chore: sync ORCID publications

Author: cfranken

.github/workflows/orcid-sync.yml

@@ -0,0 +1,51 @@
+name: ORCID Sync
+
+on:
+  schedule:
+    - cron: "0 3 * * 0"
+  workflow_dispatch:
+
+jobs:
+  sync:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.11"
+
+      - name: Install dependencies
+        run: python -m pip install --upgrade pip && pip install -r requirements.txt
+
+      - name: Sync ORCID
+        env:
+          ORCID_ID: "0000-0002-0546-5857"
+          UNPAYWALL_EMAIL: ${{ secrets.UNPAYWALL_EMAIL }}
+        run: |
+          python scripts/orcid_sync.py \
+            --orcid "$ORCID_ID" \
+            --bib-file publications/publications.bib \
+            --publications-dir publications \
+            --full
+
+      - name: Regenerate QMD files
+        run: |
+          python scripts/parsePubs.py \
+            --bib publications/publications.bib \
+            --out-dir publications \
+            --include-preprints
+
+      - name: Commit changes
+        run: |
+          if git status --porcelain | grep -q .; then
+            git config user.name "github-actions[bot]"
+            git config user.email "github-actions[bot]@users.noreply.github.com"
+            git add publications/publications.bib publications publications/preprints
+            git commit -m "chore: sync ORCID publications"
+            git push
+          else
+            echo "No changes to commit."
+          fi

.gitignore

@@ -9,3 +9,5 @@ _site
 # vim
 *~
 *swp
+
+**/*.quarto_ipynb

README.md

@@ -1,3 +1,81 @@
 # RSFraLab.github.io
 The Lab Website built using Quarto:
 https://rsfralab.github.io/
+
+## Publications sync (ORCID)
+
+This site can generate new publication entries directly from ORCID and Crossref.
+
+### One-time setup
+
+- Install Python dependencies: `pip install requests bibtexparser`
+
+### Sync new publications
+
+```
+python scripts/orcid_sync.py --orcid YOUR-ORCID-ID --full
+```
+
+This will:
+
+- Read your ORCID works
+- Pull metadata from Crossref using DOIs
+- Rebuild publications/publications.bib from ORCID
+- Optionally create QMD files under publications/ (unless --no-qmd)
+
+### ORCID-only workflow
+
+Use ORCID as the single source of truth and regenerate the BibTeX each time:
+
+```
+python scripts/orcid_sync.py --orcid YOUR-ORCID-ID --full
+```
+
+To skip QMD creation:
+
+```
+python scripts/orcid_sync.py --orcid YOUR-ORCID-ID --full --no-qmd
+```
+
+### Preprints
+
+By default, preprints are excluded when generating QMDs from the BibTeX file. To include them:
+
+```
+python scripts/parsePubs.py --bib publications/publications.bib --out-dir publications --include-preprints
+```
+
+Preprints are written to publications/preprints and shown on preprints.qmd.
+
+### PDF links
+
+If you want a PDF link to appear for a paper, place a PDF at:
+
+```
+publications/pdfs/<generated-filename>.pdf
+```
+
+The listing template will show a “PDF” link when `materials` is set. You can also manually set `materials` in any publication QMD front matter to an external URL.
+
+### External PDF hosting (recommended for large files)
+
+Use a URL template so new entries get a PDF link automatically:
+
+```
+python scripts/orcid_sync.py --orcid YOUR-ORCID-ID --materials-template "https://your-server.org/papers/{slug}.pdf"
+```
+
+Template variables:
+
+- `{slug}` = generated filename without `.qmd`
+- `{doi}` = DOI
+
+### Auto-discover and download PDFs (OA only)
+
+If you want to auto-find open-access PDFs, use Unpaywall (requires email):
+
+```
+python scripts/orcid_sync.py --orcid YOUR-ORCID-ID --unpaywall-email you@caltech.edu --download-pdfs
+```
+
+This downloads OA PDFs into publications/pdfs and sets `materials` to that local path.

