Bump to v.1.3.7

Author: npurson

.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

.github/workflows/build-preview.yaml

@@ -21,12 +21,13 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-      # for debugging
-      - name: Print contexts
-        uses: crazy-max/ghaction-dump-context@v1
+      - name: Debug dump
+        if: runner.debug == '1'
+        uses: crazy-max/ghaction-dump-context@v2
 
       - name: Checkout branch contents
-        uses: actions/checkout@v3
+        if: github.event.action != 'closed'
+        uses: actions/checkout@v4
         with:
           repository: ${{ github.event.pull_request.head.repo.full_name }}
           ref: ${{ github.head_ref }}
@@ -35,23 +36,48 @@ jobs:
         if: github.event.action != 'closed'
         uses: ruby/setup-ruby@v1
         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
+
+      - name: SSH debug
+        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
+        if: github.event.action != 'closed'
+        uses: rossjrw/[email protected]
         with:
           source-dir: _site
           umbrella-dir: ${{ env.PREVIEWS_FOLDER }}
+
+      - name: Checkout Pages branch
+        uses: actions/checkout@v4
+        with:
+          ref: gh-pages
+
+      - name: Clean up preview folders
+        uses: actions/github-script@v7
+        with:
+          script: |
+            const { rm } = require("fs").promises;
+            const { PREVIEWS_FOLDER } = process.env;
+            const { owner, repo } = context.repo;
+            const prs = (await github.rest.pulls.list({ owner, repo, state: "closed" })).data;
+            for (const { number } of prs)
+              await rm(`${PREVIEWS_FOLDER}/pr-${number}`, { recursive: true, force: true });
+
+      - name: Commit changed files
+        uses: stefanzweifel/git-auto-commit-action@v5
+        with:
+          branch: gh-pages
+          commit_message: "Clean up previews"

.github/workflows/build-site.yaml

@@ -20,31 +20,37 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-      # for debugging
-      - name: Print contexts
-        uses: crazy-max/ghaction-dump-context@v1
+      - name: Debug dump
+        if: runner.debug == '1'
+        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
         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
+
+      - name: SSH debug
+        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 }}

.github/workflows/first-time-setup.yaml

@@ -13,74 +13,83 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-      # for debugging
-      - name: Print contexts
-        uses: crazy-max/ghaction-dump-context@v1
+      - name: Debug dump
+        if: runner.debug == '1'
+        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
 
+      - name: SSH debug
+        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
+        run: rm -rf ./* .github .docker .gitignore
 
       # prevent GitHub from running Jekyll a second time after build
       - name: Make .nojekyll file
         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}" >> $GITHUB_ENV
+          printf "\nUSER=%s" "$user" >> "$GITHUB_ENV"
+          printf "\nDESCRIPTION=%s" "$description" >> "$GITHUB_ENV"
 
       - name: Personalize readme for user
         run: |
-          echo "
-          # ${{ env.USER }}'s Website
+          printf "
+            ![on-push](../../actions/workflows/on-push.yaml/badge.svg)
+            ![on-pull-request](../../actions/workflows/on-pull-request.yaml/badge.svg)
+            ![on-schedule](../../actions/workflows/on-schedule.yaml/badge.svg)
+
+            # %s's Website
 
-          Visit **[website url](#)** 🚀
+            Visit **[website url](#)** 🚀
 
-          _Built with [Lab Website Template](https://greene-lab.gitbook.io/lab-website-template-docs)_
-          " > README.md
+            _Built with [Lab Website Template](https://greene-lab.gitbook.io/lab-website-template-docs)_
+          " "${{ env.USER }}" > 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 +106,7 @@ 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 +118,6 @@ 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"
+          commit_message: "Set up repo"

.github/workflows/on-pages.yaml

@@ -20,6 +20,7 @@ jobs:
     # only run on user instance of template, not template itself
     if: github.repository != 'greenelab/lab-website-template'
     uses: ./.github/workflows/update-url.yaml
+
   build-site:
     needs: update-url
     if: needs.update-url.outputs.changed == 'true'

.github/workflows/on-pull-request.yml renamed to .github/workflows/on-pull-request.yaml

@@ -14,9 +14,9 @@ permissions:
   pull-requests: write
 
 jobs:
-  # update-citations:
-  #   uses: ./.github/workflows/update-citations.yaml
+  update-citations:
+    uses: ./.github/workflows/update-citations.yaml
 
   build-preview:
-    # needs: update-citations
+    needs: update-citations
     uses: ./.github/workflows/build-preview.yaml

.github/workflows/on-push.yml renamed to .github/workflows/on-push.yaml

@@ -14,11 +14,11 @@ permissions:
   pull-requests: write
 
 jobs:
-  # update-citations:
-  #   # skip first run because nothing enabled or setup yet
-  #   if: github.run_number != 1
-  #   uses: ./.github/workflows/update-citations.yaml
+  update-citations:
+    # skip first run because nothing enabled or setup yet
+    if: github.run_number != 1
+    uses: ./.github/workflows/update-citations.yaml
 
   build-site:
-    # needs: update-citations
+    needs: update-citations
     uses: ./.github/workflows/build-site.yaml

.github/workflows/update-citations.yaml

@@ -28,54 +28,74 @@ jobs:
     timeout-minutes: 15
 
     steps:
-      # for debugging
-      - name: Print contexts
-        uses: crazy-max/ghaction-dump-context@v1
+      - name: Debug dump
+        if: runner.debug == '1'
+        uses: crazy-max/ghaction-dump-context@v2
 
       - name: Checkout branch contents
-        uses: actions/checkout@v3
+        if: github.event.action != 'closed'
+        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
+      - name: Set up Python
+        if: github.event.action != 'closed'
+        uses: actions/setup-python@v5
         with:
           python-version: "3.11"
           cache: "pip"
           cache-dependency-path: "**/requirements.txt"
 
       - name: Install Python packages
+        if: github.event.action != 'closed'
         run: |
           python -m pip install --upgrade --requirement ./_cite/requirements.txt
 
+      - name: SSH debug
+        if: runner.debug == '1'
+        uses: mxschmitt/action-tmate@v3
+
       - name: Build updated citations
+        if: github.event.action != 'closed'
         run: python _cite/cite.py
         timeout-minutes: 15
 
+      - name: Commit cache
+        if: failure()
+        uses: stefanzweifel/git-auto-commit-action@v5
+        with:
+          file_pattern: "**/.cache/**"
+          commit_message: "Commit cache"
+
       - name: Check if citations changed
+        if: github.event.action != 'closed'
         id: changed
-        uses: tj-actions/verify-changed-files@v13
+        uses: tj-actions/verify-changed-files@v18
         with:
           files: |
             _data/citations.yaml
 
       - name: Commit updated citations to branch
         if: |
+          github.event.action != 'closed' &&
           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: |
+          github.event.action != 'closed' &&
           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
+          body: |
+            To see a live preview of this PR, close (don't merge) and reopen it.
 
     outputs:
-      changed: ${{ steps.changed.outputs.files_changed }}
+      changed: ${{ steps.changed.outputs.files_changed || false }}