Update to v1.2.1 (#122)

* Update to v1.2.0 * add pull_request trigger * v1.2.1 * remove extra pr trigger
greenelab · Apr 1, 2024 · bbb10ec · bbb10ec
1 parent c272d00
commit bbb10ec
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diff --git a/.docker/entrypoint.sh b/.docker/entrypoint.sh
@@ -1,10 +1,8 @@
 #! /bin/bash
 
 # print folder contents for debugging
-echo "Contents:"
-echo ""
+printf "\n\nContents:\n\n"
 ls
-echo ""
 
 # run cite process
 python3 _cite/cite.py

diff --git a/.github/workflows/build-preview.yaml b/.github/workflows/build-preview.yaml
@@ -22,36 +22,37 @@ jobs:
 
     steps:
       # for debugging
-      - name: Print contexts
-        uses: crazy-max/ghaction-dump-context@v1
+      - uses: crazy-max/ghaction-dump-context@v2
 
       - name: Checkout branch contents
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           repository: ${{ github.event.pull_request.head.repo.full_name }}
           ref: ${{ github.head_ref }}
 
       - name: Install Ruby packages
         if: github.event.action != 'closed'
-        uses: ruby/setup-ruby@v1
+        uses: ruby/setup-ruby@v1.172.0
         with:
-          ruby-version: "3.0"
+          ruby-version: "3.1"
           bundler-cache: true
 
       - name: Get Pages url
         if: github.event.action != 'closed'
         id: pages
-        uses: actions/configure-pages@v2
-        with:
-          enablement: false
+        uses: actions/configure-pages@v4
+
+      # for debugging
+      - if: runner.debug == '1'
+        uses: mxschmitt/action-tmate@v3
 
       - name: Build preview version of site
         if: github.event.action != 'closed'
         run: |
           JEKYLL_ENV=production bundle exec jekyll build --baseurl "${{ steps.pages.outputs.base_path || '' }}/${{ env.PREVIEWS_FOLDER }}/pr-${{ github.event.number }}"
 
       - name: Commit preview to Pages branch
-        uses: rossjrw/pr-preview-action@v1
+        uses: rossjrw/pr-preview-action@v1.4.7
         with:
           source-dir: _site
           umbrella-dir: ${{ env.PREVIEWS_FOLDER }}
diff --git a/.github/workflows/build-site.yaml b/.github/workflows/build-site.yaml
@@ -21,30 +21,35 @@ jobs:
 
     steps:
       # for debugging
-      - name: Print contexts
-        uses: crazy-max/ghaction-dump-context@v1
+      - uses: crazy-max/ghaction-dump-context@v2
 
       - name: Checkout branch contents
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       - name: Install Ruby packages
-        uses: ruby/setup-ruby@v1
+        uses: ruby/setup-ruby@v1.172.0
         with:
-          ruby-version: "3.0"
+          ruby-version: "3.1"
           bundler-cache: true
 
       - name: Get Pages url
         id: pages
-        uses: actions/configure-pages@v2
-        with:
-          enablement: false
+        uses: actions/configure-pages@v4
+
+      # for debugging
+      - if: runner.debug == '1'
+        uses: mxschmitt/action-tmate@v3
+
+      - name: Set root url
+        run: |
+          printf "\n\nurl: ${{ steps.pages.outputs.origin }}" >> _config.yaml
 
       - name: Build live version of site
         run: |
           JEKYLL_ENV=production bundle exec jekyll build --baseurl "${{ steps.pages.outputs.base_path || '' }}"
 
       - name: Commit live site to Pages branch
-        uses: JamesIves/github-pages-deploy-action@v4
+        uses: JamesIves/github-pages-deploy-action@v4.5.0
         with:
           folder: _site
           clean-exclude: ${{ env.PREVIEWS_FOLDER }}

diff --git a/.github/workflows/first-time-setup.yaml b/.github/workflows/first-time-setup.yaml
@@ -14,21 +14,24 @@ jobs:
 
     steps:
       # for debugging
-      - name: Print contexts
-        uses: crazy-max/ghaction-dump-context@v1
+      - uses: crazy-max/ghaction-dump-context@v2
 
       - name: Create Pages branch
-        uses: peterjgrainger/action-create-branch@v2.4.0
+        uses: peterjgrainger/action-create-branch@v3.0.0
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
         with:
           branch: "gh-pages"
 
       - name: Checkout Pages branch
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           ref: gh-pages
 
+      # for debugging
+      - if: runner.debug == '1'
+        uses: mxschmitt/action-tmate@v3
+
       # clean slate, as if starting from orphan branch
       - name: Clear Pages branch
         run: rm -rf * .github .docker .gitignore
@@ -38,40 +41,41 @@ jobs:
         run: touch .nojekyll
 
       - name: Make placeholder homepage
-        run: echo "Placeholder homepage" > index.html
+        run: printf "Placeholder homepage" > index.html
 
       - name: Commit changes to Pages branch
-        uses: stefanzweifel/git-auto-commit-action@v4
+        uses: stefanzweifel/git-auto-commit-action@v5
         with:
           branch: gh-pages
           commit_message: "Clear branch"
 