_quarto.yml

@@ -26,7 +26,7 @@ website:
     #  - text: "Trademark"
     #    href: trademark.qmd
     right:
-      - text: "{{< ai google-scholar >}} Google Scholar"
+      - text: "{{< iconify academicons google-scholar >}} Google Scholar"
         href: https://scholar.google.com/citations?user=7XYDtdYAAAAJ&hl=en 
       - icon: twitter
         href: https://twitter.com/chr_fronge
@@ -51,7 +51,7 @@ website:
         text: Blog
     right:
       - href: https://scholar.google.com/citations?user=7XYDtdYAAAAJ&hl=en
-        text: "{{< ai google-scholar >}}"
+        text: "{{< iconify academicons google-scholar >}}"
         aria-label: Google Scholar 
       - icon: github
         href: https://github.com/cfranken
@@ -69,6 +69,8 @@ format:
       dark: [darkly, custom.scss]
     toc: true
     css: custom.css
+    include-in-header:
+      - text: "<link rel=\"stylesheet\" href=\"https://cdn.jsdelivr.net/gh/jpswalsh/academicons@1/css/academicons.min.css\">"
     grid:
       sidebar-width: 0px
       body-width: 1000px

custom.css

@@ -1,3 +1,127 @@
 .navbar {
     height: 50px; /* Adjust this value as needed */
+}
+
+.pubs-layout {
+    margin-top: 10px;
+    position: relative;
+    display: flex;
+    gap: 24px;
+    align-items: flex-start;
+}
+
+.pubs-sidebar {
+    position: sticky;
+    top: 80px;
+    align-self: flex-start;
+    max-height: calc(100vh - 120px);
+    overflow-y: auto;
+    padding-left: 16px;
+    border-left: 1px solid #eee;
+    background: #fff;
+    z-index: 10;
+    pointer-events: auto;
+    flex: 0 0 180px;
+}
+
+.pubs-content {
+    position: relative;
+    z-index: 1;
+    flex: 1 1 auto;
+    min-width: 0;
+}
+
+.pubs-sidebar-title {
+    font-weight: 600;
+    margin-bottom: 8px;
+}
+
+.pubs-year-list {
+    list-style: none;
+    padding-left: 0;
+    margin: 0;
+}
+
+.pubs-year-list li {
+    margin: 4px 0;
+}
+
+.pubs-year-list a {
+    text-decoration: none;
+    color: #444;
+    cursor: pointer;
+    pointer-events: auto;
+}
+
+.pubs-year-list a.active {
+    color: #FF6C0C;
+    font-weight: 600;
+}
+
+.pubs-type-filters {
+    margin-bottom: 12px;
+}
+
+.pubs-type-option {
+    display: flex;
+    align-items: center;
+    gap: 6px;
+    margin: 4px 0;
+    font-size: 0.9rem;
+}
+
+.pubs-type-option input {
+    margin: 0;
+}
+
+.pub-list {
+    padding-left: 0;
+}
+
+.pub-list li {
+    list-style: none;
+    padding: 8px 0;
+    border-bottom: 1px solid #f0f0f0;
+}
+
+.pub-item {
+    line-height: 1.35;
+}
+
+.pub-title {
+    font-size: 1.02rem;
+    font-weight: 600;
+    color: #2c3e50;
+    margin-bottom: 2px;
+}
+
+.pub-authors {
+    font-size: 0.92rem;
+    color: #444;
+    margin-bottom: 2px;
+}
+
+.pub-meta {
+    font-size: 0.9rem;
+    color: #666;
+    margin-bottom: 4px;
+}
+
+.pub-links a {
+    font-size: 0.85rem;
+    margin-right: 10px;
+    text-decoration: none;
+}
+
+@media (max-width: 768px) {
+    .pubs-sidebar {
+        position: static;
+        max-height: none;
+        border-left: none;
+        padding-left: 0;
+        margin-top: 12px;
+    }
+    .pubs-layout {
+        flex-direction: column;
+    }
 }

