merged changes upstream

.github/workflows/build-preview.yaml

@@ -21,8 +21,8 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-      # for debugging
-      - uses: crazy-max/ghaction-dump-context@v2
+      - name: Debug dump
+        uses: crazy-max/ghaction-dump-context@v2
 
       - name: Checkout branch contents
         uses: actions/checkout@v4
@@ -32,7 +32,11 @@ jobs:
 
       - name: Install Ruby packages
         if: github.event.action != 'closed'
+<<<<<<< HEAD
         uses: ruby/[email protected]
+=======
+        uses: ruby/setup-ruby@v1
+>>>>>>> upstream/main
         with:
           ruby-version: "3.1"
           bundler-cache: true
@@ -42,14 +46,22 @@ jobs:
         id: pages
         uses: actions/configure-pages@v4
 
-      # for debugging
-      - if: runner.debug == '1'
+      - uses: jwalton/gh-find-current-pr@master
+        if: github.event.action != 'closed'
+        id: pr
+        with:
+          state: all
+
+      - 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-${{ github.event.number }}"
+          JEKYLL_ENV=production bundle exec jekyll build --baseurl "${{ steps.pages.outputs.base_path || '' }}/${{ env.PREVIEWS_FOLDER }}/pr-${{ env.pr }}"
+        env:
+          pr: ${{ steps.pr.outputs.pr }}
 
       - name: Commit preview to Pages branch
         uses: rossjrw/[email protected]

.github/workflows/build-site.yaml

@@ -20,14 +20,18 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-      # for debugging
-      - uses: crazy-max/ghaction-dump-context@v2
+      - name: Debug dump
+        uses: crazy-max/ghaction-dump-context@v2
 
       - name: Checkout branch contents
         uses: actions/checkout@v4
 
       - name: Install Ruby packages
+<<<<<<< HEAD
         uses: ruby/[email protected]
+=======
+        uses: ruby/setup-ruby@v1
+>>>>>>> upstream/main
         with:
           ruby-version: "3.1"
           bundler-cache: true
@@ -36,8 +40,8 @@ jobs:
         id: pages
         uses: actions/configure-pages@v4
 
-      # for debugging
-      - if: runner.debug == '1'
+      - name: SSH debug
+        if: runner.debug == '1'
         uses: mxschmitt/action-tmate@v3
 
       - name: Set root url

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

@@ -13,8 +13,8 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-      # for debugging
-      - uses: crazy-max/ghaction-dump-context@v2
+      - name: Debug dump
+        uses: crazy-max/ghaction-dump-context@v2
 
       - name: Create Pages branch
         uses: peterjgrainger/[email protected]
@@ -28,8 +28,8 @@ jobs:
         with:
           ref: gh-pages
 
-      # for debugging
-      - if: runner.debug == '1'
+      - name: SSH debug
+        if: runner.debug == '1'
         uses: mxschmitt/action-tmate@v3
 
       # clean slate, as if starting from orphan branch
@@ -70,8 +70,8 @@ jobs:
         run: |
           user="${{ github.repository_owner }}"
           description="An engaging 1-3 sentence description of your lab."
-          printf "USER=${user}" >> $GITHUB_ENV
-          printf "DESCRIPTION=${description}" >> $GITHUB_ENV
+          printf "\nUSER=${user}" >> $GITHUB_ENV
+          printf "\nDESCRIPTION=${description}" >> $GITHUB_ENV
 
       - name: Personalize readme for user
         run: |

.github/workflows/on-schedule.yaml

@@ -20,8 +20,3 @@ jobs:
     uses: ./.github/workflows/update-citations.yaml
     with:
       open-pr: true
-
-  build-preview:
-    needs: update-citations
-    if: needs.update-citations.outputs.changed == 'true'
-    uses: ./.github/workflows/build-preview.yaml

.github/workflows/update-citations.yaml

@@ -28,35 +28,47 @@ jobs:
     timeout-minutes: 15
 
     steps:
-      # for debugging
-      - uses: crazy-max/ghaction-dump-context@v2
+      - name: Debug dump
+        uses: crazy-max/ghaction-dump-context@v2
 
       - name: Checkout branch contents
+        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
+        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
 
-      # for debugging
-      - if: runner.debug == '1'
+      - 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@v18
         with:
@@ -65,6 +77,7 @@ jobs:
 
       - 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@v5
@@ -73,12 +86,15 @@ jobs:
 
       - 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@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 }}

.github/workflows/update-url.yaml

@@ -19,8 +19,8 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-      # for debugging
-      - uses: crazy-max/ghaction-dump-context@v2
+      - name: Debug dump
+        uses: crazy-max/ghaction-dump-context@v2
 
       - name: Get Pages url
         id: pages
@@ -29,8 +29,8 @@ jobs:
       - name: Checkout branch contents
         uses: actions/checkout@v4
 
-      # for debugging
-      - if: runner.debug == '1'
+      - name: SSH debug
+        if: runner.debug == '1'
         uses: mxschmitt/action-tmate@v3
 
       # update link to site in readme

.github/workflows/versioning.yaml

@@ -20,8 +20,8 @@ jobs:
       github.event_name == 'pull_request'
     runs-on: ubuntu-latest
     steps:
-      # for debugging
-      - uses: crazy-max/ghaction-dump-context@v2
+      - name: Debug dump
+        uses: crazy-max/ghaction-dump-context@v2
       - if: runner.debug == '1'
         uses: mxschmitt/action-tmate@v3
 
