add github actions workflow for building and deploying docs

.github/workflows/docs.yml

@@ -0,0 +1,47 @@
+name: Build and deploy docs
+
+on:
+  push:
+    branches: [ main ]
+  pull_request:
+
+permissions:
+  contents: read
+  pages: write
+  id-token: write
+
+jobs:
+  docs:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout repo
+        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 docs/requirements.txt
+
+      - name: Generate API docs
+        run: |
+          sphinx-apidoc -f -o docs/source/api src/longitudinal_ecg_analysis
+
+      - name: Build Sphinx docs
+        run: |
+          sphinx-build -W -b html docs/source docs/build/html
+
+      - name: Upload Pages artifact
+        uses: actions/upload-pages-artifact@v3
+        with:
+          path: docs/build/html
+
+      - name: Deploy to GitHub Pages
+        if: github.ref == 'refs/heads/main'
+        uses: actions/deploy-pages@v4
+

.gitignore

@@ -1,4 +1,5 @@
 .DS_Store
 venv/
 __pycache__/
-*.py[cod]
+*.py[cod]
+docs/build/

docs/build/html/_sources/index.rst.txt

@@ -65,5 +65,5 @@ Further details of this example are provided in the :ref:`Running demo analysis
    examples
    variables
    maintenance
-   API Documentation <modules>
+   API Documentation <api/modules>
 

docs/build/html/_sources/maintenance.rst.txt

@@ -23,7 +23,7 @@ The documentation is a mixture of manually written pages, and auto-generated API
 * Update the auto-generated API documentation using::
 
    cd longitudinal-ecg-analysis/
-   sphinx-apidoc -f -o docs/source ./src/longitudinal_ecg_analysis
+   sphinx-apidoc -f -o docs/source/api ./src/longitudinal_ecg_analysis
    cd docs
    make html
    cd ..

docs/build/html/_static/basic.css

@@ -741,14 +741,6 @@ abbr, acronym {
     cursor: help;
 }
 
-.translated {
-    background-color: rgba(207, 255, 207, 0.2)
-}
-
-.untranslated {
-    background-color: rgba(255, 207, 207, 0.2)
-}
-
 /* -- code displays --------------------------------------------------------- */
 
 pre {

docs/build/html/_static/searchtools.js

@@ -513,9 +513,11 @@ const Search = {
     // perform the search on the required terms
     searchTerms.forEach((word) => {
       const files = [];
+      // find documents, if any, containing the query word in their text/title term indices
+      // use Object.hasOwnProperty to avoid mismatching against prototype properties
       const arr = [
-        { files: terms[word], score: Scorer.term },
-        { files: titleTerms[word], score: Scorer.title },
+        { files: terms.hasOwnProperty(word) ? terms[word] : undefined, score: Scorer.term },
+        { files: titleTerms.hasOwnProperty(word) ? titleTerms[word] : undefined, score: Scorer.title },
       ];
       // add support for partial matches
       if (word.length > 2) {
@@ -547,8 +549,9 @@ const Search = {
 
         // set score for the word in each file
         recordFiles.forEach((file) => {
-          if (!scoreMap.has(file)) scoreMap.set(file, {});
-          scoreMap.get(file)[word] = record.score;
+          if (!scoreMap.has(file)) scoreMap.set(file, new Map());
+          const fileScores = scoreMap.get(file);
+          fileScores.set(word, record.score);
         });
       });
 
@@ -587,7 +590,7 @@ const Search = {
         break;
 
       // select one (max) score for the file.
-      const score = Math.max(...wordList.map((w) => scoreMap.get(file)[w]));
+      const score = Math.max(...wordList.map((w) => scoreMap.get(file).get(w)));
       // add result to the result list
       results.push([
         docNames[file],

docs/build/html/datasets.html

@@ -53,7 +53,7 @@
 <li class="toctree-l1"><a class="reference internal" href="examples.html">Examples</a></li>
 <li class="toctree-l1"><a class="reference internal" href="variables.html">Variables</a></li>
 <li class="toctree-l1"><a class="reference internal" href="maintenance.html">Maintenance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="modules.html">API Documentation</a></li>
+<li class="toctree-l1"><a class="reference internal" href="api/modules.html">API Documentation</a></li>
 </ul>
 
         </div>

docs/build/html/examples.html

@@ -91,7 +91,7 @@
 </li>
 <li class="toctree-l1"><a class="reference internal" href="variables.html">Variables</a></li>
 <li class="toctree-l1"><a class="reference internal" href="maintenance.html">Maintenance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="modules.html">API Documentation</a></li>
+<li class="toctree-l1"><a class="reference internal" href="api/modules.html">API Documentation</a></li>
 </ul>
 
         </div>