Set up uv for dependency management and add PR preview workflow

.github/PR_PREVIEW_SETUP.md

@@ -0,0 +1,87 @@
+# PR Preview Setup Guide
+
+This repository includes workflows for deploying PR previews to either Netlify or Vercel. Choose one and follow the setup instructions below.
+
+## Option 1: Netlify (Recommended)
+
+Netlify offers a generous free tier and is easy to set up.
+
+### Setup Steps:
+
+1. **Create a Netlify account** at https://netlify.com
+
+2. **Create a new site**:
+   - Go to your Netlify dashboard
+   - Click "Add new site" → "Configure manually"
+   - Note the Site ID
+
+3. **Get your auth token**:
+   - Go to User Settings → Applications → Personal Access Tokens
+   - Create a new token and save it
+
+4. **Add GitHub Secrets**:
+   - Go to your GitHub repository settings
+   - Navigate to Secrets and Variables → Actions
+   - Add these secrets:
+     - `NETLIFY_AUTH_TOKEN`: Your personal access token
+     - `NETLIFY_SITE_ID`: Your site ID
+
+5. **Enable the workflow**:
+   - Keep `pr-preview-netlify.yml` 
+   - Delete `pr-preview-vercel.yml` if not using Vercel
+
+## Option 2: Vercel
+
+Vercel is also free for open source projects and offers excellent performance.
+
+### Setup Steps:
+
+1. **Create a Vercel account** at https://vercel.com
+
+2. **Install Vercel CLI** locally:
+   ```bash
+   npm i -g vercel
+   ```
+
+3. **Link your project**:
+   ```bash
+   vercel link
+   ```
+   This will create a `.vercel` folder with your project settings
+
+4. **Get your tokens**:
+   - Create a token at: https://vercel.com/account/tokens
+   - Get your Org ID and Project ID from `.vercel/project.json`
+
+5. **Add GitHub Secrets**:
+   - Go to your GitHub repository settings
+   - Navigate to Secrets and Variables → Actions
+   - Add these secrets:
+     - `VERCEL_TOKEN`: Your access token
+     - `VERCEL_ORG_ID`: Your organization ID
+     - `VERCEL_PROJECT_ID`: Your project ID
+
+6. **Enable the workflow**:
+   - Keep `pr-preview-vercel.yml`
+   - Delete `pr-preview-netlify.yml` if not using Netlify
+
+## Security Benefits
+
+Using Netlify or Vercel for PR previews instead of GitHub Pages provides:
+
+- **Isolation**: PR previews are completely separate from your production site
+- **No write access**: PRs cannot modify your main GitHub Pages deployment
+- **Automatic cleanup**: Previews are automatically removed after PRs are merged
+- **Access control**: You can add password protection if needed (paid feature)
+
+## Choosing Between Services
+
+| Feature | Netlify | Vercel |
+|---------|---------|--------|
+| Free tier | 100GB bandwidth/month | 100GB bandwidth/month |
+| Build minutes | 300 min/month | 6000 min/month |
+| Setup complexity | Simple | Moderate |
+| Preview URLs | Custom aliases | Automatic unique URLs |
+| Comments on PR | ✅ Automatic | ✅ Automatic |
+
+Both services work great for PR previews. Choose based on your preference and existing infrastructure.

.github/workflows/gh-pages.yml

@@ -23,15 +23,19 @@ jobs:
     steps:
     - uses: actions/checkout@v4
 
-    # Install dependencies
-    - name: Set up Python 3.11
-      uses: actions/setup-python@v5
+    # Install uv for faster dependency management
+    - name: Install uv
+      uses: astral-sh/setup-uv@v4
       with:
-        python-version: '3.11'
-        cache: pip # Implicitly uses requirements.txt for cache key
+        enable-cache: true
 
+    # Set up Python using uv
+    - name: Set up Python
+      run: uv python install 3.11
+
+    # Install dependencies using uv
     - name: Install dependencies
-      run: pip install -r requirements.txt
+      run: uv sync
 
     # (optional) Cache your executed notebooks between runs
     # if you have config:
@@ -41,12 +45,12 @@ jobs:
       uses: actions/cache@v4
       with:
         path: _build/.jupyter_cache
-        key: jupyter-book-cache-${{ hashFiles('requirements.txt') }}
+        key: jupyter-book-cache-${{ hashFiles('uv.lock') }}
 
     # Build the book
     - name: Build the book
       run: |
-        jupyter-book build .
+        uv run jupyter-book build .
 
