The curly braces are recommended if you use URLs as keys:
+> `[@{https://example.com/bib?name=foobar&date=2000}, p. 33]`.
+
+If a citation key does not fully match [this online regex](https://regex101.com/r/mXZyY2/latest)
+(for example, contains characters such as `;` or `=` or end with a non-alphanumeric character such as `/`),
+make sure to surround it with curly braces or use the [citation aliases](#citation-aliases) workaround below.
+<!-- See [jgm/pandoc#6026](https://github.com/jgm/pandoc/issues/6026) on the curly-brace syntax for Markdown citation keys, which was introduced in Pandoc 2.14. -->
 
 Prior to Rootstock commit [`6636b91`](https://github.com/manubot/rootstock/commit/6636b912c6b41593acd2041d34cd4158c1b317fb) on 2020-01-14, Manubot processed citations separately from Pandoc.
 Switching to a Pandoc filter improved reliability on complex documents, but restricted the syntax of citation keys slightly.
diff --git a/build/assets/style.csl b/build/assets/style.csl
index 942a043..b836f7b 100644
--- a/build/assets/style.csl
+++ b/build/assets/style.csl
@@ -47,7 +47,7 @@
       <text variable="citation-number"/>
     </layout>
   </citation>
-  <bibliography hanging-indent="true" second-field-align="flush">
+  <bibliography second-field-align="flush">
     <layout>
       <text variable="citation-number" suffix=". "/>
       <group delimiter=" ">
diff --git a/build/environment.yml b/build/environment.yml
index abee7fb..40abf49 100644
--- a/build/environment.yml
+++ b/build/environment.yml
@@ -5,11 +5,10 @@ dependencies:
   - cairo=1.14.12
   - cairocffi=0.8.0
   - cffi=1.12.3
-  - ghp-import=0.5.5
+  - ghp-import=1.0.0
   - jinja2=2.11.2
   - jsonschema=3.2.0
-  - pandoc=2.9.2
-  - panflute=1.12.5
+  - pandoc=2.14
   - pango=1.40.14
   - pip=20.2
   - psutil=5.7.3
@@ -21,14 +20,15 @@ dependencies:
   - yamllint=1.25.0
   - pip:
     - errorhandler==2.0.1
-    - git+https://github.com/manubot/manubot@553090a16ac24a9fdc3f8df241a91b790c140865
+    - git+https://github.com/manubot/manubot@2c028a7a87be24a76e2dec3ac7db6e8754ae6d4a
     - isbnlib==3.10.3
     - opentimestamps-client==0.7.0
     - opentimestamps==0.4.1
-    - pandoc-eqnos==2.3.0
-    - pandoc-fignos==2.3.1
-    - pandoc-tablenos==2.2.2
-    - pandoc-xnos==2.4.3
+    - pandoc-eqnos==2.5.0
+    - pandoc-fignos==2.4.0
+    - pandoc-tablenos==2.3.0
+    - pandoc-xnos==2.5.0
+    - panflute==2.1.0
     - pybase62==0.4.3
     - pysha3==1.0.2
     - python-bitcoinlib==0.10.2
diff --git a/build/pandoc/defaults/common.yaml b/build/pandoc/defaults/common.yaml
index 12c0c34..bfa5d97 100644
--- a/build/pandoc/defaults/common.yaml
+++ b/build/pandoc/defaults/common.yaml
@@ -6,7 +6,7 @@ filters:
 - pandoc-eqnos
 - pandoc-tablenos
 - pandoc-manubot-cite
-- pandoc-citeproc
+- citeproc
 wrap: preserve
 metadata:
   csl: build/assets/style.csl
diff --git a/build/pandoc/defaults/html.yaml b/build/pandoc/defaults/html.yaml
index 50d2981..8aff336 100644
--- a/build/pandoc/defaults/html.yaml
+++ b/build/pandoc/defaults/html.yaml
@@ -25,6 +25,7 @@ include-after-body:
 - build/plugins/mathjax.html
 #- build/plugins/scite.html
 variables:
+  document-css: false
   math: ""
 html-math-method:
   method: mathjax
diff --git a/build/plugins/anchors.html b/build/plugins/anchors.html
index 68f1225..7149501 100644
--- a/build/plugins/anchors.html
+++ b/build/plugins/anchors.html
@@ -10,7 +10,8 @@
 <script type="module">
   // which types of elements to add anchors next to, in "document.querySelector"
   // format
-  const typesQuery = 'h1, h2, h3, [id^="fig:"], [id^="tbl:"], [id^="eq:"]';
+  const typesQuery =
+    'h1, h2, h3, div[id^="fig:"], div[id^="tbl:"], span[id^="eq:"]';
 
   // start script
   function start() {
diff --git a/build/plugins/jump-to-first.html b/build/plugins/jump-to-first.html
index d205093..da7df4a 100644
--- a/build/plugins/jump-to-first.html
+++ b/build/plugins/jump-to-first.html
@@ -15,9 +15,11 @@
 
   // start script
   function start() {
-    if (references !== "false") makeButtons("ref-", "p", "reference");
-    if (figures !== "false") makeButtons("fig:", "figcaption", "figure");
-    if (tables !== "false") makeButtons("tbl:", "caption", "table");
+    if (references !== "false")
+      makeButtons(`div[id^="ref-"]`, ".csl-left-margin", "reference");
+    if (figures !== "false")
+      makeButtons(`div[id^="fig:"]`, "figcaption", "figure");
+    if (tables !== "false") makeButtons(`div[id^="tbl:"]`, "caption", "table");
   }
 
   // when jump button clicked
@@ -45,7 +47,7 @@
 
   // add button next to each reference entry, figure, or table
   function makeButtons(query, containerQuery, subject) {
-    const elements = document.querySelectorAll(`[id^="${query}"`);
+    const elements = document.querySelectorAll(query);
     for (const element of elements) {
       const id = element.id;
       const buttonContainer = element.querySelector(containerQuery);
diff --git a/build/plugins/tooltips.html b/build/plugins/tooltips.html
index b6fc505..e023e3a 100644
--- a/build/plugins/tooltips.html
+++ b/build/plugins/tooltips.html
@@ -230,6 +230,7 @@
       "data-selected",
       "data-highlighted",
       "data-glow",
+      "class",
     ];
     for (const attribute of attributes) {
       sourceCopy.removeAttribute(attribute);
@@ -290,9 +291,8 @@
     prevButton.classList.add("icon_button");
     nextButton.classList.add("icon_button");
     prevButton.innerHTML = document.querySelector(".icon_caret_left").innerHTML;
-    nextButton.innerHTML = document.querySelector(
-      ".icon_caret_right"
-    ).innerHTML;
+    nextButton.innerHTML =
+      document.querySelector(".icon_caret_right").innerHTML;
     navBar.appendChild(prevButton);
     navBar.appendChild(document.createTextNode(text));
     navBar.appendChild(nextButton);
@@ -336,7 +336,7 @@
     if (!target) return;
 
     // if ref or figure, modify target to get expected element
-    if (id.indexOf("ref-") === 0) target = target.querySelector("p");
+    if (id.indexOf("ref-") === 0) target = target.querySelector(":nth-child(2)");
     else if (id.indexOf("fig:") === 0) target = target.querySelector("figure");
 
     return target;
diff --git a/build/themes/default.html b/build/themes/default.html
index 2396cc4..b3298fe 100644
--- a/build/themes/default.html
+++ b/build/themes/default.html
@@ -267,8 +267,7 @@
   }
 
   /* table auto-number */
-  table > caption > span:first-of-type,
-  div.table_wrapper > table > caption > span:first-of-type {
+  table > caption > span:first-of-type {
     font-weight: bold;
     margin-right: 5px;
   }
@@ -495,6 +494,15 @@
     top: 0.125em;
   }
 
+  /* -------------------------------------------------- */
+  /* references */
+  /* -------------------------------------------------- */
+
+  .csl-entry {
+    margin-top: 15px;
+    margin-bottom: 15px;
+  }
+
   /* -------------------------------------------------- */
   /* print control */
   /* -------------------------------------------------- */
@@ -626,7 +634,6 @@
 
   /* tablenos wrapper */
   .tablenos {
-    /* show scrollbar on tables if necessary to prevent overflow */
     width: 100%;
     margin: 20px 0;
   }
diff --git a/content/02.delete-me.md b/content/02.delete-me.md
index c2b1fd0..387c467 100644
--- a/content/02.delete-me.md
+++ b/content/02.delete-me.md
@@ -107,7 +107,7 @@ Citation by Wikidata ID [@wikidata:Q56458321].
 
 Citation by ISBN [@isbn:9780262517638].
 
-Citation by URL [@https://greenelab.github.io/meta-review/].
+Citation by URL [@{https://greenelab.github.io/meta-review/}].
 
 Citation by alias [@deep-review].
 

From 09776607f7007d20f97a773a6da30f56b0f554b1 Mon Sep 17 00:00:00 2001
From: Daniel Himmelstein <daniel.himmelstein@gmail.com>
Date: Thu, 26 Aug 2021 14:01:06 -0400
Subject: [PATCH 26/50] GitHub Actions workflow_dispatch

merges https://github.com/manubot/rootstock/pull/436

* allows ad-hoc builds of main that can set BUILD_DOCX=true
* upgrade manubot to fix GitHub Actions URLs
* build.sh: set variable defaults and lowercase
---
 .github/workflows/manubot.yaml | 17 +++++++++++++++++
 build/build.sh                 | 27 +++++++++++++++++----------
 build/environment.yml          |  2 +-
 3 files changed, 35 insertions(+), 11 deletions(-)

diff --git a/.github/workflows/manubot.yaml b/.github/workflows/manubot.yaml
index 9a7d576..3d390d6 100644
--- a/.github/workflows/manubot.yaml
+++ b/.github/workflows/manubot.yaml
@@ -8,6 +8,17 @@ on:
     branches:
       - main
       - master
+  workflow_dispatch:
+    inputs:
+      BUILD_PDF:
+        description: generate PDF output (true or false)
+        default: "true"
+      BUILD_DOCX:
+        description: generate DOCX output (true or false)
+        default: "false"
+      BUILD_LATEX:
+        description: generate LaTeX output (true or false)
+        default: "false"
 jobs:
   manubot:
     name: Manubot
@@ -21,6 +32,12 @@ jobs:
         with:
           # fetch entire commit history to support get_rootstock_commit
           fetch-depth: 0
+      - name: Set Environment Variables (Workflow Dispatch)
+        if: github.event_name == 'workflow_dispatch'
+        run: |
+          echo "BUILD_PDF=${{ github.event.inputs.BUILD_PDF }}" >> $GITHUB_ENV
+          echo "BUILD_DOCX=${{ github.event.inputs.BUILD_DOCX }}" >> $GITHUB_ENV
+          echo "BUILD_LATEX=${{ github.event.inputs.BUILD_LATEX }}" >> $GITHUB_ENV
       - name: Set Environment Variables
         run: |
           TRIGGERING_SHA=${GITHUB_PULL_REQUEST_SHA:-$GITHUB_SHA}
diff --git a/build/build.sh b/build/build.sh
index 5cebfc5..778c958 100755
--- a/build/build.sh
+++ b/build/build.sh
@@ -11,6 +11,16 @@ export TZ=Etc/UTC
 # Default Python to read/write text files using UTF-8 encoding
 export LC_ALL=en_US.UTF-8
 
+# Set option defaults
+CI="${CI:-false}"
+BUILD_PDF="${BUILD_PDF:-true}"
+BUILD_DOCX="${BUILD_DOCX:-false}"
+BUILD_LATEX="${BUILD_LATEX:-false}"
+SPELLCHECK="${SPELLCHECK:-false}"
+# Pandoc's configuration is specified via files of option defaults
+# located in the $PANDOC_DATA_DIR/defaults directory.
+PANDOC_DATA_DIR="${PANDOC_DATA_DIR:-build/pandoc}"
+
 # Generate reference information
 echo >&2 "Retrieving and processing reference metadata"
 manubot process \
@@ -20,10 +30,6 @@ manubot process \
   --skip-citations \
   --log-level=INFO
 
-# Pandoc's configuration is specified via files of option defaults
-# located in the $PANDOC_DATA_DIR/defaults directory.
-PANDOC_DATA_DIR="${PANDOC_DATA_DIR:-build/pandoc}"
-
 # Make output directory
 mkdir -p output
 
@@ -39,8 +45,9 @@ pandoc --verbose \
 DOCKER_RUNNING="$(docker info &> /dev/null && echo "yes" || true)"
 
 # Create PDF output (unless BUILD_PDF environment variable equals "false")
+# The double-commas (,,) lowercase the variable.
 # If Docker is not available, use WeasyPrint to create PDF
-if [ "${BUILD_PDF:-}" != "false" ] && [ -z "$DOCKER_RUNNING" ]; then
+if [ "${BUILD_PDF,,}" != "false" ] && [ -z "$DOCKER_RUNNING" ]; then
   echo >&2 "Exporting PDF manuscript using WeasyPrint"
   if [ -L images ]; then rm images; fi  # if images is a symlink, remove it
   ln -s content/images
@@ -53,9 +60,9 @@ if [ "${BUILD_PDF:-}" != "false" ] && [ -z "$DOCKER_RUNNING" ]; then
 fi
 
 # If Docker is available, use athenapdf to create PDF
-if [ "${BUILD_PDF:-}" != "false" ] && [ -n "$DOCKER_RUNNING" ]; then
+if [ "${BUILD_PDF,,}" != "false" ] && [ -n "$DOCKER_RUNNING" ]; then
   echo >&2 "Exporting PDF manuscript using Docker + Athena"
-  if [ "${CI:-}" = "true" ]; then
+  if [ "${CI,,}" = "true" ]; then
     # Incease --delay for CI builds to ensure the webpage fully renders, even when the CI server is under high load.
     # Local builds default to a shorter --delay to minimize runtime, assuming proper rendering is less crucial.
     MANUBOT_ATHENAPDF_DELAY="${MANUBOT_ATHENAPDF_DELAY:-5000}"
@@ -77,7 +84,7 @@ if [ "${BUILD_PDF:-}" != "false" ] && [ -n "$DOCKER_RUNNING" ]; then
 fi
 
 # Create DOCX output (if BUILD_DOCX environment variable equals "true")
-if [ "${BUILD_DOCX:-}" = "true" ]; then
+if [ "${BUILD_DOCX,,}" = "true" ]; then
   echo >&2 "Exporting Word Docx manuscript"
   pandoc --verbose \
     --data-dir="$PANDOC_DATA_DIR" \
@@ -86,7 +93,7 @@ if [ "${BUILD_DOCX:-}" = "true" ]; then
 fi
 
 # Create LaTeX output (if BUILD_LATEX environment variable equals "true")
-if [ "${BUILD_LATEX:-}" = "true" ]; then
+if [ "${BUILD_LATEX,,}" = "true" ]; then
   echo >&2 "Exporting LaTeX manuscript"
   pandoc \
     --data-dir="$PANDOC_DATA_DIR" \
@@ -95,7 +102,7 @@ if [ "${BUILD_LATEX:-}" = "true" ]; then
 fi
 
 # Spellcheck
-if [ "${SPELLCHECK:-}" = "true" ]; then
+if [ "${SPELLCHECK,,}" = "true" ]; then
   export ASPELL_CONF="add-extra-dicts $(pwd)/build/assets/custom-dictionary.txt; ignore-case true"
 
   # Identify and store spelling errors
diff --git a/build/environment.yml b/build/environment.yml
index 40abf49..8cac427 100644
--- a/build/environment.yml
+++ b/build/environment.yml
@@ -20,7 +20,7 @@ dependencies:
   - yamllint=1.25.0
   - pip:
     - errorhandler==2.0.1
-    - git+https://github.com/manubot/manubot@2c028a7a87be24a76e2dec3ac7db6e8754ae6d4a
+    - git+https://github.com/manubot/manubot@2fc85b57be896c6262398f343b550197127c0ccb
     - isbnlib==3.10.3
     - opentimestamps-client==0.7.0
     - opentimestamps==0.4.1

From 03427bf38582356e4f0951cb0917c4486c30c261 Mon Sep 17 00:00:00 2001
From: Daniel Himmelstein <daniel.himmelstein@gmail.com>
Date: Thu, 26 Aug 2021 15:15:39 -0400
Subject: [PATCH 27/50] GitHub Actions: fix CI_JOB_WEB_URL

---
 .github/workflows/manubot.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/manubot.yaml b/.github/workflows/manubot.yaml
index 3d390d6..c196f95 100644
--- a/.github/workflows/manubot.yaml
+++ b/.github/workflows/manubot.yaml
@@ -81,6 +81,6 @@ jobs:
           MANUBOT_ACCESS_TOKEN: ${{ secrets.GITHUB_TOKEN }}
           MANUBOT_SSH_PRIVATE_KEY: ${{ secrets.MANUBOT_SSH_PRIVATE_KEY }}
           CI_BUILD_WEB_URL: https://github.com/${{ github.repository }}/commit/${{ github.sha }}/checks
-          CI_JOB_WEB_URL: https://github.com/${{ github.repository }}/runs/${{ github.run_id }}
+          CI_JOB_WEB_URL: https://github.com/${{ github.repository }}/actions/runs/${{ github.run_id }}
         shell: bash --login {0}
         run: bash ci/deploy.sh

From d2ca9953a443537288a4eb4f8707847b6fe39336 Mon Sep 17 00:00:00 2001
From: Daniel Himmelstein <daniel.himmelstein@gmail.com>
Date: Thu, 26 Aug 2021 15:26:09 -0400
Subject: [PATCH 28/50] GitHub Actions: enable deployment on workflow_dispatch

fixes 09776607f7007d20f97a773a6da30f56b0f554b1
---
 .github/workflows/manubot.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/manubot.yaml b/.github/workflows/manubot.yaml
index c196f95..7f8a630 100644
--- a/.github/workflows/manubot.yaml
+++ b/.github/workflows/manubot.yaml
@@ -76,7 +76,7 @@ jobs:
           name: manuscript-${{ github.run_id }}-${{ env.TRIGGERING_SHA_7 }}
           path: output
       - name: Deploy Manuscript
-        if: github.ref == env.DEFAULT_BRANCH_REF && github.event_name == 'push' && !github.event.repository.fork
+        if: github.ref == env.DEFAULT_BRANCH_REF && github.event_name != 'pull_request' && !github.event.repository.fork
         env:
           MANUBOT_ACCESS_TOKEN: ${{ secrets.GITHUB_TOKEN }}
           MANUBOT_SSH_PRIVATE_KEY: ${{ secrets.MANUBOT_SSH_PRIVATE_KEY }}

From 4e8f9b1040b2456db1947fe30fc628bf48f8fb3b Mon Sep 17 00:00:00 2001
From: Vincent Rubinetti <vince.rubinetti@gmail.com>
Date: Thu, 23 Sep 2021 16:26:28 -0400
Subject: [PATCH 29/50] HTML plugins: collapse sections, prioritize attributes

merges https://github.com/manubot/rootstock/pull/438
---
 build/plugins/accordion.html  | 3 ++-
 build/plugins/attributes.html | 5 +++--
 build/plugins/hypothesis.html | 2 +-
 build/plugins/scite.html      | 2 +-
 4 files changed, 7 insertions(+), 5 deletions(-)

diff --git a/build/plugins/accordion.html b/build/plugins/accordion.html
index 98ba165..f620135 100644
--- a/build/plugins/accordion.html
+++ b/build/plugins/accordion.html
@@ -19,7 +19,8 @@
       // start expanded/collapsed based on option
       if (
         startCollapsed === "true" ||
-        (startCollapsed === "auto" && isSmallScreen())
+        (startCollapsed === "auto" && isSmallScreen()) ||
+        heading.dataset.collapsed === "true"
       )
         collapseHeading(heading);
       else expandElement(heading);
diff --git a/build/plugins/attributes.html b/build/plugins/attributes.html
index 7009782..85077da 100644
--- a/build/plugins/attributes.html
+++ b/build/plugins/attributes.html
@@ -79,6 +79,7 @@
     }
   }
 
-  // start script when document is finished loading
-  window.addEventListener("load", start);
+  // start script on DOMContentLoaded instead of load to ensure this plugins
+  // runs before other plugins
+  window.addEventListener("DOMContentLoaded", start);
 </script>
diff --git a/build/plugins/hypothesis.html b/build/plugins/hypothesis.html
index 1986d36..3cd5e10 100644
--- a/build/plugins/hypothesis.html
+++ b/build/plugins/hypothesis.html
@@ -4,7 +4,7 @@
   Allows public annotation of the  manuscript. See https://web.hypothes.is/.
 -->
 
-<script>
+<script type="module">
   // configuration
   window.hypothesisConfig = function () {
     return {
diff --git a/build/plugins/scite.html b/build/plugins/scite.html
index 4d62049..60bb9a6 100644
--- a/build/plugins/scite.html
+++ b/build/plugins/scite.html
@@ -11,7 +11,7 @@
   src="https://cdn.scite.ai/badge/scite-badge-latest.min.js"
 ></script>
 
-<script>
+<script type="module">
   // start script
   function start() {
     // if printing, exit and don't run badges

From 9a448fe6edb477fb98065d5b83d206b1ca489cee Mon Sep 17 00:00:00 2001
From: Travis Wrightsman <traviswrightsman@gmail.com>
Date: Wed, 29 Sep 2021 21:04:48 -0400
Subject: [PATCH 30/50] Fix front-matter logo dimensions in DOCX

merges https://github.com/manubot/rootstock/pull/439
closes https://github.com/manubot/rootstock/issues/437
---
 content/00.front-matter.md | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/content/00.front-matter.md b/content/00.front-matter.md
index e6eafd5..5f1a8eb 100644
--- a/content/00.front-matter.md
+++ b/content/00.front-matter.md
@@ -29,15 +29,15 @@ on {{manubot.date}}.
 {% for author in manubot.authors %}
 + **{{author.name}}**<br>
   {%- if author.orcid is defined and author.orcid is not none %}
-    ![ORCID icon](images/orcid.svg){.inline_icon}
+    ![ORCID icon](images/orcid.svg){.inline_icon width=16 height=16}
     [{{author.orcid}}](https://orcid.org/{{author.orcid}})
   {%- endif %}
   {%- if author.github is defined and author.github is not none %}
-    · ![GitHub icon](images/github.svg){.inline_icon}
+    · ![GitHub icon](images/github.svg){.inline_icon width=16 height=16}
     [{{author.github}}](https://github.com/{{author.github}})
   {%- endif %}
   {%- if author.twitter is defined and author.twitter is not none %}
-    · ![Twitter icon](images/twitter.svg){.inline_icon}
+    · ![Twitter icon](images/twitter.svg){.inline_icon width=16 height=16}
     [{{author.twitter}}](https://twitter.com/{{author.twitter}})
   {%- endif %}<br>
   <small>

From f51c566b7d4cf038222d82fabe5c599b6bfbba26 Mon Sep 17 00:00:00 2001
From: mariojmdavid <mariojmdavid@gmail.com>
Date: Thu, 4 Nov 2021 07:45:34 +0100
Subject: [PATCH 31/50] spell check

---
 content/02.document-log.md     | 1 +
 content/06.quality_criteria.md | 8 ++++----
 webpage/images                 | 1 -
 webpage/index.html             | 1 -
 webpage/manuscript.pdf         | 1 -
 5 files changed, 5 insertions(+), 7 deletions(-)
 delete mode 120000 webpage/images
 delete mode 120000 webpage/index.html
 delete mode 120000 webpage/manuscript.pdf

diff --git a/content/02.document-log.md b/content/02.document-log.md
index 16f85f8..f9bd59d 100644
--- a/content/02.document-log.md
+++ b/content/02.document-log.md
@@ -6,3 +6,4 @@
 | v0.2         | 28/02/2020 | Second draft version |
 | v1.0-beta03  | 09/06/2020 | beta03 draft version |
 | v1.0         | 12/06/2020 | v1.0 release         |
+| v1.1         | 11/2021 | v1.1 release         |
diff --git a/content/06.quality_criteria.md b/content/06.quality_criteria.md
index 726e355..41beca1 100644
--- a/content/06.quality_criteria.md
+++ b/content/06.quality_criteria.md
@@ -133,7 +133,7 @@ findable and accessible. [SQA-QC.Doc03].
 * **[SvcQC.Doc03]** Documentation MUST be version controlled. [SQA-QC.Doc01.1].
 
 * **[SvcQC.Doc04]** Documentation MUST be updated on new **Service** versions
-involving any change in the installation, configuration or behaviour of
+involving any change in the installation, configuration or behavior of
 the **Service**. [SQA-QC.Doc04].
 
