Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

docs: add extensive externally hosted docs #177

Open
wants to merge 49 commits into
base: dev
Choose a base branch
from
Open
Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
49 commits
Select commit Hold shift + click to select a range
8003399
docs: describe ZARP output
fgypas Sep 18, 2024
5011f23
Add multiqc output files
fgypas Oct 8, 2024
19db053
Fix typo
fgypas Oct 8, 2024
2779ae9
Add output file description
fgypas Oct 8, 2024
6570e36
Update README
fgypas Oct 8, 2024
6b6a39a
Update README and citation
fgypas Oct 9, 2024
f85a648
Test deployment from branch
fgypas Oct 9, 2024
21c571d
docs:add installation guide
mkatsanto Oct 10, 2024
25d1291
Move description of output files in github page outputs.md
fgypas Oct 12, 2024
fc22d04
Add section in nav bar
fgypas Oct 12, 2024
dc26daa
Test images path
fgypas Oct 12, 2024
06b4ce1
Change path of images under guides
fgypas Oct 12, 2024
5724434
Fix paths
fgypas Oct 12, 2024
0b22ff3
Move execution documentation to the docs page
fgypas Oct 13, 2024
acef1cf
Update usage and outputs
fgypas Oct 13, 2024
ed8aeeb
Add outputs for HTSinfer
fgypas Oct 13, 2024
0f9a991
Add contribute section
fgypas Oct 13, 2024
ea99f3c
Add contribute options
fgypas Oct 13, 2024
caa9cad
Fix indentation
fgypas Oct 13, 2024
1e98a25
guides/contribute.md -> guides/parameterization.md
fgypas Oct 14, 2024
b631f14
Documentation
fgypas Oct 14, 2024
caefd94
Dockerfile, add docker test and update in samtools dependency
fgypas Oct 20, 2024
588d6a6
Remove TTY option and interactive mode from docker execution
fgypas Oct 21, 2024
2c4562c
Remove md5sum
fgypas Oct 21, 2024
caae76f
Debug data ownership in docker test
fgypas Oct 21, 2024
f5b780e
Add clean up step
fgypas Oct 22, 2024
062005f
Add docker instructions
fgypas Oct 27, 2024
984b266
Add section Expand zarp with a new package in documentation
fgypas Dec 2, 2024
3221b08
Fix header
fgypas Dec 2, 2024
339b9d2
Try to fix ssl issue
fgypas Dec 5, 2024
82cbf0c
Add openssl in yml
fgypas Dec 5, 2024
e9a7979
Disable openssl
fgypas Dec 5, 2024
8b2d32f
Disable lint test
fgypas Dec 5, 2024
32e37ca
Disable rulegraph test
fgypas Dec 5, 2024
f7162e3
Disable dag test
fgypas Dec 5, 2024
96f9bc0
Add pyopenssl
fgypas Dec 5, 2024
91a29f2
Use mamba version lower than 2
fgypas Dec 5, 2024
6a0a7aa
Show mamba version
fgypas Dec 5, 2024
1dc9bbe
Restrict to version 1 of mamba in tests
fgypas Dec 5, 2024
b67cb2b
Apply to all tests
fgypas Dec 5, 2024
40fa1cb
Remove docker from PR
fgypas Dec 19, 2024
fce4260
Simplify main README.md
fgypas Dec 19, 2024
95b18c7
Render list
fgypas Dec 19, 2024
3684cd1
Improve usage.md
fgypas Dec 19, 2024
d7af25e
Update documentation based on PR feedback
fgypas Dec 22, 2024
e6961e7
Fix small rendering issues
fgypas Dec 22, 2024
f1e00f5
Fix CI
fgypas Dec 22, 2024
625edfd
Update CI
fgypas Dec 22, 2024
53ed475
Specify exact version of base R
fgypas Dec 22, 2024
File filter

