Spring 26 Updates

.devcontainer/devcontainer.json

@@ -9,7 +9,7 @@
     "ghcr.io/rocker-org/devcontainer-features/apt-packages:1": {
       "packages": "build-essential,imagemagick,inotify-tools,jupyter-nbconvert,procps,ruby-full,zlib1g-dev"
     },
-    "ghcr.io/devcontainers-contrib/features/prettier:1": {}
+    "ghcr.io/devcontainers-extra/features/prettier:1.0.2": {}
   },
 
   // Optionally: run jekyll serve automatically on container entering using the Docker entrypoint

.gitattributes

@@ -0,0 +1,2 @@
+# Force LF line endings, needed for Docker to work on Windows
+*.sh text eol=lf

.github/workflows/axe.yml

@@ -43,6 +43,7 @@ jobs:
             }
       - name: Install and Build 🔧
         run: |
+          sudo apt-get update && sudo apt-get install -y imagemagick
           pip3 install --upgrade jupyter
           export JEKYLL_ENV=production
           bundle exec jekyll build

.github/workflows/broken-links-site.yml

@@ -31,6 +31,7 @@ jobs:
             }
       - name: Install and Build 🔧
         run: |
+          sudo apt-get update && sudo apt-get install -y imagemagick
           pip3 install --upgrade jupyter
           export JEKYLL_ENV=production
           bundle exec jekyll build
@@ -39,7 +40,7 @@ jobs:
           npm install -g purgecss
           purgecss -c purgecss.config.js
       - name: Link Checker 🔗
-        uses: lycheeverse/lychee-action@v1.9.0
+        uses: lycheeverse/lychee-action@v2.0.2
         with:
           fail: false
           # only check local links

.github/workflows/broken-links.yml

@@ -0,0 +1,54 @@
+name: Check for broken links
+
+on:
+  push:
+    branches:
+      - master
+      - main
+    paths:
+      - "assets/**"
+      - "**.html"
+      - "**.js"
+      - "**.liquid"
+      - "**/*.md"
+      - "**.yml"
+      - "!.github/workflows/axe.yml"
+      - "!.github/workflows/deploy-docker-tag.yml"
+      - "!.github/workflows/deploy-image.yml"
+      - "!.github/workflows/docker-slim.yml"
+      - "!.github/workflows/lighthouse-badger.yml"
+      - "!.github/workflows/prettier.yml"
+      - "!lighthouse_results/**"
+  pull_request:
+    branches:
+      - master
+      - main
+    paths:
+      - "assets/**"
+      - "**.html"
+      - "**.js"
+      - "**.liquid"
+      - "**/*.md"
+      - "**.yml"
+      - "!.github/workflows/axe.yml"
+      - "!.github/workflows/deploy-docker-tag.yml"
+      - "!.github/workflows/deploy-image.yml"
+      - "!.github/workflows/docker-slim.yml"
+      - "!.github/workflows/lighthouse-badger.yml"
+      - "!.github/workflows/prettier.yml"
+      - "!lighthouse_results/**"
+
+jobs:
+  link-checker:
+    runs-on: ubuntu-latest
+    # only run on the main repo
+    if: github.repository == 'alshedivat/al-folio'
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Link Checker 🔗
+        uses: lycheeverse/[email protected]
+        with:
+          fail: true
+          # removed md files that include liquid tags
+          args: --user-agent 'curl/7.54' --exclude-path README.md --exclude-path _pages/404.md --exclude-path _pages/blog.md --exclude-path _posts/2018-12-22-distill.md --exclude-path _posts/2023-04-24-videos.md --exclude-path _books/the_godfather.md --verbose --no-progress './**/*.md' './**/*.html'