 * **[SvcQC.Doc05]** Documentation MUST be updated whenever reported
@@ -231,11 +231,11 @@ good practices.
 * **[SvcQC.Sec07]** IaC testing, from [SvcQC.Aud02] criterion, MUST cover the
 security auditing of the IaC templates (_SaC_) in
 order to assure the deployment of secured **Services**. For all the third-party
-dependencies used in the IaC templates (including all kind of software artefacts,
+dependencies used in the IaC templates (including all kind of software artifacts,
 such as Linux packages or container-based images):
   * **[SvcQC.Sec07.1]** SaC MUST perform vulnerability scanning of the
   artefact versions in use.
-  * **[SvcQC.Sec07.2]** SaC SHOULD verify that the artefacts are trusted and
+  * **[SvcQC.Sec07.2]** SaC SHOULD verify that the artifacts are trusted and
   digitally signed.
   * **[SvcQC.Sec07.3]** SaC MUST scan IaC templates to uncover misalignments
   with widely-accepted security policies from [SvcQC.Sec06] criteria, such as
@@ -246,7 +246,7 @@ such as Linux packages or container-based images):
 
 ### Policies [SvcQC.Pol]
 
-Policy documents describe what are the user's expected behaviour when using the
+Policy documents describe what are the user's expected behavior when using the
 **Service**, how they can access it and what they can expect regarding privacy
 of their data.
 
diff --git a/webpage/images b/webpage/images
deleted file mode 120000
index 2b55bac..0000000
--- a/webpage/images
+++ /dev/null
@@ -1 +0,0 @@
-v/latest/images
\ No newline at end of file
diff --git a/webpage/index.html b/webpage/index.html
deleted file mode 120000
index 2f982ac..0000000
--- a/webpage/index.html
+++ /dev/null
@@ -1 +0,0 @@
-v/latest/index.html
\ No newline at end of file
diff --git a/webpage/manuscript.pdf b/webpage/manuscript.pdf
deleted file mode 120000
index b886727..0000000
--- a/webpage/manuscript.pdf
+++ /dev/null
@@ -1 +0,0 @@
-v/latest/manuscript.pdf
\ No newline at end of file

From 2822b694b5b12dcc79dd7137d6189d526be1947e Mon Sep 17 00:00:00 2001
From: mariojmdavid <mariojmdavid@gmail.com>
Date: Thu, 4 Nov 2021 09:59:40 +0100
Subject: [PATCH 32/50] add justified text

---
 build/themes/default.html | 8 ++++++++
 1 file changed, 8 insertions(+)

diff --git a/build/themes/default.html b/build/themes/default.html
index b3298fe..7da007c 100644
--- a/build/themes/default.html
+++ b/build/themes/default.html
@@ -192,6 +192,14 @@
     margin-bottom: 20px;
   }
 
+p {
+  text-align: justify;
+}
+
+#refs p {
+  text-align: left;
+}
+
   /* -------------------------------------------------- */
   /* figures */
   /* -------------------------------------------------- */

From 748dac79b6d9c4b744c3cfa961ebf0fb11c2b158 Mon Sep 17 00:00:00 2001
From: mariojmdavid <mariojmdavid@gmail.com>
Date: Thu, 4 Nov 2021 12:43:01 +0100
Subject: [PATCH 33/50] issue #25

---
 content/01.abstract.md               |   4 +-
 content/02.0.copyright-ack.md        |   6 +-
 content/02.document-log.md           |   2 +-
 content/03.intro.md                  |  41 +++--
 content/04.goals.md                  |  23 ++-
 content/05.notational_conventions.md |   2 +-
 content/06.quality_criteria.md       | 265 ++++++++++++++++-----------
 content/07.glossary.md               |   2 +-
 content/99.back-matter.md            |   2 +-
 9 files changed, 197 insertions(+), 150 deletions(-)

diff --git a/content/01.abstract.md b/content/01.abstract.md
index 6789a0f..58868dd 100644
--- a/content/01.abstract.md
+++ b/content/01.abstract.md
@@ -1,7 +1,7 @@
-## Abstract {.page_break_before}
+# Abstract {.page_break_before}
 
 The purpose of this document is to define a set of quality standards,
 procedures and best practices to conform a Service Quality Assurance
-plan to serve as a reference within the European research ecosystem 
+plan, to serve as a reference within the European research ecosystem 
 related projects for the adequate development, deployment, operation
 and integration of services into production research infrastructures.
diff --git a/content/02.0.copyright-ack.md b/content/02.0.copyright-ack.md
index 51074ed..36fde0c 100644
--- a/content/02.0.copyright-ack.md
+++ b/content/02.0.copyright-ack.md
@@ -1,8 +1,8 @@
-## Copyright Notice
+# Copyright Notice
 
-Copyright © Members of the EOSC-Synergy collaboration, 2019-2020.
+Copyright © Members of the EOSC-Synergy collaboration, 2019-2021.
 
-## Acknowledgements
+# Acknowledgements
 
 The EOSC-Synergy project received funding from the European Union’s 
 Horizon 2020 research and innovation programme under grant agreement 
diff --git a/content/02.document-log.md b/content/02.document-log.md
index f9bd59d..a762943 100644
--- a/content/02.document-log.md
+++ b/content/02.document-log.md
@@ -1,4 +1,4 @@
-## Document Log
+# Document Log {.page_break_before}
 
 | Issue        | Date       | Comment              |
 |--------------|------------|----------------------|
diff --git a/content/03.intro.md b/content/03.intro.md
index a2b383a..867c2fe 100644
--- a/content/03.intro.md
+++ b/content/03.intro.md
@@ -1,8 +1,7 @@
-## Introduction
+# 1. Introduction {.page_break_before}
 
-The Open Science realization in Europe is already taking its first steps by
-means of the implementation of the European Open Science Cloud (EOSC). The
-EOSC aims at providing researchers with a unique, federated and inclusive
+The Open Science realization in Europe is implementing the European Open Science Cloud (EOSC).
+The EOSC aims at providing researchers with a unique, federated and inclusive
 view of fit-for-purpose services, developed and operated by the diverse European
 research infrastructures, including the underlying e-Infrastructures. Consequently,
 the ultimate success of the EOSC heavily relies on the quality aspects of those
@@ -24,7 +23,7 @@ narrows down the scope to meet the user expectations by acting exclusively on
 the quality features of the **Service**, which is seen as an aggregate of software
 components in operation.
 
-## Purpose
+# 2. Purpose
 
 This document provides an initial approach to **Service Quality Assurance**,
 meant to be applied in the integration process of the **Services** existing
@@ -32,35 +31,39 @@ under the EOSC-Synergy project, which eventually will be accessible as part
 of the EOSC offerings.
 
 The criteria compiled in this document favours a pragmatic and systematic
-approach that puts emphasis on the programmatic assessment of the quality
-conventions. To this end, the criteria herein compiled builds on the DevOps
+approach, putting emphasis on the programmatic assessment of the quality
+conventions. As such, the criteria herein compiled builds on the DevOps
 culture already established in the preceding Software Quality Assurance baseline
 document [@url:https://digital.csic.es/handle/10261/160086] to outline the set
-of good practices that seek the usability and
-reliability of **Services**, and meet the user expectations in terms of functional
-requirements.
+of good practices that seek the usability and reliability of **Services**, and meet
+the user expectations in terms of functional requirements.
 
-## Contextualization of a Service
+# 3. Contextualization of a Service
 
 As a result, a **Service**, as conceived in this document, represents the following:
 
 * **Web Service** [@url:https://techterms.com/definition/web_service]:
-    * A **Web Service** is an application or data source that is accessible via
+
+  * A **Web Service** is an application or data source that is accessible via
     a standard web protocol (HTTP or HTTPS).
-    * **Web Services** are designed to communicate with other programs,
+
+  * **Web Services** are designed to communicate with other programs,
     rather than directly with users.
-    * Most **Web Services** provide an API, or a set of functions and commands,
+
+  * Most **Web Services** provide an API, or a set of functions and commands,
     that can be used to access the data.
 
 * **Web Application** [@url:https://techterms.com/definition/web_application]:
-    * A **Web Application** or "Web App" is a software program that is delivered over
+
+  * A **Web Application** or "Web App" is a software program that is delivered over
     the Internet and is accessed through a web browser.
 
 * **Platform** or **Service Composition**
-[@url:https://csrc.nist.gov/glossary/term/Service_Composition]:
-    * Aggregation of multiple small services into larger services,
+  [@url:https://csrc.nist.gov/glossary/term/Service_Composition]:
+
+  * Aggregation of multiple small services into larger services,
     according to a service-oriented (SOA) and/or microservices architecture.
-    * An integrated set of **Web Services**, **Web Applications** and software components.
 
-Examples are: Web portals, Scientific portals and gateways, data repositories.
+  * An integrated set of **Web Services**, **Web Applications** and software components.
 
+Examples are: Web portals, Scientific portals and gateways, data repositories.
diff --git a/content/04.goals.md b/content/04.goals.md
index 3775266..1f3610f 100644
--- a/content/04.goals.md
+++ b/content/04.goals.md
@@ -1,4 +1,4 @@
-## Goals
+# 5. Goals
 
 The herein proposed baseline harnesses the capabilities of the quality factors
 in the underlying software to lay out the principles for attaining quality in
@@ -8,18 +8,17 @@ services.
 
 The Service Quality baseline aims at fulfilling the following goals:
 
-* Complement with a DevOps approach the existing approaches to assess and
-assure the quality and maturity of services within the EOSC, i.e. Technology
-Readiness Levels (TRLs) and EOSC Service Management System (SMS).
+1. Complement with a DevOps approach the existing approaches to assess and
+   assure the quality and maturity of services within the EOSC, i.e. Technology
+   Readiness Levels (TRLs) and EOSC Service Management System (SMS).
 
-* Build trust on the users by strengthening the reliability and stability of
-the services, with a focus on the underlying software, thus ensuring a proper
-realization of the verification and validation processes.
+2. Build trust on the users by strengthening the reliability and stability of
+   the services, with a focus on the underlying software, thus ensuring a proper
+   realization of the verification and validation processes.
 
-* Ensure the functional suitability of the service by promoting testing
-techniques that check the compliance with the user requirements.
+3. Ensure the functional suitability of the service by promoting testing
+   techniques that check the compliance with the user requirements.
 
-* Improve the usability by identifying the set of criteria that fosters the
-service adoption.
+4. Improve the usability by identifying the set of criteria that fosters the service adoption.
 
-* Promote the automated validation of the service quality criteria.
+5. Promote the automated validation of the service quality criteria.
diff --git a/content/05.notational_conventions.md b/content/05.notational_conventions.md
index f3dbe7a..e5e1160 100644
--- a/content/05.notational_conventions.md
+++ b/content/05.notational_conventions.md
@@ -1,4 +1,4 @@
-## Notational Conventions
+# 6. Notational Conventions
 
 The keywords “MUST”, “MUST NOT”, “REQUIRED”, “SHALL”, “SHALL NOT”, “SHOULD”,
 “SHOULD NOT”, “RECOMMENDED”, “MAY”, and “OPTIONAL” in this document are to be
diff --git a/content/06.quality_criteria.md b/content/06.quality_criteria.md
index 41beca1..890408e 100644
--- a/content/06.quality_criteria.md
+++ b/content/06.quality_criteria.md
@@ -1,4 +1,4 @@
-## Quality Criteria
+# 7. Quality Criteria
 
 The following sections describe the quality conventions and best
 practices that apply to the development, operation and integration
@@ -12,7 +12,7 @@ document "Software Quality Assurance baseline"
 following tag is added to the criteria: [SQA-QC.XyNN] where QC.XyNN is
 the codename of the criteria in that document.
 
-### API Testing [SvcQC.Api]
+## 7.1. API Testing [SvcQC.Api]
 
 Web services commonly use application programming interfaces (APIs) to expose
 the available features to external consumers, which can be either oriented to
@@ -25,12 +25,14 @@ compose, consume and validate APIs. The following requirements assume the
 presence of such an API specification.
 
 * **[SvcQC.Api01]** API testing MUST cover the validation of the features
-outlined in the specification (aka _contract testing_).
+  outlined in the specification (aka _contract testing_).
+
   * **[SvcQC.Api01.1]** Any change in the API not compliant with the OAS MUST
-  NOT pass contract testing.
+    NOT pass contract testing.
+
   * **[SvcQC.Api01.2]** The use of OAS SHOULD narrow down the applicable set of
-  test cases to the features described in the specification, avoiding unnecessary
-  assertions.
+    test cases to the features described in the specification, avoiding unnecessary
+    assertions.
   <!--
   * [Future Link to the SW baseline] OAS fosters test-driven development (TDD)
   as the de-facto scenario for API development: i) writing the specification,
@@ -41,28 +43,29 @@ outlined in the specification (aka _contract testing_).
   security-related criteria outlined in [SvcQC.Sec] section.
 
 * **[SvcQC.Api03]** API testing SHOULD involve the use of test doubles, such
-as mock servers or stubs, that act as a validation layer for the incoming
-requests.
+  as mock servers or stubs, that act as a validation layer for the incoming requests.
 
-### Integration Testing [SvcQC.Int]
+## 7.2. Integration Testing [SvcQC.Int]
 
 Integration testing refers to the evaluation of the interactions among
 coupled **Services** or parts of a system that cooperate to achieve a given
 functionality.
 
 * **[SvcQC.Int01]** Whenever a new functionality is involved, integration
-testing MUST guarantee the operation of any previously-working interaction
-with external **Services**. [SQA-QC.Int01].
+  testing MUST guarantee the operation of any previously-working interaction
+  with external **Services**. [SQA-QC.Int01].
+
   * When using APIs, contract testing MUST detect any disruption in the
-  communication between provider and consumer endpoints, through the validation
-  of the API specification [SvcQC.Api01].
+    communication between provider and consumer endpoints, through the validation
+    of the API specification [SvcQC.Api01].
 
 * **[SvcQC.Int02]** Integration testing SHOULD be automated.
 
 * **[SvcQC.Int03]** Ad-hoc pilot **Service** infrastructures and/or local
-testbeds MAY be used to cope with the integration testing requirements. [SQA-QC.Int04].
+  testbeds MAY be used to cope with the integration testing requirements. [SQA-QC.Int04].
+
+## 7.3. Functional tests [SvcQC.Fun]
 
-### Functional tests [SvcQC.Fun]
 Functional testing is a type of black-box testing. It involves the verification
 of the **Service** identified functionality, based on requested requirements and
 agreed design specifications. This type of **Service** testing focuses on the evaluation
@@ -70,20 +73,22 @@ of the functionality that the **Service** exposes, leaving apart any internal
 design analysis or side-effects to external systems.
 
 * **[SvcQC.Fun01]** Functional testing SHOULD tend to cover the full scope
---e.g. positive, negative, edge cases-- for the set of functionality that the
-**Service** claims to provide. [SQA-QC.Fun01].
+  --e.g. positive, negative, edge cases-- for the set of functionality that the
+  **Service** claims to provide. [SQA-QC.Fun01].
+
   * **[SvcQC.Fun01.1]** When using APIs, contract testing MUST detect any
-  disruption in the features exposed by the provider to the consumer, through
-  the validation of the API specification. [SvcQC.Api01].
+    disruption in the features exposed by the provider to the consumer, through
+    the validation of the API specification. [SvcQC.Api01].
+
   * **[SvcQC.Fun01.2]** Functional tests SHOULD include the Web interface of
-  the **Service**.
+    the **Service**.
 
 * **[SvcQC.Fun02]** Functional tests SHOULD be checked automatically.
 
 * **[SvcQC.Fun03]** Functional tests SHOULD be provided by the developers
   of the underlying software. [SQA-QC.Fun04].
 
-### Performance tests [SvcQC.Per]
+## 7.4. Performance tests [SvcQC.Per]
 
 Performance testing verifies that the software meets the specified performance
 requirements and assesses performance characteristics - for instance,
@@ -119,51 +124,67 @@ to variable demand or workload for those service(s) [@doi:10.1186/s13677-019-013
 * **[SvcQC.Per04]** Elasticity testing MAY be carried out to check the
   **Service** ability to scale out or scale in, depending on its demand or workload.
 
-### Documentation [SvcQC.Doc]
+## 7.5. Documentation [SvcQC.Doc]
 
 Documentation is an integral part of any Software or Service. For example,
 it describes how and what users can use and interact with it, or how operators can
 deploy, configure and manage a given Software or Service.
 
 * **[SvcQC.Doc01]** Documentation MUST be available online, easily
-findable and accessible. [SQA-QC.Doc03].
+  findable and accessible. [SQA-QC.Doc03].
 
 * **[SvcQC.Doc02]** Documentation SHOULD have a Persistent Identifier (PID).
 
 * **[SvcQC.Doc03]** Documentation MUST be version controlled. [SQA-QC.Doc01.1].
 
 * **[SvcQC.Doc04]** Documentation MUST be updated on new **Service** versions
-involving any change in the installation, configuration or behavior of
-the **Service**. [SQA-QC.Doc04].
+  involving any change in the installation, configuration or behavior of
+  the **Service**. [SQA-QC.Doc04].
 
 * **[SvcQC.Doc05]** Documentation MUST be updated whenever reported
-as inaccurate or unclear. [SQA-QC.Doc05].
+  as inaccurate or unclear. [SQA-QC.Doc05].
 
 * **[SvcQC.Doc06]** Documentation MUST have a non-software license.
 
 * **[SvcQC.Doc07]** Documentation MUST be produced according to the
-target audience, varying according to the **Service** specification.
-The identified types of documentation and their RECOMMENDED content are:
+  target audience, varying according to the **Service** specification.
+  The identified types of documentation and their RECOMMENDED content are:
 
   * **[SvcQC.Doc07.2]** Deployment and Administration. [SQA-QC.Doc06.3]:
+
     * Installation and configuration guides.
+
     * Service Reference Card, with the following RECOMMENDED content:
+
       * Brief functional description.
+
       * List of processes or daemons.
+
       * Init scripts and options.
+
       * List of configuration files, location and example or template.
+
       * Log files location and other useful audit information.
+
       * List of ports.
+
       * Service state information.
+
       * List of cron jobs.
+
       * Security information.
+
       * FAQs and troubleshooting.
+
   * **[SvcQC.Doc07.3]** User. [SQA-QC.Doc06.4]:
+
     * Detailed User Guide for the **Service**.
+
     * Public API documentation (if applicable).
+
     * Command-line (CLI) reference (if applicable).
 
-### Security [SvcQC.Sec]
+## 7.6. Security [SvcQC.Sec]
 
 Security assessment is essential for any production **Service**. While an 
 effective implementation of the security requirements applies to every stage in 
@@ -180,92 +201,107 @@ through the _Security as Code_ (_SaC_) capabilities. SaC is a particularly
 suitable tool for endorsing security of **Service Composition** deployments.
 
 * **[SvcQC.Sec01]** The **Service** public endpoints and APIs MUST be secured
-with data encryption.
+  with data encryption.
+
   * **[SvcQC.Sec01.1]** The **Service** MUST use strong ciphers for data
-  encryption.
+    encryption.
 
 * **[SvcQC.Sec02]** The **Service** SHOULD have an authentication mechanism.
+
   * **[SvcQC.Sec02.1]** Whenever dealing with a **Service Composition**, such
-  as microservice architectures, the **Services** SHOULD be managed by a
-  centralized authentication mechanism.
+    as microservice architectures, the **Services** SHOULD be managed by a
+    centralized authentication mechanism.
+
   * **[SvcQC.Sec02.2]** In publicly-accessible APIs, **Service**
-  authentication SHOULD be handled through an API gateway in order to control
-  the traffic and protect the backend services from overuse.
+    authentication SHOULD be handled through an API gateway in order to control
+    the traffic and protect the backend services from overuse.
 
 * **[SvcQC.Sec03]** The **Service** SHOULD implement an authorization mechanism.
+
   * **[SvcQC.Sec03.1]** In **Service Composition** environments, the
-  authorization mechanism SHOULD uniquely grant the essential access
-  permissions for each **Service** according to the principle of least privilege
-  (PoLP).
+    authorization mechanism SHOULD uniquely grant the essential access
+    permissions for each **Service** according to the principle of least privilege
+    (PoLP).
 
 * **[SvcQC.Sec04]** The **Service** MUST validate the credentials and signatures.
+
   * **[SvcQC.Sec04.1]** Credentials used in the **Service** MUST be signed by
-  a recognized and trusted certification authority.
+    a recognized and trusted certification authority.
 
 * **[SvcQC.Sec05]** The **Service** MUST handle personal data in compliance with
-the applicable regulations, such as the General Data Protection Regulation
-(GDPR) within the European boundaries.
+  the applicable regulations, such as the General Data Protection Regulation
+  (GDPR) within the European boundaries.
 
 * **[SvcQC.Sec06]** The **Service** SHOULD be audited in accordance with the
-black-box testing criteria identified by de-facto (cyber)security standards and
-good practices.
+  black-box testing criteria identified by de-facto (cyber)security standards and
+  good practices.
+
   * **[SvcQC.Sec06.1]** DAST checks MUST be executed, through the use of ad-hoc
-  tools, directly to an operational **Service** in order to uncover runtime
-  security vulnerabilities and any other environment-related issues (e.g. SQL
-  injection, cross-site scripting or DDOS). The latest release of OWASP's Web
-  Security Testing Guide
-  [@url:https://owasp.org/www-project-web-security-testing-guide/stable/] and
-  the NIST's Technical Guide to Information Security Testing and Assessment
-  [@url:https://doi.org/10.6028/NIST.SP.800-115] MUST be considered for 
-  carrying out comprehensive **Service** security testing.
+    tools, directly to an operational **Service** in order to uncover runtime
+    security vulnerabilities and any other environment-related issues (e.g. SQL
+    injection, cross-site scripting or DDOS). The latest release of OWASP's Web
+    Security Testing Guide
+    [@url:https://owasp.org/www-project-web-security-testing-guide/stable/] and
+    the NIST's Technical Guide to Information Security Testing and Assessment
+    [@url:https://doi.org/10.6028/NIST.SP.800-115] MUST be considered for 
+    carrying out comprehensive **Service** security testing.
+
   * **[SvcQC.Sec06.2]** Penetration testing (manual or automated) MAY be part of
-  the application security verification effort. [SQA-QC.Sec04].
+    the application security verification effort. [SQA-QC.Sec04].
+
   * **[SvcQC.Sec06.3]** The security assessment of the target system 
-  configuration is particularly important to reduce the risk of security
-  attacks. The benchmarks delivered by the Center for Internet
-  Security (CIS) [@url:https://www.cisecurity.org/cis-benchmarks/] and the
-  NIST's Security Assurance Requirements for Linux Application Container
-  Deployments [@url:https://doi.org/10.6028/NIST.IR.8176] MUST be considered
-  for this task.
+    configuration is particularly important to reduce the risk of security
+    attacks. The benchmarks delivered by the Center for Internet
+    Security (CIS) [@url:https://www.cisecurity.org/cis-benchmarks/] and the
+    NIST's Security Assurance Requirements for Linux Application Container
+    Deployments [@url:https://doi.org/10.6028/NIST.IR.8176] MUST be considered
+    for this task.
 
 * **[SvcQC.Sec07]** IaC testing, from [SvcQC.Aud02] criterion, MUST cover the
-security auditing of the IaC templates (_SaC_) in
-order to assure the deployment of secured **Services**. For all the third-party
-dependencies used in the IaC templates (including all kind of software artifacts,
-such as Linux packages or container-based images):
+  security auditing of the IaC templates (_SaC_) in
+  order to assure the deployment of secured **Services**. For all the third-party
+  dependencies used in the IaC templates (including all kind of software artifacts,
+  such as Linux packages or container-based images):
+
   * **[SvcQC.Sec07.1]** SaC MUST perform vulnerability scanning of the
-  artefact versions in use.
+    artefact versions in use.
+
   * **[SvcQC.Sec07.2]** SaC SHOULD verify that the artifacts are trusted and
   digitally signed.
+
   * **[SvcQC.Sec07.3]** SaC MUST scan IaC templates to uncover misalignments
-  with widely-accepted security policies from [SvcQC.Sec06] criteria, such as
-  non-encrypted secrets or disabled audit logs.
+    with widely-accepted security policies from [SvcQC.Sec06] criteria, such as
+    non-encrypted secrets or disabled audit logs.
+
   * **[SvcQC.Sec07.4]** SaC MAY be used to seek, in the IaC templates, for
-  violations of security requirements outlined in the applicable regulations
-  from criterion [SvcQC.Sec05].
+    violations of security requirements outlined in the applicable regulations
+    from criterion [SvcQC.Sec05].
 
-### Policies [SvcQC.Pol]
+## 7.7. Policies [SvcQC.Pol]
 
 Policy documents describe what are the user's expected behavior when using the
 **Service**, how they can access it and what they can expect regarding privacy
 of their data.
 
 * **[SvcQC.Pol01]** The **Service** MUST include the following policy documents:
+
   * **[SvcQC.Pol01.1]** Acceptable Usage Policy (AUP): Is a set of rules applied
-  by the owner, creator or administrator of a network, **Service** or system, that
-  restrict the ways in which the network, **Service** or system may be used and sets
-  guidelines as to how it should be used. The AUP can also be referred to as: Acceptable
-  Use Policy or Fair Use Policy.
+    by the owner, creator or administrator of a network, **Service** or system, that
+    restrict the ways in which the network, **Service** or system may be used and sets
+    guidelines as to how it should be used. The AUP can also be referred to as: Acceptable
+    Use Policy or Fair Use Policy.
+
   * **[SvcQC.Pol01.2]** Access Policy or Terms of Use: represent a binding legal
-  contract between the users (and/or customers), and the Provider of the **Service**.
-  The Access Policy mandates the users (and/or customers) access to and the use of
-  the Provider’s **Service**.
+    contract between the users (and/or customers), and the Provider of the **Service**.
+    The Access Policy mandates the users (and/or customers) access to and the use of
+    the Provider’s **Service**.
+
   * **[SvcQC.Pol01.3]** Privacy Policy: Data privacy statement informing the users
-  (and/or customers), about which personal data is collected and processed when they
-  use and interact with the **Service**. It states which rights the users (and/or customers)
-  have regarding the processing of their data.
+    (and/or customers), about which personal data is collected and processed when they
+    use and interact with the **Service**. It states which rights the users (and/or customers)
+    have regarding the processing of their data.
 
-### Support [SvcQC.Sup]
+## 7.8. Support [SvcQC.Sup]
 
 Support is the formal way by which users and operators of the **Service**
 communicate with other operators and/or developers of the **Service**,
@@ -274,18 +310,18 @@ in case of problems, be it operational problems or bugs in the
 and even documentation issues.
 