Filter by extension

Filter by extension


Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
17 changes: 9 additions & 8 deletions .github/workflows/ci.yml
Original file line number Diff line number Diff line change
Expand Up @@ -25,7 +25,7 @@ jobs:
uses: conda-incubator/setup-miniconda@v3
with:
python-version: "3.10"
mamba-version: "*"
mamba-version: "1"
channels: conda-forge
channel-priority: true
auto-update-conda: false
Expand Down Expand Up @@ -73,7 +73,7 @@ jobs:
uses: conda-incubator/setup-miniconda@v3
with:
python-version: "3.10"
mamba-version: "*"
mamba-version: "1"
channels: conda-forge
channel-priority: true
auto-update-conda: false
Expand All @@ -82,7 +82,9 @@ jobs:
auto-activate-base: false

- name: Update zarp env with root. packages
run: mamba env update -p $CONDA_PREFIX -f install/environment.root.yml
run: |
mamba --version
mamba env update -p $CONDA_PREFIX -f install/environment.root.yml

- name: Update zarp env with dev. packages
run: mamba env update -p $CONDA_PREFIX -f install/environment.dev.yml
Expand Down Expand Up @@ -116,7 +118,7 @@ jobs:
uses: conda-incubator/setup-miniconda@v3
with:
python-version: "3.10"
mamba-version: "*"
mamba-version: "1"
channels: conda-forge
channel-priority: true
auto-update-conda: false
Expand Down Expand Up @@ -153,7 +155,7 @@ jobs:
uses: conda-incubator/setup-miniconda@v3
with:
python-version: "3.10"
mamba-version: "*"
mamba-version: "1"
channels: conda-forge
channel-priority: true
auto-update-conda: false
Expand Down Expand Up @@ -190,7 +192,7 @@ jobs:
uses: conda-incubator/setup-miniconda@v3
with:
python-version: "3.10"
mamba-version: "*"
mamba-version: "1"
channels: conda-forge
channel-priority: true
auto-update-conda: false
Expand All @@ -212,5 +214,4 @@ jobs:
run: bash tests/test_htsinfer_with_conda/test.local.sh

- name: Run SRA downloads workflow
run: bash tests/test_sra_download_with_conda/test.local.sh

run: bash tests/test_sra_download_with_conda/test.local.sh
4 changes: 2 additions & 2 deletions .github/workflows/docs.yml
Original file line number Diff line number Diff line change
Expand Up @@ -2,7 +2,7 @@ name: Docs

on:
push:
branches: [main, dev]
branches: [main, dev, docs-describe-zarp-outputs]
workflow_dispatch:

jobs:
Expand All @@ -21,7 +21,7 @@ jobs:
uses: conda-incubator/setup-miniconda@v3
with:
python-version: "3.10"
mamba-version: "*"
mamba-version: "1"
channels: conda-forge
channel-priority: true
auto-update-conda: false
Expand Down
31 changes: 22 additions & 9 deletions CITATION.cff
Original file line number Diff line number Diff line change
@@ -1,9 +1,10 @@
cff-version: 1.2.0
message: "If you use this software, please cite it as below."
title: "ZARP: An automated workflow for processing of RNA-seq data"
version: 0.3.0
doi: 10.1101/2021.11.18.469017
date-released: 2021-11-18
title: "ZARP: A user-friendly and versatile RNA-seq analysis workflow"

version: 1.0.0
doi: 10.12688/f1000research.149237.1
date-released: 2024-05-24
url: "https://github.com/zavolanlab/zarp"
preferred-citation:
type: article
Expand Down Expand Up @@ -32,6 +33,18 @@ preferred-citation:
- family-names: "Ataman"
given-names: "Meric"
orcid: "https://orcid.org/0000-0002-7942-9226"
- family-names: "Balajti"
given-names: "Máté"
orcid: "https://orcid.org/0009-0000-3932-3964"
- family-names: "Pozzan"
given-names: "Noè"
- family-names: "Schlusser"
given-names: "Niels"
- family-names: "Moon"
given-names: "Youngbin"
orcid: "https://orcid.org/0009-0001-5728-3959"
- family-names: "Mironov"
given-names: "Aleksei"
- family-names: "Boersch"
given-names: "Anastasiya"
orcid: "https://orcid.org/0000-0003-3392-5272"
Expand All @@ -41,8 +54,8 @@ preferred-citation:
- family-names: "Kanitz"
given-names: "Alexander"
orcid: "https://orcid.org/0000-0002-3468-0652"
doi: "10.1101/2021.11.18.469017"
journal: "bioRxiv"
month: 11
title: "ZARP: An automated workflow for processing of RNA-seq data"
year: 2021
doi: "10.12688/f1000research.149237.1"
journal: "F1000Research"
month: 05
title: "ZARP: A user-friendly and versatile RNA-seq analysis workflow"
year: 2024
170 changes: 170 additions & 0 deletions CONTRIBUTING.md
Original file line number Diff line number Diff line change
@@ -0,0 +1,170 @@
# Guidelines for contributing