.github/workflows/codeql.yml

@@ -0,0 +1,94 @@
+# For most projects, this workflow file will not need changing; you simply need
+# to commit it to your repository.
+#
+# You may wish to alter this file to override the set of languages analyzed,
+# or to provide custom queries or build logic.
+#
+# ******** NOTE ********
+# We have attempted to detect the languages in your repository. Please check
+# the `language` matrix defined below to confirm you have the correct set of
+# supported CodeQL languages.
+#
+name: "CodeQL Advanced"
+
+on:
+  push:
+    branches: ["main"]
+  pull_request:
+    branches: ["main"]
+  schedule:
+    - cron: "45 4 * * 3"
+
+jobs:
+  analyze:
+    name: Analyze (${{ matrix.language }})
+    # Runner size impacts CodeQL analysis time. To learn more, please see:
+    #   - https://gh.io/recommended-hardware-resources-for-running-codeql
+    #   - https://gh.io/supported-runners-and-hardware-resources
+    #   - https://gh.io/using-larger-runners (GitHub.com only)
+    # Consider using larger runners or machines with greater resources for possible analysis time improvements.
+    runs-on: ${{ (matrix.language == 'swift' && 'macos-latest') || 'ubuntu-latest' }}
+    permissions:
+      # required for all workflows
+      security-events: write
+
+      # required to fetch internal or private CodeQL packs
+      packages: read
+
+      # only required for workflows in private repositories
+      actions: read
+      contents: read
+
+    strategy:
+      fail-fast: false
+      matrix:
+        include:
+          - language: javascript-typescript
+            build-mode: none
+          - language: ruby
+            build-mode: none
+        # CodeQL supports the following values keywords for 'language': 'c-cpp', 'csharp', 'go', 'java-kotlin', 'javascript-typescript', 'python', 'ruby', 'swift'
+        # Use `c-cpp` to analyze code written in C, C++ or both
+        # Use 'java-kotlin' to analyze code written in Java, Kotlin or both
+        # Use 'javascript-typescript' to analyze code written in JavaScript, TypeScript or both
+        # To learn more about changing the languages that are analyzed or customizing the build mode for your analysis,
+        # see https://docs.github.com/en/code-security/code-scanning/creating-an-advanced-setup-for-code-scanning/customizing-your-advanced-setup-for-code-scanning.
+        # If you are analyzing a compiled language, you can modify the 'build-mode' for that language to customize how
+        # your codebase is analyzed, see https://docs.github.com/en/code-security/code-scanning/creating-an-advanced-setup-for-code-scanning/codeql-code-scanning-for-compiled-languages
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+
+      # Initializes the CodeQL tools for scanning.
+      - name: Initialize CodeQL
+        uses: github/codeql-action/init@v3
+        with:
+          languages: ${{ matrix.language }}
+          build-mode: ${{ matrix.build-mode }}
+          # If you wish to specify custom queries, you can do so here or in a config file.
+          # By default, queries listed here will override any specified in a config file.
+          # Prefix the list here with "+" to use these queries and those in the config file.
+
+          # For more details on CodeQL's query packs, refer to: https://docs.github.com/en/code-security/code-scanning/automatically-scanning-your-code-for-vulnerabilities-and-errors/configuring-code-scanning#using-queries-in-ql-packs
+          # queries: security-extended,security-and-quality
+
+      # If the analyze step fails for one of the languages you are analyzing with
+      # "We were unable to automatically build your code", modify the matrix above
+      # to set the build mode to "manual" for that language. Then modify this step
+      # to build your code.
+      # ℹ️ Command-line programs to run using the OS shell.
+      # 📚 See https://docs.github.com/en/actions/using-workflows/workflow-syntax-for-github-actions#jobsjob_idstepsrun
+      - if: matrix.build-mode == 'manual'
+        shell: bash
+        run: |
+          echo 'If you are using a "manual" build mode for one or more of the' \
+            'languages you are analyzing, replace this with the commands to build' \
+            'your code, for example:'
+          echo '  make bootstrap'
+          echo '  make release'
+          exit 1
+
+      - name: Perform CodeQL Analysis
+        uses: github/codeql-action/analyze@v3
+        with:
+          category: "/language:${{matrix.language}}"

.github/workflows/deploy.yml

@@ -7,6 +7,8 @@ on:
       - main
     paths:
       - "assets/**"
+      - "_sass/**"
+      - "_scripts/**"
       - "**.bib"
       - "**.html"
       - "**.js"
@@ -34,6 +36,8 @@ on:
       - main
     paths:
       - "assets/**"
+      - "_sass/**"
+      - "_scripts/**"
       - "**.bib"
       - "**.html"
       - "**.js"
@@ -86,6 +90,7 @@ jobs:
           value: ${{ github.repository }}
       - name: Install and Build 🔧
         run: |
+          sudo apt-get update && sudo apt-get install -y imagemagick
           pip3 install --upgrade nbconvert
           export JEKYLL_ENV=production
           bundle exec jekyll build

.github/workflows/docker-slim.yml

@@ -12,11 +12,7 @@ on:
     workflows: ["Docker Image CI"]
     types:
       - completed
-
-# on:
-#   push:
-#     branches:
-#       - 'master'
+  workflow_dispatch:
 
 jobs:
   build:
@@ -43,7 +39,7 @@ jobs:
           sed -i "s|\.:|${{ github.workspace }}:|g" ${{ github.workspace }}/docker-compose.yml
           cat ${{ github.workspace }}/docker-compose.yml
 