 * **[SvcQC.Sup01]** The **Service** MUST have a tracker or helpdesk
-for operational and users issues.
+  for operational and users issues.
 
 * **[SvcQC.Sup02]** The **Service** SHOULD have a tracker for the
-underlying software issues. [SQA-QC.Man01].
+  underlying software issues. [SQA-QC.Man01].
 
 * **[SvcQC.Sup03]** The **Service** SHOULD include an Operational
-Level Agreement (OLA) with the infrastructure where it is integrated.
+  Level Agreement (OLA) with the infrastructure where it is integrated.
 
 * **[SvcQC.Sup04]** The **Service** MAY include Service Level
-Agreement (SLA) with user communities.
+  Agreement (SLA) with user communities.
 
-### Automated Deployment [SvcQC.Aud]
+## 7.9. Automated Deployment [SvcQC.Aud]
 
 The automated deployment of **Services** implies the use of code to install and
 configure them in the target infrastructures. Infrastructure as Code (IaC)
@@ -298,18 +334,19 @@ redeployed. An immutable infrastructure simplifies maintenance and enhances
 repeatability and reliability.
 
 * **[SvcQC.Aud01]** A production-ready **Service** SHOULD be deployed as a
-workable system with the minimal user or system administrator interaction
-leveraging IaC templates.
+  workable system with the minimal user or system administrator interaction
+  leveraging IaC templates.
 
 * **[SvcQC.Aud02]** Any future change to a deployed **Service** SHOULD be
   done in the form of a new deployment, in order to preserve immutable
   infrastructures.
 
 * **[SvcQC.Aud03]** IaC SHOULD be validated by specific (unit) testing
-frameworks for every change being done.
+  frameworks for every change being done.
+
   * **[SvcQC.Aud03.1]** IaC (unit) tests MUST be idempotent.
 
-### Monitoring [SvcQC.Mon]
+## 7.10. Monitoring [SvcQC.Mon]
 
 Monitoring is a periodic testing of the **Service**. It requires a monitoring
 service from where tests are executed or sent and results of those tests are shown.
@@ -321,29 +358,35 @@ where the **Service** is foreseen to be integrated.
 
 * **[SvcQC.Mon01]** The **Service** in an operational production state SHOULD
   be monitored for functional-related criteria:
+
   * **[SvcQC.Mon01.1]** The **Service** public endpoints MUST be monitored.
+
   * **[SvcQC.Mon01.2]** The **Service** public APIs MUST be monitored. Use
-  functional tests of criteria [SvcQC.Fun01.2].
+    functional tests of criteria [SvcQC.Fun01.2].
+
   * **[SvcQC.Mon01.3]** The **Service** Web interface MAY be monitored. Use
-  functional tests of criteria [SvcQC.Fun01.3].
+    functional tests of criteria [SvcQC.Fun01.3].
 
 * **[SvcQC.Mon02]** The **Service** MUST be monitored for security-related
   criteria:
+
   * **[SvcQC.Mon02.1]** The **Service** MUST be monitored for public endpoints
-  and APIs secured and strong ciphers for encryption. Use Security tests of
-  criteria [SvcQC.Sec02] and [SvcQC.Sec05].
+    and APIs secured and strong ciphers for encryption. Use Security tests of
+    criteria [SvcQC.Sec02] and [SvcQC.Sec05].
+
   * **[SvcQC.Mon02.2]** The **Service** SHOULD be monitored with DAST checks.
-  Use Security tests of criteria [SvcQC.Sec06].
+    Use Security tests of criteria [SvcQC.Sec06].
 
 * **[SvcQC.Mon03]** The **Service** MUST be monitored for infrastructure-related
   criteria:
+
   * **[SvcQC.Mon03.1]** IaC (unit) tests [SvcQC.Aud02] SHOULD be reused as
-  monitoring tests, thus avoiding duplication.
+    monitoring tests, thus avoiding duplication.
 
-### Metrics [SvcQC.Met]
+## 7.1. Metrics [SvcQC.Met]
 
-A metric is a quantifiable measure that is used to track and assess
-the status of a specific process.
+A metric is a quantifiable measure that is used to track and assess the status of a specific
+process.
 
 In the case of **Services**, some relevant metrics are the number
 of users registered in the **Service**, or using it actively. Also
@@ -354,18 +397,20 @@ Although the metrics may be published in external services managed
 by the infrastructure, this is a common case in federated
 infrastructures such as EOSC.
 
-* **[SvcQC.Met01]** The **Service** SHOULD implement the collection
-of metrics.
-  * **[SvcQC.Met01.1]** The collection of metrics SHOULD be cumulative
-  over time and timestamped, so that the values can be queried per
-  time interval.
-  * **[SvcQC.Met01.2]** The metric *Number of registered users* SHOULD
-  be collected.
+* **[SvcQC.Met01]** The **Service** SHOULD implement the collection of metrics.
+
+  * **[SvcQC.Met01.1]** The collection of metrics SHOULD be cumulative over time and
+    timestamped, so that the values can be queried per time interval.
+
+  * **[SvcQC.Met01.2]** The metric *Number of registered users* SHOULD be collected.
+
   * **[SvcQC.Met01.3]** The metric *Number of active users over a given period of time*
-  MAY be collected.
-  * **[SvcQC.Met01.4]** The metric *Amount of computing resources per user or per group*
-  MAY be collected. The metric unit depends on the type of service and infrastructure.
-  An example is CPU x hours.
+    MAY be collected.
+
+  * **[SvcQC.Met01.4]** The metric *Amount of computing resources per user or per group* MAY be
+    collected. The metric unit depends on the type of service and infrastructure. An example
+    is CPU x hours.
+
   * **[SvcQC.Met01.5]** The metric *Amount of storage resources per user or per group*
-  MAY be collected. The metric unit depends on the type of service and infrastructure.
-  An example is GByte x hours.
+    MAY be collected. The metric unit depends on the type of service and infrastructure.
+    An example is GByte x hours.
diff --git a/content/07.glossary.md b/content/07.glossary.md
index c5ad4ea..dd8062a 100644
--- a/content/07.glossary.md
+++ b/content/07.glossary.md
@@ -1,4 +1,4 @@
-## Glossary
+# 8. Glossary
 
 __API__
 : Application Programming Interface
diff --git a/content/99.back-matter.md b/content/99.back-matter.md
index 339b33c..907573a 100644
--- a/content/99.back-matter.md
+++ b/content/99.back-matter.md
@@ -1,4 +1,4 @@
-## References {.page_break_before}
+# References {.page_break_before}
 
 <!-- Explicitly insert bibliography here -->
 <div id="refs"></div>

From 006c1b17851ec07eb184ec655b2c9ba49bfd9e8f Mon Sep 17 00:00:00 2001
From: mariojmdavid <mariojmdavid@gmail.com>
Date: Fri, 5 Nov 2021 12:18:48 +0100
Subject: [PATCH 34/50] fix section number

---
 content/00.front-matter.md           | 14 +++++++-------
 content/04.goals.md                  |  2 +-
 content/05.notational_conventions.md |  2 +-
 content/06.quality_criteria.md       | 24 ++++++++++++------------
 content/07.glossary.md               |  2 +-
 content/metadata.yaml                |  2 +-
 6 files changed, 23 insertions(+), 23 deletions(-)

diff --git a/content/00.front-matter.md b/content/00.front-matter.md
index a5f641f..cff78a6 100644
--- a/content/00.front-matter.md
+++ b/content/00.front-matter.md
@@ -29,23 +29,23 @@ on {{date}}.
 {% for author in manubot.authors %}
 + **{{author.name}}**<br>
   {%- if author.orcid is defined and author.orcid is not none %}
-    ![ORCID icon](images/orcid.svg){.inline_icon width=16 height=16}
+    ![ORCID icon](images/orcid.svg){.inline_icon}
     [{{author.orcid}}](https://orcid.org/{{author.orcid}})
   {%- endif %}
   {%- if author.github is defined and author.github is not none %}
-    · ![GitHub icon](images/github.svg){.inline_icon width=16 height=16}
+    · ![GitHub icon](images/github.svg){.inline_icon}
     [{{author.github}}](https://github.com/{{author.github}})
   {%- endif %}
   {%- if author.twitter is defined and author.twitter is not none %}
-    · ![Twitter icon](images/twitter.svg){.inline_icon width=16 height=16}
+    · ![Twitter icon](images/twitter.svg){.inline_icon}
     [{{author.twitter}}](https://twitter.com/{{author.twitter}})
   {%- endif %}<br>
   <small>
-  {%- if auth.affiliations is defined and auth.affiliations|length %}
-     {{auth.affiliations | join('; ')}}
+  {%- if author.affiliations is defined and author.affiliations|length %}
+     {{author.affiliations | join('; ')}}
   {%- endif %}
-  {%- if auth.funders is defined and auth.funders|length %}
-     · Funded by {{auth.funders}}
+  {%- if author.funders is defined and author.funders|length %}
+     · Funded by {{author.funders | join('; ')}}
   {%- endif %}
   </small>
 {% endfor %}
diff --git a/content/04.goals.md b/content/04.goals.md
index 1f3610f..790b62d 100644
--- a/content/04.goals.md
+++ b/content/04.goals.md
@@ -1,4 +1,4 @@
-# 5. Goals
+# 4. Goals
 
 The herein proposed baseline harnesses the capabilities of the quality factors
 in the underlying software to lay out the principles for attaining quality in
diff --git a/content/05.notational_conventions.md b/content/05.notational_conventions.md
index e5e1160..e7c08c5 100644
--- a/content/05.notational_conventions.md
+++ b/content/05.notational_conventions.md
@@ -1,4 +1,4 @@
-# 6. Notational Conventions
+# 5. Notational Conventions
 
 The keywords “MUST”, “MUST NOT”, “REQUIRED”, “SHALL”, “SHALL NOT”, “SHOULD”,
 “SHOULD NOT”, “RECOMMENDED”, “MAY”, and “OPTIONAL” in this document are to be
diff --git a/content/06.quality_criteria.md b/content/06.quality_criteria.md
index 890408e..9f4b83a 100644
--- a/content/06.quality_criteria.md
+++ b/content/06.quality_criteria.md
@@ -1,4 +1,4 @@
-# 7. Quality Criteria
+# 6. Quality Criteria {.page_break_before}
 
 The following sections describe the quality conventions and best
 practices that apply to the development, operation and integration
@@ -12,7 +12,7 @@ document "Software Quality Assurance baseline"
 following tag is added to the criteria: [SQA-QC.XyNN] where QC.XyNN is
 the codename of the criteria in that document.
 
-## 7.1. API Testing [SvcQC.Api]
+## 6.1. API Testing [SvcQC.Api]
 
 Web services commonly use application programming interfaces (APIs) to expose
 the available features to external consumers, which can be either oriented to
@@ -45,7 +45,7 @@ presence of such an API specification.
 * **[SvcQC.Api03]** API testing SHOULD involve the use of test doubles, such
   as mock servers or stubs, that act as a validation layer for the incoming requests.
 
-## 7.2. Integration Testing [SvcQC.Int]
+## 6.2. Integration Testing [SvcQC.Int]
 
 Integration testing refers to the evaluation of the interactions among
 coupled **Services** or parts of a system that cooperate to achieve a given
@@ -64,7 +64,7 @@ functionality.
 * **[SvcQC.Int03]** Ad-hoc pilot **Service** infrastructures and/or local
   testbeds MAY be used to cope with the integration testing requirements. [SQA-QC.Int04].
 
-## 7.3. Functional tests [SvcQC.Fun]
+## 6.3. Functional tests [SvcQC.Fun]
 
 Functional testing is a type of black-box testing. It involves the verification
 of the **Service** identified functionality, based on requested requirements and
@@ -88,7 +88,7 @@ design analysis or side-effects to external systems.
 * **[SvcQC.Fun03]** Functional tests SHOULD be provided by the developers
   of the underlying software. [SQA-QC.Fun04].
 
-## 7.4. Performance tests [SvcQC.Per]
+## 6.4. Performance tests [SvcQC.Per]
 
 Performance testing verifies that the software meets the specified performance
 requirements and assesses performance characteristics - for instance,
@@ -124,7 +124,7 @@ to variable demand or workload for those service(s) [@doi:10.1186/s13677-019-013
 * **[SvcQC.Per04]** Elasticity testing MAY be carried out to check the
   **Service** ability to scale out or scale in, depending on its demand or workload.
 
-## 7.5. Documentation [SvcQC.Doc]
+## 6.5. Documentation [SvcQC.Doc]
 
 Documentation is an integral part of any Software or Service. For example,
 it describes how and what users can use and interact with it, or how operators can
@@ -184,7 +184,7 @@ deploy, configure and manage a given Software or Service.
 
     * Command-line (CLI) reference (if applicable).
 
-## 7.6. Security [SvcQC.Sec]
+## 6.6. Security [SvcQC.Sec]
 
 Security assessment is essential for any production **Service**. While an 
 effective implementation of the security requirements applies to every stage in 
@@ -277,7 +277,7 @@ suitable tool for endorsing security of **Service Composition** deployments.
     violations of security requirements outlined in the applicable regulations
     from criterion [SvcQC.Sec05].
 
-## 7.7. Policies [SvcQC.Pol]
+## 6.7. Policies [SvcQC.Pol]
 
 Policy documents describe what are the user's expected behavior when using the
 **Service**, how they can access it and what they can expect regarding privacy
@@ -301,7 +301,7 @@ of their data.
     use and interact with the **Service**. It states which rights the users (and/or customers)
     have regarding the processing of their data.
 
-## 7.8. Support [SvcQC.Sup]
+## 6.8. Support [SvcQC.Sup]
 
 Support is the formal way by which users and operators of the **Service**
 communicate with other operators and/or developers of the **Service**,
@@ -321,7 +321,7 @@ and even documentation issues.
 * **[SvcQC.Sup04]** The **Service** MAY include Service Level
   Agreement (SLA) with user communities.
 
-## 7.9. Automated Deployment [SvcQC.Aud]
+## 6.9. Automated Deployment [SvcQC.Aud]
 
 The automated deployment of **Services** implies the use of code to install and
 configure them in the target infrastructures. Infrastructure as Code (IaC)
@@ -346,7 +346,7 @@ repeatability and reliability.
 
   * **[SvcQC.Aud03.1]** IaC (unit) tests MUST be idempotent.
 
-## 7.10. Monitoring [SvcQC.Mon]
+## 6.10. Monitoring [SvcQC.Mon]
 
 Monitoring is a periodic testing of the **Service**. It requires a monitoring
 service from where tests are executed or sent and results of those tests are shown.
@@ -383,7 +383,7 @@ where the **Service** is foreseen to be integrated.
   * **[SvcQC.Mon03.1]** IaC (unit) tests [SvcQC.Aud02] SHOULD be reused as
     monitoring tests, thus avoiding duplication.
 
-## 7.1. Metrics [SvcQC.Met]
+## 6.11. Metrics [SvcQC.Met]
 
 A metric is a quantifiable measure that is used to track and assess the status of a specific
 process.
diff --git a/content/07.glossary.md b/content/07.glossary.md
index dd8062a..5262f68 100644
--- a/content/07.glossary.md
+++ b/content/07.glossary.md
@@ -1,4 +1,4 @@
-# 8. Glossary
+# 7. Glossary {.page_break_before}
 
 __API__
 : Application Programming Interface
diff --git a/content/metadata.yaml b/content/metadata.yaml
index 9e6f41d..e161ab4 100644
--- a/content/metadata.yaml
+++ b/content/metadata.yaml
@@ -9,7 +9,7 @@ keywords:
   - agile development
 lang: en-US
 date: 29-04-2020
-author:
+authors:
   -
     name: Pablo Orviz
     github: orviz

From 9aa0b79b6a5b098a169bd56bbb518523e637af79 Mon Sep 17 00:00:00 2001
From: mariojmdavid <mariojmdavid@gmail.com>
Date: Mon, 22 Nov 2021 15:04:20 +0000
Subject: [PATCH 35/50] move sections, adapt SvcQC.Int02 to remove from SQA
 criteria,

---
 content/06.quality_criteria.md | 180 +++++++++++++++++----------------
 1 file changed, 92 insertions(+), 88 deletions(-)

diff --git a/content/06.quality_criteria.md b/content/06.quality_criteria.md
index 9f4b83a..505e5c2 100644
--- a/content/06.quality_criteria.md
+++ b/content/06.quality_criteria.md
@@ -12,6 +12,31 @@ document "Software Quality Assurance baseline"
 following tag is added to the criteria: [SQA-QC.XyNN] where QC.XyNN is
 the codename of the criteria in that document.
 
+## 6.9. Automated Deployment [SvcQC.Aud]
+
+The automated deployment of **Services** implies the use of code to install and
+configure them in the target infrastructures. Infrastructure as Code (IaC)
+templates allow operations teams to treat service provisioning and deployment in
+a similar fashion as developers manage the software code.
+
+Consequently, IaC enables the paradigm of immutable infrastructure deployment
+and maintenance, where **Services** are never updated, but deprovisioned and
+redeployed. An immutable infrastructure simplifies maintenance and enhances
+repeatability and reliability.
+
+* **[SvcQC.Aud01]** A production-ready **Service** SHOULD be deployed as a
+  workable system with the minimal user or system administrator interaction
+  leveraging IaC templates.
+
+* **[SvcQC.Aud02]** Any future change to a deployed **Service** SHOULD be
+  done in the form of a new deployment, in order to preserve immutable
+  infrastructures.
+
+* **[SvcQC.Aud03]** IaC SHOULD be validated by specific (unit) testing
+  frameworks for every change being done.
+
+  * **[SvcQC.Aud03.1]** IaC (unit) tests MUST be idempotent.
+
 ## 6.1. API Testing [SvcQC.Api]
 
 Web services commonly use application programming interfaces (APIs) to expose
@@ -53,16 +78,20 @@ functionality.
 
 * **[SvcQC.Int01]** Whenever a new functionality is involved, integration
   testing MUST guarantee the operation of any previously-working interaction
-  with external **Services**. [SQA-QC.Int01].
+  with external **Services**.
 
   * When using APIs, contract testing MUST detect any disruption in the
     communication between provider and consumer endpoints, through the validation
     of the API specification [SvcQC.Api01].
 
-* **[SvcQC.Int02]** Integration testing SHOULD be automated.
+* **[SvcQC.Int02]** Integration testing MUST NOT rely on non-operational or out-of-the-warranty services.
+  * **[SvcQC.Int02.1]** On lack of automation, pilot service infrastructures or local testbeds
+    MAY be used.
+  * **[SvcQC.Int02.2]** In the presence of CI environments, integration tests SHOULD be suitable for
+    the automated testing.
 
 * **[SvcQC.Int03]** Ad-hoc pilot **Service** infrastructures and/or local
-  testbeds MAY be used to cope with the integration testing requirements. [SQA-QC.Int04].
+  testbeds MAY be used to cope with the integration testing requirements.
 
 ## 6.3. Functional tests [SvcQC.Fun]
 
@@ -124,66 +153,6 @@ to variable demand or workload for those service(s) [@doi:10.1186/s13677-019-013
 * **[SvcQC.Per04]** Elasticity testing MAY be carried out to check the
   **Service** ability to scale out or scale in, depending on its demand or workload.
 
-## 6.5. Documentation [SvcQC.Doc]
-
-Documentation is an integral part of any Software or Service. For example,
-it describes how and what users can use and interact with it, or how operators can
-deploy, configure and manage a given Software or Service.
-
-* **[SvcQC.Doc01]** Documentation MUST be available online, easily
-  findable and accessible. [SQA-QC.Doc03].
-
-* **[SvcQC.Doc02]** Documentation SHOULD have a Persistent Identifier (PID).
-
-* **[SvcQC.Doc03]** Documentation MUST be version controlled. [SQA-QC.Doc01.1].
-
-* **[SvcQC.Doc04]** Documentation MUST be updated on new **Service** versions
-  involving any change in the installation, configuration or behavior of
-  the **Service**. [SQA-QC.Doc04].
-
-* **[SvcQC.Doc05]** Documentation MUST be updated whenever reported
-  as inaccurate or unclear. [SQA-QC.Doc05].
-
-* **[SvcQC.Doc06]** Documentation MUST have a non-software license.
-
-* **[SvcQC.Doc07]** Documentation MUST be produced according to the
-  target audience, varying according to the **Service** specification.
-  The identified types of documentation and their RECOMMENDED content are:
-
-  * **[SvcQC.Doc07.2]** Deployment and Administration. [SQA-QC.Doc06.3]:
-
-    * Installation and configuration guides.
-
-    * Service Reference Card, with the following RECOMMENDED content:
-
-      * Brief functional description.
-
-      * List of processes or daemons.
-
-      * Init scripts and options.
-
-      * List of configuration files, location and example or template.
-
-      * Log files location and other useful audit information.
-
-      * List of ports.
-
-      * Service state information.
-
-      * List of cron jobs.
-
-      * Security information.
-
-      * FAQs and troubleshooting.
-
-  * **[SvcQC.Doc07.3]** User. [SQA-QC.Doc06.4]:
-
-    * Detailed User Guide for the **Service**.
-
-    * Public API documentation (if applicable).
-
-    * Command-line (CLI) reference (if applicable).
-
 ## 6.6. Security [SvcQC.Sec]
 
 Security assessment is essential for any production **Service**. While an 
@@ -277,6 +246,66 @@ suitable tool for endorsing security of **Service Composition** deployments.
     violations of security requirements outlined in the applicable regulations
     from criterion [SvcQC.Sec05].
 
+## 6.5. Documentation [SvcQC.Doc]
+
+Documentation is an integral part of any Software or Service. For example,
+it describes how and what users can use and interact with it, or how operators can
+deploy, configure and manage a given Software or Service.
+
+* **[SvcQC.Doc01]** Documentation MUST be available online, easily
+  findable and accessible. [SQA-QC.Doc03].
+
+* **[SvcQC.Doc02]** Documentation SHOULD have a Persistent Identifier (PID).
+
+* **[SvcQC.Doc03]** Documentation MUST be version controlled. [SQA-QC.Doc01.1].
+
+* **[SvcQC.Doc04]** Documentation MUST be updated on new **Service** versions
+  involving any change in the installation, configuration or behavior of
+  the **Service**. [SQA-QC.Doc04].
+
+* **[SvcQC.Doc05]** Documentation MUST be updated whenever reported
+  as inaccurate or unclear. [SQA-QC.Doc05].
+
+* **[SvcQC.Doc06]** Documentation MUST have a non-software license.
+
+* **[SvcQC.Doc07]** Documentation MUST be produced according to the
+  target audience, varying according to the **Service** specification.
+  The identified types of documentation and their RECOMMENDED content are:
+
+  * **[SvcQC.Doc07.2]** Deployment and Administration. [SQA-QC.Doc06.3]:
+
+    * Installation and configuration guides.
+
+    * Service Reference Card, with the following RECOMMENDED content:
+
+      * Brief functional description.
+
+      * List of processes or daemons.
+
+      * Init scripts and options.
+
+      * List of configuration files, location and example or template.
+
+      * Log files location and other useful audit information.
+
+      * List of ports.
+
+      * Service state information.
+
+      * List of cron jobs.
+
+      * Security information.
+
+      * FAQs and troubleshooting.
+
+  * **[SvcQC.Doc07.3]** User. [SQA-QC.Doc06.4]:
+
+    * Detailed User Guide for the **Service**.
+
+    * Public API documentation (if applicable).
+
+    * Command-line (CLI) reference (if applicable).
+
 ## 6.7. Policies [SvcQC.Pol]
 
 Policy documents describe what are the user's expected behavior when using the
@@ -321,31 +350,6 @@ and even documentation issues.
 * **[SvcQC.Sup04]** The **Service** MAY include Service Level
   Agreement (SLA) with user communities.
 
-## 6.9. Automated Deployment [SvcQC.Aud]
-
-The automated deployment of **Services** implies the use of code to install and
-configure them in the target infrastructures. Infrastructure as Code (IaC)
-templates allow operations teams to treat service provisioning and deployment in
-a similar fashion as developers manage the software code.
-
-Consequently, IaC enables the paradigm of immutable infrastructure deployment
-and maintenance, where **Services** are never updated, but deprovisioned and
-redeployed. An immutable infrastructure simplifies maintenance and enhances
-repeatability and reliability.
-
-* **[SvcQC.Aud01]** A production-ready **Service** SHOULD be deployed as a
-  workable system with the minimal user or system administrator interaction
-  leveraging IaC templates.
-
-* **[SvcQC.Aud02]** Any future change to a deployed **Service** SHOULD be
-  done in the form of a new deployment, in order to preserve immutable
-  infrastructures.
-
-* **[SvcQC.Aud03]** IaC SHOULD be validated by specific (unit) testing
-  frameworks for every change being done.
-
-  * **[SvcQC.Aud03.1]** IaC (unit) tests MUST be idempotent.
-
 ## 6.10. Monitoring [SvcQC.Mon]
 
 Monitoring is a periodic testing of the **Service**. It requires a monitoring

From 28e20fa9dfa4f26beea24ff5c9133fab2a28bf67 Mon Sep 17 00:00:00 2001
From: mariojmdavid <mariojmdavid@gmail.com>
Date: Tue, 23 Nov 2021 18:43:04 +0000
Subject: [PATCH 36/50] update doc log, glossary, wip on issue #27

---
 content/02.document-log.md     |  2 +-
 content/06.quality_criteria.md | 77 +++++++++++++++++++++-------------
 content/07.glossary.md         |  4 +-
 3 files changed, 51 insertions(+), 32 deletions(-)

diff --git a/content/02.document-log.md b/content/02.document-log.md
index a762943..c105ca2 100644
--- a/content/02.document-log.md
+++ b/content/02.document-log.md
@@ -6,4 +6,4 @@
 | v0.2         | 28/02/2020 | Second draft version |
 | v1.0-beta03  | 09/06/2020 | beta03 draft version |
 | v1.0         | 12/06/2020 | v1.0 release         |
-| v1.1         | 11/2021 | v1.1 release         |
+| v1.1         | 11/2021 | Issues: #25        |
diff --git a/content/06.quality_criteria.md b/content/06.quality_criteria.md
index 505e5c2..503cc10 100644
--- a/content/06.quality_criteria.md
+++ b/content/06.quality_criteria.md
@@ -6,13 +6,15 @@ phases of a **Service** with a production infrastructure for research,
 such as the EOSC ecosystem. These guidelines rule the **Service** development
 and operation process within the framework of the EOSC-Synergy project.
 