       - name: Checkout main branch
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       - name: Remove files user doesn't need
         run: |
           rm -rf \
             CHANGELOG.md \
             testbed.md \
             .github/ISSUE_TEMPLATE \
+            .github/DISCUSSION_TEMPLATE \
             .github/workflows/versioning.yaml \
             .github/pull_request_template.md \
-      
+
       - name: Rename files
         run: |
-          mv .github/user_pull_request_template.md .github/pull_request_template.md
+          mv -f .github/user_pull_request_template.md .github/pull_request_template.md
 
       - name: Set vars for personalization
         run: |
           user="${{ github.repository_owner }}"
           description="An engaging 1-3 sentence description of your lab."
-          echo "USER=${user}" >> $GITHUB_ENV
-          echo "DESCRIPTION=${description}" >> $GITHUB_ENV
+          printf "USER=${user}" >> $GITHUB_ENV
+          printf "DESCRIPTION=${description}" >> $GITHUB_ENV
 
       - name: Personalize readme for user
         run: |
-          echo "
+          printf "
           # ${{ env.USER }}'s Website
 
           Visit **[website url](#)** 🚀
@@ -80,7 +84,7 @@ jobs:
           " > README.md
 
       - name: Personalize Jekyll config for user
-        uses: actions/github-script@v6
+        uses: actions/github-script@v7
         with:
           script: |
             const { readFileSync, writeFileSync } = require("fs");
@@ -97,7 +101,7 @@ jobs:
             writeFileSync(file, contents);
 
       - name: Personalize homepage for user
-        uses: actions/github-script@v6
+        uses: actions/github-script@v7
         with:
           script: |
             const { readFileSync, writeFileSync } = require("fs");
@@ -109,6 +113,6 @@ jobs:
             writeFileSync(file, contents);
 
       - name: Commit changed files
-        uses: stefanzweifel/git-auto-commit-action@v4
+        uses: stefanzweifel/git-auto-commit-action@v5
         with:
           commit_message: "Setup repo"
diff --git a/.github/workflows/update-citations.yaml b/.github/workflows/update-citations.yaml
@@ -29,17 +29,16 @@ jobs:
 
     steps:
       # for debugging
-      - name: Print contexts
-        uses: crazy-max/ghaction-dump-context@v1
+      - uses: crazy-max/ghaction-dump-context@v2
 
       - name: Checkout branch contents
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           repository: ${{ github.event.pull_request.head.repo.full_name }}
           ref: ${{ github.head_ref }}
 
       - name: Setup Python
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: "3.11"
           cache: "pip"
@@ -49,13 +48,17 @@ jobs:
         run: |
           python -m pip install --upgrade --requirement ./_cite/requirements.txt
 
+      # for debugging
+      - if: runner.debug == '1'
+        uses: mxschmitt/action-tmate@v3
+
       - name: Build updated citations
         run: python _cite/cite.py
         timeout-minutes: 15
 
       - name: Check if citations changed
         id: changed
-        uses: tj-actions/verify-changed-files@v13
+        uses: tj-actions/verify-changed-files@v18
         with:
           files: |
             _data/citations.yaml
@@ -64,15 +67,15 @@ jobs:
         if: |
           steps.changed.outputs.files_changed == 'true' &&
           inputs.open-pr != true
-        uses: stefanzweifel/git-auto-commit-action@v4
+        uses: stefanzweifel/git-auto-commit-action@v5
         with:
           commit_message: "Update citations"
 
       - name: Open pull request with updated citations
         if: |
           steps.changed.outputs.files_changed == 'true' &&
           inputs.open-pr == true
-        uses: peter-evans/create-pull-request@v4
+        uses: peter-evans/create-pull-request@v6
         with:
           branch: citation-update
           title: Periodic citation update

diff --git a/.github/workflows/update-url.yaml b/.github/workflows/update-url.yaml
@@ -20,21 +20,22 @@ jobs:
 
     steps:
       # for debugging
-      - name: Print contexts
-        uses: crazy-max/ghaction-dump-context@v1
+      - uses: crazy-max/ghaction-dump-context@v2
 
       - name: Get Pages url
         id: pages
-        uses: actions/configure-pages@v2
-        with:
-          enablement: false
+        uses: actions/configure-pages@v4
 
       - name: Checkout branch contents
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
+
+      # for debugging
+      - if: runner.debug == '1'
+        uses: mxschmitt/action-tmate@v3
 
       # update link to site in readme
       - name: Update readme
-        uses: actions/github-script@v6
+        uses: actions/github-script@v7
         with:
           script: |
             const { readFileSync, writeFileSync } = require("fs");
@@ -53,14 +54,14 @@ jobs:
 
       - name: Check if readme changed
         id: changed
-        uses: tj-actions/verify-changed-files@v13
+        uses: tj-actions/verify-changed-files@v18
         with:
           files: |
             README.md
 
       - name: Commit changed files
         if: steps.changed.outputs.files_changed == 'true'
-        uses: stefanzweifel/git-auto-commit-action@v4
+        uses: stefanzweifel/git-auto-commit-action@v5
         with:
           commit_message: "Update url"