Add maintenance guardrails for CI and local workflow

.github/workflows/jekyll.yml

@@ -2,9 +2,9 @@ name: Jekyll site CI
 
 on:
   push:
-    branches: [ "main" ]
+    branches: ["main"]
   pull_request:
-    branches: [ "main" ]
+    branches: ["main"]
 
 permissions:
   contents: read
@@ -15,61 +15,72 @@ jobs:
   build:
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v4
-      with:
-        fetch-depth: 0
-
-    - name: Block node_modules changes on pull requests
-      if: github.event_name == 'pull_request'
-      run: |
-        BASE_SHA="${{ github.event.pull_request.base.sha }}"
-        HEAD_SHA="${{ github.event.pull_request.head.sha }}"
-        CHANGED_NODE_MODULES="$(git diff --name-only "${BASE_SHA}...${HEAD_SHA}" -- 'node_modules/**')"
-
-        if [ -n "${CHANGED_NODE_MODULES}" ]; then
-          echo "::error title=Blocked path::Pull request includes changes under node_modules/."
-          echo "${CHANGED_NODE_MODULES}"
-          exit 1
-        fi
-
-    - name: Block node_modules changes on pushes
-      if: github.event_name == 'push'
-      run: |
-        BASE_SHA="${{ github.event.before }}"
-        HEAD_SHA="${{ github.sha }}"
-        ZERO_SHA="0000000000000000000000000000000000000000"
-
-        if [ "${BASE_SHA}" = "${ZERO_SHA}" ]; then
-          echo "Initial push detected; skipping node_modules diff guard."
-          exit 0
-        fi
-
-        CHANGED_NODE_MODULES="$(git diff --name-only "${BASE_SHA}...${HEAD_SHA}" -- 'node_modules/**')"
-
-        if [ -n "${CHANGED_NODE_MODULES}" ]; then
-          echo "::error title=Blocked path::Push includes changes under node_modules/."
-          echo "${CHANGED_NODE_MODULES}"
-          exit 1
-        fi
-
-    - name: Verify thesis navigation docs stay in sync
-      run: |
-        chmod +x scripts/check-phd-thesis-nav-docs.sh
-        ./scripts/check-phd-thesis-nav-docs.sh
-
-    - name: Set up Ruby
-      uses: ruby/setup-ruby@v1
-      with:
-        ruby-version: '3.2'
-        bundler-cache: true
-
-    - name: Build site and search database
-      run: |
-        chmod +x scripts/build.sh
-        ./scripts/build.sh
-
-    - name: Upload artifact
-      uses: actions/upload-pages-artifact@v3
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+
+      - name: Block node_modules changes on pull requests
+        if: github.event_name == 'pull_request'
+        run: |
+          BASE_SHA="${{ github.event.pull_request.base.sha }}"
+          HEAD_SHA="${{ github.event.pull_request.head.sha }}"
+          CHANGED_NODE_MODULES="$(git diff --name-only "${BASE_SHA}...${HEAD_SHA}" -- 'node_modules/**')"
+
+          if [ -n "${CHANGED_NODE_MODULES}" ]; then
+            echo "::error title=Blocked path::Pull request includes changes under node_modules/."
+            echo "${CHANGED_NODE_MODULES}"
+            exit 1
+          fi
+
+      - name: Block node_modules changes on pushes
+        if: github.event_name == 'push'
+        run: |
+          BASE_SHA="${{ github.event.before }}"
+          HEAD_SHA="${{ github.sha }}"
+          ZERO_SHA="0000000000000000000000000000000000000000"
+
+          if [ "${BASE_SHA}" = "${ZERO_SHA}" ]; then
+            echo "Initial push detected; skipping node_modules diff guard."
+            exit 0
+          fi
+
+          CHANGED_NODE_MODULES="$(git diff --name-only "${BASE_SHA}...${HEAD_SHA}" -- 'node_modules/**')"
+
+          if [ -n "${CHANGED_NODE_MODULES}" ]; then
+            echo "::error title=Blocked path::Push includes changes under node_modules/."
+            echo "${CHANGED_NODE_MODULES}"
+            exit 1
+          fi
+
+      - name: Verify thesis navigation docs stay in sync
+        run: |
+          chmod +x scripts/check-phd-thesis-nav-docs.sh
+          ./scripts/check-phd-thesis-nav-docs.sh
+
+      - name: Set up Node.js
+        uses: actions/setup-node@v4
+        with:
+          node-version: "22.16.0"
+          cache: "npm"
+
+      - name: Lint markdown
+        run: |
+          npm ci --no-fund --no-audit --ignore-scripts
+          npm run lint:md
+
+      - name: Set up Ruby
+        uses: ruby/setup-ruby@v1
+        with:
+          ruby-version: "3.2"
+          bundler-cache: true
+
+      - name: Build site and search database
+        run: |
+          chmod +x scripts/build.sh
+          ./scripts/build.sh
+
+      - name: Upload artifact
+        uses: actions/upload-pages-artifact@v3
 