+**REVIEW - criteria here is complementary to SQA baseline**
+
 Some of the criteria in this document is similar or based on the
 document "Software Quality Assurance baseline"
 [@url:https://digital.csic.es/handle/10261/160086]. For such cases the
 following tag is added to the criteria: [SQA-QC.XyNN] where QC.XyNN is
 the codename of the criteria in that document.
 
-## 6.9. Automated Deployment [SvcQC.Aud]
+## 6.1. Automated Deployment [SvcQC.Aud]
 
 The automated deployment of **Services** implies the use of code to install and
 configure them in the target infrastructures. Infrastructure as Code (IaC)
@@ -37,7 +39,7 @@ repeatability and reliability.
 
   * **[SvcQC.Aud03.1]** IaC (unit) tests MUST be idempotent.
 
-## 6.1. API Testing [SvcQC.Api]
+## 6.2. API Testing [SvcQC.Api]
 
 Web services commonly use application programming interfaces (APIs) to expose
 the available features to external consumers, which can be either oriented to
@@ -58,11 +60,12 @@ presence of such an API specification.
   * **[SvcQC.Api01.2]** The use of OAS SHOULD narrow down the applicable set of
     test cases to the features described in the specification, avoiding unnecessary
     assertions.
-  <!--
-  * [Future Link to the SW baseline] OAS fosters test-driven development (TDD)
-  as the de-facto scenario for API development: i) writing the specification,
-  ii) writing tests, and iii) implementing the API endpoints
-  -->
+
+<!--
+* [Future Link to the SW baseline] OAS fosters test-driven development (TDD)
+as the de-facto scenario for API development: i) writing the specification,
+ii) writing tests, and iii) implementing the API endpoints
+-->
 
 * **[SvcQC.Api02]** API testing MUST include the assessment of the
   security-related criteria outlined in [SvcQC.Sec] section.
@@ -70,7 +73,7 @@ presence of such an API specification.
 * **[SvcQC.Api03]** API testing SHOULD involve the use of test doubles, such
   as mock servers or stubs, that act as a validation layer for the incoming requests.
 
-## 6.2. Integration Testing [SvcQC.Int]
+## 6.3. Integration Testing [SvcQC.Int]
 
 Integration testing refers to the evaluation of the interactions among
 coupled **Services** or parts of a system that cooperate to achieve a given
@@ -85,15 +88,17 @@ functionality.
     of the API specification [SvcQC.Api01].
 
 * **[SvcQC.Int02]** Integration testing MUST NOT rely on non-operational or out-of-the-warranty services.
+
   * **[SvcQC.Int02.1]** On lack of automation, pilot service infrastructures or local testbeds
     MAY be used.
+
   * **[SvcQC.Int02.2]** In the presence of CI environments, integration tests SHOULD be suitable for
     the automated testing.
 
 * **[SvcQC.Int03]** Ad-hoc pilot **Service** infrastructures and/or local
   testbeds MAY be used to cope with the integration testing requirements.
 
-## 6.3. Functional tests [SvcQC.Fun]
+## 6.4. Functional tests [SvcQC.Fun]
 
 Functional testing is a type of black-box testing. It involves the verification
 of the **Service** identified functionality, based on requested requirements and
@@ -103,7 +108,7 @@ design analysis or side-effects to external systems.
 
 * **[SvcQC.Fun01]** Functional testing SHOULD tend to cover the full scope
   --e.g. positive, negative, edge cases-- for the set of functionality that the
-  **Service** claims to provide. [SQA-QC.Fun01].
+  **Service** claims to provide.
 
   * **[SvcQC.Fun01.1]** When using APIs, contract testing MUST detect any
     disruption in the features exposed by the provider to the consumer, through
@@ -115,9 +120,9 @@ design analysis or side-effects to external systems.
 * **[SvcQC.Fun02]** Functional tests SHOULD be checked automatically.
 
 * **[SvcQC.Fun03]** Functional tests SHOULD be provided by the developers
-  of the underlying software. [SQA-QC.Fun04].
+  of the underlying software.
 
-## 6.4. Performance tests [SvcQC.Per]
+## 6.5. Performance tests [SvcQC.Per]
 
 Performance testing verifies that the software meets the specified performance
 requirements and assesses performance characteristics - for instance,
@@ -155,14 +160,14 @@ to variable demand or workload for those service(s) [@doi:10.1186/s13677-019-013
 
 ## 6.6. Security [SvcQC.Sec]
 
-Security assessment is essential for any production **Service**. While an 
-effective implementation of the security requirements applies to every stage in 
-the software development life cycle (SDLC) --especially effective at the source 
-code level, as discussed in [SQA-QC.Sec]--, the security testing of a 
-**Service** is also --similarly to the diverse testing strategies previously 
+Security assessment is essential for any production **Service**. While an
+effective implementation of the security requirements applies to every stage in
+the software development life cycle (SDLC) --especially effective at the source
+code level, as discussed in [SQA-QC.Sec]--, the security testing of a
+**Service** is also --similarly to the diverse testing strategies previously
 covered-- a black-box type of testing. Hence, this section focuses on the
 runtime analysis of security-related requirements, as part of the _Dynamic
-Application Security Testing_  (_DAST_). 
+Application Security Testing_  (_DAST_).
 
 Additionally, the compliance with security policies and regulations complements
 the analysis, which can be implemented, continuously validated and monitored
@@ -205,7 +210,8 @@ suitable tool for endorsing security of **Service Composition** deployments.
   black-box testing criteria identified by de-facto (cyber)security standards and
   good practices.
 
-  * **[SvcQC.Sec06.1]** DAST checks MUST be executed, through the use of ad-hoc
+  * **[SvcQC.Sec06.1]** Dynamic application security testing (DAST)
+    checks MUST be executed, through the use of ad-hoc
     tools, directly to an operational **Service** in order to uncover runtime
     security vulnerabilities and any other environment-related issues (e.g. SQL
     injection, cross-site scripting or DDOS). The latest release of OWASP's Web
@@ -215,10 +221,16 @@ suitable tool for endorsing security of **Service Composition** deployments.
     [@url:https://doi.org/10.6028/NIST.SP.800-115] MUST be considered for 
     carrying out comprehensive **Service** security testing.
 
+  * **[SvcQC.Sec06.2]** Interactive Application Security Testing (IAST)
+    [@https://www.veracode.com/security/interactive-application-security-testing-iast],
+    analyzes code for security vulnerabilities while the app is run by an automated test. IAST SHOULD
+    be performed to software components in an operating state, while Functional Testing **[SvcQC.Fun]**,
+    is running.
+
   * **[SvcQC.Sec06.2]** Penetration testing (manual or automated) MAY be part of
-    the application security verification effort. [SQA-QC.Sec04].
+    the application security verification effort.
 
-  * **[SvcQC.Sec06.3]** The security assessment of the target system 
+  * **[SvcQC.Sec06.3]** The security assessment of the target system
     configuration is particularly important to reduce the risk of security
     attacks. The benchmarks delivered by the Center for Internet
     Security (CIS) [@url:https://www.cisecurity.org/cis-benchmarks/] and the
@@ -246,25 +258,30 @@ suitable tool for endorsing security of **Service Composition** deployments.
     violations of security requirements outlined in the applicable regulations
     from criterion [SvcQC.Sec05].
 
-## 6.5. Documentation [SvcQC.Doc]
+  * **[SvcQC.Sec07.5]** World-writable files SHOULD NOT be created while the service is in
+    operation. Whenever they are required, the relevant files MUST be documented.
+
+  * **[SvcQC.Sec07.6]** World-readable files MUST NOT contain passwords.
+
+## 6.7. Documentation [SvcQC.Doc]
 
 Documentation is an integral part of any Software or Service. For example,
 it describes how and what users can use and interact with it, or how operators can
 deploy, configure and manage a given Software or Service.
 
 * **[SvcQC.Doc01]** Documentation MUST be available online, easily
-  findable and accessible. [SQA-QC.Doc03].
+  findable and accessible.
 
 * **[SvcQC.Doc02]** Documentation SHOULD have a Persistent Identifier (PID).
 
-* **[SvcQC.Doc03]** Documentation MUST be version controlled. [SQA-QC.Doc01.1].
+* **[SvcQC.Doc03]** Documentation MUST be version controlled.
 
 * **[SvcQC.Doc04]** Documentation MUST be updated on new **Service** versions
   involving any change in the installation, configuration or behavior of
-  the **Service**. [SQA-QC.Doc04].
+  the **Service**.
 
 * **[SvcQC.Doc05]** Documentation MUST be updated whenever reported
-  as inaccurate or unclear. [SQA-QC.Doc05].
+  as inaccurate or unclear.
 
 * **[SvcQC.Doc06]** Documentation MUST have a non-software license.
 
@@ -272,7 +289,7 @@ deploy, configure and manage a given Software or Service.
   target audience, varying according to the **Service** specification.
   The identified types of documentation and their RECOMMENDED content are:
 
-  * **[SvcQC.Doc07.2]** Deployment and Administration. [SQA-QC.Doc06.3]:
+  * **[SvcQC.Doc07.2]** Deployment and Administration:
 
     * Installation and configuration guides.
 
@@ -298,7 +315,7 @@ deploy, configure and manage a given Software or Service.
 
       * FAQs and troubleshooting.
 
-  * **[SvcQC.Doc07.3]** User. [SQA-QC.Doc06.4]:
+  * **[SvcQC.Doc07.3]** User:
 
     * Detailed User Guide for the **Service**.
 
@@ -306,7 +323,7 @@ deploy, configure and manage a given Software or Service.
 
     * Command-line (CLI) reference (if applicable).
 
-## 6.7. Policies [SvcQC.Pol]
+## 6.8. Policies [SvcQC.Pol]
 
 Policy documents describe what are the user's expected behavior when using the
 **Service**, how they can access it and what they can expect regarding privacy
@@ -330,7 +347,7 @@ of their data.
     use and interact with the **Service**. It states which rights the users (and/or customers)
     have regarding the processing of their data.
 
-## 6.8. Support [SvcQC.Sup]
+## 6.9. Support [SvcQC.Sup]
 
 Support is the formal way by which users and operators of the **Service**
 communicate with other operators and/or developers of the **Service**,
diff --git a/content/07.glossary.md b/content/07.glossary.md
index 5262f68..f2410d5 100644
--- a/content/07.glossary.md
+++ b/content/07.glossary.md
@@ -21,8 +21,10 @@ __GDPR__
 __IaC__
 : Infrastructure as Code
 
-__ITSM__
+__IAST__
+: Interactive Application Security Testing
 
+__ITSM__
 : IT Service Management
 
 __NIST__

From 1366643dfb9c2661af2bfbec533df5497e792b30 Mon Sep 17 00:00:00 2001
From: mariojmdavid <mariojmdavid@gmail.com>
Date: Wed, 24 Nov 2021 11:37:47 +0000
Subject: [PATCH 37/50] mardown format, typos spell, issues #27, #29

---
 content/01.abstract.md                     |   9 +-
 content/02.0.copyright-ack.md              |   5 +-
 content/03.intro.md                        |  88 +++++----
 content/04.goals.md                        |  25 ++-
 content/05.notational_conventions.md       |   6 +-
 content/06.quality_criteria.md             | 201 ++++-----------------
 content/07.ops_quality_criteria.md         | 118 ++++++++++++
 content/{07.glossary.md => 08.glossary.md} |   0
 8 files changed, 219 insertions(+), 233 deletions(-)
 create mode 100644 content/07.ops_quality_criteria.md
 rename content/{07.glossary.md => 08.glossary.md} (100%)

diff --git a/content/01.abstract.md b/content/01.abstract.md
index 58868dd..465c462 100644
--- a/content/01.abstract.md
+++ b/content/01.abstract.md
@@ -1,7 +1,6 @@
 # Abstract {.page_break_before}
 
-The purpose of this document is to define a set of quality standards,
-procedures and best practices to conform a Service Quality Assurance
-plan, to serve as a reference within the European research ecosystem 
-related projects for the adequate development, deployment, operation
-and integration of services into production research infrastructures.
+The purpose of this document is to define a set of quality standards, procedures and best practices
+to conform a Service Quality Assurance plan, to serve as a reference within the European research
+ecosystem related projects for the adequate development, deployment, operation and integration of
+services into production research infrastructures.
diff --git a/content/02.0.copyright-ack.md b/content/02.0.copyright-ack.md
index 36fde0c..fb8cd2f 100644
--- a/content/02.0.copyright-ack.md
+++ b/content/02.0.copyright-ack.md
@@ -4,9 +4,8 @@ Copyright © Members of the EOSC-Synergy collaboration, 2019-2021.
 
 # Acknowledgements
 
-The EOSC-Synergy project received funding from the European Union’s 
-Horizon 2020 research and innovation programme under grant agreement 
-number 857647.
+The EOSC-Synergy project received funding from the European Union’s Horizon 2020 research and
+innovation programme under grant agreement number 857647.
 
 <p align="center">
   <img src="https://encrypted-tbn0.gstatic.com/images?q=tbn:ANd9GcT1WF4g5KH3PnQE_Ve10QFRS-gZ0NpCQ7Qr-_km1RqnOCEF1fQt">
diff --git a/content/03.intro.md b/content/03.intro.md
index 867c2fe..e57b4ad 100644
--- a/content/03.intro.md
+++ b/content/03.intro.md
@@ -1,68 +1,62 @@
 # 1. Introduction {.page_break_before}
 
-The Open Science realization in Europe is implementing the European Open Science Cloud (EOSC).
-The EOSC aims at providing researchers with a unique, federated and inclusive
-view of fit-for-purpose services, developed and operated by the diverse European
-research infrastructures, including the underlying e-Infrastructures. Consequently,
-the ultimate success of the EOSC heavily relies on the quality aspects of those
-services, such as their stability or functional suitability.
-
-The meaning of **Service** can be regarded from different perspectives.
-From an IT Service Management (ITSM) standpoint, such as the EOSC Service Management
-System (SMS) process model, a **Service** is devised as a means to "provide value
-to the customer". The same goal is shared by the DevOps paradigm, but in this
-case there is a more pragmatic vision that the customer satisfaction is achieved
-through the continuous delivery of quality-assured **Services**, with a shorter
-life cycle, as the final outcome of a comprehensive software development process.
-
-The ITSM model has a broader focus. A **Service** is an "intangible asset" that
-also includes additional activities such as customer engagement and support.
-Consequently, it is a much heavier process that might not be appropriate to
-be applicable for all types of **Services**. The DevOps model, on the other hand,
-narrows down the scope to meet the user expectations by acting exclusively on
-the quality features of the **Service**, which is seen as an aggregate of software
-components in operation.
+The Open Science realization in Europe is implementing the European Open Science Cloud (EOSC). The
+EOSC aims at providing researchers with a unique, federated and inclusive view of fit-for-purpose
+services, developed and operated by the diverse European research infrastructures, including the
+underlying e-Infrastructures. Consequently, the ultimate success of the EOSC heavily relies on the
+quality aspects of those services, such as their stability or functional suitability.
+
+The meaning of **Service** can be regarded from different perspectives. From an IT Service
+Management (ITSM) standpoint, such as the EOSC Service Management System (SMS) process model, a
+**Service** is devised as a means to "provide value to the customer". The same goal is shared by the
+DevOps paradigm, but in this case there is a more pragmatic vision that the customer satisfaction is
+achieved through the continuous delivery of quality-assured **Services**, with a shorter life cycle,
+as the final outcome of a comprehensive software development process.
+
+The ITSM model has a broader focus. A **Service** is an "intangible asset" that also includes
+additional activities such as customer engagement and support. Consequently, it is a much heavier
+process that might not be appropriately applicable for all types of **Services**. The DevOps model,
+on the other hand, narrows down the scope to meet the user expectations by acting exclusively on the
+quality features of the **Service**, which is seen as an aggregate of software components in
+operation.
 
 # 2. Purpose
 
-This document provides an initial approach to **Service Quality Assurance**,
-meant to be applied in the integration process of the **Services** existing
-under the EOSC-Synergy project, which eventually will be accessible as part
-of the EOSC offerings.
+This document provides an initial approach to **Service Quality Assurance**, meant to be applied in
+the integration process of the **Services** existing under the EOSC-Synergy project, which
+eventually will be accessible as part of the EOSC offerings.
 
-The criteria compiled in this document favours a pragmatic and systematic
-approach, putting emphasis on the programmatic assessment of the quality
-conventions. As such, the criteria herein compiled builds on the DevOps
-culture already established in the preceding Software Quality Assurance baseline
-document [@url:https://digital.csic.es/handle/10261/160086] to outline the set
-of good practices that seek the usability and reliability of **Services**, and meet
-the user expectations in terms of functional requirements.
+The criteria compiled in this document favours a pragmatic and systematic approach, putting emphasis
+on the programmatic assessment of the quality conventions. As such, the criteria herein compiled
+builds on the DevOps culture already established in the Software Quality Assurance baseline document
+[@https://digital.csic.es/handle/10261/160086], to outline the set of good practices that seek the
+usability and reliability of **Services**, and meet the user expectations in terms of functional
+requirements.
 
 # 3. Contextualization of a Service
 
 As a result, a **Service**, as conceived in this document, represents the following:
 
-* **Web Service** [@url:https://techterms.com/definition/web_service]:
+* **Web Service** [@https://techterms.com/definition/web_service]:
 
-  * A **Web Service** is an application or data source that is accessible via
-    a standard web protocol (HTTP or HTTPS).
+  * A **Web Service** is an application or data source that is accessible via a standard web
+    protocol (HTTP or HTTPS).
 
-  * **Web Services** are designed to communicate with other programs,
-    rather than directly with users.
+  * **Web Services** are designed to communicate with other programs, rather than directly with
+    users.
 
-  * Most **Web Services** provide an API, or a set of functions and commands,
-    that can be used to access the data.
+  * Most **Web Services** provide an API, or a set of functions and commands, that can be used to
+    access the data.
 
-* **Web Application** [@url:https://techterms.com/definition/web_application]:
+* **Web Application** [@https://techterms.com/definition/web_application]:
 
-  * A **Web Application** or "Web App" is a software program that is delivered over
-    the Internet and is accessed through a web browser.
+  * A **Web Application** or "Web App" is a software program that is delivered over the Internet and
+    is accessed through a web browser.
 
-* **Platform** or **Service Composition**
-  [@url:https://csrc.nist.gov/glossary/term/Service_Composition]:
+* **Platform / Service Composition** [@https://csrc.nist.gov/glossary/term/Service_Composition]:
 
-  * Aggregation of multiple small services into larger services,
-    according to a service-oriented (SOA) and/or microservices architecture.
+  * Aggregation of multiple small services into larger services, according to a service-oriented
+    (SOA) and/or microservices architecture.
 
   * An integrated set of **Web Services**, **Web Applications** and software components.
 
diff --git a/content/04.goals.md b/content/04.goals.md
index 790b62d..9073279 100644
--- a/content/04.goals.md
+++ b/content/04.goals.md
@@ -1,23 +1,22 @@
 # 4. Goals
 
-The herein proposed baseline harnesses the capabilities of the quality factors
-in the underlying software to lay out the principles for attaining quality in
-the enabled services within the EOSC context. According to this view, service
-quality is the foundation to shape user-centric, reliable and fit-for-purpose
-services. 
+The herein proposed baseline, harnesses the capabilities of the quality factors in the underlying
+software to lay out the principles for attaining quality in the enabled services within the EOSC
+context. According to this view, service quality is the foundation to shape user-centric, reliable
+and fit-for-purpose services.
 
 The Service Quality baseline aims at fulfilling the following goals:
 
-1. Complement with a DevOps approach the existing approaches to assess and
-   assure the quality and maturity of services within the EOSC, i.e. Technology
-   Readiness Levels (TRLs) and EOSC Service Management System (SMS).
+1. Complement with a DevOps approach the existing approaches to assess and assure the quality and
+   maturity of services within the EOSC, i.e. Technology Readiness Levels (TRLs) and EOSC Service
+   Management System (SMS).
 
-2. Build trust on the users by strengthening the reliability and stability of
-   the services, with a focus on the underlying software, thus ensuring a proper
-   realization of the verification and validation processes.
+2. Build trust on the users by strengthening the reliability and stability of the services, with a
+   focus on the underlying software, thus ensuring a proper realization of the verification and
+   validation processes.
 
-3. Ensure the functional suitability of the service by promoting testing
-   techniques that check the compliance with the user requirements.
+3. Ensure the functional suitability of the service by promoting testing techniques that check the
+   compliance with the user requirements.
 
 4. Improve the usability by identifying the set of criteria that fosters the service adoption.
 
diff --git a/content/05.notational_conventions.md b/content/05.notational_conventions.md
index e7c08c5..ab55759 100644
--- a/content/05.notational_conventions.md
+++ b/content/05.notational_conventions.md
@@ -1,5 +1,5 @@
 # 5. Notational Conventions
 
-The keywords “MUST”, “MUST NOT”, “REQUIRED”, “SHALL”, “SHALL NOT”, “SHOULD”,
-“SHOULD NOT”, “RECOMMENDED”, “MAY”, and “OPTIONAL” in this document are to be
-interpreted as described in RFC 2119 [@url:https://www.ietf.org/rfc/rfc2119.txt].
+The keywords "MUST", "MUST NOT", "REQUIRED", "SHALL", "SHALL NOT", "SHOULD", "SHOULD NOT",
+"RECOMMENDED", "MAY", and "OPTIONAL" in this document are to be interpreted as described in RFC 2119
+[@https://www.rfc-editor.org/info/rfc2119].
diff --git a/content/06.quality_criteria.md b/content/06.quality_criteria.md
index 503cc10..e54d34a 100644
--- a/content/06.quality_criteria.md
+++ b/content/06.quality_criteria.md
@@ -1,41 +1,32 @@
 # 6. Quality Criteria {.page_break_before}
 
-The following sections describe the quality conventions and best
-practices that apply to the development, operation and integration
-phases of a **Service** with a production infrastructure for research,
-such as the EOSC ecosystem. These guidelines rule the **Service** development
-and operation process within the framework of the EOSC-Synergy project.
+The following sections describe the quality conventions and best practices that apply to the
+development, operation and integration phases of a **Service** with a production infrastructure for
+research, such as the EOSC ecosystem. These guidelines rule the **Service** development and
+operation process within the framework of the EOSC-Synergy project.
 
-**REVIEW - criteria here is complementary to SQA baseline**
-
-Some of the criteria in this document is similar or based on the
-document "Software Quality Assurance baseline"
-[@url:https://digital.csic.es/handle/10261/160086]. For such cases the
-following tag is added to the criteria: [SQA-QC.XyNN] where QC.XyNN is
-the codename of the criteria in that document.
+The criteria in this document complements the criteria described in the "Software Quality Assurance
+baseline" [@https://digital.csic.es/handle/10261/160086], while following the same pragmatic DevOps
+approach of automation.
 
 ## 6.1. Automated Deployment [SvcQC.Aud]
 
-The automated deployment of **Services** implies the use of code to install and
-configure them in the target infrastructures. Infrastructure as Code (IaC)
-templates allow operations teams to treat service provisioning and deployment in
-a similar fashion as developers manage the software code.
+The automated deployment of **Services** implies the use of code to install and configure them in
+the target infrastructures. Infrastructure as Code (IaC) templates allow operations teams to treat
+service provisioning and deployment in a similar fashion as developers manage the software code.
 
-Consequently, IaC enables the paradigm of immutable infrastructure deployment
-and maintenance, where **Services** are never updated, but deprovisioned and
-redeployed. An immutable infrastructure simplifies maintenance and enhances
-repeatability and reliability.
+Consequently, IaC enables the paradigm of immutable infrastructure deployment and maintenance, where
+**Services** are never updated, but deprovisioned and redeployed. An immutable infrastructure
+simplifies maintenance and enhances repeatability and reliability.
 
-* **[SvcQC.Aud01]** A production-ready **Service** SHOULD be deployed as a
-  workable system with the minimal user or system administrator interaction
-  leveraging IaC templates.
+* **[SvcQC.Aud01]** A production-ready **Service** SHOULD be deployed as a workable system with the
+  minimal user or system administrator interaction leveraging IaC templates.
 
-* **[SvcQC.Aud02]** Any future change to a deployed **Service** SHOULD be
-  done in the form of a new deployment, in order to preserve immutable
-  infrastructures.
+* **[SvcQC.Aud02]** Any future change to a deployed **Service** SHOULD be done in the form of a new
+  deployment, in order to preserve immutable infrastructures.
 
-* **[SvcQC.Aud03]** IaC SHOULD be validated by specific (unit) testing
-  frameworks for every change being done.
+* **[SvcQC.Aud03]** IaC SHOULD be validated by specific (unit) testing frameworks for every change
+  being done.
 
   * **[SvcQC.Aud03.1]** IaC (unit) tests MUST be idempotent.
 
@@ -47,7 +38,7 @@ the end-user or suitable for machine-to-machine communications.
 