@@ -85,17 +85,17 @@ jobs:
       github.event_name == 'push'
     runs-on: ubuntu-latest
     steps:
-      # for debugging
-      - uses: crazy-max/ghaction-dump-context@v2
+      - name: Debug dump
+        uses: crazy-max/ghaction-dump-context@v2
 
       - name: Checkout branch contents
         uses: actions/checkout@v4
 
       - name: Install packages
         run: npm install yaml semver
 
-      # for debugging
-      - if: runner.debug == '1'
+      - name: SSH debug
+        if: runner.debug == '1'
         uses: mxschmitt/action-tmate@v3
 
       - name: Get version and body

.gitignore

@@ -8,8 +8,6 @@ _site
 vendor
 debug.log
 __pycache__
-.cache
-!cache.db
 .DS_STORE
 .env*
 package.json

CHANGELOG.md

@@ -2,6 +2,28 @@
 
 Reference: common-changelog.org
 
+## 1.3.1 - 2024-11-11
+
+### Changed
+
+- Update and improve workflows for building site and citations
+- Escape user inputs better in rare edge cases
+
+## 1.3.0 - 2024-08-16
+
+### Changed
+
+- List component `filters` parameter changed to `filter` and now takes any Ruby expression instead of the existing custom syntax.
+  Example: `filters="publisher: bioRxiv, date: ^2020"` becomes `filter="publisher == 'bioRxiv' and date =~ /^2020/"`.
+  See docs for more info.
+- Fix rare bug where data (e.g. a paper title) containing certain characters (e.g. a double quote) can mess up HTML rendering.
+- Fix "first time setup" workflow bug.
+- Tweak GitHub Actions debugging/logging.
+
+### Added
+
+- Styling for `<details>` HTML element.
+
 ## 1.2.2 - 2024-06-05
 
 ### Added
@@ -37,7 +59,7 @@ Reference: common-changelog.org
 
 - Add `image` param to support blog post thumbnails.
 - Add `html-proofer` plugin that checks for broken images/links/etc.
-- Add `remove` flag to remove a source from a metasource. 
+- Add `remove` flag to remove a source from a metasource.
 
 ## 1.1.6 - 2023-10-06
 

CITATION.cff

@@ -1,8 +1,8 @@
 # citation metadata for the template itself
 
 title: "Lab Website Template"
-version: 1.2.2
-date-released: 2024-06-05
+version: 1.3.1
+date-released: 2024-11-11
 url: "https://github.com/greenelab/lab-website-template"
 authors:
   - family-names: "Rubinetti"

_includes/button.html

@@ -7,13 +7,13 @@
       class="button"
       href="{{ button.link | replace: "$LINK", button.link | relative_url }}"
       {% if button.tooltip %}
-        data-tooltip="{{ button.tooltip }}"
+        data-tooltip="{{ button.tooltip | xml_escape }}"
       {% endif %}
       data-style="{{ include.style }}"
       {% if include.flip %}
         data-flip
       {% endif %}
-      aria-label="{{ button.tooltip | default: button.icon | default: "button" }}"
+      aria-label="{{ button.tooltip | default: button.icon | default: "button" | regex_strip }}"
     >
       {% include icon.html icon=button.icon %}
       {% if button.text and button.text != "" %}

_includes/card.html

@@ -2,14 +2,14 @@
 <div class="card" data-style="{{ include.style }}">
   <a
     {% if include.link %}
-      href="{{ include.link | relative_url }}"
+      href="{{ include.link | relative_url | uri_escape }}"
     {% endif %}
-    aria-label="{{ include.title | default: "card link" }}"
+    aria-label="{{ include.title | default: "card link" | regex_strip }}"
     class="card-image"
   >
     <img
-      src="{{ include.image | relative_url }}"
-      alt="{{ include.title | default: "card image" }}"
+      src="{{ include.image | relative_url | uri_escape }}"
+      alt="{{ include.title | default: "card image" | regex_strip }}"
       loading="lazy"
       {% include fallback.html %}
     >
@@ -19,10 +19,10 @@
     {% if include.title %}
       <a
         {% if include.link %}
-          href="{{ include.link | relative_url }}"
+          href="{{ include.link | relative_url | uri_escape }}"
         {% endif %}
         {% if include.tooltip %}
-          data-tooltip="{{ include.tooltip }}"
+          data-tooltip="{{ include.tooltip | xml_escape }}"
         {% endif %}
         class="card-title"
       >

_includes/citation.html

@@ -13,14 +13,14 @@
     {% if include.style == "rich" %}
       <a
         {% if citation.link %}
-          href="{{ citation.link | relative_url }}"
+          href="{{ citation.link | relative_url | uri_escape }}"
         {% endif %}
         class="citation-image"
-        aria-label="{{ citation.title | default: "citation link" }}"
+        aria-label="{{ citation.title | default: "citation link" | regex_strip }}"
       >
         <img
-          src="{{ citation.image | relative_url }}"
-          alt="{{ citation.title | default: "citation image" }}"
+          src="{{ citation.image | relative_url | uri_escape }}"
+          alt="{{ citation.title | default: "citation image" | regex_strip }}"
           loading="lazy"
           {% include fallback.html %}
         >
@@ -33,7 +33,7 @@
 
       <a
         {% if citation.link %}
-          href="{{ citation.link | relative_url }}"
+          href="{{ citation.link | relative_url | xml_escape }}"
         {% endif %}
         class="citation-title"
       >
@@ -43,7 +43,7 @@
       <div
         class="citation-authors"
         {% if citation.authors.size > 10 %}
-          data-tooltip="{{ citation.authors | join: ", " }} "
+          data-tooltip="{{ citation.authors | join: ", " | xml_escape }}"
         {% endif %}
         tabindex="0"
       >