   deploy:
     # Only run deploy job on push to main, not on PRs

.github/workflows/update-search.yml

@@ -39,22 +39,29 @@ jobs:
         run: |
           GITHUB_ORG="${GITHUB_REPOSITORY%%/*}"
           SEARCH_REPO="${SEARCH_REPO:-comphy-search}"
-          echo "Attempting to clone search database from ${GITHUB_ORG}/${SEARCH_REPO}..."
+          SEARCH_BRANCH="${SEARCH_BRANCH:-main}"
+          CLONE_URL="https://github.com/${GITHUB_ORG}/${SEARCH_REPO}.git"
+          CLONE_LOG="$(mktemp)"
 
-          if git clone "https://github.com/${GITHUB_ORG}/${SEARCH_REPO}.git"; then
+          echo "Attempting to clone search database from ${GITHUB_ORG}/${SEARCH_REPO} (${SEARCH_BRANCH})..."
+
+          if git clone --single-branch --branch "${SEARCH_BRANCH}" "${CLONE_URL}" 2>"${CLONE_LOG}"; then
             mkdir -p assets/js
             echo "clone_ok=true" >> "${GITHUB_OUTPUT}"
             echo "Search database repository cloned successfully"
           else
             echo "clone_ok=false" >> "${GITHUB_OUTPUT}"
-            echo "Warning: Could not clone ${GITHUB_ORG}/${SEARCH_REPO}"
-            echo "Search functionality may be limited. This is expected if the search repository does not exist."
-            echo "::warning title=Search DB clone failed::Could not clone ${GITHUB_ORG}/${SEARCH_REPO}. Search update will be skipped."
+            CLONE_ERROR="$(tr '\n' ' ' < "${CLONE_LOG}" | sed 's/[[:space:]]\+/ /g; s/^ //; s/ $//')"
+            echo "::error title=Search DB clone failed::Could not clone ${GITHUB_ORG}/${SEARCH_REPO} (${SEARCH_BRANCH})."
             {
-              echo "### Search DB update skipped"
-              echo "- Clone failed for \`${GITHUB_ORG}/${SEARCH_REPO}\`."
+              echo "### Search DB clone failed"
+              echo "- Repository: \`${GITHUB_ORG}/${SEARCH_REPO}\`"
+              echo "- Branch: \`${SEARCH_BRANCH}\`"
+              echo "- URL: \`${CLONE_URL}\`"
+              echo "- Error: \`${CLONE_ERROR}\`"
             } >> "${GITHUB_STEP_SUMMARY}"
-            exit 0
+            cat "${CLONE_LOG}" >&2
+            exit 1
           fi
 
       - name: Copy search database

.husky/pre-commit

@@ -0,0 +1,12 @@
+#!/usr/bin/env sh
+
+set -e
+
+REPO_ROOT="$(git rev-parse --show-toplevel 2>/dev/null)"
+
+if [ -z "$REPO_ROOT" ]; then
+  echo "Unable to determine repository root for pre-commit checks."
+  exit 1
+fi
+
+sh "$REPO_ROOT/scripts/check-node-modules.sh"

.markdownlint-cli2.jsonc

@@ -1,5 +1,6 @@
 {
   "config": {
+    "default": false,
     "MD034": true,
   },
   "ignores": ["node_modules/**", "assets/css/academicons-1.7.0/README.md"],

AGENTS.md

@@ -94,6 +94,12 @@ The following pages redirect to the CoMPhy Lab website:
 - Escape literal dollar signs in content as `\$` to prevent accidental math
   parsing.
 