 An accurate implementation of a publicly-accessible API is driven by a clearly
 defined specification. The OpenAPI Specification (OAS)
-[@url:https://www.openapis.org/] provides the most suitable way to describe,
+[@https://www.openapis.org] provides the most suitable way to describe,
 compose, consume and validate APIs. The following requirements assume the
 presence of such an API specification.
 
@@ -126,23 +117,23 @@ design analysis or side-effects to external systems.
 
 Performance testing verifies that the software meets the specified performance
 requirements and assesses performance characteristics - for instance,
-capacity and response time [@url:http://www.swebok.org].
+capacity and response time [@http://www.swebok.org].
 
 Stress or Load testing, exercises software at the maximum design load, as well as beyond it,
 with the goal of determining the behavioral limits, and to test defense
-mechanisms in critical systems [@url:http://www.swebok.org]. *Stress testing is
+mechanisms in critical systems [@http://www.swebok.org]. *Stress testing is
 a subset of Performance testing*
-[@url:https://www.geeksforgeeks.org/difference-between-performance-and-stress-testing/].
+[@https://www.geeksforgeeks.org/difference-between-performance-and-stress-testing].
 
 Scalability testing is a test methodology in which an application’s or **Service**
 performance is measured in terms of its ability to scale up *and/or* scale out the
 number of user requests or other such performance measure attributes, through
 an increase in the amount of available resources. The definition
-is based on [@url:https://dl.acm.org/doi/10.1145/2737182.2737185].
+is based on [@doi:10.1145/2737182.2737185].
 *Scalability testing is a subset of Performance testing*.
 
 Elasticity is based on how quickly **Services** in an infrastructure are able to
-adapt [@url:https://dl.acm.org/doi/10.1145/2737182.2737185], in response
+adapt [@doi:10.1145/2737182.2737185], in response
 to variable demand or workload for those service(s) [@doi:10.1186/s13677-019-0134-y].
 *Elasticity testing is a subset of Performance testing*.
 
@@ -163,11 +154,11 @@ to variable demand or workload for those service(s) [@doi:10.1186/s13677-019-013
 Security assessment is essential for any production **Service**. While an
 effective implementation of the security requirements applies to every stage in
 the software development life cycle (SDLC) --especially effective at the source
-code level, as discussed in [SQA-QC.Sec]--, the security testing of a
+code level, as discussed in [@https://digital.csic.es/handle/10261/160086], section [SQA-QC.Sec]--, the security testing of a
 **Service** is also --similarly to the diverse testing strategies previously
 covered-- a black-box type of testing. Hence, this section focuses on the
 runtime analysis of security-related requirements, as part of the _Dynamic
-Application Security Testing_  (_DAST_).
+Application Security Testing_  (_DAST_) as well as the _Interactive Application Security Testing_ (_IAST_).
 
 Additionally, the compliance with security policies and regulations complements
 the analysis, which can be implemented, continuously validated and monitored
@@ -194,8 +185,8 @@ suitable tool for endorsing security of **Service Composition** deployments.
 
   * **[SvcQC.Sec03.1]** In **Service Composition** environments, the
     authorization mechanism SHOULD uniquely grant the essential access
-    permissions for each **Service** according to the principle of least privilege
-    (PoLP).
+    permissions for each **Service** according to the _Principle of Least Privilege_
+    (_PoLP_).
 
 * **[SvcQC.Sec04]** The **Service** MUST validate the credentials and signatures.
 
@@ -216,26 +207,25 @@ suitable tool for endorsing security of **Service Composition** deployments.
     security vulnerabilities and any other environment-related issues (e.g. SQL
     injection, cross-site scripting or DDOS). The latest release of OWASP's Web
     Security Testing Guide
-    [@url:https://owasp.org/www-project-web-security-testing-guide/stable/] and
+    [@https://owasp.org/www-project-web-security-testing-guide/stable] and
     the NIST's Technical Guide to Information Security Testing and Assessment
-    [@url:https://doi.org/10.6028/NIST.SP.800-115] MUST be considered for 
+    [@doi:10.6028/NIST.SP.800-115] MUST be considered for
     carrying out comprehensive **Service** security testing.
 
   * **[SvcQC.Sec06.2]** Interactive Application Security Testing (IAST)
     [@https://www.veracode.com/security/interactive-application-security-testing-iast],
     analyzes code for security vulnerabilities while the app is run by an automated test. IAST SHOULD
-    be performed to software components in an operating state, while Functional Testing **[SvcQC.Fun]**,
-    is running.
+    be performed to a service in an operating state.
 
-  * **[SvcQC.Sec06.2]** Penetration testing (manual or automated) MAY be part of
+  * **[SvcQC.Sec06.3]** Penetration testing (manual or automated) MAY be part of
     the application security verification effort.
 
-  * **[SvcQC.Sec06.3]** The security assessment of the target system
+  * **[SvcQC.Sec06.4]** The security assessment of the target system
     configuration is particularly important to reduce the risk of security
     attacks. The benchmarks delivered by the Center for Internet
-    Security (CIS) [@url:https://www.cisecurity.org/cis-benchmarks/] and the
+    Security (CIS) [@https://www.cisecurity.org/cis-benchmarks] and the
     NIST's Security Assurance Requirements for Linux Application Container
-    Deployments [@url:https://doi.org/10.6028/NIST.IR.8176] MUST be considered
+    Deployments [@doi:10.6028/NIST.IR.8176] MUST be considered
     for this task.
 
 * **[SvcQC.Sec07]** IaC testing, from [SvcQC.Aud02] criterion, MUST cover the
@@ -248,7 +238,7 @@ suitable tool for endorsing security of **Service Composition** deployments.
     artefact versions in use.
 
   * **[SvcQC.Sec07.2]** SaC SHOULD verify that the artifacts are trusted and
-  digitally signed.
+    digitally signed.
 
   * **[SvcQC.Sec07.3]** SaC MUST scan IaC templates to uncover misalignments
     with widely-accepted security policies from [SvcQC.Sec06] criteria, such as
@@ -289,7 +279,7 @@ deploy, configure and manage a given Software or Service.
   target audience, varying according to the **Service** specification.
   The identified types of documentation and their RECOMMENDED content are:
 
-  * **[SvcQC.Doc07.2]** Deployment and Administration:
+  * **[SvcQC.Doc07.1]** Deployment and Administration:
 
     * Installation and configuration guides.
 
@@ -315,123 +305,10 @@ deploy, configure and manage a given Software or Service.
 
       * FAQs and troubleshooting.
 
-  * **[SvcQC.Doc07.3]** User:
+  * **[SvcQC.Doc07.2]** User:
 
     * Detailed User Guide for the **Service**.
 
     * Public API documentation (if applicable).
 
     * Command-line (CLI) reference (if applicable).
-
-## 6.8. Policies [SvcQC.Pol]
-
-Policy documents describe what are the user's expected behavior when using the
-**Service**, how they can access it and what they can expect regarding privacy
-of their data.
-
-* **[SvcQC.Pol01]** The **Service** MUST include the following policy documents:
-
-  * **[SvcQC.Pol01.1]** Acceptable Usage Policy (AUP): Is a set of rules applied
-    by the owner, creator or administrator of a network, **Service** or system, that
-    restrict the ways in which the network, **Service** or system may be used and sets
-    guidelines as to how it should be used. The AUP can also be referred to as: Acceptable
-    Use Policy or Fair Use Policy.
-
-  * **[SvcQC.Pol01.2]** Access Policy or Terms of Use: represent a binding legal
-    contract between the users (and/or customers), and the Provider of the **Service**.
-    The Access Policy mandates the users (and/or customers) access to and the use of
-    the Provider’s **Service**.
-
-  * **[SvcQC.Pol01.3]** Privacy Policy: Data privacy statement informing the users
-    (and/or customers), about which personal data is collected and processed when they
-    use and interact with the **Service**. It states which rights the users (and/or customers)
-    have regarding the processing of their data.
-
-## 6.9. Support [SvcQC.Sup]
-
-Support is the formal way by which users and operators of the **Service**
-communicate with other operators and/or developers of the **Service**,
-in case of problems, be it operational problems or bugs in the
-**Service** or underlying Software. Reporting of enhancements, improvements
-and even documentation issues.
-
-* **[SvcQC.Sup01]** The **Service** MUST have a tracker or helpdesk
-  for operational and users issues.
-
-* **[SvcQC.Sup02]** The **Service** SHOULD have a tracker for the
-  underlying software issues. [SQA-QC.Man01].
-
-* **[SvcQC.Sup03]** The **Service** SHOULD include an Operational
-  Level Agreement (OLA) with the infrastructure where it is integrated.
-
-* **[SvcQC.Sup04]** The **Service** MAY include Service Level
-  Agreement (SLA) with user communities.
-
-## 6.10. Monitoring [SvcQC.Mon]
-
-Monitoring is a periodic testing of the **Service**. It requires a monitoring
-service from where tests are executed or sent and results of those tests are shown.
-The tests can be the same, in part or in total of the Functional, Security and
-Infrastructure tests.
-The technology used for the monitoring is left to the developers of the underlying
-software to decide eventually with input from the infrastructure(s),
-where the **Service** is foreseen to be integrated.
-
-* **[SvcQC.Mon01]** The **Service** in an operational production state SHOULD
-  be monitored for functional-related criteria:
-
-  * **[SvcQC.Mon01.1]** The **Service** public endpoints MUST be monitored.
-
-  * **[SvcQC.Mon01.2]** The **Service** public APIs MUST be monitored. Use
-    functional tests of criteria [SvcQC.Fun01.2].
-
-  * **[SvcQC.Mon01.3]** The **Service** Web interface MAY be monitored. Use
-    functional tests of criteria [SvcQC.Fun01.3].
-
-* **[SvcQC.Mon02]** The **Service** MUST be monitored for security-related
-  criteria:
-
-  * **[SvcQC.Mon02.1]** The **Service** MUST be monitored for public endpoints
-    and APIs secured and strong ciphers for encryption. Use Security tests of
-    criteria [SvcQC.Sec02] and [SvcQC.Sec05].
-
-  * **[SvcQC.Mon02.2]** The **Service** SHOULD be monitored with DAST checks.
-    Use Security tests of criteria [SvcQC.Sec06].
-
-* **[SvcQC.Mon03]** The **Service** MUST be monitored for infrastructure-related
-  criteria:
-
-  * **[SvcQC.Mon03.1]** IaC (unit) tests [SvcQC.Aud02] SHOULD be reused as
-    monitoring tests, thus avoiding duplication.
-
-## 6.11. Metrics [SvcQC.Met]
-
-A metric is a quantifiable measure that is used to track and assess the status of a specific
-process.
-
-In the case of **Services**, some relevant metrics are the number
-of users registered in the **Service**, or using it actively. Also
-accounting is important to track resource usage per user or group
-of users, either or both computing and storage resources.
-
-Although the metrics may be published in external services managed
-by the infrastructure, this is a common case in federated
-infrastructures such as EOSC.
-
-* **[SvcQC.Met01]** The **Service** SHOULD implement the collection of metrics.
-
-  * **[SvcQC.Met01.1]** The collection of metrics SHOULD be cumulative over time and
-    timestamped, so that the values can be queried per time interval.
-
-  * **[SvcQC.Met01.2]** The metric *Number of registered users* SHOULD be collected.
-
-  * **[SvcQC.Met01.3]** The metric *Number of active users over a given period of time*
-    MAY be collected.
-
-  * **[SvcQC.Met01.4]** The metric *Amount of computing resources per user or per group* MAY be
-    collected. The metric unit depends on the type of service and infrastructure. An example
-    is CPU x hours.
-
-  * **[SvcQC.Met01.5]** The metric *Amount of storage resources per user or per group*
-    MAY be collected. The metric unit depends on the type of service and infrastructure.
-    An example is GByte x hours.
diff --git a/content/07.ops_quality_criteria.md b/content/07.ops_quality_criteria.md
new file mode 100644
index 0000000..29f9ba6
--- /dev/null
+++ b/content/07.ops_quality_criteria.md
@@ -0,0 +1,118 @@
+# 7. Operational Quality Criteria {.page_break_before}
+
+The following sections describe the operational quality criteria that is not fit for automation, but
+that contribute to the assessment of the quality of the service when it's in an operational
+production state.
+
+## 7.1. Policies [SvcQC.Pol]
+
+Policy documents describe what are the user's expected behavior when using the
+**Service**, how they can access it and what they can expect regarding privacy
+of their data.
+
+* **[SvcQC.Pol01]** The **Service** MUST include the following policy documents:
+
+  * **[SvcQC.Pol01.1]** Acceptable Usage Policy (AUP): Is a set of rules applied
+    by the owner, creator or administrator of a network, **Service** or system, that
+    restrict the ways in which the network, **Service** or system may be used and sets
+    guidelines as to how it should be used. The AUP can also be referred to as: Acceptable
+    Use Policy or Fair Use Policy.
+
+  * **[SvcQC.Pol01.2]** Access Policy or Terms of Use: represent a binding legal
+    contract between the users (and/or customers), and the Provider of the **Service**.
+    The Access Policy mandates the users (and/or customers) access to and the use of
+    the Provider’s **Service**.
+
+  * **[SvcQC.Pol01.3]** Privacy Policy: Data privacy statement informing the users
+    (and/or customers), about which personal data is collected and processed when they
+    use and interact with the **Service**. It states which rights the users (and/or customers)
+    have regarding the processing of their data.
+
+## 7.2. Support [SvcQC.Sup]
+
+Support is the formal way by which users and operators of the **Service**
+communicate with other operators and/or developers of the **Service**
+in case of problems, be it operational problems or bugs in the
+**Service** or underlying Software. Reporting of enhancements, improvements
+and documentation issues.
+
+* **[SvcQC.Sup01]** The **Service** MUST have a tracker or helpdesk
+  for operational and users issues.
+
+* **[SvcQC.Sup02]** The **Service** SHOULD have a tracker for the
+  underlying software issues. [SQA-QC.Man01].
+
+* **[SvcQC.Sup03]** The **Service** SHOULD include an Operational
+  Level Agreement (OLA) with the infrastructure where it is integrated.
+
+* **[SvcQC.Sup04]** The **Service** MAY include Service Level
+  Agreement (SLA) with user communities.
+
+## 7.3. Monitoring [SvcQC.Mon]
+
+Monitoring is a periodic testing of the **Service**. It requires a monitoring
+service from where tests are executed or sent and results of those tests are shown.
+The tests can be the same, in part or in total of the Functional, Security and
+Infrastructure tests.
+The technology used for the monitoring is left to the developers of the underlying
+software to decide eventually with input from the infrastructure(s),
+where the **Service** is foreseen to be integrated.
+
+* **[SvcQC.Mon01]** The **Service** in an operational production state SHOULD
+  be monitored for functional-related criteria:
+
+  * **[SvcQC.Mon01.1]** The **Service** public endpoints MUST be monitored.
+
+  * **[SvcQC.Mon01.2]** The **Service** public APIs MUST be monitored. Use
+    functional tests of criteria [SvcQC.Fun01.1].
+
+  * **[SvcQC.Mon01.3]** The **Service** Web interface MAY be monitored. Use
+    functional tests of criteria [SvcQC.Fun01.2].
+
+* **[SvcQC.Mon02]** The **Service** MUST be monitored for security-related
+  criteria:
+
+  * **[SvcQC.Mon02.1]** The **Service** MUST be monitored for public endpoints
+    and APIs secured and strong ciphers for encryption. Use Security tests of
+    criteria [SvcQC.Sec01].
+
+  * **[SvcQC.Mon02.2]** The **Service** SHOULD be monitored with DAST checks.
+    Use Security tests of criteria [SvcQC.Sec06.1].
+
+* **[SvcQC.Mon03]** The **Service** MUST be monitored for infrastructure-related
+  criteria:
+
+  * **[SvcQC.Mon03.1]** IaC (unit) tests [SvcQC.Aud02] SHOULD be reused as
+    monitoring tests, thus avoiding duplication.
+
+## 7.4. Metrics [SvcQC.Met]
+
+A metric is a quantifiable measure that is used to track and assess the status of a specific
+process.
+
+In the case of **Services**, some relevant metrics are the number
+of users registered in the **Service**, or of active users. Also
+accounting is important to track resource usage per user or group
+of users, either or both computing and storage resources.
+
+Although the metrics may be published in external services managed
+by the infrastructure, this is a common case in federated
+infrastructures such as EOSC.
+
+* **[SvcQC.Met01]** The **Service** SHOULD implement the collection of metrics.
+
+  * **[SvcQC.Met01.1]** The collection of metrics SHOULD be cumulative over time and
+    timestamped, so that the values can be queried per time interval.
+
+  * **[SvcQC.Met01.2]** The metric *Number of registered users* SHOULD be collected.
+
+  * **[SvcQC.Met01.3]** The metric *Number of active users over a given period of time*
+    MAY be collected.
+
+  * **[SvcQC.Met01.4]** The metric *Amount of computing resources per user or per group* MAY be
+    collected. The metric unit depends on the type of service and infrastructure. An example
+    is CPU x hours.
+
+  * **[SvcQC.Met01.5]** The metric *Amount of storage resources per user or per group*
+    MAY be collected. The metric unit depends on the type of service and infrastructure.
+    An example is GByte x hours.
diff --git a/content/07.glossary.md b/content/08.glossary.md
similarity index 100%
rename from content/07.glossary.md
rename to content/08.glossary.md

From abb2e634d16c7f5ec72f6956eaef615eae0785e3 Mon Sep 17 00:00:00 2001
From: mariojmdavid <mariojmdavid@gmail.com>
Date: Wed, 24 Nov 2021 11:50:50 +0000
Subject: [PATCH 38/50] issue #28

---
 content/06.quality_criteria.md     | 111 ++++++++++++++---------------
 content/07.ops_quality_criteria.md |  30 ++++----
 2 files changed, 70 insertions(+), 71 deletions(-)

diff --git a/content/06.quality_criteria.md b/content/06.quality_criteria.md
index e54d34a..416173e 100644
--- a/content/06.quality_criteria.md
+++ b/content/06.quality_criteria.md
@@ -19,16 +19,16 @@ Consequently, IaC enables the paradigm of immutable infrastructure deployment an
 **Services** are never updated, but deprovisioned and redeployed. An immutable infrastructure
 simplifies maintenance and enhances repeatability and reliability.
 
-* **[SvcQC.Aud01]** A production-ready **Service** SHOULD be deployed as a workable system with the
+* **[SvcQC.Aud01]** A production-ready **Service** **SHOULD** be deployed as a workable system with the
   minimal user or system administrator interaction leveraging IaC templates.
 
-* **[SvcQC.Aud02]** Any future change to a deployed **Service** SHOULD be done in the form of a new
+* **[SvcQC.Aud02]** Any future change to a deployed **Service** **SHOULD** be done in the form of a new
   deployment, in order to preserve immutable infrastructures.
 
-* **[SvcQC.Aud03]** IaC SHOULD be validated by specific (unit) testing frameworks for every change
+* **[SvcQC.Aud03]** IaC **SHOULD** be validated by specific (unit) testing frameworks for every change
   being done.
 
-  * **[SvcQC.Aud03.1]** IaC (unit) tests MUST be idempotent.
+  * **[SvcQC.Aud03.1]** IaC (unit) tests **MUST** be idempotent.
 
 ## 6.2. API Testing [SvcQC.Api]
 
@@ -42,13 +42,12 @@ defined specification. The OpenAPI Specification (OAS)
 compose, consume and validate APIs. The following requirements assume the
 presence of such an API specification.
 
-* **[SvcQC.Api01]** API testing MUST cover the validation of the features
+* **[SvcQC.Api01]** API testing **MUST** cover the validation of the features
   outlined in the specification (aka _contract testing_).
 
-  * **[SvcQC.Api01.1]** Any change in the API not compliant with the OAS MUST
-    NOT pass contract testing.
+  * **[SvcQC.Api01.1]** Any change in the API not compliant with the OAS **MUST NOT** pass contract testing.
 
-  * **[SvcQC.Api01.2]** The use of OAS SHOULD narrow down the applicable set of
+  * **[SvcQC.Api01.2]** The use of OAS **SHOULD** narrow down the applicable set of
     test cases to the features described in the specification, avoiding unnecessary
     assertions.
 
@@ -58,10 +57,10 @@ as the de-facto scenario for API development: i) writing the specification,
 ii) writing tests, and iii) implementing the API endpoints
 -->
 
-* **[SvcQC.Api02]** API testing MUST include the assessment of the
+* **[SvcQC.Api02]** API testing **MUST** include the assessment of the
   security-related criteria outlined in [SvcQC.Sec] section.
 
-* **[SvcQC.Api03]** API testing SHOULD involve the use of test doubles, such
+* **[SvcQC.Api03]** API testing **SHOULD** involve the use of test doubles, such
   as mock servers or stubs, that act as a validation layer for the incoming requests.
 
 ## 6.3. Integration Testing [SvcQC.Int]
@@ -71,23 +70,23 @@ coupled **Services** or parts of a system that cooperate to achieve a given
 functionality.
 
 * **[SvcQC.Int01]** Whenever a new functionality is involved, integration
-  testing MUST guarantee the operation of any previously-working interaction
+  testing **MUST** guarantee the operation of any previously-working interaction
   with external **Services**.
 
-  * When using APIs, contract testing MUST detect any disruption in the
+  * When using APIs, contract testing **MUST** detect any disruption in the
     communication between provider and consumer endpoints, through the validation
     of the API specification [SvcQC.Api01].
 
-* **[SvcQC.Int02]** Integration testing MUST NOT rely on non-operational or out-of-the-warranty services.
+* **[SvcQC.Int02]** Integration testing **MUST NOT** rely on non-operational or out-of-the-warranty services.
 
   * **[SvcQC.Int02.1]** On lack of automation, pilot service infrastructures or local testbeds
-    MAY be used.
+    **MAY** be used.
 
-  * **[SvcQC.Int02.2]** In the presence of CI environments, integration tests SHOULD be suitable for
+  * **[SvcQC.Int02.2]** In the presence of CI environments, integration tests **SHOULD** be suitable for
     the automated testing.
 
 * **[SvcQC.Int03]** Ad-hoc pilot **Service** infrastructures and/or local
-  testbeds MAY be used to cope with the integration testing requirements.
+  testbeds **MAY** be used to cope with the integration testing requirements.
 
 ## 6.4. Functional tests [SvcQC.Fun]
 
@@ -97,20 +96,20 @@ agreed design specifications. This type of **Service** testing focuses on the ev
 of the functionality that the **Service** exposes, leaving apart any internal
 design analysis or side-effects to external systems.
 
-* **[SvcQC.Fun01]** Functional testing SHOULD tend to cover the full scope
+* **[SvcQC.Fun01]** Functional testing **SHOULD** tend to cover the full scope
   --e.g. positive, negative, edge cases-- for the set of functionality that the
   **Service** claims to provide.
 
-  * **[SvcQC.Fun01.1]** When using APIs, contract testing MUST detect any
+  * **[SvcQC.Fun01.1]** When using APIs, contract testing **MUST** detect any
     disruption in the features exposed by the provider to the consumer, through
     the validation of the API specification. [SvcQC.Api01].
 
-  * **[SvcQC.Fun01.2]** Functional tests SHOULD include the Web interface of
+  * **[SvcQC.Fun01.2]** Functional tests **SHOULD** include the Web interface of
     the **Service**.
 
-* **[SvcQC.Fun02]** Functional tests SHOULD be checked automatically.
+* **[SvcQC.Fun02]** Functional tests **SHOULD** be checked automatically.
 
-* **[SvcQC.Fun03]** Functional tests SHOULD be provided by the developers
+* **[SvcQC.Fun03]** Functional tests **SHOULD** be provided by the developers
   of the underlying software.
 
 ## 6.5. Performance tests [SvcQC.Per]
@@ -137,16 +136,16 @@ adapt [@doi:10.1145/2737182.2737185], in response
 to variable demand or workload for those service(s) [@doi:10.1186/s13677-019-0134-y].
 *Elasticity testing is a subset of Performance testing*.
 
-* **[SvcQC.Per01]** Performance testing SHOULD be carried out to check the
+* **[SvcQC.Per01]** Performance testing **SHOULD** be carried out to check the
   **Service** performance under varying loads.
 
-* **[SvcQC.Per02]** Stress testing SHOULD be carried out to check the
+* **[SvcQC.Per02]** Stress testing **SHOULD** be carried out to check the
   **Service** to determine the behavioral limits under sudden increased load.
 
-* **[SvcQC.Per03]** Scalability testing MAY be carried out to check the
+* **[SvcQC.Per03]** Scalability testing **MAY** be carried out to check the
   **Service** ability to scale up *and/or* scale out when its load reaches the limits.
 
-* **[SvcQC.Per04]** Elasticity testing MAY be carried out to check the
+* **[SvcQC.Per04]** Elasticity testing **MAY** be carried out to check the
   **Service** ability to scale out or scale in, depending on its demand or workload.
 
 ## 6.6. Security [SvcQC.Sec]
@@ -165,59 +164,59 @@ the analysis, which can be implemented, continuously validated and monitored
 through the _Security as Code_ (_SaC_) capabilities. SaC is a particularly
 suitable tool for endorsing security of **Service Composition** deployments.
 
-* **[SvcQC.Sec01]** The **Service** public endpoints and APIs MUST be secured
+* **[SvcQC.Sec01]** The **Service** public endpoints and APIs **MUST** be secured
   with data encryption.
 
-  * **[SvcQC.Sec01.1]** The **Service** MUST use strong ciphers for data
+  * **[SvcQC.Sec01.1]** The **Service** **MUST** use strong ciphers for data
     encryption.
 
