style: modern code blocks — dark surface, ghost labels, brand accents

.github/workflows/deploy-docs.yml

@@ -2,35 +2,62 @@ name: Deploy Documentation
 
 on:
   push:
-    branches: ["main"]
+    branches: [main]
+    paths:
+      - 'docs/**'
+      - 'mkdocs.yml'
+      - '.github/workflows/deploy-docs.yml'
+  pull_request:
+    paths:
+      - 'docs/**'
+      - 'mkdocs.yml'
   workflow_dispatch:
 
 permissions:
-  contents: write
+  contents: read
+  pages: write
+  id-token: write
+
+concurrency:
+  group: "pages"
+  cancel-in-progress: false
 
 jobs:
-  deploy-docs:
+  build:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v4
-        with:
-          fetch-depth: 0
+      - name: Checkout
+        uses: actions/checkout@v4
 
-      - name: Set up Python 3.10
-        uses: actions/setup-python@v4
+      - name: Setup Python
+        uses: actions/setup-python@v5
         with:
-          python-version: "3.10"
+          python-version: '3.11'
 
-      - name: Cache pip dependencies
-        uses: actions/cache@v3
-        with:
-          path: ~/.cache/pip
-          key: ${{ runner.os }}-pip-docs-${{ hashFiles('requirements-docs.txt') }}
-          restore-keys: |
-            ${{ runner.os }}-pip-docs-
+      - name: Install MkDocs
+        run: pip install mkdocs-material
+
+      - name: Build docs
+        run: mkdocs build --site-dir site
 
-      - name: Install documentation dependencies
-        run: pip install -r requirements-docs.txt
+      - name: Setup Pages
+        if: github.ref == 'refs/heads/main'
+        uses: actions/configure-pages@v5
 
-      - name: Build and deploy documentation
-        run: 'mkdocs gh-deploy --force --message "docs: deploy documentation [skip ci]"'
+      - name: Upload artifact
+        if: github.ref == 'refs/heads/main'
+        uses: actions/upload-pages-artifact@v3
+        with:
+          path: site
+
+  deploy:
+    if: github.ref == 'refs/heads/main'
+    environment:
+      name: github-pages
+      url: ${{ steps.deployment.outputs.page_url }}
+    runs-on: ubuntu-latest
+    needs: build
+    steps:
+      - name: Deploy to GitHub Pages
+        id: deployment
+        uses: actions/deploy-pages@v4

.gitignore

@@ -248,3 +248,4 @@ tests/example/QCprofile.pdf
 poetry.lock
 .vscode/
 .DS_Store
+tmp/

docs/overrides/main.html

@@ -0,0 +1,67 @@
+{% extends "base.html" %}
+
+{% block footer %}
+<footer class="md-footer">
+  {% if page.previous_page or page.next_page %}
+  <nav class="md-footer__inner md-grid" aria-label="Footer">
+    {% if page.previous_page %}
+    <a href="{{ page.previous_page.url | url }}" class="md-footer__link md-footer__link--prev">
+      <div class="md-footer__button md-icon">
+        <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path d="M20 11v2H8l5.5 5.5-1.42 1.42L4.16 12l7.92-7.92L13.5 5.5 8 11z"/></svg>
+      </div>
+      <div class="md-footer__title">
+        <span class="md-footer__direction">Previous</span>
+        {{ page.previous_page.title }}
+      </div>
+    </a>
+    {% endif %}
+    {% if page.next_page %}
+    <a href="{{ page.next_page.url | url }}" class="md-footer__link md-footer__link--next">
+      <div class="md-footer__title">
+        <span class="md-footer__direction">Next</span>
+        {{ page.next_page.title }}
+      </div>
+      <div class="md-footer__button md-icon">
+        <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path d="M4 11v2h12l-5.5 5.5 1.42 1.42L19.84 12l-7.92-7.92L10.5 5.5 16 11z"/></svg>
+      </div>
+    </a>
+    {% endif %}
+  </nav>
+  {% endif %}
+  <div class="qms-ecosystem-banner">
+    <div class="qms-banner-inner">
+      <div>
+        <div class="qms-brand"><svg width="20" height="20" viewBox="0 0 70 70" fill="none"><polygon points="35,56 10,46 35,36 60,46" fill="#60a5fa" opacity="0.4"/><polygon points="35,48 14,40 35,32 56,40" fill="#818cf8" opacity="0.6"/><polygon points="35,40 18,34 35,28 52,34" fill="#a78bfa" opacity="0.75"/><rect x="28" y="14" width="2.5" height="12" rx="0.8" fill="#c4b5fd" opacity="0.55"/><rect x="32" y="8" width="2.5" height="18" rx="0.8" fill="#a78bfa" opacity="0.9"/><rect x="36" y="12" width="2.5" height="14" rx="0.8" fill="#c4b5fd" opacity="0.6"/></svg><span class="qms-brand-text">quant<span>ms</span></span></div>
+        <p>A complete, open-source ecosystem for quantitative proteomics analysis.</p>
+      </div>
+      <div>
+        <h4>Pipelines</h4>
+        <ul>
+          <li><a href="https://docs.quantms.org" target="_blank">quantms (DDA)</a></li>
+          <li><a href="https://github.com/bigbio/quantmsdiann" target="_blank">quantmsdiann (DIA)</a></li>
+        </ul>
+      </div>
+      <div>
+        <h4>Libraries</h4>
+        <ul>
+          <li><a href="https://mokume.quantms.org" target="_blank">mokume</a></li>
+          <li><a href="https://qpx.quantms.org" target="_blank">qpx</a></li>
+          <li><a href="https://pmultiqc.quantms.org" target="_blank">pmultiqc</a></li>
+        </ul>
+      </div>
+      <div>
+        <h4>Resources</h4>
+        <ul>
+          <li><a href="https://quantms.org" target="_blank">quantms.org</a></li>
+          <li><a href="https://portal.quantms.org" target="_blank">Data Portal</a></li>
+          <li><a href="https://github.com/bigbio" target="_blank">GitHub</a></li>
+        </ul>
+      </div>
+      <div class="qms-bottom">
+        <span>&copy; 2024-2026 BigBio Team</span>
+        <span>Built with open science</span>
+      </div>
+    </div>
+  </div>
+</footer>
+{% endblock %}

