Public-Health-Scotland · Jennit07 · Jan 10, 2025 · Jan 14, 2025 · Jan 14, 2025
diff --git a/.github/workflows/pkgdown.yaml b/.github/workflows/pkgdown.yaml
@@ -2,14 +2,15 @@
 # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
 on:
   push:
-    branches: [master]
-  issue_comment:
-    types: [created]
+    branches: [main, master]
+  pull_request:
   release:
     types: [published]
   workflow_dispatch:
 
-name: pkgdown
+name: pkgdown.yaml
+
+permissions: read-all
 
 jobs:
   pkgdown:
@@ -19,63 +20,30 @@ jobs:
       group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }}
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
-      NETLIFY_AUTH_TOKEN: ${{ secrets.NETLIFY_AUTH_TOKEN }}
-      NETLIFY_SITE_ID: ${{ secrets.NETLIFY_SITE_ID }}
-      isPush: ${{ github.event_name == 'push' }}
-      isPR: ${{ github.event.issue.pull_request && startsWith(github.event.comment.body, '/pkgdown') }}
-
+    permissions:
+      contents: write
     steps:
-      - name: Checkout repo
-        uses: actions/checkout@v4
-
-      - name: Checkout Pull Request
-        if: contains(env.isPR, 'true')
-        run: hub pr checkout ${{ github.event.issue.number }}
-        env:
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-pandoc@v2
 
-      - name: Setup R
-        uses: r-lib/actions/setup-r@v2
+      - uses: r-lib/actions/setup-r@v2
         with:
           use-public-rspm: true
 
-      - name: Install dependencies
-        uses: r-lib/actions/setup-r-dependencies@v2
+      - uses: r-lib/actions/setup-r-dependencies@v2
         with:
           extra-packages: any::pkgdown, local::.
           needs: website
 
-      - name: Install package
-        run: R CMD INSTALL .
-
-      - name: Build and deploy pkgdown site to GitHub pages 🚀
-        if: contains(env.isPush, 'true')
-        run: |
-          git config --local user.name "$GITHUB_ACTOR"
-          git config --local user.email "[email protected]"
-          Rscript -e 'pkgdown::deploy_to_branch(new_process = FALSE)'
-
-      - name: Create website
-        if: contains(env.isPR, 'true')
-        run: |
-          pkgdown::build_site()
+      - name: Build site
+        run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
         shell: Rscript {0}
 
-      - name: Create index file
-        if: contains(env.isPR, 'true')
-        run: |
-          echo '<!DOCTYPE html><html><head><meta http-equiv="refresh" content="0;URL=/dev/index.html" />  <script language="javascript"> window.location.replace('/dev/index.html')</script></head></html>' > ./docs/index.html
-
-      - name: Deploy to Netlify
-        if: contains(env.isPR, 'true')
-        id: netlify-deploy
-        uses: nwtgck/actions-netlify@v3
+      - name: Deploy to GitHub pages 🚀
+        if: github.event_name != 'pull_request'
+        uses: JamesIves/[email protected]
         with:
-          publish-dir: './docs'
-          production-branch: main-R
-          github-token: ${{ secrets.GITHUB_TOKEN }}
-          deploy-message:
-            'Deploy from GHA: ${{ github.event.pull_request.title || github.event.head_commit.message }} (${{ github.sha }})'
-          timeout-minutes: 12
+          clean: false
+          branch: gh-pages
+          folder: docs
diff --git a/_pkgdown.yml b/_pkgdown.yml
@@ -3,200 +3,3 @@
 url: https://public-health-scotland.github.io/source-linkage-files
 template:
   bootstrap: 5
-
-reference:
-
-  - title: Connection to PHS database
-    desc: Connection to PHS database
-  - contents:
-    - phs_db_connection
-
-
-  - title: Check
-    desc: Checks within vectors
-  - contents:
-    - is_missing
-    - check_variables_exist
-    - check_year_valid
-    - check_it_reference
-
-
-  - title: Years & Dates
-  - subtitle: Dates within Financial Year
-    desc: Functions to compute the start, end and midpoint dates of a financial year, and convert date types
-  - contents:
-    - has_concept("date functions")
-    - ends_with("_fy")
-    - fy_interval
-    - contains("_date")
-  - subtitle: Year Format
-    desc: Functions to convert between financial year and calendar year, and check that the year variable is in the correct format
-  - contents:
-    - has_concept("year functions")
-    - ends_with("year")
-    - contains("year_format")
-  - subtitle: Ages
-    desc: Functions to deal with ages of clients
-  - contents:
-    - contains("_age")
-
-
-  - title: Clean-Up
-    desc: Clean up the data
-  - contents:
-    - starts_with("clean_up")
-    - fill_ch_names
-    - cascade_geographies
-    - correct_demographics
-
-
-  - title: Create
-  - subtitle: ID
-    desc: Functions to create ID variables
-  - contents:
-    - has_concept("id functions")
-    - contains("_id")
-  - subtitle: Costs
-    desc: Functions to create costs variables and fix costs
-  - contents:
-    - ends_with("_costs")
-  - subtitle: Flags
-    desc: Functions to create flag variables
-  - contents:
-    - has_concept("flag functions")
-    - ends_with("_flags")
-  - subtitle: Monthly
-    desc: Functions to convert monthly variables, beddays
-  - contents:
-    - contains("_monthly_rows")
-    - contains("_beddays")
-
-
-  - title: Codes
-    desc: Convert various codes to alternate forms
-  - contents:
-    - has_concept("code functions")
-    - has_concept("Codes")
-    - contains("_to_lca")
-    - contains("to_dummy")
-    - contains("_hb_to")
-    - contains("_hscp_to")
-    - contains("_chi")
-    - contains("lca")
-    - la_code_lookup
-
-  - title: Writing data
-    desc: Functions which mask the typical data write functions to add some nice defaults and importantly fix file permissions.
-  - contents:
-    - write_file
-
-
-  - title: Initialisation
-    desc: Get the date of update, period, and extract number
-  - contents:
-    - has_concept("initialisation")
-    - ends_with("_period")
-    - ends_with("_update")
-    - starts_with("it_extract")
-    - gzip_files
-    - make_lowercase_ext
-
-
-  - title: Files
-  - subtitle: Directories
-    desc: File Directories for SLF's
-  - contents:
-    - has_concept("directories")
-    - ends_with("_dir")
-  - subtitle: Paths
-    desc: File Paths for SLF's
-  - contents:
-    - has_concept("file path functions")
-    - has_concept("lookup file paths")
-    - has_concept("slf lookup file paths")
-    - has_concept("costs lookup file paths")
-    - has_concept("extract file paths")
-    - has_concept("social care lookup file paths")
-    - has_concept("social care episodes file paths")
-    - has_concept("cohort lookup file paths")
-    - ends_with("_file")
-    - ends_with("_path")
-
-  - title: Read extracts
-    desc: Process SLF Extracts
-  - contents:
-    - has_concept("read extracts")
-    - starts_with("read_")
-    - get_gpprac_opendata
-
-
-  - title: Process extracts
-    desc: Process SLF Extracts
-  - contents:
-    - has_concept("process extracts")
-    - starts_with("process_")
-
-
-  - title: Episode file
-    desc: Building the episode file
-  - contents:
-    - has_concept("episode_file")
-    - fill_geographies
-  - subtitle: Lookups
-  - contents:
-    - has_concept("Demographic and Service Use Cohort functions")
-    - join_sparra_hhg
-    - join_deaths_data
-    - join_sc_client
-    - match_on_ltcs
-
-
-  - title: Individual file
-    desc: Building the episode file
-  - contents:
-    - has_concept("individual_file")
-  - subtitle: Lookups
-  - contents:
-    - has_concept("Demographic and Service Use Cohort functions")
-    - join_sparra_hhg
-    - join_cohort_lookups
-    - join_deaths_data
-    - join_slf_lookup_vars
-    - match_on_ltcs
-
-  - title: Demographics
-    desc: Things related to demographic lookups
-  - contents:
-    - fill_geographies
-    - get_gpprac_opendata
-    - make_gpprac_lookup
-    - make_postcode_lookup
-    - recode_health_boards
-    - recode_hscp
-    - la_code_lookup
-
-
-  - title: Miscellaneous functions
-    desc: Miscellaneous functions.
-  - subtitle: Homelessness
-  - contents:
-    - fix_east_ayrshire_duplicates
-    - fix_west_dun_duplicates
-    - produce_homelessness_completeness
-  - subtitle: Helper functions
-  - contents:
-    - vars_end_with
-    - has_concept("helper_funs")
-
-
-  - title: Testing
-    desc: Tests for the SLF Extracts
-  - contents:
-    - has_concept("test functions")
-    - has_concept("extract test functions")
-    - has_concept("slf test functions")
-    - has_concept("social care test functions")
-    - contains("_tests")
-    - contains("_measures")
-    - starts_with("produce_test")
-