-* **[SvcQC.Sec02]** The **Service** SHOULD have an authentication mechanism.
+* **[SvcQC.Sec02]** The **Service** **SHOULD** have an authentication mechanism.
 
   * **[SvcQC.Sec02.1]** Whenever dealing with a **Service Composition**, such
-    as microservice architectures, the **Services** SHOULD be managed by a
+    as microservice architectures, the **Services** **SHOULD** be managed by a
     centralized authentication mechanism.
 
   * **[SvcQC.Sec02.2]** In publicly-accessible APIs, **Service**
-    authentication SHOULD be handled through an API gateway in order to control
+    authentication **SHOULD** be handled through an API gateway in order to control
     the traffic and protect the backend services from overuse.
 
-* **[SvcQC.Sec03]** The **Service** SHOULD implement an authorization mechanism.
+* **[SvcQC.Sec03]** The **Service** **SHOULD** implement an authorization mechanism.
 
   * **[SvcQC.Sec03.1]** In **Service Composition** environments, the
-    authorization mechanism SHOULD uniquely grant the essential access
+    authorization mechanism **SHOULD** uniquely grant the essential access
     permissions for each **Service** according to the _Principle of Least Privilege_
     (_PoLP_).
 
-* **[SvcQC.Sec04]** The **Service** MUST validate the credentials and signatures.
+* **[SvcQC.Sec04]** The **Service** **MUST** validate the credentials and signatures.
 
-  * **[SvcQC.Sec04.1]** Credentials used in the **Service** MUST be signed by
+  * **[SvcQC.Sec04.1]** Credentials used in the **Service** **MUST** be signed by
     a recognized and trusted certification authority.
 
-* **[SvcQC.Sec05]** The **Service** MUST handle personal data in compliance with
+* **[SvcQC.Sec05]** The **Service** **MUST** handle personal data in compliance with
   the applicable regulations, such as the General Data Protection Regulation
   (GDPR) within the European boundaries.
 
-* **[SvcQC.Sec06]** The **Service** SHOULD be audited in accordance with the
+* **[SvcQC.Sec06]** The **Service** **SHOULD** be audited in accordance with the
   black-box testing criteria identified by de-facto (cyber)security standards and
   good practices.
 
   * **[SvcQC.Sec06.1]** Dynamic application security testing (DAST)
-    checks MUST be executed, through the use of ad-hoc
+    checks **MUST** be executed, through the use of ad-hoc
     tools, directly to an operational **Service** in order to uncover runtime
     security vulnerabilities and any other environment-related issues (e.g. SQL
     injection, cross-site scripting or DDOS). The latest release of OWASP's Web
     Security Testing Guide
     [@https://owasp.org/www-project-web-security-testing-guide/stable] and
     the NIST's Technical Guide to Information Security Testing and Assessment
-    [@doi:10.6028/NIST.SP.800-115] MUST be considered for
+    [@doi:10.6028/NIST.SP.800-115] **MUST** be considered for
     carrying out comprehensive **Service** security testing.
 
   * **[SvcQC.Sec06.2]** Interactive Application Security Testing (IAST)
     [@https://www.veracode.com/security/interactive-application-security-testing-iast],
-    analyzes code for security vulnerabilities while the app is run by an automated test. IAST SHOULD
+    analyzes code for security vulnerabilities while the app is run by an automated test. IAST **SHOULD**
     be performed to a service in an operating state.
 
-  * **[SvcQC.Sec06.3]** Penetration testing (manual or automated) MAY be part of
+  * **[SvcQC.Sec06.3]** Penetration testing (manual or automated) **MAY** be part of
     the application security verification effort.
 
   * **[SvcQC.Sec06.4]** The security assessment of the target system
@@ -225,33 +224,33 @@ suitable tool for endorsing security of **Service Composition** deployments.
     attacks. The benchmarks delivered by the Center for Internet
     Security (CIS) [@https://www.cisecurity.org/cis-benchmarks] and the
     NIST's Security Assurance Requirements for Linux Application Container
-    Deployments [@doi:10.6028/NIST.IR.8176] MUST be considered
+    Deployments [@doi:10.6028/NIST.IR.8176] **MUST** be considered
     for this task.
 
-* **[SvcQC.Sec07]** IaC testing, from [SvcQC.Aud02] criterion, MUST cover the
+* **[SvcQC.Sec07]** IaC testing, from [SvcQC.Aud02] criterion, **MUST** cover the
   security auditing of the IaC templates (_SaC_) in
   order to assure the deployment of secured **Services**. For all the third-party
   dependencies used in the IaC templates (including all kind of software artifacts,
   such as Linux packages or container-based images):
 
-  * **[SvcQC.Sec07.1]** SaC MUST perform vulnerability scanning of the
+  * **[SvcQC.Sec07.1]** SaC **MUST** perform vulnerability scanning of the
     artefact versions in use.
 
-  * **[SvcQC.Sec07.2]** SaC SHOULD verify that the artifacts are trusted and
+  * **[SvcQC.Sec07.2]** SaC **SHOULD** verify that the artifacts are trusted and
     digitally signed.
 
-  * **[SvcQC.Sec07.3]** SaC MUST scan IaC templates to uncover misalignments
+  * **[SvcQC.Sec07.3]** SaC **MUST** scan IaC templates to uncover misalignments
     with widely-accepted security policies from [SvcQC.Sec06] criteria, such as
     non-encrypted secrets or disabled audit logs.
 
-  * **[SvcQC.Sec07.4]** SaC MAY be used to seek, in the IaC templates, for
+  * **[SvcQC.Sec07.4]** SaC **MAY** be used to seek, in the IaC templates, for
     violations of security requirements outlined in the applicable regulations
     from criterion [SvcQC.Sec05].
 
-  * **[SvcQC.Sec07.5]** World-writable files SHOULD NOT be created while the service is in
-    operation. Whenever they are required, the relevant files MUST be documented.
+  * **[SvcQC.Sec07.5]** World-writable files **SHOULD NOT** be created while the service is in
+    operation. Whenever they are required, the relevant files **MUST** be documented.
 
-  * **[SvcQC.Sec07.6]** World-readable files MUST NOT contain passwords.
+  * **[SvcQC.Sec07.6]** World-readable files **MUST NOT** contain passwords.
 
 ## 6.7. Documentation [SvcQC.Doc]
 
@@ -259,23 +258,23 @@ Documentation is an integral part of any Software or Service. For example,
 it describes how and what users can use and interact with it, or how operators can
 deploy, configure and manage a given Software or Service.
 
-* **[SvcQC.Doc01]** Documentation MUST be available online, easily
+* **[SvcQC.Doc01]** Documentation **MUST** be available online, easily
   findable and accessible.
 
-* **[SvcQC.Doc02]** Documentation SHOULD have a Persistent Identifier (PID).
+* **[SvcQC.Doc02]** Documentation **SHOULD** have a Persistent Identifier (PID).
 
-* **[SvcQC.Doc03]** Documentation MUST be version controlled.
+* **[SvcQC.Doc03]** Documentation **MUST** be version controlled.
 
-* **[SvcQC.Doc04]** Documentation MUST be updated on new **Service** versions
+* **[SvcQC.Doc04]** Documentation **MUST** be updated on new **Service** versions
   involving any change in the installation, configuration or behavior of
   the **Service**.
 
-* **[SvcQC.Doc05]** Documentation MUST be updated whenever reported
+* **[SvcQC.Doc05]** Documentation **MUST** be updated whenever reported
   as inaccurate or unclear.
 
-* **[SvcQC.Doc06]** Documentation MUST have a non-software license.
+* **[SvcQC.Doc06]** Documentation **MUST** have a non-software license.
 
-* **[SvcQC.Doc07]** Documentation MUST be produced according to the
+* **[SvcQC.Doc07]** Documentation **MUST** be produced according to the
   target audience, varying according to the **Service** specification.
   The identified types of documentation and their RECOMMENDED content are:
 
diff --git a/content/07.ops_quality_criteria.md b/content/07.ops_quality_criteria.md
index 29f9ba6..8e94fd4 100644
--- a/content/07.ops_quality_criteria.md
+++ b/content/07.ops_quality_criteria.md
@@ -10,7 +10,7 @@ Policy documents describe what are the user's expected behavior when using the
 **Service**, how they can access it and what they can expect regarding privacy
 of their data.
 
-* **[SvcQC.Pol01]** The **Service** MUST include the following policy documents:
+* **[SvcQC.Pol01]** The **Service** **MUST** include the following policy documents:
 
   * **[SvcQC.Pol01.1]** Acceptable Usage Policy (AUP): Is a set of rules applied
     by the owner, creator or administrator of a network, **Service** or system, that
@@ -36,13 +36,13 @@ in case of problems, be it operational problems or bugs in the
 **Service** or underlying Software. Reporting of enhancements, improvements
 and documentation issues.
 
-* **[SvcQC.Sup01]** The **Service** MUST have a tracker or helpdesk
+* **[SvcQC.Sup01]** The **Service** **MUST** have a tracker or helpdesk
   for operational and users issues.
 
-* **[SvcQC.Sup02]** The **Service** SHOULD have a tracker for the
+* **[SvcQC.Sup02]** The **Service** **SHOULD** have a tracker for the
   underlying software issues. [SQA-QC.Man01].
 
-* **[SvcQC.Sup03]** The **Service** SHOULD include an Operational
+* **[SvcQC.Sup03]** The **Service** **SHOULD** include an Operational
   Level Agreement (OLA) with the infrastructure where it is integrated.
 
 * **[SvcQC.Sup04]** The **Service** MAY include Service Level
@@ -58,31 +58,31 @@ The technology used for the monitoring is left to the developers of the underlyi
 software to decide eventually with input from the infrastructure(s),
 where the **Service** is foreseen to be integrated.
 
-* **[SvcQC.Mon01]** The **Service** in an operational production state SHOULD
+* **[SvcQC.Mon01]** The **Service** in an operational production state **SHOULD**
   be monitored for functional-related criteria:
 
-  * **[SvcQC.Mon01.1]** The **Service** public endpoints MUST be monitored.
+  * **[SvcQC.Mon01.1]** The **Service** public endpoints **MUST** be monitored.
 
-  * **[SvcQC.Mon01.2]** The **Service** public APIs MUST be monitored. Use
+  * **[SvcQC.Mon01.2]** The **Service** public APIs **MUST** be monitored. Use
     functional tests of criteria [SvcQC.Fun01.1].
 
   * **[SvcQC.Mon01.3]** The **Service** Web interface MAY be monitored. Use
     functional tests of criteria [SvcQC.Fun01.2].
 
-* **[SvcQC.Mon02]** The **Service** MUST be monitored for security-related
+* **[SvcQC.Mon02]** The **Service** **MUST** be monitored for security-related
   criteria:
 
-  * **[SvcQC.Mon02.1]** The **Service** MUST be monitored for public endpoints
+  * **[SvcQC.Mon02.1]** The **Service** **MUST** be monitored for public endpoints
     and APIs secured and strong ciphers for encryption. Use Security tests of
     criteria [SvcQC.Sec01].
 
-  * **[SvcQC.Mon02.2]** The **Service** SHOULD be monitored with DAST checks.
+  * **[SvcQC.Mon02.2]** The **Service** **SHOULD** be monitored with DAST checks.
     Use Security tests of criteria [SvcQC.Sec06.1].
 
-* **[SvcQC.Mon03]** The **Service** MUST be monitored for infrastructure-related
+* **[SvcQC.Mon03]** The **Service** **MUST** be monitored for infrastructure-related
   criteria:
 
-  * **[SvcQC.Mon03.1]** IaC (unit) tests [SvcQC.Aud02] SHOULD be reused as
+  * **[SvcQC.Mon03.1]** IaC (unit) tests [SvcQC.Aud02] **SHOULD** be reused as
     monitoring tests, thus avoiding duplication.
 
 ## 7.4. Metrics [SvcQC.Met]
@@ -99,12 +99,12 @@ Although the metrics may be published in external services managed
 by the infrastructure, this is a common case in federated
 infrastructures such as EOSC.
 
-* **[SvcQC.Met01]** The **Service** SHOULD implement the collection of metrics.
+* **[SvcQC.Met01]** The **Service** **SHOULD** implement the collection of metrics.
 
-  * **[SvcQC.Met01.1]** The collection of metrics SHOULD be cumulative over time and
+  * **[SvcQC.Met01.1]** The collection of metrics **SHOULD** be cumulative over time and
     timestamped, so that the values can be queried per time interval.
 
-  * **[SvcQC.Met01.2]** The metric *Number of registered users* SHOULD be collected.
+  * **[SvcQC.Met01.2]** The metric *Number of registered users* **SHOULD** be collected.
 
   * **[SvcQC.Met01.3]** The metric *Number of active users over a given period of time*
     MAY be collected.

From 1e295847362b5597f14f3e74c31dc217fcce6fcc Mon Sep 17 00:00:00 2001
From: mariojmdavid <mariojmdavid@gmail.com>
Date: Wed, 24 Nov 2021 11:53:03 +0000
Subject: [PATCH 39/50] issue #30

---
 content/06.quality_criteria.md | 11 ++++-------
 1 file changed, 4 insertions(+), 7 deletions(-)

diff --git a/content/06.quality_criteria.md b/content/06.quality_criteria.md
index 416173e..5102032 100644
--- a/content/06.quality_criteria.md
+++ b/content/06.quality_criteria.md
@@ -79,14 +79,11 @@ functionality.
 
 * **[SvcQC.Int02]** Integration testing **MUST NOT** rely on non-operational or out-of-the-warranty services.
 
-  * **[SvcQC.Int02.1]** On lack of automation, pilot service infrastructures or local testbeds
-    **MAY** be used.
-
-  * **[SvcQC.Int02.2]** In the presence of CI environments, integration tests **SHOULD** be suitable for
-    the automated testing.
-
-* **[SvcQC.Int03]** Ad-hoc pilot **Service** infrastructures and/or local
+* **[SvcQC.Int03]** On lack of automation, ad-hoc pilot **Service** infrastructures and/or local
   testbeds **MAY** be used to cope with the integration testing requirements.
+  
+* **[SvcQC.Int04]** In the presence of CI environments, integration tests **SHOULD** be suitable for
+  the automated testing.
 
 ## 6.4. Functional tests [SvcQC.Fun]
 

From b5327999c8a5ccbb15aa8b425149399815a035c7 Mon Sep 17 00:00:00 2001
From: mariojmdavid <mariojmdavid@gmail.com>
Date: Wed, 24 Nov 2021 14:03:44 +0000
Subject: [PATCH 40/50] issue #6

---
 content/06.quality_criteria.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/content/06.quality_criteria.md b/content/06.quality_criteria.md
index 5102032..e88e3f8 100644
--- a/content/06.quality_criteria.md
+++ b/content/06.quality_criteria.md
@@ -269,7 +269,7 @@ deploy, configure and manage a given Software or Service.
 * **[SvcQC.Doc05]** Documentation **MUST** be updated whenever reported
   as inaccurate or unclear.
 
-* **[SvcQC.Doc06]** Documentation **MUST** have a non-software license.
+* **[SvcQC.Doc06]** Documentation **SHOULD** have a non-software license.
 
 * **[SvcQC.Doc07]** Documentation **MUST** be produced according to the
   target audience, varying according to the **Service** specification.

From 21666cc93f8d2c9ac6918810aa3e854543be0990 Mon Sep 17 00:00:00 2001
From: mariojmdavid <mariojmdavid@gmail.com>
Date: Wed, 24 Nov 2021 14:50:43 +0000
Subject: [PATCH 41/50] issue #15

---
 content/06.quality_criteria.md     | 20 ++++++++++----------
 content/07.ops_quality_criteria.md | 10 +++++-----
 2 files changed, 15 insertions(+), 15 deletions(-)

diff --git a/content/06.quality_criteria.md b/content/06.quality_criteria.md
index e88e3f8..51b66ac 100644
--- a/content/06.quality_criteria.md
+++ b/content/06.quality_criteria.md
@@ -9,7 +9,7 @@ The criteria in this document complements the criteria described in the "Softwar
 baseline" [@https://digital.csic.es/handle/10261/160086], while following the same pragmatic DevOps
 approach of automation.
 
-## 6.1. Automated Deployment [SvcQC.Aud]
+## 6.1. Automated Deployment [SvcQC.Aud] {#aud}
 
 The automated deployment of **Services** implies the use of code to install and configure them in
 the target infrastructures. Infrastructure as Code (IaC) templates allow operations teams to treat
@@ -30,7 +30,7 @@ simplifies maintenance and enhances repeatability and reliability.
 
   * **[SvcQC.Aud03.1]** IaC (unit) tests **MUST** be idempotent.
 
-## 6.2. API Testing [SvcQC.Api]
+## 6.2. API Testing [SvcQC.Api] {#api01}
 
 Web services commonly use application programming interfaces (APIs) to expose
 the available features to external consumers, which can be either oriented to
@@ -58,7 +58,7 @@ ii) writing tests, and iii) implementing the API endpoints
 -->
 
 * **[SvcQC.Api02]** API testing **MUST** include the assessment of the
-  security-related criteria outlined in [SvcQC.Sec] section.
+  security-related criteria outlined in [SvcQC.Sec](#security) section.
 
 * **[SvcQC.Api03]** API testing **SHOULD** involve the use of test doubles, such
   as mock servers or stubs, that act as a validation layer for the incoming requests.
@@ -75,7 +75,7 @@ functionality.
 
   * When using APIs, contract testing **MUST** detect any disruption in the
     communication between provider and consumer endpoints, through the validation
-    of the API specification [SvcQC.Api01].
+    of the API specification [SvcQC.Api01](#api01).
 
 * **[SvcQC.Int02]** Integration testing **MUST NOT** rely on non-operational or out-of-the-warranty services.
 
@@ -85,7 +85,7 @@ functionality.
 * **[SvcQC.Int04]** In the presence of CI environments, integration tests **SHOULD** be suitable for
   the automated testing.
 
-## 6.4. Functional tests [SvcQC.Fun]
+## 6.4. Functional tests [SvcQC.Fun] {#fun}
 
 Functional testing is a type of black-box testing. It involves the verification
 of the **Service** identified functionality, based on requested requirements and
@@ -99,7 +99,7 @@ design analysis or side-effects to external systems.
 
   * **[SvcQC.Fun01.1]** When using APIs, contract testing **MUST** detect any
     disruption in the features exposed by the provider to the consumer, through
-    the validation of the API specification. [SvcQC.Api01].
+    the validation of the API specification. [SvcQC.Api01](#api01).
 
   * **[SvcQC.Fun01.2]** Functional tests **SHOULD** include the Web interface of
     the **Service**.
@@ -145,7 +145,7 @@ to variable demand or workload for those service(s) [@doi:10.1186/s13677-019-013
 * **[SvcQC.Per04]** Elasticity testing **MAY** be carried out to check the
   **Service** ability to scale out or scale in, depending on its demand or workload.
 
-## 6.6. Security [SvcQC.Sec]
+## 6.6. Security [SvcQC.Sec] {#security}
 
 Security assessment is essential for any production **Service**. While an
 effective implementation of the security requirements applies to every stage in
@@ -224,7 +224,7 @@ suitable tool for endorsing security of **Service Composition** deployments.
     Deployments [@doi:10.6028/NIST.IR.8176] **MUST** be considered
     for this task.
 
-* **[SvcQC.Sec07]** IaC testing, from [SvcQC.Aud02] criterion, **MUST** cover the
+* **[SvcQC.Sec07]** IaC testing, from [SvcQC.Aud02](#aud) criterion, **MUST** cover the
   security auditing of the IaC templates (_SaC_) in
   order to assure the deployment of secured **Services**. For all the third-party
   dependencies used in the IaC templates (including all kind of software artifacts,
@@ -237,12 +237,12 @@ suitable tool for endorsing security of **Service Composition** deployments.
     digitally signed.
 
   * **[SvcQC.Sec07.3]** SaC **MUST** scan IaC templates to uncover misalignments
-    with widely-accepted security policies from [SvcQC.Sec06] criteria, such as
+    with widely-accepted security policies from [SvcQC.Sec06](#security) criteria, such as
     non-encrypted secrets or disabled audit logs.
 
   * **[SvcQC.Sec07.4]** SaC **MAY** be used to seek, in the IaC templates, for
     violations of security requirements outlined in the applicable regulations
-    from criterion [SvcQC.Sec05].
+    from criterion [SvcQC.Sec05](#security).
 
   * **[SvcQC.Sec07.5]** World-writable files **SHOULD NOT** be created while the service is in
     operation. Whenever they are required, the relevant files **MUST** be documented.
diff --git a/content/07.ops_quality_criteria.md b/content/07.ops_quality_criteria.md
index 8e94fd4..1015a07 100644
--- a/content/07.ops_quality_criteria.md
+++ b/content/07.ops_quality_criteria.md
@@ -40,7 +40,7 @@ and documentation issues.
   for operational and users issues.
 
 * **[SvcQC.Sup02]** The **Service** **SHOULD** have a tracker for the
-  underlying software issues. [SQA-QC.Man01].
+  underlying software issues [@https://digital.csic.es/handle/10261/160086], section [SQA-QC.Man01].
 
 * **[SvcQC.Sup03]** The **Service** **SHOULD** include an Operational
   Level Agreement (OLA) with the infrastructure where it is integrated.
@@ -64,10 +64,10 @@ where the **Service** is foreseen to be integrated.
   * **[SvcQC.Mon01.1]** The **Service** public endpoints **MUST** be monitored.
 
   * **[SvcQC.Mon01.2]** The **Service** public APIs **MUST** be monitored. Use
-    functional tests of criteria [SvcQC.Fun01.1].
+    functional tests of criteria [SvcQC.Fun01.1](#fun).
 
   * **[SvcQC.Mon01.3]** The **Service** Web interface MAY be monitored. Use
-    functional tests of criteria [SvcQC.Fun01.2].
+    functional tests of criteria [SvcQC.Fun01.2](#fun).
 
 * **[SvcQC.Mon02]** The **Service** **MUST** be monitored for security-related
   criteria:
@@ -77,12 +77,12 @@ where the **Service** is foreseen to be integrated.
     criteria [SvcQC.Sec01].
 
   * **[SvcQC.Mon02.2]** The **Service** **SHOULD** be monitored with DAST checks.
-    Use Security tests of criteria [SvcQC.Sec06.1].
+    Use Security tests of criteria [SvcQC.Sec06.1](#security).
 
 * **[SvcQC.Mon03]** The **Service** **MUST** be monitored for infrastructure-related
   criteria:
 
-  * **[SvcQC.Mon03.1]** IaC (unit) tests [SvcQC.Aud02] **SHOULD** be reused as
+  * **[SvcQC.Mon03.1]** IaC (unit) tests [SvcQC.Aud02](#aud) **SHOULD** be reused as
     monitoring tests, thus avoiding duplication.
 
 ## 7.4. Metrics [SvcQC.Met]

From f62b0a135babdb813655dfcad72b0b8439553e9f Mon Sep 17 00:00:00 2001
From: mariojmdavid <mariojmdavid@gmail.com>
Date: Wed, 24 Nov 2021 15:05:41 +0000
Subject: [PATCH 42/50] issue #23

---
 content/06.quality_criteria.md | 2 +-
 content/08.glossary.md         | 3 +++
 2 files changed, 4 insertions(+), 1 deletion(-)

diff --git a/content/06.quality_criteria.md b/content/06.quality_criteria.md
index 51b66ac..149a913 100644
--- a/content/06.quality_criteria.md
+++ b/content/06.quality_criteria.md
@@ -101,7 +101,7 @@ design analysis or side-effects to external systems.
     disruption in the features exposed by the provider to the consumer, through
     the validation of the API specification. [SvcQC.Api01](#api01).
 
-  * **[SvcQC.Fun01.2]** Functional tests **SHOULD** include the Web interface of
+  * **[SvcQC.Fun01.2]** Functional tests **SHOULD** include the Web Interface or Graphical User Interface (GUI)) of
     the **Service**.
 
 * **[SvcQC.Fun02]** Functional tests **SHOULD** be checked automatically.
diff --git a/content/08.glossary.md b/content/08.glossary.md
index f2410d5..14b3555 100644
--- a/content/08.glossary.md
+++ b/content/08.glossary.md
@@ -18,6 +18,9 @@ __EOSC__
 __GDPR__
 : General Data Protection Regulation
 
+__GUI__
+: Graphical User Interface
+
 __IaC__
 : Infrastructure as Code
 

From 25396c8bc6398ca1f41064a3fa2b6646532a2db9 Mon Sep 17 00:00:00 2001
From: mariojmdavid <mariojmdavid@gmail.com>
Date: Wed, 24 Nov 2021 16:05:31 +0000
Subject: [PATCH 43/50] MD formating

---
 content/02.document-log.md         |   2 +-
 content/06.quality_criteria.md     | 293 +++++++++++++----------------
 content/07.ops_quality_criteria.md | 127 ++++++-------
 3 files changed, 193 insertions(+), 229 deletions(-)

diff --git a/content/02.document-log.md b/content/02.document-log.md
index c105ca2..e88e67a 100644
--- a/content/02.document-log.md
+++ b/content/02.document-log.md
@@ -6,4 +6,4 @@
 | v0.2         | 28/02/2020 | Second draft version |
 | v1.0-beta03  | 09/06/2020 | beta03 draft version |
 | v1.0         | 12/06/2020 | v1.0 release         |
-| v1.1         | 11/2021 | Issues: #25        |
+| v1.1         | 11/2021 | Issues: #6, #15, #23, #25, #27, #28, #29, #30 |
diff --git a/content/06.quality_criteria.md b/content/06.quality_criteria.md
index 149a913..30a1e0b 100644
--- a/content/06.quality_criteria.md
+++ b/content/06.quality_criteria.md
@@ -19,37 +19,36 @@ Consequently, IaC enables the paradigm of immutable infrastructure deployment an
 **Services** are never updated, but deprovisioned and redeployed. An immutable infrastructure
 simplifies maintenance and enhances repeatability and reliability.
 