     # Upload the book's HTML as an artifact
     - name: Upload artifact

.github/workflows/pr-preview-netlify.yml

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+name: Deploy PR Preview to Netlify
+
+on:
+  pull_request:
+    types: [opened, synchronize, reopened]
+
+jobs:
+  build-and-deploy:
+    runs-on: ubuntu-latest
+    permissions:
+      pull-requests: write  # To comment on the PR
+    steps:
+    - uses: actions/checkout@v4
+
+    # Install uv for faster dependency management
+    - name: Install uv
+      uses: astral-sh/setup-uv@v4
+      with:
+        enable-cache: true
+
+    # Set up Python using uv
+    - name: Set up Python
+      run: uv python install 3.11
+
+    # Install dependencies using uv
+    - name: Install dependencies
+      run: uv sync
+
+    # Cache executed notebooks between runs
+    - name: Cache executed notebooks
+      uses: actions/cache@v4
+      with:
+        path: _build/.jupyter_cache
+        key: jupyter-book-cache-${{ hashFiles('uv.lock') }}
+
+    # Build the book
+    - name: Build the book
+      run: |
+        uv run jupyter-book build .
+
+    # Deploy to Netlify
+    - name: Deploy to Netlify
+      uses: nwtgck/[email protected]
+      with:
+        publish-dir: './_build/html'
+        production-deploy: false
+        github-token: ${{ secrets.GITHUB_TOKEN }}
+        deploy-message: "Deploy PR ${{ github.event.pull_request.number }}: ${{ github.event.pull_request.title }}"
+        enable-pull-request-comment: true
+        enable-commit-comment: false
+        overwrites-pull-request-comment: true
+        alias: pr-${{ github.event.pull_request.number }}
+      env:
+        NETLIFY_AUTH_TOKEN: ${{ secrets.NETLIFY_AUTH_TOKEN }}
+        NETLIFY_SITE_ID: ${{ secrets.NETLIFY_SITE_ID }}
+      timeout-minutes: 5

.github/workflows/pr-preview.yml

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+name: PR Preview
+
+# Build the book on pull requests for preview
+on:
+  pull_request:
+    branches:
+      - main
+      - master
+
+jobs:
+  build-preview:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v4
+
+    # Install uv for faster dependency management
+    - name: Install uv
+      uses: astral-sh/setup-uv@v4
+      with:
+        enable-cache: true
+
+    # Set up Python using uv
+    - name: Set up Python
+      run: uv python install 3.11
+
+    # Install dependencies using uv
+    - name: Install dependencies
+      run: uv sync
+
+    # Cache executed notebooks between runs
+    - name: Cache executed notebooks
+      uses: actions/cache@v4
+      with:
+        path: _build/.jupyter_cache
+        key: jupyter-book-cache-${{ hashFiles('uv.lock') }}
+
+    # Build the book
+    - name: Build the book
+      run: |
+        uv run jupyter-book build .
+
+    # Upload the book's HTML as an artifact
+    - name: Upload book artifact
+      uses: actions/upload-artifact@v4
+      with:
+        name: book-html-${{ github.event.pull_request.number }}
+        path: "_build/html"
+        retention-days: 7
+
+    # Post comment with artifact link
+    - name: Comment PR
+      uses: actions/github-script@v7
+      if: github.event_name == 'pull_request'
+      with:
+        script: |
+          const artifactUrl = `https://github.com/${context.repo.owner}/${context.repo.repo}/actions/runs/${context.runId}`;
+          github.rest.issues.createComment({
+            issue_number: context.issue.number,
+            owner: context.repo.owner,
+            repo: context.repo.repo,
+            body: `📚 Book preview build completed! [Download the artifact](${artifactUrl}) to view the HTML locally.`
+          })

pyproject.toml

@@ -0,0 +1,14 @@
+[project]
+name = "xarray-for-biology"
+version = "0.1.0"
+description = "Add your description here"
+readme = "README.md"
+requires-python = ">=3.13"
+dependencies = [
+    "flox>=0.10.6",
+    "jupyter-book>=1.0.4.post1",
+    "jupyterlab>=4.4.7",
+    "matplotlib>=3.10.6",
+    "numpy>=2.3.2",
+    "xarray>=2025.8.0",
+]

test.md

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+# Testing Netlify