ejs/article.ejs

@@ -2,16 +2,82 @@
 ```{=html}
 <ul class="pub-list list">
 <% for (const item of items) { %>
+  <% const decodeEntitiesOnce = (value) => (value || '')
+       .replace(/&lt;/g, '<')
+       .replace(/&gt;/g, '>')
+       .replace(/&quot;/g, '"')
+       .replace(/&#39;/g, "'")
+       .replace(/&amp;/g, '&')
+       .replace(/&#(\d+);/g, (_m, code) => String.fromCharCode(Number(code)))
+       .replace(/&#x([0-9a-fA-F]+);/g, (_m, code) => String.fromCharCode(parseInt(code, 16)));
+     const decodeEntities = (value) => {
+       let current = value || '';
+       for (let i = 0; i < 3; i += 1) {
+         const next = decodeEntitiesOnce(current);
+         if (next === current) break;
+         current = next;
+       }
+       return current;
+     };
+     const titleDecoded = decodeEntities(item.title || '');
+     const titleHtml = titleDecoded.replace(/\$\\mathrm\{([^}]+)\}\$/g, (_m, formula) => {
+       const plain = formula.replace(/_\{?(\d+)\}?/g, '$1');
+       return plain.replace(/([A-Za-z])([0-9]+)/g, '$1<sub>$2</sub>');
+     }).replace(/\b([A-Z][a-z]?)(\d+)\b/g, '$1<sub>$2</sub>'); %>
+  <% const formatAuthors = (value) => {
+       const raw = (value || '').trim();
+       if (!raw) return '';
+       const parts = raw.split(/\s+and\s+/i).map((p) => p.trim()).filter(Boolean);
+       const formatted = parts.map((p) => {
+         const cleaned = p.replace(/\s+/g, ' ').replace(/[{}]/g, '').trim();
+         if (!cleaned) return '';
+         if (cleaned.includes(',')) {
+           const [last, rest] = cleaned.split(',').map((s) => s.trim());
+           const initials = (rest || '')
+             .split(/\s+/)
+             .map((token) => token.replace(/[^A-Za-z-]/g, ''))
+             .filter(Boolean)
+             .map((token) => `${token[0]}.`)
+             .join(' ');
+           return `${last}${initials ? `, ${initials}` : ''}`;
+         }
+         const tokens = cleaned.split(/\s+/).filter(Boolean);
+         if (tokens.length === 1) return tokens[0];
+         const last = tokens[tokens.length - 1];
+         const initials = tokens.slice(0, -1).map((token) => `${token[0]}.`).join(' ');
+         return `${last}${initials ? `, ${initials}` : ''}`;
+       }).filter(Boolean);
+       if (formatted.length <= 1) return formatted.join('');
+       return `${formatted.slice(0, -1).join(', ')} and ${formatted[formatted.length - 1]}`;
+     };
+     const authorsFormatted = formatAuthors(item.author); %>
   <li <%= metadataAttrs(item) %>>
-    <span class="listing-title lead" style="color:orange;font-weight:bold"><%= item.title %></span><br />
-    <span class="listing-author"><%= item.author %></span>
-    <span class="listing-publication fst-italic "><%= item.publication %></span>
-    <span class="listing-year">(<%= item.year %>)</span>
+    <div class="pub-item">
+      <div class="listing-title pub-title"><%- titleHtml %></div>
+      <div class="listing-author pub-authors"><%= authorsFormatted %></div>
+      <span class="listing-type pub-type" style="display:none"><%= item.type %></span>
+      <div class="pub-meta">
+        <span class="listing-publication pub-publication"><%= item.publication %></span>
+        <span class="listing-year pub-year">(<%= item.year %>)</span>
+      </div>
+      <div class="pub-links">
     <% if (item.doi) { %>
     <a href="https://doi.org/<%- item.doi %>">
       DOI
     </a>
     <% } %>
+    <% if (item.materials) { %>
+    <a href="<%- item.materials %>">
+      PDF
+    </a>
+    <% } %>
+    <% if (item.supplement) { %>
+    <a href="<%- item.supplement %>">
+      Supplement
+    </a>
+    <% } %>
+      </div>
+    </div>
   </li>
 <% } %>
 </ul>