-* **[SvcQC.Aud01]** A production-ready **Service** **SHOULD** be deployed as a workable system with the
-  minimal user or system administrator interaction leveraging IaC templates.
+* **[SvcQC.Aud01]** A production-ready **Service** **SHOULD** be deployed as a workable system with
+  the minimal user or system administrator interaction leveraging IaC templates.
 
-* **[SvcQC.Aud02]** Any future change to a deployed **Service** **SHOULD** be done in the form of a new
-  deployment, in order to preserve immutable infrastructures.
+* **[SvcQC.Aud02]** Any future change to a deployed **Service** **SHOULD** be done in the form of a
+  new deployment, in order to preserve immutable infrastructures.
 
-* **[SvcQC.Aud03]** IaC **SHOULD** be validated by specific (unit) testing frameworks for every change
-  being done.
+* **[SvcQC.Aud03]** IaC **SHOULD** be validated by specific (unit) testing frameworks for every
+  change being done.
 
   * **[SvcQC.Aud03.1]** IaC (unit) tests **MUST** be idempotent.
 
 ## 6.2. API Testing [SvcQC.Api] {#api01}
 
-Web services commonly use application programming interfaces (APIs) to expose
-the available features to external consumers, which can be either oriented to
-the end-user or suitable for machine-to-machine communications.
+Web services commonly use application programming interfaces (APIs) to expose the available features
+to external consumers, which can be either oriented to the end-user or suitable for
+machine-to-machine communications.
 
-An accurate implementation of a publicly-accessible API is driven by a clearly
-defined specification. The OpenAPI Specification (OAS)
-[@https://www.openapis.org] provides the most suitable way to describe,
-compose, consume and validate APIs. The following requirements assume the
-presence of such an API specification.
+Accurate implementation of a publicly-accessible API, is driven by a clearly defined specification.
+The OpenAPI Specification (OAS) [@https://www.openapis.org] provides the most suitable way to
+describe, compose, consume and validate APIs. The following requirements assume the presence of such
+an API specification.
 
-* **[SvcQC.Api01]** API testing **MUST** cover the validation of the features
-  outlined in the specification (aka _contract testing_).
+* **[SvcQC.Api01]** API testing **MUST** cover the validation of the features outlined in the
+  specification (aka _contract testing_).
 
-  * **[SvcQC.Api01.1]** Any change in the API not compliant with the OAS **MUST NOT** pass contract testing.
+  * **[SvcQC.Api01.1]** Any change in the API not compliant with the OAS **MUST NOT** pass contract
+    testing.
 
-  * **[SvcQC.Api01.2]** The use of OAS **SHOULD** narrow down the applicable set of
-    test cases to the features described in the specification, avoiding unnecessary
-    assertions.
+  * **[SvcQC.Api01.2]** The use of OAS **SHOULD** narrow down the applicable set of test cases to
+    the features described in the specification, avoiding unnecessary assertions.
 
 <!--
 * [Future Link to the SW baseline] OAS fosters test-driven development (TDD)
@@ -57,27 +56,26 @@ as the de-facto scenario for API development: i) writing the specification,
 ii) writing tests, and iii) implementing the API endpoints
 -->
 
-* **[SvcQC.Api02]** API testing **MUST** include the assessment of the
-  security-related criteria outlined in [SvcQC.Sec](#security) section.
+* **[SvcQC.Api02]** API testing **MUST** include the assessment of the security-related criteria
+  outlined in [SvcQC.Sec](#security) section.
 
-* **[SvcQC.Api03]** API testing **SHOULD** involve the use of test doubles, such
-  as mock servers or stubs, that act as a validation layer for the incoming requests.
+* **[SvcQC.Api03]** API testing **SHOULD** involve the use of test doubles, such as mock servers or
+  stubs, that act as a validation layer for the incoming requests.
 
 ## 6.3. Integration Testing [SvcQC.Int]
 
-Integration testing refers to the evaluation of the interactions among
-coupled **Services** or parts of a system that cooperate to achieve a given
-functionality.
+Integration testing refers to the evaluation of the interactions among coupled **Services** or parts
+of a system that cooperate to achieve a given functionality.
 
-* **[SvcQC.Int01]** Whenever a new functionality is involved, integration
-  testing **MUST** guarantee the operation of any previously-working interaction
-  with external **Services**.
+* **[SvcQC.Int01]** Whenever a new functionality is involved, integration testing **MUST** guarantee
+  the operation of any previously-working interaction with external **Services**.
 
-  * When using APIs, contract testing **MUST** detect any disruption in the
-    communication between provider and consumer endpoints, through the validation
-    of the API specification [SvcQC.Api01](#api01).
+  * When using APIs, contract testing **MUST** detect any disruption in the communication between
+    provider and consumer endpoints, through the validation of the API specification
+    [SvcQC.Api01](#api01).
 
-* **[SvcQC.Int02]** Integration testing **MUST NOT** rely on non-operational or out-of-the-warranty services.
+* **[SvcQC.Int02]** Integration testing **MUST NOT** rely on non-operational or out-of-the-warranty
+  services.
 
 * **[SvcQC.Int03]** On lack of automation, ad-hoc pilot **Service** infrastructures and/or local
   testbeds **MAY** be used to cope with the integration testing requirements.
@@ -87,162 +85,144 @@ functionality.
 
 ## 6.4. Functional tests [SvcQC.Fun] {#fun}
 
-Functional testing is a type of black-box testing. It involves the verification
-of the **Service** identified functionality, based on requested requirements and
-agreed design specifications. This type of **Service** testing focuses on the evaluation
-of the functionality that the **Service** exposes, leaving apart any internal
-design analysis or side-effects to external systems.
+Functional testing is a type of black-box testing. It involves the verification of the **Service**
+identified functionality, based on requested requirements and agreed design specifications. This
+type of **Service** testing focuses on the evaluation of the functionality that the **Service**
+exposes, leaving apart any internal design analysis or side-effects to external systems.
 
-* **[SvcQC.Fun01]** Functional testing **SHOULD** tend to cover the full scope
-  --e.g. positive, negative, edge cases-- for the set of functionality that the
-  **Service** claims to provide.
+* **[SvcQC.Fun01]** Functional testing **SHOULD** tend to cover the full scope --e.g. positive,
+  negative, edge cases-- for the set of functionality that the **Service** claims to provide.
 
-  * **[SvcQC.Fun01.1]** When using APIs, contract testing **MUST** detect any
-    disruption in the features exposed by the provider to the consumer, through
-    the validation of the API specification. [SvcQC.Api01](#api01).
+  * **[SvcQC.Fun01.1]** When using APIs, contract testing **MUST** detect any disruption in the
+    features exposed by the provider to the consumer, through the validation of the API
+    specification. [SvcQC.Api01](#api01).
 
-  * **[SvcQC.Fun01.2]** Functional tests **SHOULD** include the Web Interface or Graphical User Interface (GUI)) of
-    the **Service**.
+  * **[SvcQC.Fun01.2]** Functional tests **SHOULD** include the Web Interface or Graphical User
+    Interface (GUI)) of the **Service**.
 
 * **[SvcQC.Fun02]** Functional tests **SHOULD** be checked automatically.
 
-* **[SvcQC.Fun03]** Functional tests **SHOULD** be provided by the developers
-  of the underlying software.
+* **[SvcQC.Fun03]** Functional tests **SHOULD** be provided by the developers of the underlying
+  software.
 
 ## 6.5. Performance tests [SvcQC.Per]
 
-Performance testing verifies that the software meets the specified performance
-requirements and assesses performance characteristics - for instance,
-capacity and response time [@http://www.swebok.org].
+Performance testing verifies that the software meets the specified performance requirements and
+assesses performance characteristics - for instance, capacity and response time
+[@http://www.swebok.org].
 
-Stress or Load testing, exercises software at the maximum design load, as well as beyond it,
-with the goal of determining the behavioral limits, and to test defense
-mechanisms in critical systems [@http://www.swebok.org]. *Stress testing is
-a subset of Performance testing*
+Stress or Load testing, exercises software at the maximum design load, as well as beyond it, with
+the goal of determining the behavioral limits, and to test defense mechanisms in critical systems
+[@http://www.swebok.org]. *Stress testing is a subset of Performance testing*
 [@https://www.geeksforgeeks.org/difference-between-performance-and-stress-testing].
 
-Scalability testing is a test methodology in which an application’s or **Service**
-performance is measured in terms of its ability to scale up *and/or* scale out the
-number of user requests or other such performance measure attributes, through
-an increase in the amount of available resources. The definition
-is based on [@doi:10.1145/2737182.2737185].
-*Scalability testing is a subset of Performance testing*.
+Scalability testing is a test methodology in which an application’s or **Service** performance is
+measured in terms of its ability to scale up *and/or* scale out the number of user requests or
+other such performance measure attributes, through an increase in the amount of available resources.
+The definition is based on [@doi:10.1145/2737182.2737185]. *Scalability testing is a subset of
+Performance testing*.
 
-Elasticity is based on how quickly **Services** in an infrastructure are able to
-adapt [@doi:10.1145/2737182.2737185], in response
-to variable demand or workload for those service(s) [@doi:10.1186/s13677-019-0134-y].
-*Elasticity testing is a subset of Performance testing*.
+Elasticity is based on how quickly **Services** in an infrastructure are able to adapt
+[@doi:10.1145/2737182.2737185], in response to variable demand or workload for those service(s)
+[@doi:10.1186/s13677-019-0134-y]. *Elasticity testing is a subset of Performance testing*.
 
-* **[SvcQC.Per01]** Performance testing **SHOULD** be carried out to check the
-  **Service** performance under varying loads.
+* **[SvcQC.Per01]** Performance testing **SHOULD** be carried out to check the **Service**
+  performance under varying loads.
 
-* **[SvcQC.Per02]** Stress testing **SHOULD** be carried out to check the
-  **Service** to determine the behavioral limits under sudden increased load.
+* **[SvcQC.Per02]** Stress testing **SHOULD** be carried out to check the **Service** to determine
+  the behavioral limits under sudden increased load.
 
-* **[SvcQC.Per03]** Scalability testing **MAY** be carried out to check the
-  **Service** ability to scale up *and/or* scale out when its load reaches the limits.
+* **[SvcQC.Per03]** Scalability testing **MAY** be carried out to check the **Service** ability to
+  scale up *and/or* scale out when its load reaches the limits.
 
-* **[SvcQC.Per04]** Elasticity testing **MAY** be carried out to check the
-  **Service** ability to scale out or scale in, depending on its demand or workload.
+* **[SvcQC.Per04]** Elasticity testing **MAY** be carried out to check the **Service** ability to
+  scale out or scale in, depending on its demand or workload.
 
 ## 6.6. Security [SvcQC.Sec] {#security}
 
-Security assessment is essential for any production **Service**. While an
-effective implementation of the security requirements applies to every stage in
-the software development life cycle (SDLC) --especially effective at the source
-code level, as discussed in [@https://digital.csic.es/handle/10261/160086], section [SQA-QC.Sec]--, the security testing of a
-**Service** is also --similarly to the diverse testing strategies previously
-covered-- a black-box type of testing. Hence, this section focuses on the
-runtime analysis of security-related requirements, as part of the _Dynamic
-Application Security Testing_  (_DAST_) as well as the _Interactive Application Security Testing_ (_IAST_).
+Security assessment is essential for any production **Service**. While an effective implementation
+of the security requirements applies to every stage in the software development life cycle (SDLC)
+--especially effective at the source code level, as discussed in
+[@https://digital.csic.es/handle/10261/160086], section [SQA-QC.Sec]--, the security testing of a
+**Service** is also --similarly to the diverse testing strategies previously covered-- a black-box
+type of testing. Hence, this section focuses on the runtime analysis of security-related
+requirements, as part of the _Dynamic Application Security Testing_  (_DAST_) as well as the
+_Interactive Application Security Testing_ (_IAST_).
 
-Additionally, the compliance with security policies and regulations complements
-the analysis, which can be implemented, continuously validated and monitored
-through the _Security as Code_ (_SaC_) capabilities. SaC is a particularly
-suitable tool for endorsing security of **Service Composition** deployments.
+Additionally, the compliance with security policies and regulations complements the analysis, which
+can be implemented, continuously validated and monitored through the _Security as Code_ (_SaC_)
+capabilities. SaC is a particularly suitable tool for endorsing security of **Service Composition**
+deployments.
 
-* **[SvcQC.Sec01]** The **Service** public endpoints and APIs **MUST** be secured
-  with data encryption.
+* **[SvcQC.Sec01]** The **Service** public endpoints and APIs **MUST** be secured with data
+  encryption.
 
-  * **[SvcQC.Sec01.1]** The **Service** **MUST** use strong ciphers for data
-    encryption.
+  * **[SvcQC.Sec01.1]** The **Service** **MUST** use strong ciphers for data encryption.
 
 * **[SvcQC.Sec02]** The **Service** **SHOULD** have an authentication mechanism.
 
-  * **[SvcQC.Sec02.1]** Whenever dealing with a **Service Composition**, such
-    as microservice architectures, the **Services** **SHOULD** be managed by a
-    centralized authentication mechanism.
+  * **[SvcQC.Sec02.1]** Whenever dealing with a **Service Composition**, such as microservice
+    architectures, the **Services** **SHOULD** be managed by a centralized authentication mechanism.
 
-  * **[SvcQC.Sec02.2]** In publicly-accessible APIs, **Service**
-    authentication **SHOULD** be handled through an API gateway in order to control
-    the traffic and protect the backend services from overuse.
+  * **[SvcQC.Sec02.2]** In publicly-accessible APIs, **Service** authentication **SHOULD** be
+    handled through an API gateway in order to control the traffic and protect the backend services
+    from overuse.
 
 * **[SvcQC.Sec03]** The **Service** **SHOULD** implement an authorization mechanism.
 
-  * **[SvcQC.Sec03.1]** In **Service Composition** environments, the
-    authorization mechanism **SHOULD** uniquely grant the essential access
-    permissions for each **Service** according to the _Principle of Least Privilege_
-    (_PoLP_).
+  * **[SvcQC.Sec03.1]** In **Service Composition** environments, the authorization mechanism
+    **SHOULD** uniquely grant the essential access permissions for each **Service** according to the
+    _Principle of Least Privilege_ (_PoLP_).
 
 * **[SvcQC.Sec04]** The **Service** **MUST** validate the credentials and signatures.
 
-  * **[SvcQC.Sec04.1]** Credentials used in the **Service** **MUST** be signed by
-    a recognized and trusted certification authority.
+  * **[SvcQC.Sec04.1]** Credentials used in the **Service** **MUST** be signed by a recognized and
+    trusted certification authority.
 
-* **[SvcQC.Sec05]** The **Service** **MUST** handle personal data in compliance with
-  the applicable regulations, such as the General Data Protection Regulation
-  (GDPR) within the European boundaries.
+* **[SvcQC.Sec05]** The **Service** **MUST** handle personal data in compliance with the applicable
+  regulations, such as the General Data Protection Regulation (GDPR) within the European boundaries.
 
-* **[SvcQC.Sec06]** The **Service** **SHOULD** be audited in accordance with the
-  black-box testing criteria identified by de-facto (cyber)security standards and
-  good practices.
+* **[SvcQC.Sec06]** The **Service** **SHOULD** be audited in accordance with the black-box testing
+  criteria identified by de-facto (cyber)security standards and good practices.
 
-  * **[SvcQC.Sec06.1]** Dynamic application security testing (DAST)
-    checks **MUST** be executed, through the use of ad-hoc
-    tools, directly to an operational **Service** in order to uncover runtime
-    security vulnerabilities and any other environment-related issues (e.g. SQL
-    injection, cross-site scripting or DDOS). The latest release of OWASP's Web
-    Security Testing Guide
-    [@https://owasp.org/www-project-web-security-testing-guide/stable] and
-    the NIST's Technical Guide to Information Security Testing and Assessment
-    [@doi:10.6028/NIST.SP.800-115] **MUST** be considered for
-    carrying out comprehensive **Service** security testing.
+  * **[SvcQC.Sec06.1]** Dynamic application security testing (DAST) checks **MUST** be executed,
+    through the use of ad-hoc tools, directly to an operational **Service** in order to uncover
+    runtime security vulnerabilities and any other environment-related issues (e.g. SQL injection,
+    cross-site scripting or DDOS). The latest release of OWASP's Web Security Testing Guide
+    [@https://owasp.org/www-project-web-security-testing-guide/stable] and the NIST's Technical
+    Guide to Information Security Testing and Assessment [@doi:10.6028/NIST.SP.800-115] **MUST** be
+    considered for carrying out comprehensive **Service** security testing.
 
   * **[SvcQC.Sec06.2]** Interactive Application Security Testing (IAST)
-    [@https://www.veracode.com/security/interactive-application-security-testing-iast],
-    analyzes code for security vulnerabilities while the app is run by an automated test. IAST **SHOULD**
-    be performed to a service in an operating state.
+    [@https://www.veracode.com/security/interactive-application-security-testing-iast], analyzes
+    code for security vulnerabilities while the app is run by an automated test. IAST **SHOULD** be
+    performed to a service in an operating state.
 
-  * **[SvcQC.Sec06.3]** Penetration testing (manual or automated) **MAY** be part of
-    the application security verification effort.
+  * **[SvcQC.Sec06.3]** Penetration testing (manual or automated) **MAY** be part of the application
+    security verification effort.
 
-  * **[SvcQC.Sec06.4]** The security assessment of the target system
-    configuration is particularly important to reduce the risk of security
-    attacks. The benchmarks delivered by the Center for Internet
-    Security (CIS) [@https://www.cisecurity.org/cis-benchmarks] and the
-    NIST's Security Assurance Requirements for Linux Application Container
-    Deployments [@doi:10.6028/NIST.IR.8176] **MUST** be considered
-    for this task.
+  * **[SvcQC.Sec06.4]** The security assessment of the target system configuration is particularly
+    important to reduce the risk of security attacks. The benchmarks delivered by the Center for
+    Internet Security (CIS) [@https://www.cisecurity.org/cis-benchmarks] and the NIST's Security
+    Assurance Requirements for Linux Application Container Deployments [@doi:10.6028/NIST.IR.8176]
+    **MUST** be considered for this task.
 
-* **[SvcQC.Sec07]** IaC testing, from [SvcQC.Aud02](#aud) criterion, **MUST** cover the
-  security auditing of the IaC templates (_SaC_) in
-  order to assure the deployment of secured **Services**. For all the third-party
-  dependencies used in the IaC templates (including all kind of software artifacts,
-  such as Linux packages or container-based images):
+* **[SvcQC.Sec07]** IaC testing, from [SvcQC.Aud02](#aud) criterion, **MUST** cover the security
+  auditing of the IaC templates (_SaC_) in order to assure the deployment of secured **Services**.
+  For all the third-party dependencies used in the IaC templates (including all kind of software
+  artifacts, such as Linux packages or container-based images):
 
-  * **[SvcQC.Sec07.1]** SaC **MUST** perform vulnerability scanning of the
-    artefact versions in use.
+  * **[SvcQC.Sec07.1]** SaC **MUST** perform vulnerability scanning of the artefact versions in use.
 
-  * **[SvcQC.Sec07.2]** SaC **SHOULD** verify that the artifacts are trusted and
-    digitally signed.
+  * **[SvcQC.Sec07.2]** SaC **SHOULD** verify that the artifacts are trusted and digitally signed.
 
-  * **[SvcQC.Sec07.3]** SaC **MUST** scan IaC templates to uncover misalignments
-    with widely-accepted security policies from [SvcQC.Sec06](#security) criteria, such as
-    non-encrypted secrets or disabled audit logs.
+  * **[SvcQC.Sec07.3]** SaC **MUST** scan IaC templates to uncover misalignments with widely
+    accepted security policies from [SvcQC.Sec06](#security) criteria, such as non-encrypted secrets
+    or disabled audit logs.
 
-  * **[SvcQC.Sec07.4]** SaC **MAY** be used to seek, in the IaC templates, for
-    violations of security requirements outlined in the applicable regulations
-    from criterion [SvcQC.Sec05](#security).
+  * **[SvcQC.Sec07.4]** SaC **MAY** be used to seek, in the IaC templates, for violations of
+    security requirements outlined in the applicable regulations from criterion
+    [SvcQC.Sec05](#security).
 
   * **[SvcQC.Sec07.5]** World-writable files **SHOULD NOT** be created while the service is in
     operation. Whenever they are required, the relevant files **MUST** be documented.
@@ -251,29 +231,26 @@ suitable tool for endorsing security of **Service Composition** deployments.
 
 ## 6.7. Documentation [SvcQC.Doc]
 
-Documentation is an integral part of any Software or Service. For example,
-it describes how and what users can use and interact with it, or how operators can
-deploy, configure and manage a given Software or Service.
+Documentation is an integral part of any Software or Service. For example, it describes how and what
+users can use and interact with it, or how operators can deploy, configure and manage a given
+Software or Service.
 
-* **[SvcQC.Doc01]** Documentation **MUST** be available online, easily
-  findable and accessible.
+* **[SvcQC.Doc01]** Documentation **MUST** be available online, easily findable and accessible.
 
 * **[SvcQC.Doc02]** Documentation **SHOULD** have a Persistent Identifier (PID).
 
 * **[SvcQC.Doc03]** Documentation **MUST** be version controlled.
 
-* **[SvcQC.Doc04]** Documentation **MUST** be updated on new **Service** versions
-  involving any change in the installation, configuration or behavior of
-  the **Service**.
+* **[SvcQC.Doc04]** Documentation **MUST** be updated on new **Service** versions involving any
+  change in the installation, configuration or behavior of the **Service**.
 
-* **[SvcQC.Doc05]** Documentation **MUST** be updated whenever reported
-  as inaccurate or unclear.
+* **[SvcQC.Doc05]** Documentation **MUST** be updated whenever reported as inaccurate or unclear.
 
 * **[SvcQC.Doc06]** Documentation **SHOULD** have a non-software license.
 
-* **[SvcQC.Doc07]** Documentation **MUST** be produced according to the
-  target audience, varying according to the **Service** specification.
-  The identified types of documentation and their RECOMMENDED content are:
+* **[SvcQC.Doc07]** Documentation **MUST** be produced according to the target audience, varying
+  according to the **Service** specification. The identified types of documentation and their
+  RECOMMENDED content are:
 
   * **[SvcQC.Doc07.1]** Deployment and Administration:
 
diff --git a/content/07.ops_quality_criteria.md b/content/07.ops_quality_criteria.md
index 1015a07..1e5ab94 100644
--- a/content/07.ops_quality_criteria.md
+++ b/content/07.ops_quality_criteria.md
@@ -6,98 +6,85 @@ production state.
 
 ## 7.1. Policies [SvcQC.Pol]
 
-Policy documents describe what are the user's expected behavior when using the
-**Service**, how they can access it and what they can expect regarding privacy
-of their data.
+Policy documents describe what are the user's expected behavior when using the **Service**, how they
+can access it and what they can expect regarding privacy of their data.
 
 * **[SvcQC.Pol01]** The **Service** **MUST** include the following policy documents:
 
-  * **[SvcQC.Pol01.1]** Acceptable Usage Policy (AUP): Is a set of rules applied
-    by the owner, creator or administrator of a network, **Service** or system, that
-    restrict the ways in which the network, **Service** or system may be used and sets
-    guidelines as to how it should be used. The AUP can also be referred to as: Acceptable
-    Use Policy or Fair Use Policy.
+  * **[SvcQC.Pol01.1]** Acceptable Usage Policy (AUP): Is a set of rules applied by the owner,
+    creator or administrator of a network, **Service** or system, that restrict the ways in which
+    the network, **Service** or system may be used and sets guidelines as to how it should be used.
+    The AUP can also be referred to as: Acceptable Use Policy or Fair Use Policy.
 
-  * **[SvcQC.Pol01.2]** Access Policy or Terms of Use: represent a binding legal
-    contract between the users (and/or customers), and the Provider of the **Service**.
-    The Access Policy mandates the users (and/or customers) access to and the use of
-    the Provider’s **Service**.
+  * **[SvcQC.Pol01.2]** Access Policy or Terms of Use: represent a binding legal contract between
+    the users (and/or customers), and the Provider of the **Service**. The Access Policy mandates
+    the users (and/or customers) access to and the use of the Provider’s **Service**.
 
-  * **[SvcQC.Pol01.3]** Privacy Policy: Data privacy statement informing the users
-    (and/or customers), about which personal data is collected and processed when they
-    use and interact with the **Service**. It states which rights the users (and/or customers)
-    have regarding the processing of their data.
+  * **[SvcQC.Pol01.3]** Privacy Policy: Data privacy statement informing the users (and/or
+    customers), about which personal data is collected and processed when they use and interact with
+    the **Service**. It states which rights the users (and/or customers) have regarding the
+    processing of their data.
 
 ## 7.2. Support [SvcQC.Sup]
 
-Support is the formal way by which users and operators of the **Service**
-communicate with other operators and/or developers of the **Service**
-in case of problems, be it operational problems or bugs in the
-**Service** or underlying Software. Reporting of enhancements, improvements
-and documentation issues.
+Support is the formal way by which users and operators of the **Service** communicate with other
+operators and/or developers of the **Service** in case of problems, be it operational problems or
+bugs in the **Service** or underlying Software. Reporting of enhancements, improvements and
+documentation issues.
 