+### MathJax Update Checklist
+
+- Refresh vendored MathJax at `assets/js/mathjax/tex-svg.js`.
+- Update pinned fallback URL and SRI hash in `_layouts/default.html`.
+- Re-run `scripts/check-phd-thesis-nav-docs.sh` and `npm run lint:md`.
+
 ### Content Management
 
 - Team information and research papers are managed at the CoMPhy Lab

Gemfile.lock

@@ -10,12 +10,12 @@ GEM
       eventmachine (>= 0.12.9)
       http_parser.rb (~> 0)
     eventmachine (1.2.7)
-    faraday (2.12.2)
+    faraday (2.14.1)
       faraday-net_http (>= 2.0, < 3.5)
       json
       logger
-    faraday-net_http (3.4.0)
-      net-http (>= 0.5.0)
+    faraday-net_http (3.4.2)
+      net-http (~> 0.5)
     ffi (1.17.1)
     ffi (1.17.1-aarch64-linux-gnu)
     ffi (1.17.1-aarch64-linux-musl)
@@ -80,7 +80,7 @@ GEM
       jekyll (>= 3.7, < 5.0)
     jekyll-watch (2.2.1)
       listen (~> 3.0)
-    json (2.9.1)
+    json (2.18.1)
     kramdown (2.5.1)
       rexml (>= 3.3.9)
     kramdown-parser-gfm (1.1.0)
@@ -89,10 +89,10 @@ GEM
     listen (3.9.0)
       rb-fsevent (~> 0.10, >= 0.10.3)
       rb-inotify (~> 0.9, >= 0.9.10)
-    logger (1.6.5)
+    logger (1.7.0)
     mercenary (0.4.0)
-    net-http (0.6.0)
-      uri
+    net-http (0.9.1)
+      uri (>= 0.11.1)
     octokit (4.25.1)
       faraday (>= 1, < 3)
       sawyer (~> 0.9)

README.md

@@ -47,40 +47,54 @@ The personal website for Vatsal Sanjay, hosted at [comphy-lab.org/vatsalsy](http
    - Bundler (`gem install bundler`)
 
 2. **Install Dependencies**
+
    ```bash
    bundle install
    ```
 
 3. **Run Local Server**
+
    ```bash
    bundle exec jekyll serve
    ```
+
    - Visit <http://localhost:4000> in the browser
    - Changes in source files trigger automatic rebuilds
 
 4. **Deployment**
    - Typically managed via GitHub Pages when merged/pushed to the main branch
    - Local testing is recommended before committing changes
 
+### Commit Guardrails
+
+- Run `./scripts/check-node-modules.sh` before commits if you touch dependencies.
+- If `node_modules/` changes were accidental, clean them with:
+  - `git restore --staged --worktree -- node_modules`
+  - `git clean -fdX -- node_modules/`
+- Install hooks with `npm install` so `.husky/pre-commit` blocks staged `node_modules/` changes automatically.
+
 ### Content Management
 
 #### About Page & Content
+
 - `about.md`: Redirects to the About section on the homepage (/#about)
 - `aboutVatsal.md`: Contains the About section content loaded via JavaScript on the homepage
 - The main.js file fetches and renders aboutVatsal.md in the #about-content element
 
 **IMPORTANT**: When updating `aboutVatsal.md`, you must also update the fallback content in `about.md` (lines 15-37) to keep them synchronized. The fallback content is displayed when JavaScript is disabled.
 
 #### Research Pages
+
 - `research-interests.md`: Redirects to comphy-lab.org/research
 - `research-interest.md`: Redirects to comphy-lab.org/research
 - `phd-thesis.md`: Redirects to comphy-lab.org/research#thesis
 - `talks.md`: Redirects to comphy-lab.org/research
 
 #### Contact Page
+
 - `contact.md`: Redirects to comphy-lab.org/join
 
-#### Adding or Editing Team 
+#### Adding or Editing Team
 
 See: [comphy-lab.org/team](https://comphy-lab.org/team) and to edit, see: [github](https://github.com/comphy-lab/comphy-lab.github.io)
 