-      - uses: kitabisa/docker-slim-action@v1.1.1
+      - uses: kitabisa/docker-slim-action@v1.2.0
         env:
           DSLIM_PULL: true
           DSLIM_COMPOSE_FILE: ${{ github.workspace }}/docker-compose.yml

.github/workflows/update-citations.yml

@@ -0,0 +1,116 @@
+name: Update Google Scholar Citations
+
+on:
+  schedule:
+    - cron: "0 0 * * 1" # Monday
+    - cron: "0 0 * * 3" # Wednesday
+    - cron: "0 0 * * 5" # Friday
+  workflow_dispatch:
+
+jobs:
+  update-citations:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+        with:
+          # Use PAT if provided, otherwise fall back to GitHub token so `act` runs cleanly.
+          token: ${{ secrets.PAT || github.token }}
+
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: "3.13"
+
+      - name: Install dependencies
+        run: |
+          echo "🔧 Installing dependencies..."
+          python -m pip install --upgrade pip
+          pip install -r requirements.txt
+
+      - name: Save current citations.yml hash
+        id: before
+        run: |
+          echo "📦 Checking existing citations.yml hash..."
+          if [ -f _data/citations.yml ]; then
+            sha_before=$(sha256sum _data/citations.yml | awk '{print $1}')
+            echo "sha_before=$sha_before" >> $GITHUB_OUTPUT
+            echo "📝 SHA before: $sha_before"
+          else
+            echo "sha_before=none" >> $GITHUB_OUTPUT
+            echo "📝 No existing citations.yml file found."
+          fi
+
+      - name: Run citation update script
+        id: run_citation_update
+        shell: bash
+        run: |
+          set +e
+          max_attempts=2
+          attempt=1
+          status=1
+          while [ $attempt -le $max_attempts ]; do
+            echo "🚀 Attempt $attempt/$max_attempts: running citation update (timeout 180s)..."
+            start_time=$(date)
+            timeout 360 python bin/update_scholar_citations.py
+            status=$?
+            end_time=$(date)
+            if [ $status -eq 0 ]; then
+              echo "✅ Citation update succeeded on attempt $attempt (started at $start_time, ended at $end_time)."
+              echo "✅ Citation update succeeded." >> $GITHUB_STEP_SUMMARY
+              break
+            else
+              echo "❌ Citation update failed on attempt $attempt with exit code $status (started at $start_time, ended at $end_time)."
+              if [ $attempt -lt $max_attempts ]; then
+                echo "⏳ Retrying after brief pause..."
+                sleep 5
+              fi
+            fi
+            attempt=$((attempt+1))
+          done
+
+          if [ $status -ne 0 ]; then
+            echo "❌ Citation update script failed after $max_attempts attempt(s) with exit code $status." >> $GITHUB_STEP_SUMMARY
+          fi
+          set -e
+
+      - name: Save new citations.yml hash
+        id: after
+        run: |
+          echo "🔍 Checking updated citations.yml hash..."
+          if [ -f _data/citations.yml ]; then
+            sha_after=$(sha256sum _data/citations.yml | awk '{print $1}')
+            echo "sha_after=$sha_after" >> $GITHUB_OUTPUT
+            echo "📝 SHA after: $sha_after"
+          else
+            echo "sha_after=none" >> $GITHUB_OUTPUT
+            echo "📝 citations.yml was not created or is missing."
+          fi
+
+      - name: Report citations.yml change in summary
+        run: |
+          echo "📋 Comparing citation file hashes..."
+          if [ "${{ steps.before.outputs.sha_before }}" != "${{ steps.after.outputs.sha_after }}" ]; then
+            echo "✅ _data/citations.yml was updated."
+            echo "✅ _data/citations.yml was updated." >> $GITHUB_STEP_SUMMARY
+          else
+            echo "ℹ️ _data/citations.yml was not changed."
+            echo "ℹ️ _data/citations.yml was not changed." >> $GITHUB_STEP_SUMMARY
+          fi
+
+      - name: Configure Git
+        run: |
+          git config --local user.email "[email protected]"
+          git config --local user.name "GitHub Actions"
+          echo "🔧 Git configured."
+
+      - name: Commit and push if changed
+        if: ${{ !env.ACT }} # skip pushing when running under act
+        run: |
+          git add _data/citations.yml
+          git diff --staged --quiet || (
+            echo "📤 Committing and pushing changes..."
+            git commit -m "Update Google Scholar citations"
+            git push
+          )