From c2260a5d07193662691849a3de29e78833f8c9dd Mon Sep 17 00:00:00 2001
From: Iahn Cajigas <iahncajigas@Iahns-MacBook-Pro-310.local>
Date: Mon, 23 Mar 2026 22:52:26 -0400
Subject: [PATCH] Add GitHub Pages deployment workflow with sphinx_rtd_theme

- New deploy-docs.yml: builds Sphinx HTML and deploys to GitHub Pages
  on every push to main (uses actions/deploy-pages v4)
- docs/conf.py: switch to sphinx_rtd_theme with navigation options;
  exclude superpowers/ specs from build
- pyproject.toml: add sphinx-rtd-theme>=3.0 to dev dependencies
- Add .nojekyll marker in build step to preserve _static/ directories
- Includes design spec at docs/superpowers/specs/

The live site at cajigaslab.github.io/nSTAT-python/ has been frozen
since Feb 28 because no deployment workflow existed. This fix will
automatically deploy fresh docs on every merge to main.

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
---
 .github/workflows/deploy-docs.yml             | 53 +++++++++++++++++++
 docs/conf.py                                  |  8 ++-
 ...26-03-24-github-pages-deployment-design.md | 38 +++++++++++++
 pyproject.toml                                |  1 +
 4 files changed, 99 insertions(+), 1 deletion(-)
 create mode 100644 .github/workflows/deploy-docs.yml
 create mode 100644 docs/superpowers/specs/2026-03-24-github-pages-deployment-design.md

diff --git a/.github/workflows/deploy-docs.yml b/.github/workflows/deploy-docs.yml
new file mode 100644
index 00000000..3d28cb1a
--- /dev/null
+++ b/.github/workflows/deploy-docs.yml
@@ -0,0 +1,53 @@
+name: deploy-docs
+
+on:
+  push:
+    branches: [main]
+  workflow_dispatch:
+
+permissions:
+  contents: read
+  pages: write
+  id-token: write
+
+concurrency:
+  group: pages
+  cancel-in-progress: false
+
+jobs:
+  deploy:
+    runs-on: ubuntu-latest
+    environment:
+      name: github-pages
+      url: ${{ steps.deployment.outputs.page_url }}
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.12"
+
+      - name: Install dependencies
+        run: pip install -e .[dev]
+
+      - name: Regenerate paper gallery artifacts
+        run: python tools/paper_examples/build_gallery.py
+
+      - name: Build Sphinx docs
+        run: python -m sphinx -W -b html docs docs/_build/html
+
+      - name: Add .nojekyll marker
+        run: touch docs/_build/html/.nojekyll
+
+      - name: Configure Pages
+        uses: actions/configure-pages@v5
+
+      - name: Upload Pages artifact
+        uses: actions/upload-pages-artifact@v3
+        with:
+          path: docs/_build/html
+
+      - name: Deploy to GitHub Pages
+        id: deployment
+        uses: actions/deploy-pages@v4
diff --git a/docs/conf.py b/docs/conf.py
index 86790cb6..d2dad863 100644
--- a/docs/conf.py
+++ b/docs/conf.py
@@ -2,5 +2,11 @@
 author = "Cajigas Lab"
 release = "0.3.0"
 extensions = ["myst_parser"]
-exclude_patterns = ["_build", "Thumbs.db", ".DS_Store"]
+exclude_patterns = ["_build", "Thumbs.db", ".DS_Store", "superpowers"]
 master_doc = "index"
+
+html_theme = "sphinx_rtd_theme"
+html_theme_options = {
+    "navigation_depth": 3,
+    "collapse_navigation": False,
+}
diff --git a/docs/superpowers/specs/2026-03-24-github-pages-deployment-design.md b/docs/superpowers/specs/2026-03-24-github-pages-deployment-design.md
new file mode 100644
index 00000000..30843e9a
--- /dev/null
+++ b/docs/superpowers/specs/2026-03-24-github-pages-deployment-design.md
@@ -0,0 +1,38 @@
+# GitHub Pages Deployment Design
+
+**Date:** 2026-03-24
+**Status:** Approved
+
+## Problem
+
+The Python nSTAT GitHub Pages site (cajigaslab.github.io/nSTAT-python/) is frozen at a Feb 28, 2026 commit. The `docs-build` CI job verifies Sphinx compilation but never deploys the output. Over 20 merges to main have had no effect on the live site.
+
+## Solution
+
+A dedicated `deploy-docs.yml` workflow that builds Sphinx HTML with the Read the Docs theme and deploys it to GitHub Pages on every push to main.
+
+## Components
+
+### 1. `.github/workflows/deploy-docs.yml`
+
+New workflow triggered by push to main and workflow_dispatch. Uses GitHub's artifact-based Pages deployment (`actions/upload-pages-artifact` + `actions/deploy-pages`). Requires `pages: write` and `id-token: write` permissions. Concurrency group prevents overlapping deployments.
+
+### 2. `docs/conf.py` updates
+
+Switch from Alabaster (default) to `sphinx_rtd_theme`. Keep `myst_parser` extension. Set project metadata.
+
+### 3. `pyproject.toml` updates
+
+Add `sphinx-rtd-theme` to dev dependencies if not already present.
+
+### 4. `.nojekyll` marker
+
+Created during build to prevent Jekyll from ignoring `_static/` directories.
+
+## What Gets Deployed
+
+The existing docs/index.rst toctree: help home, paper overview, class definitions, examples, API reference, paper examples gallery with figure thumbnails.
+
+## What Doesn't Change
+
+The existing `docs-build` job in ci.yml remains as a PR build-verification step.
diff --git a/pyproject.toml b/pyproject.toml
index c119b14c..4dfa3094 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -26,6 +26,7 @@ dev = [
   "pytest>=8.0",
   "scikit-image>=0.22",
   "sphinx>=8.0",
+  "sphinx-rtd-theme>=3.0",
   "myst-parser>=4.0",
 ]