mkdocs.yml

@@ -8,22 +8,22 @@ repo_url: https://github.com/bigbio/mokume
 
 theme:
   name: material
+  custom_dir: docs/overrides
+  font: false
   palette:
     - scheme: default
-      primary: indigo
+      primary: blue
       accent: indigo
       toggle:
         icon: material/brightness-7
         name: Switch to dark mode
     - scheme: slate
-      primary: indigo
+      primary: blue
       accent: indigo
       toggle:
         icon: material/brightness-4
         name: Switch to light mode
   features:
-    - navigation.tabs
-    - navigation.tabs.sticky
     - navigation.sections
     - navigation.expand
     - navigation.path
@@ -36,7 +36,6 @@ theme:
     - search.highlight
     - search.share
     - toc.follow
-    - toc.integrate
     - content.code.copy
     - content.code.annotate
     - content.tabs.link
@@ -99,31 +98,34 @@ plugins:
         - en
 
 nav:
-  - Home:
+  - Getting Started:
       - Home: index.md
       - Installation: installation.md
       - Quick Start: quickstart.md
-  - Concepts:
+      - Community: community.md
+  - Library:
       - concepts/index.md
       - Quantification Methods: concepts/quantification.md
       - Normalization: concepts/normalization.md
       - Batch Correction: concepts/batch-correction.md
       - IRS Normalization: concepts/irs.md
-      - Preprocessing Filters: concepts/preprocessing.md
-  - User Guide:
+      - Preprocessing: concepts/preprocessing.md
+  - CLI:
       - user-guide/index.md
-      - "features2proteins: Unified Pipeline": user-guide/features2proteins.md
-      - "features2peptides: Peptide Normalization": user-guide/features2peptides.md
-      - "peptides2protein: Protein Quantification": user-guide/peptides2protein.md
-      - "batch-correct: Batch Correction": user-guide/batch-correct.md
-      - Visualization & Reports: user-guide/visualization.md
-  - Reference:
+      - features2proteins: user-guide/features2proteins.md
+      - features2peptides: user-guide/features2peptides.md
+      - peptides2protein: user-guide/peptides2protein.md
+      - batch-correct: user-guide/batch-correct.md
+      - Visualization: user-guide/visualization.md
+  - API Reference:
       - reference/index.md
-      - CLI Reference: reference/cli.md
+      - CLI Options: reference/cli.md
       - Python API: reference/python-api.md
       - Configuration: reference/configuration.md
       - Computed Values: reference/computed-values.md
-  - Community: community.md
+
+extra_css:
+  - https://quantms.org/css/quantms-theme.css
 
 extra:
   social: