bookdown

Author: mikemartinez99

.github/workflows/deploy-pages.yml

@@ -0,0 +1,59 @@
+name: Deploy to GitHub Pages
+
+on:
+  push:
+    branches:
+      - main
+      - master
+      - bookdown
+  workflow_dispatch:
+
+permissions:
+  contents: read
+  pages: write
+  id-token: write
+
+concurrency:
+  group: "pages"
+  cancel-in-progress: false
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+      
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: '3.9'
+      
+      - name: Install dependencies
+        run: |
+          python3 -m pip install --upgrade pip
+          pip install markdown
+      
+      - name: Build site
+        run: |
+          python3 build_site.py
+      
+      - name: Setup Pages
+        uses: actions/configure-pages@v4
+      
+      - 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
+

GITHUB_PAGES_SETUP.md

@@ -0,0 +1,62 @@
+# GitHub Pages Setup Guide
+
+This repository is configured to automatically deploy to GitHub Pages using GitHub Actions.
+
+## Automatic Deployment
+
+The site will automatically build and deploy when you push to the `main`, `master`, or `bookdown` branch.
+
+### Setup Steps:
+
+1. **Enable GitHub Pages in your repository:**
+   - Go to your repository on GitHub
+   - Click on **Settings** → **Pages**
+   - Under "Source", select **GitHub Actions** (not "Deploy from a branch")
+   - Save the settings
+
+2. **Push your changes:**
+   - The GitHub Actions workflow (`.github/workflows/deploy-pages.yml`) will automatically:
+     - Build the site using the `build_site.py` script
+     - Deploy it to GitHub Pages
+   - Your site will be available at: `https://[your-username].github.io/RNA-seq-Differential-Expression-workshop-June-2022/`
+
+## Manual Deployment (Alternative)
+
+If you prefer to deploy manually:
+
+1. Build the site locally:
+   ```bash
+   python3 build_site.py
+   ```
+
+2. Push the `docs/` directory to the `gh-pages` branch:
+   ```bash
+   git subtree push --prefix docs origin gh-pages
+   ```
+
+   Or if the `gh-pages` branch doesn't exist:
+   ```bash
+   git checkout --orphan gh-pages
+   git rm -rf .
+   cp -r docs/* .
+   git add .
+   git commit -m "Deploy site"
+   git push origin gh-pages
+   ```
+
+3. Configure GitHub Pages to use the `gh-pages` branch as the source.
+
+## Custom Domain (Optional)
+
+If you want to use a custom domain:
+
+1. Create a `CNAME` file in the `docs/` directory with your domain name
+2. Update your DNS settings to point to GitHub Pages
+3. The workflow will automatically include the CNAME file in deployments
+
+## Troubleshooting
+
+- **Images not showing:** Make sure all image paths in markdown files use `../figures/` or `figures/` (the build script normalizes these)
+- **Build fails:** Check that Python 3.9+ is available and the `markdown` package is installed
+- **Pages not updating:** Wait a few minutes after pushing, GitHub Pages can take 1-2 minutes to update
+