## General workflow

We are using [Git][git], [GitHub][github] and [Git Flow][git-flow].

> **Note:** If you are a **beginner** and do not have a lot of experience with
> this sort of workflow, please do not feel overwhelmed. We will guide you
> through the process until you feel comfortable using it. And do not worry
> about mistakes either - everybody does them. Often! Our project layout makes
> it very very hard for anyone to cause irreversible harm, so relax, try things
> out, take your time and enjoy the work! :)

We would kindly ask you to abide by our [Code of Conduct][coc] in all
interactions with the community when contributing to this project, regardless
of the type of contribution. We will not accept any offensive or demeaning
behavior towards others and will take any necessary steps to ensure that
everyone is treated with respect and dignity.

## Issue tracker

Please use each project's GitHub [issue tracker][issue-tracker] to:

- find issues to work on
- report bugs
- propose features
- discuss future directions

## Submitting issues

Please choose a template when submitting an issue: choose the [**bug report**
template][bug-report] only when reporting bugs; for all other issues,
choose the [**feature request** template][bug-report]. Please follow the
instructions in the templates.

You do not need to worry about adding labels or milestones for an issue, the
project maintainers will do that for you. However, it is important that all
issues are written concisely, yet with enough detail and with proper
references (links, screenshots, etc.) to allow other contributors to start
working on them. For bug reports, it is essential that they include all
information required to reproduce the bug.

Please **do not** use the issue tracker to ask usage questions, installation
problems etc., unless they appear to be bugs. For these issues, please use
the [communication channels](#communication) outlined below.

## Communication

Send us an [email][contact] if you want to reach out to us
work on)

## Code style and testing

To make it easier for everyone to maintain, read and contribute to the code,
as well as to ensure that the code base is robust and of high quality, we
would kindly ask you to stick to the following guidelines for code style and
testing.

- Please use a recent version of [Python 3][py] (3.7.4+)
- Please try to conform to the used code, docstring and commenting style within
a project to maintain consistency
- Please use [type hints][py-typing] for all function/method signatures
(exception: tests)
- Please use the following linters (see configuration files in repository root
directory, e.g., `setup.cfg`, for settings):
- [`flake8`][py-flake8]
- [`pylint`][py-pylint] (use available [configuration][py-pylint-conf])
- [`mypy`][py-mypy] OR [`pyright`][py-pyright] to help with type hints
- Please use the following test suites:
- [`pytest`][py-pytest]
- [`coverage`][py-coverage]

## Commit messages

In an effort to increase consistency, simplify maintenance and enable automated
change logs, we would like to kindly ask you to write _semantic commit
messages_, as described in the [Conventional Commits
specification][conv-commits].

The general structure of _Conventional Commits_ is as follows:

```console
<type>[optional scope]: <description>

[optional body]

[optional footer]
```

