fix: enable Jekyll to render markdown documentation

Author: pycckuu

.github/workflows/docs.yml

@@ -19,10 +19,7 @@ concurrency:
   cancel-in-progress: false
 
 jobs:
-  deploy:
-    environment:
-      name: github-pages
-      url: ${{ steps.deployment.outputs.page_url }}
+  build:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout
@@ -31,11 +28,22 @@ jobs:
       - name: Setup Pages
         uses: actions/configure-pages@v4
 
+      - name: Build with Jekyll
+        uses: actions/jekyll-build-pages@v1
+        with:
+          source: ./docs
+          destination: ./_site
+
       - name: Upload artifact
         uses: actions/upload-pages-artifact@v3
-        with:
-          path: 'docs'
 
+  deploy:
+    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

docs/_config.yml

@@ -0,0 +1,16 @@
+title: PorousMediaLab Documentation
+description: Python toolbox for batch and 1D reactive transport modeling in porous media
+remote_theme: pages-themes/cayman@v0.2.0
+plugins:
+  - jekyll-remote-theme
+
+markdown: kramdown
+kramdown:
+  input: GFM
+  syntax_highlighter: rouge
+
+defaults:
+  - scope:
+      path: ""
+    values:
+      layout: default

docs/index.html

@@ -35,16 +35,16 @@ <h1>PorousMediaLab Documentation</h1>
 
     <h2>Quick Links</h2>
     <table class="nav-table">
-        <tr><td><a href="quickstart.md">Quickstart</a></td><td>Get started in 5 minutes</td></tr>
-        <tr><td><a href="batch-guide.md">Batch Guide</a></td><td>Complete guide to 0D batch reactor simulations</td></tr>
-        <tr><td><a href="column-guide.md">Column Guide</a></td><td>Complete guide to 1D reactive transport</td></tr>
+        <tr><td><a href="quickstart.html">Quickstart</a></td><td>Get started in 5 minutes</td></tr>
+        <tr><td><a href="batch-guide.html">Batch Guide</a></td><td>Complete guide to 0D batch reactor simulations</td></tr>
+        <tr><td><a href="column-guide.html">Column Guide</a></td><td>Complete guide to 1D reactive transport</td></tr>
     </table>
 
     <h2>Tutorials</h2>
     <p>Step-by-step tutorials with real-world examples:</p>
     <ul>
-        <li><a href="tutorials/batch-roden.md">Organic Matter Degradation</a> - Batch reactor modeling following Roden 2008</li>
-        <li><a href="tutorials/sediment-column.md">Sediment Diagenesis</a> - 1D column transport with complex reactions</li>
+        <li><a href="tutorials/batch-roden.html">Organic Matter Degradation</a> - Batch reactor modeling following Roden 2008</li>
+        <li><a href="tutorials/sediment-column.html">Sediment Diagenesis</a> - 1D column transport with complex reactions</li>
     </ul>
 
     <h2>Features</h2>