ci: replace auto-ci with commands

.github/pull_request_template.md

@@ -14,6 +14,11 @@ Please:
       (backwards-incompatible changes to the documented interface) are noted.
       Collect the changes under the next release number (e.g. if you are on
       1.7.2, then write your changes under the 1.8 heading).
+- [ ] Styling and documentation checks. Make a PR comment with:
+  - `/document` to check the package documentation and fix any issues.
+  - `/style` to check the style and fix any issues.
+  - `/preview-docs` to preview the docs.
+  - See Actions GitHub tab to track progress of these commands.
 - See [DEVELOPMENT.md](DEVELOPMENT.md) for more information on the development
   process.
 

.github/workflows/lint.yaml

@@ -1,27 +1,23 @@
 # Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
 # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
-#
-# Modifications:
-#   * workflow_dispatch added to allow manual triggering of the workflow
-#   * trigger branches changed
-#   * API key secrets.DELPHI_GITHUB_ACTIONS_EPIDATA_API_KEY
 on:
   push:
     branches: [main, dev]
   pull_request:
     branches: [main, dev]
   workflow_dispatch:
 
-name: Lint
+name: lint.yaml
+
+permissions: read-all
 
 jobs:
   lint:
     runs-on: ubuntu-latest
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
-      DELPHI_EPIDATA_KEY: ${{ secrets.DELPHI_GITHUB_ACTIONS_EPIDATA_API_KEY }}
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-r@v2
         with:

.github/workflows/pr-commands.yaml

@@ -0,0 +1,149 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+# Modifications:
+# - Allow more roles to trigger each PR command
+# - Document builds README.md from README.Rmd with devtools::build_readme()
+# - Include a doc-preview command (uses Netlify to preview the docs)
+on:
+  issue_comment:
+    types: [created]
+
+name: pr-commands.yaml
+
+permissions: read-all
+
+jobs:
+  document:
+    if: ${{ github.event.issue.pull_request && (github.event.comment.author_association == 'COLLABORATOR' || github.event.comment.author_association == 'CONTRIBUTOR' || github.event.comment.author_association == 'MEMBER' || github.event.comment.author_association == 'OWNER') && startsWith(github.event.comment.body, '/document') }}
+    name: document
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    permissions:
+      contents: write
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/pr-fetch@v2
+        with:
+          repo-token: ${{ secrets.GITHUB_TOKEN }}
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::roxygen2
+          needs: pr-document
+
+      - name: Document
+        run: roxygen2::roxygenise()
+        shell: Rscript {0}
+
+      - name: Build README.md from README.Rmd
+        run: Rscript -e 'if (file.exists("README.Rmd")) devtools::build_readme()'
+
+      - name: commit
+        run: |
+          git config --local user.name "$GITHUB_ACTOR"
+          git config --local user.email "$GITHUB_ACTOR@users.noreply.github.com"
+          git add man/\* NAMESPACE
+          git commit -m 'Document'
+
+      - uses: r-lib/actions/pr-push@v2
+        with:
+          repo-token: ${{ secrets.GITHUB_TOKEN }}
+
+  style:
+    if: ${{ github.event.issue.pull_request && (github.event.comment.author_association == 'COLLABORATOR' || github.event.comment.author_association == 'CONTRIBUTOR' || github.event.comment.author_association == 'MEMBER' || github.event.comment.author_association == 'OWNER') && startsWith(github.event.comment.body, '/style') }}
+    name: style
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    permissions:
+      contents: write
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/pr-fetch@v2
+        with:
+          repo-token: ${{ secrets.GITHUB_TOKEN }}
+
+      - uses: r-lib/actions/setup-r@v2
+
+      - name: Install dependencies
+        run: install.packages("styler")
+        shell: Rscript {0}
+
+      - name: Style
+        run: styler::style_pkg()
+        shell: Rscript {0}
+
+      - name: commit
+        run: |
+          git config --local user.name "$GITHUB_ACTOR"
+          git config --local user.email "$GITHUB_ACTOR@users.noreply.github.com"
+          git add \*.R
+          git commit -m 'Style'
+
+      - uses: r-lib/actions/pr-push@v2
+        with:
+          repo-token: ${{ secrets.GITHUB_TOKEN }}
+
+  preview:
+    if: ${{ github.event.issue.pull_request && (github.event.comment.author_association == 'COLLABORATOR' || github.event.comment.author_association == 'CONTRIBUTOR' || github.event.comment.author_association == 'MEMBER' || github.event.comment.author_association == 'OWNER') && startsWith(github.event.comment.body, '/preview-docs') }}
+
+    runs-on: ubuntu-latest
+    permissions:
+      # Needed to write a comment on the PR
+      pull-requests: write
+      # Needed to read the PR branch
+      contents: read
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          # Checkout the PR branch
+          ref: refs/pull/${{ github.event.issue.number }}/head
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::pkgdown, local::.
+          needs: website
+
+      - name: Build site
+        run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
+        shell: Rscript {0}
+
+      - name: Deploy to Netlify
+        uses: nwtgck/actions-netlify@v3.0
+        with:
+          # Standard config
+          github-token: ${{ secrets.GITHUB_TOKEN }}
+          deploy-message: "Deploy from GitHub Actions"
+          # 'docs/' is the default directory for pkgdown::build_site()
+          # we add 'dev' because _pkgdown.yml has 'development: mode: devel'
+          publish-dir: './docs/dev'
+          # Development deploys only
+          production-deploy: false
+          # Enable pull request comment (default)
+          enable-pull-request-comment: true
+          # Overwrite the pull request comment with updated link (default)
+          overwrites-pull-request-comment: true
+          # Don't deploy to GitHub
+          enable-github-deployment: false
+          # Don't update the status of the commit
+          enable-commit-status: false
+          # Don't comment on the commit
+          enable-commit-comment: false
+        env:
+          # Netlify credentials (currently from Dmitry's account)
+          NETLIFY_AUTH_TOKEN: ${{ secrets.NETLIFY_AUTH_TOKEN }}
+          NETLIFY_SITE_ID: ${{ secrets.NETLIFY_SITE_ID }}
+        timeout-minutes: 1