Depending on the changes, please use one of the following **type** prefixes:

| Type | Description |
| --- | --- |
| build | The build type (formerly known as chore) is used to identify development changes related to the build system (involving scripts, configurations or tools) and package dependencies. |
| ci | The ci type is used to identify development changes related to the continuous integration and deployment system - involving scripts, configurations or tools. |
| docs | The docs type is used to identify documentation changes related to the project - whether intended externally for the end users (in case of a library) or internally for the developers. |
| feat | The feat type is used to identify production changes related to new backward-compatible abilities or functionality. |
| fix | The fix type is used to identify production changes related to backward-compatible bug fixes. |
| perf | The perf type is used to identify production changes related to backward-compatible performance improvements. |
| refactor | The refactor type is used to identify development changes related to modifying the codebase, which neither adds a feature nor fixes a bug - such as removing redundant code, simplifying the code, renaming variables, etc. |
| revert | For commits that revert one or more previous commits. |
| style | The style type is used to identify development changes related to styling the codebase, regardless of the meaning - such as indentations, semi-colons, quotes, trailing commas and so on. |
| test | The test type is used to identify development changes related to tests - such as refactoring existing tests or adding new tests. |

In order to ensure that the format of your commit messages adheres to the
Conventional Commits specification and the defined type vocabulary, you can
use the [dedicated linter][conv-commits-lint]. More information about
_Conventional Commits_ can also be found in this [blog
post][conv-commits-blog].

## Merging your code

Here is a check list that you can follow to make sure that code merges
happen smoothly:

1. [Open an issue](#submitting-issues) _first_ to give other contributors a
chance to discuss the proposed changes (alternatively: assign yourself
to one of the existing issues)
2. Clone the repository, create a feature branch off of the default branch
(never commit changes to protected branches directly) and implement your
code changes
3. If applicable, update relevant sections of the [documentation][docs]
4. Add or update tests; untested code will not be merged; refer to the
[guidelines](#code-style-and-testing) above for details
5. Ensure that your coding style is in line with the
[guidelines](#code-style-and-testing) described above
6. Ensure that all tests and linter checks configured in the [Travis
CI][travis-docs] [continuous integration][ci-cd] (CI) pipeline pass without
issues
7. If necessary, clean up excessive commits with `git rebase`; cherry-pick and
merge commits as you see fit; use concise and descriptive commit messages
8. Push your clean, tested and documented feature branch to the remote; make
sure the [Travis CI][travis-docs] [CI][ci-cd] pipeline passes
9. Issue a pull request against the default branch; follow the instructions in
the [template][pull-request]; importantly, describe your changes in
detail, yet with concise language, and do not forget to indicate which
issue(s) the code changes resolve or refer to; assign a project maintainer
to review your changes

## Becoming a co-maintainer

If you are as interested in the project as we are and have contributed some
code, suggested some features or bug reports and have taken part in
discussions on where to go with the project, we will very likely to have you
on board as a co-maintainer. If you are intersted in that, please let us
know. You can reach us by [email][contact].

[bug-report]: .github/ISSUE_TEMPLATE/bug_report.mdrequest.md
[ci-cd]: <https://en.wikipedia.org/wiki/Continuous_integration>
[coc]: CODE_OF_CONDUCT.md
[contact]: <[email protected]>
[conv-commits]: <https://www.conventionalcommits.org/en/v1.0.0-beta.2/#specification>
[conv-commits-blog]: <https://nitayneeman.com/posts/understanding-semantic-commit-messages-using-git-and-angular/>
[conv-commits-lint]: <https://github.com/conventional-changelog/commitlint>
[docs]: README.md
[git]: <https://git-scm.com/>
[git-flow]: <https://nvie.com/posts/a-successful-git-branching-model/>
[github]: <https://github.com>
[issue-tracker]: <https://github.com/zavolanlab/zarp/issues>
[pull-request]: PULL_REQUEST_TEMPLATE.md
[py]: <https://www.python.org/>
[py-flake8]: <https://gitlab.com/pycqa/flake8>
[py-mypy]: <http://mypy-lang.org/>
[py-pylint]: <https://www.pylint.org/>
[py-pylint-conf]: pylint.cfg
[py-pyright]: <https://github.com/microsoft/pyright>
[py-pytest]: <https://docs.pytest.org/en/latest/>
[py-coverage]: <https://pypi.org/project/coverage/>
[py-typing]: <https://docs.python.org/3/library/typing.html>
[travis-docs]: <https://docs.travis-ci.com/>
Loading
Loading