-* **[SvcQC.Sup01]** The **Service** **MUST** have a tracker or helpdesk
-  for operational and users issues.
+* **[SvcQC.Sup01]** The **Service** **MUST** have a tracker or helpdesk for operational and users
+  issues.
 
-* **[SvcQC.Sup02]** The **Service** **SHOULD** have a tracker for the
-  underlying software issues [@https://digital.csic.es/handle/10261/160086], section [SQA-QC.Man01].
+* **[SvcQC.Sup02]** The **Service** **SHOULD** have a tracker for the underlying software issues
+  [@https://digital.csic.es/handle/10261/160086], section [SQA-QC.Man01].
 
-* **[SvcQC.Sup03]** The **Service** **SHOULD** include an Operational
-  Level Agreement (OLA) with the infrastructure where it is integrated.
+* **[SvcQC.Sup03]** The **Service** **SHOULD** include an Operational Level Agreement (OLA) with the
+  infrastructure where it is integrated.
 
-* **[SvcQC.Sup04]** The **Service** MAY include Service Level
-  Agreement (SLA) with user communities.
+* **[SvcQC.Sup04]** The **Service** MAY include Service Level Agreement (SLA) with user communities.
 
 ## 7.3. Monitoring [SvcQC.Mon]
 
-Monitoring is a periodic testing of the **Service**. It requires a monitoring
-service from where tests are executed or sent and results of those tests are shown.
-The tests can be the same, in part or in total of the Functional, Security and
-Infrastructure tests.
-The technology used for the monitoring is left to the developers of the underlying
-software to decide eventually with input from the infrastructure(s),
-where the **Service** is foreseen to be integrated.
+Monitoring is a periodic testing of the **Service**. It requires a monitoring service from where
+tests are executed or sent and results of those tests are shown. The tests can be the same, in part
+or in total of the Functional, Security and Infrastructure tests. The technology used for the
+monitoring is left to the developers of the underlying software to decide eventually with input
+from the infrastructure(s), where the **Service** is foreseen to be integrated.
 
-* **[SvcQC.Mon01]** The **Service** in an operational production state **SHOULD**
-  be monitored for functional-related criteria:
+* **[SvcQC.Mon01]** The **Service** in an operational production state **SHOULD** be monitored for
+  functional-related criteria:
 
   * **[SvcQC.Mon01.1]** The **Service** public endpoints **MUST** be monitored.
 
-  * **[SvcQC.Mon01.2]** The **Service** public APIs **MUST** be monitored. Use
-    functional tests of criteria [SvcQC.Fun01.1](#fun).
+  * **[SvcQC.Mon01.2]** The **Service** public APIs **MUST** be monitored. Use functional tests of
+    criteria [SvcQC.Fun01.1](#fun).
 
-  * **[SvcQC.Mon01.3]** The **Service** Web interface MAY be monitored. Use
-    functional tests of criteria [SvcQC.Fun01.2](#fun).
+  * **[SvcQC.Mon01.3]** The **Service** Web interface MAY be monitored. Use functional tests of
+    criteria [SvcQC.Fun01.2](#fun).
 
-* **[SvcQC.Mon02]** The **Service** **MUST** be monitored for security-related
-  criteria:
+* **[SvcQC.Mon02]** The **Service** **MUST** be monitored for security-related criteria:
 
-  * **[SvcQC.Mon02.1]** The **Service** **MUST** be monitored for public endpoints
-    and APIs secured and strong ciphers for encryption. Use Security tests of
-    criteria [SvcQC.Sec01].
+  * **[SvcQC.Mon02.1]** The **Service** **MUST** be monitored for public endpoints and APIs secured
+    and strong ciphers for encryption. Use Security tests of criteria [SvcQC.Sec01].
 
-  * **[SvcQC.Mon02.2]** The **Service** **SHOULD** be monitored with DAST checks.
-    Use Security tests of criteria [SvcQC.Sec06.1](#security).
+  * **[SvcQC.Mon02.2]** The **Service** **SHOULD** be monitored with DAST checks. Use Security tests
+    of criteria [SvcQC.Sec06.1](#security).
 
-* **[SvcQC.Mon03]** The **Service** **MUST** be monitored for infrastructure-related
-  criteria:
+* **[SvcQC.Mon03]** The **Service** **MUST** be monitored for infrastructure-related criteria:
 
-  * **[SvcQC.Mon03.1]** IaC (unit) tests [SvcQC.Aud02](#aud) **SHOULD** be reused as
-    monitoring tests, thus avoiding duplication.
+  * **[SvcQC.Mon03.1]** IaC (unit) tests [SvcQC.Aud02](#aud) **SHOULD** be reused as monitoring
+    tests, thus avoiding duplication.
 
 ## 7.4. Metrics [SvcQC.Met]
 
-A metric is a quantifiable measure that is used to track and assess the status of a specific
-process.
+A metric is a quantifiable measure used to track and assess the status of a specific process.
 
-In the case of **Services**, some relevant metrics are the number
-of users registered in the **Service**, or of active users. Also
-accounting is important to track resource usage per user or group
-of users, either or both computing and storage resources.
+In the case of **Services**, some relevant metrics are the number of users registered in the
+**Service**, or of active users. Also accounting is important to track resource usage per user or
+group of users, either or both computing and storage resources.
 
-Although the metrics may be published in external services managed
-by the infrastructure, this is a common case in federated
-infrastructures such as EOSC.
+Although the metrics may be published in external services managed by the infrastructure, this is a
+common case in federated infrastructures such as EOSC.
 
 * **[SvcQC.Met01]** The **Service** **SHOULD** implement the collection of metrics.
 
@@ -106,13 +93,13 @@ infrastructures such as EOSC.
 
   * **[SvcQC.Met01.2]** The metric *Number of registered users* **SHOULD** be collected.
 
-  * **[SvcQC.Met01.3]** The metric *Number of active users over a given period of time*
-    MAY be collected.
+  * **[SvcQC.Met01.3]** The metric *Number of active users over a given period of time* **MAY** be
+    collected.
 
-  * **[SvcQC.Met01.4]** The metric *Amount of computing resources per user or per group* MAY be
-    collected. The metric unit depends on the type of service and infrastructure. An example
-    is CPU x hours.
+  * **[SvcQC.Met01.4]** The metric *Amount of computing resources per user or per group* **MAY** be
+    collected. The metric unit depends on the type of service and infrastructure. An example is
+    `CPU x hours`.
 
-  * **[SvcQC.Met01.5]** The metric *Amount of storage resources per user or per group*
-    MAY be collected. The metric unit depends on the type of service and infrastructure.
-    An example is GByte x hours.
+  * **[SvcQC.Met01.5]** The metric *Amount of storage resources per user or per group* **MAY** be
+    collected. The metric unit depends on the type of service and infrastructure. An example is
+    `TByte x month`.

From 2744cd12bc0f5a26e991965f8a066908e6a124d0 Mon Sep 17 00:00:00 2001
From: mariojmdavid <mariojmdavid@gmail.com>
Date: Wed, 24 Nov 2021 16:08:16 +0000
Subject: [PATCH 44/50] typo

---
 content/07.ops_quality_criteria.md | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/content/07.ops_quality_criteria.md b/content/07.ops_quality_criteria.md
index 1e5ab94..367aa71 100644
--- a/content/07.ops_quality_criteria.md
+++ b/content/07.ops_quality_criteria.md
@@ -1,8 +1,8 @@
 # 7. Operational Quality Criteria {.page_break_before}
 
-The following sections describe the operational quality criteria that is not fit for automation, but
-that contribute to the assessment of the quality of the service when it's in an operational
-production state.
+This section describe the operational quality criteria that is not fit for automation, but that
+contribute to the assessment of the quality of the service when it's in an operational production
+state.
 
 ## 7.1. Policies [SvcQC.Pol]
 

From 3b75ea81eeccf891b7a5709292eb161f6ad8ffb6 Mon Sep 17 00:00:00 2001
From: mariojmdavid <mariojmdavid@gmail.com>
Date: Wed, 24 Nov 2021 16:09:36 +0000
Subject: [PATCH 45/50] typo

---
 content/07.ops_quality_criteria.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/content/07.ops_quality_criteria.md b/content/07.ops_quality_criteria.md
index 367aa71..a77b691 100644
--- a/content/07.ops_quality_criteria.md
+++ b/content/07.ops_quality_criteria.md
@@ -1,6 +1,6 @@
 # 7. Operational Quality Criteria {.page_break_before}
 
-This section describe the operational quality criteria that is not fit for automation, but that
+This section describes the operational quality criteria that is not fit for automation, but that
 contribute to the assessment of the quality of the service when it's in an operational production
 state.
 

From c9e682ae8c09ddada4d9512d8c77ced9a94eedd3 Mon Sep 17 00:00:00 2001
From: mariojmdavid <mariojmdavid@gmail.com>
Date: Thu, 9 Dec 2021 10:45:29 +0000
Subject: [PATCH 46/50] issues #31 #32 #33 #34 #35 #36

---
 content/06.quality_criteria.md     | 26 +++++++++++++-------------
 content/07.ops_quality_criteria.md |  4 ++--
 2 files changed, 15 insertions(+), 15 deletions(-)

diff --git a/content/06.quality_criteria.md b/content/06.quality_criteria.md
index 30a1e0b..62ca850 100644
--- a/content/06.quality_criteria.md
+++ b/content/06.quality_criteria.md
@@ -9,7 +9,7 @@ The criteria in this document complements the criteria described in the "Softwar
 baseline" [@https://digital.csic.es/handle/10261/160086], while following the same pragmatic DevOps
 approach of automation.
 
-## 6.1. Automated Deployment [SvcQC.Aud] {#aud}
+## 6.1. Automated Deployment [SvcQC.Dep] {#dep}
 
 The automated deployment of **Services** implies the use of code to install and configure them in
 the target infrastructures. Infrastructure as Code (IaC) templates allow operations teams to treat
@@ -19,16 +19,16 @@ Consequently, IaC enables the paradigm of immutable infrastructure deployment an
 **Services** are never updated, but deprovisioned and redeployed. An immutable infrastructure
 simplifies maintenance and enhances repeatability and reliability.
 
-* **[SvcQC.Aud01]** A production-ready **Service** **SHOULD** be deployed as a workable system with
+* **[SvcQC.Dep01]** A production-ready **Service** **SHOULD** be deployed as a workable system with
   the minimal user or system administrator interaction leveraging IaC templates.
 
-* **[SvcQC.Aud02]** Any future change to a deployed **Service** **SHOULD** be done in the form of a
+* **[SvcQC.Dep02]** Any future change to a deployed **Service** **SHOULD** be done in the form of a
   new deployment, in order to preserve immutable infrastructures.
 
-* **[SvcQC.Aud03]** IaC **SHOULD** be validated by specific (unit) testing frameworks for every
+* **[SvcQC.Dep03]** IaC **SHOULD** be validated by specific (unit) testing frameworks for every
   change being done.
 
-  * **[SvcQC.Aud03.1]** IaC (unit) tests **MUST** be idempotent.
+  * **[SvcQC.Dep03.1]** IaC (unit) tests **MUST** be idempotent.
 
 ## 6.2. API Testing [SvcQC.Api] {#api01}
 
@@ -70,9 +70,9 @@ of a system that cooperate to achieve a given functionality.
 * **[SvcQC.Int01]** Whenever a new functionality is involved, integration testing **MUST** guarantee
   the operation of any previously-working interaction with external **Services**.
 
-  * When using APIs, contract testing **MUST** detect any disruption in the communication between
-    provider and consumer endpoints, through the validation of the API specification
-    [SvcQC.Api01](#api01).
+  * **[SvcQC.Int01.1]** When using APIs, contract testing **MUST** detect any disruption in the
+    communication between provider and consumer endpoints, through the validation of the API
+    specification [SvcQC.Api01](#api01).
 
 * **[SvcQC.Int02]** Integration testing **MUST NOT** rely on non-operational or out-of-the-warranty
   services.
@@ -98,7 +98,7 @@ exposes, leaving apart any internal design analysis or side-effects to external
     specification. [SvcQC.Api01](#api01).
 
   * **[SvcQC.Fun01.2]** Functional tests **SHOULD** include the Web Interface or Graphical User
-    Interface (GUI)) of the **Service**.
+    Interface (GUI) of the **Service**.
 
 * **[SvcQC.Fun02]** Functional tests **SHOULD** be checked automatically.
 
@@ -143,9 +143,9 @@ Elasticity is based on how quickly **Services** in an infrastructure are able to
 Security assessment is essential for any production **Service**. While an effective implementation
 of the security requirements applies to every stage in the software development life cycle (SDLC)
 --especially effective at the source code level, as discussed in
-[@https://digital.csic.es/handle/10261/160086], section [SQA-QC.Sec]--, the security testing of a
-**Service** is also --similarly to the diverse testing strategies previously covered-- a black-box
-type of testing. Hence, this section focuses on the runtime analysis of security-related
+[@https://digital.csic.es/handle/10261/160086], section *Security **[SQA-QC.Sec]***--, the security
+testing of a **Service** is also --similarly to the diverse testing strategies previously covered--
+a black-box type of testing. Hence, this section focuses on the runtime analysis of security-related
 requirements, as part of the _Dynamic Application Security Testing_  (_DAST_) as well as the
 _Interactive Application Security Testing_ (_IAST_).
 
@@ -207,7 +207,7 @@ deployments.
     Assurance Requirements for Linux Application Container Deployments [@doi:10.6028/NIST.IR.8176]
     **MUST** be considered for this task.
 
-* **[SvcQC.Sec07]** IaC testing, from [SvcQC.Aud02](#aud) criterion, **MUST** cover the security
+* **[SvcQC.Sec07]** IaC testing, from [SvcQC.Aud02](#dep) criterion, **MUST** cover the security
   auditing of the IaC templates (_SaC_) in order to assure the deployment of secured **Services**.
   For all the third-party dependencies used in the IaC templates (including all kind of software
   artifacts, such as Linux packages or container-based images):
diff --git a/content/07.ops_quality_criteria.md b/content/07.ops_quality_criteria.md
index a77b691..e840ce7 100644
--- a/content/07.ops_quality_criteria.md
+++ b/content/07.ops_quality_criteria.md
@@ -59,13 +59,13 @@ from the infrastructure(s), where the **Service** is foreseen to be integrated.
   * **[SvcQC.Mon01.2]** The **Service** public APIs **MUST** be monitored. Use functional tests of
     criteria [SvcQC.Fun01.1](#fun).
 
-  * **[SvcQC.Mon01.3]** The **Service** Web interface MAY be monitored. Use functional tests of
+  * **[SvcQC.Mon01.3]** The **Service** Web interface **MAY** be monitored. Use functional tests of
     criteria [SvcQC.Fun01.2](#fun).
 
 * **[SvcQC.Mon02]** The **Service** **MUST** be monitored for security-related criteria:
 
   * **[SvcQC.Mon02.1]** The **Service** **MUST** be monitored for public endpoints and APIs secured
-    and strong ciphers for encryption. Use Security tests of criteria [SvcQC.Sec01].
+    and strong ciphers for encryption. Use Security tests of criteria [SvcQC.Sec01](#security).
 
   * **[SvcQC.Mon02.2]** The **Service** **SHOULD** be monitored with DAST checks. Use Security tests
     of criteria [SvcQC.Sec06.1](#security).

From 11e2a66b2eeeeedfa22a6608527869c337ae9770 Mon Sep 17 00:00:00 2001
From: mariojmdavid <mariojmdavid@gmail.com>
Date: Wed, 2 Feb 2022 13:58:24 +0000
Subject: [PATCH 47/50] update document log, md formating

---
 content/02.document-log.md     |  2 +-
 content/06.quality_criteria.md | 14 +++++++-------
 2 files changed, 8 insertions(+), 8 deletions(-)

diff --git a/content/02.document-log.md b/content/02.document-log.md
index e88e67a..c8f9108 100644
--- a/content/02.document-log.md
+++ b/content/02.document-log.md
@@ -6,4 +6,4 @@
 | v0.2         | 28/02/2020 | Second draft version |
 | v1.0-beta03  | 09/06/2020 | beta03 draft version |
 | v1.0         | 12/06/2020 | v1.0 release         |
-| v1.1         | 11/2021 | Issues: #6, #15, #23, #25, #27, #28, #29, #30 |
+| v2.0         | 02/02/2022 | Issues: #6, #15, #23, #25, #27, #28, #29, #30, #31, #32, #33, #34, #35, #36 |
diff --git a/content/06.quality_criteria.md b/content/06.quality_criteria.md
index 62ca850..8e37661 100644
--- a/content/06.quality_criteria.md
+++ b/content/06.quality_criteria.md
@@ -113,18 +113,18 @@ assesses performance characteristics - for instance, capacity and response time
 
 Stress or Load testing, exercises software at the maximum design load, as well as beyond it, with
 the goal of determining the behavioral limits, and to test defense mechanisms in critical systems
-[@http://www.swebok.org]. *Stress testing is a subset of Performance testing*
+[@http://www.swebok.org]. _Stress testing is a subset of Performance testing_
 [@https://www.geeksforgeeks.org/difference-between-performance-and-stress-testing].
 
 Scalability testing is a test methodology in which an application’s or **Service** performance is
-measured in terms of its ability to scale up *and/or* scale out the number of user requests or
+measured in terms of its ability to scale up _and/or_ scale out the number of user requests or
 other such performance measure attributes, through an increase in the amount of available resources.
-The definition is based on [@doi:10.1145/2737182.2737185]. *Scalability testing is a subset of
-Performance testing*.
+The definition is based on [@doi:10.1145/2737182.2737185]. _Scalability testing is a subset of
+Performance testing_.
 
 Elasticity is based on how quickly **Services** in an infrastructure are able to adapt
 [@doi:10.1145/2737182.2737185], in response to variable demand or workload for those service(s)
-[@doi:10.1186/s13677-019-0134-y]. *Elasticity testing is a subset of Performance testing*.
+[@doi:10.1186/s13677-019-0134-y]. _Elasticity testing is a subset of Performance testing_.
 
 * **[SvcQC.Per01]** Performance testing **SHOULD** be carried out to check the **Service**
   performance under varying loads.
@@ -133,7 +133,7 @@ Elasticity is based on how quickly **Services** in an infrastructure are able to
   the behavioral limits under sudden increased load.
 
 * **[SvcQC.Per03]** Scalability testing **MAY** be carried out to check the **Service** ability to
-  scale up *and/or* scale out when its load reaches the limits.
+  scale up _and/or_ scale out when its load reaches the limits.
 
 * **[SvcQC.Per04]** Elasticity testing **MAY** be carried out to check the **Service** ability to
   scale out or scale in, depending on its demand or workload.
@@ -143,7 +143,7 @@ Elasticity is based on how quickly **Services** in an infrastructure are able to
 Security assessment is essential for any production **Service**. While an effective implementation
 of the security requirements applies to every stage in the software development life cycle (SDLC)
 --especially effective at the source code level, as discussed in
-[@https://digital.csic.es/handle/10261/160086], section *Security **[SQA-QC.Sec]***--, the security
+[@https://digital.csic.es/handle/10261/160086], section _Security **[SQA-QC.Sec]**_--, the security
 testing of a **Service** is also --similarly to the diverse testing strategies previously covered--
 a black-box type of testing. Hence, this section focuses on the runtime analysis of security-related
 requirements, as part of the _Dynamic Application Security Testing_  (_DAST_) as well as the

From f50728c042f54ca2c34904ba33aa6a2af3d06233 Mon Sep 17 00:00:00 2001
From: mariojmdavid <mariojmdavid@gmail.com>
Date: Wed, 2 Feb 2022 15:40:04 +0000
Subject: [PATCH 48/50] update author email

---
 content/metadata.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/content/metadata.yaml b/content/metadata.yaml
index e161ab4..1eddad8 100644
--- a/content/metadata.yaml
+++ b/content/metadata.yaml
@@ -22,7 +22,7 @@ authors:
     name: Mario David
     github: mariojmdavid
     orcid: 0000-0003-1802-5356
-    email: mario@lip.pt
+    email: david@lip.pt
     affiliation: Laboratory of Instrumentation and Experimental Particle Physics (LIP)
   -
     name: Jorge Gomes

From 9e6243d930e1255f5140001d4c1e814e3fea2b13 Mon Sep 17 00:00:00 2001
From: mariojmdavid <mariojmdavid@gmail.com>
Date: Thu, 3 Feb 2022 08:45:19 +0000
Subject: [PATCH 49/50] add author, implment PR comment

---
 content/06.quality_criteria.md |  8 +-------
 content/metadata.yaml          | 19 +++++++++++++++----
 2 files changed, 16 insertions(+), 11 deletions(-)

diff --git a/content/06.quality_criteria.md b/content/06.quality_criteria.md
index 8e37661..0f28ca2 100644
--- a/content/06.quality_criteria.md
+++ b/content/06.quality_criteria.md
@@ -50,12 +50,6 @@ an API specification.
   * **[SvcQC.Api01.2]** The use of OAS **SHOULD** narrow down the applicable set of test cases to
     the features described in the specification, avoiding unnecessary assertions.
 
-<!--
-* [Future Link to the SW baseline] OAS fosters test-driven development (TDD)
-as the de-facto scenario for API development: i) writing the specification,
-ii) writing tests, and iii) implementing the API endpoints
--->
-
 * **[SvcQC.Api02]** API testing **MUST** include the assessment of the security-related criteria
   outlined in [SvcQC.Sec](#security) section.
 
@@ -133,7 +127,7 @@ Elasticity is based on how quickly **Services** in an infrastructure are able to
   the behavioral limits under sudden increased load.
 
 * **[SvcQC.Per03]** Scalability testing **MAY** be carried out to check the **Service** ability to
-  scale up _and/or_ scale out when its load reaches the limits.
+  scale up or scale down when its load reaches the limits.
 
 * **[SvcQC.Per04]** Elasticity testing **MAY** be carried out to check the **Service** ability to
   scale out or scale in, depending on its demand or workload.
diff --git a/content/metadata.yaml b/content/metadata.yaml
index 1eddad8..41570a3 100644
--- a/content/metadata.yaml
+++ b/content/metadata.yaml
@@ -23,25 +23,29 @@ authors:
     github: mariojmdavid
     orcid: 0000-0003-1802-5356
     email: david@lip.pt
-    affiliation: Laboratory of Instrumentation and Experimental Particle Physics (LIP)
+    affiliation:
+      - Laboratory of Instrumentation and Experimental Particle Physics (LIP)
   -
     name: Jorge Gomes
     github: jorge-lip
     orcid: 0000-0002-9142-2596
     email: jorge@lip.pt
-    affiliation: Laboratory of Instrumentation and Experimental Particle Physics (LIP)
+    affiliation:
+      - Laboratory of Instrumentation and Experimental Particle Physics (LIP)
   -
     name: Joao Pina
     github: jopina
     orcid: 0000-0001-8959-5044
     email: jpina@lip.pt
-    affiliation: Laboratory of Instrumentation and Experimental Particle Physics (LIP)
+    affiliation:
+      - Laboratory of Instrumentation and Experimental Particle Physics (LIP)
   -
     name: Samuel Bernardo
     github: samuelbernardolip
     orcid: 0000-0002-6175-4012
     email: samuel@lip.pt
-    affiliation: Laboratory of Instrumentation and Experimental Particle Physics (LIP)
+    affiliation:
+      - Laboratory of Instrumentation and Experimental Particle Physics (LIP)
   -
     name: Isabel Campos
     github: isabel-campos-plasencia
@@ -64,3 +68,10 @@ authors:
     email: micafer1@upv.es
     affiliations:
       - Universitat Politècnica de València (UPV)
+  -
+    name: Vyacheslav Tykhonov
+    github: 4tikhonov
+    orcid:  0000-0001-9447-9830
+    email: vyacheslav.tykhonov@dans.knaw.nl
+    affiliation:
+      - DANS-KNAW

From e9ee4ebf47d8c31d1eb9454306927a3775a50e91 Mon Sep 17 00:00:00 2001
From: mariojmdavid <mariojmdavid@gmail.com>
Date: Thu, 3 Feb 2022 08:49:38 +0000
Subject: [PATCH 50/50] fix authors affiliattions

---
 content/metadata.yaml | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/content/metadata.yaml b/content/metadata.yaml
index 41570a3..9f6305d 100644
--- a/content/metadata.yaml
+++ b/content/metadata.yaml
@@ -23,28 +23,28 @@ authors:
     github: mariojmdavid
     orcid: 0000-0003-1802-5356
     email: david@lip.pt
-    affiliation:
+    affiliations:
       - Laboratory of Instrumentation and Experimental Particle Physics (LIP)
   -
     name: Jorge Gomes
     github: jorge-lip
     orcid: 0000-0002-9142-2596
     email: jorge@lip.pt
-    affiliation:
+    affiliations:
       - Laboratory of Instrumentation and Experimental Particle Physics (LIP)
   -
     name: Joao Pina
     github: jopina
     orcid: 0000-0001-8959-5044
     email: jpina@lip.pt
-    affiliation:
+    affiliations:
       - Laboratory of Instrumentation and Experimental Particle Physics (LIP)
   -
     name: Samuel Bernardo
     github: samuelbernardolip
     orcid: 0000-0002-6175-4012
     email: samuel@lip.pt
-    affiliation:
+    affiliations:
       - Laboratory of Instrumentation and Experimental Particle Physics (LIP)
   -
     name: Isabel Campos
@@ -73,5 +73,5 @@ authors:
     github: 4tikhonov
     orcid:  0000-0001-9447-9830
     email: vyacheslav.tykhonov@dans.knaw.nl
-    affiliation:
+    affiliations:
       - DANS-KNAW