@@ -91,12 +105,14 @@ See: [comphy-lab.org/research](https://comphy-lab.org/research) and to edit, see
 ## Part B: Back-End Documentation
 
 ### Configuration and Layouts
+
 - `_config.yml`: Site-wide settings, collections, build options
 - Layout Templates in `_layouts/`
 - Partial Includes in `_includes/`
 - Assets in `assets/`
 
 ### Design Elements
+
 - **Color Scheme**
   - Gradient text (Red to Blue) for lab name
   - Warm orange tint + blur for header
@@ -109,23 +125,25 @@ See: [comphy-lab.org/research](https://comphy-lab.org/research) and to edit, see
   - Generated from CoMPhy Lab logo
 
 ### Fonts and Icons Attribution
+
 - [Academicons 1.7.0 (SIL OFL 1.1, MIT)](https://jpswalsh.github.io/academicons/)
 - [Font Awesome](https://fontawesome.com/)
 - Fontello (Various licenses)
 - Libre Baskerville (SIL Open Font License)
 - Open Sans (Apache License 2.0)
 
-
 ## Contributing Guidelines
 
 ### Issue Templates
+
 The repository includes several issue templates to streamline the process of reporting problems or requesting changes:
 
 1. **[Bug Report](https://github.com/VatsalSy/VatsalSy.github.io/issues/new?template=bug_report.yml)**: Use this template to report website issues, broken links, or display problems
 2. **[Add Team Member](https://github.com/VatsalSy/VatsalSy.github.io/issues/new?template=add_team_member.yml)**: Template for requesting addition of new lab members with their details
 3. **[Add Publication](https://github.com/VatsalSy/VatsalSy.github.io/issues/new?template=add_publication.yml)**: Template for adding new research publications with metadata
 
 To create a new issue:
+
 1. Click one of the template links above, or
 2. Go to the Issues tab in GitHub
 3. Click "New Issue"
@@ -134,14 +152,17 @@ To create a new issue:
 6. Submit the issue
 
 ### Pull Request Template
+
 When submitting changes, use the provided PR template which includes:
+
 - Description of changes
 - Type of change (bug fix, feature, content update, etc.)
 - Testing checklist
 - Related issues
 - Screenshots (if applicable)
 
 To submit a PR:
+
 1. Fork the repository
 2. Create a new branch for your changes
 3. Make and test your changes locally

about.md

@@ -52,9 +52,8 @@ We’re building a computationally focused group at Durham. If you’re excited
 - Sanjay, V., Zhang, B., Lv, C., & Lohse, D. The role of viscosity on drop impact forces on non-wetting surfaces. J. Fluid Mech., 1004, A6 (2025). [![Open Access](https://img.shields.io/badge/Open%20Access-Open-orange?logo=openaccess&logoColor=white&style=flat)](https://doi.org/10.1017/jfm.2024.982)
 
 ### Find me
-[![Location](https://img.shields.io/badge/-Physics%20of%20Fluids-4285F4?style=flat&logo=googlemaps&logoColor=white)](https://maps.app.goo.gl/jSTCYnfcndF1uZPV8)
+[![Location](https://img.shields.io/badge/-Durham%20University-4285F4?style=flat&logo=googlemaps&logoColor=white)](https://www.durham.ac.uk/staff/vatsal-sanjay/)
 [![Website](https://img.shields.io/badge/-comphy--lab.org-4285F4?style=flat&logo=googlechrome&logoColor=white)](https://comphy-lab.org)
-[![Email](https://img.shields.io/badge/-mailto:[email protected]?style=flat&logo=gmail&logoColor=white)](mailto:[email protected])
 
 <div class="email-container">
   <span class="email-text">[email protected]</span>

package.json

@@ -12,6 +12,8 @@
     "lint:js": "eslint assets/js/**/*.js",
     "lint:css": "stylelint 'assets/css/**/*.css'",
     "lint:md": "markdownlint-cli2 '**/*.md' --ignore node_modules",
+    "lint:md:fix": "markdownlint-cli2 --fix '**/*.md' --ignore node_modules",
+    "check:node-modules": "./scripts/check-node-modules.sh",
     "lint": "npm run lint:js && npm run lint:css && npm run lint:md",
     "format": "prettier --write assets/js/**/*.js assets/css/**/*.css",
     "prepare": "husky",