Update Makefile and CLAUDE.md for the uv/GitHub Actions build

Author: tdhopper

CLAUDE.md

@@ -15,6 +15,8 @@ The site is generated from a Jupyter notebook (Examples.ipynb) that contains tag
 3. Generates static HTML using Jinja2 templates
 4. Outputs PNG images and an HTML file to the `web/` directory
 
+The checked-in Examples.ipynb has no outputs; the site can only be rendered from an executed copy of the notebook.
+
 ### Key Components
 
 - **Examples.ipynb**: Source notebook containing plot examples for each library
@@ -24,7 +26,7 @@ The site is generated from a Jupyter notebook (Examples.ipynb) that contains tag
   - Parses cell source code and optional markdown comments
   - Renders the final HTML using Jinja2
 - **templates/t_index.html**: Jinja2 template for the website
-- **web/**: Output directory for generated site
+- **web/**: Output directory for generated site; web/css/ (checked in) holds custom.css and pygments-native.css
 - **INTRO.md**: Markdown content for the site introduction
 
 ### Cell Tagging System
@@ -37,40 +39,32 @@ name:scatter-plot         # Maps to names dict in render.py
 package:seaborn           # Maps to packages dict in render.py
 ```
 
-Valid plot names and packages are defined in dictionaries at the top of render.py (lines 19-43).
+Valid plot names and packages are defined in dictionaries at the top of render.py.
 
 ## Development Commands
 
 ### Setup Environment
 
 ```bash
-make dev_environment    # Installs Python and R dependencies using uv
-make setup             # Alternative command (same as dev_environment)
+make setup    # uv sync, Chrome for Kaleido, R packages
 ```
 
 **Prerequisites:**
-- Python 3.11+ installed on system
 - R 4.0+ installed separately (via Homebrew, apt, or CRAN)
-- uv package manager (auto-installed by make targets if missing)
+- uv package manager (auto-installed by make targets if missing; uv provides Python)
 
 **Manual Setup:**
 ```bash
-# Install uv
-curl -LsSf https://astral.sh/uv/install.sh | sh
-
-# Install Python dependencies
-uv pip install -r requirements.txt
-
-# Install R packages (ggplot2, mgcv)
-./setup_r.sh
+uv sync         # Python dependencies (pyproject.toml + uv.lock)
+uv run kaleido_get_chrome   # Chrome for plotly PNG export
+./setup_r.sh    # R packages (ggplot2, mgcv)
 ```
 
 ### Build Site
 
 ```bash
-make qrender           # Quick render from Examples.ipynb without executing
-make render            # Full build: execute notebook, then render (creates timestamped .ipynb)
-make                   # Full build + S3 upload
+make qrender   # Render from an already-executed Examples.ipynb (fails if outputs are stripped)
+make render    # Full build: execute notebook, then render (creates git-hash-stamped .ipynb)
 ```
 
 The render process:
@@ -83,10 +77,9 @@ The render process:
 
 ```bash
 make test              # Run pytest tests
-python -m pytest tests/
 ```
 
-The test suite (tests/test_plots.py) validates that Examples.ipynb contains all expected plot/package combinations defined in the defined_plots dictionary.
+The test suite (tests/test_plots.py) validates that Examples.ipynb contains all expected plot/package tag combinations. It reads tags only, so it works on the outputs-stripped notebook.
 
 ### Local Development
 
@@ -98,12 +91,10 @@ cd web && python -m http.server
 
 ### Image Rendering
 
-All plots are rendered to static PNG images:
-- **Plotly**: Uses Kaleido for local rendering (no authentication required with v5+)
-- **Altair**: Uses native rendering or selenium/geckodriver
-- **R/ggplot2**: Uses rpy2 to interface with system R installation
-
-**Note**: Plotly authentication is no longer needed with plotly v5+. The old authentication code in `.travis/authenticate_plotly.py` is deprecated.
+All plots are rendered to static PNG images inside the executed notebook:
+- **Plotly**: `pio.renderers.default = "png"` with Kaleido (needs Chrome; `uv run kaleido_get_chrome`)
+- **Altair**: `alt.renderers.enable("png")` with vl-convert-python (set in the notebook's first cell — do not remove)
+- **R/ggplot2**: rpy2 against the system R installation (`%%R` cell magic)
 
 ## Adding New Plots
 
@@ -113,74 +104,30 @@ All plots are rendered to static PNG images:
 4. Keep code lines under ~46 characters to avoid horizontal scrolling in the UI
 5. Optionally add a markdown comment in triple quotes on the first line
 6. Update tests/test_plots.py to include the new plot in defined_plots
-7. Run `make qrender` to test (or `make render` for full rebuild)
+7. Run `make render` and inspect web/index.html
 
 ## Technical Constraints
 
 - Plot code must generate PNG output in the notebook cell
-- For plotly, images must be generated via their server (requires credentials)
 - R code cells must start with `%%R` magic command
-- Altair cells must start with `%%altair` magic command
 - Code lines should wrap to ~46 characters for proper display
 - All image paths are MD5 hashes of the base64-encoded PNG data
 
 ## Dependencies
 
-### Python Environment
-- **Python**: 3.11+ (specified in runtime.txt and pyproject.toml)
-- **Package Manager**: uv (modern, fast alternative to pip)
-- **Jupyter**: For notebook execution
-
-### Plotting Libraries (all latest versions)
-- pandas 2.0+
-- matplotlib 3.7+
-- seaborn 0.13+
-- plotnine 0.13+
-- plotly 5.24+ (with Kaleido for image export)
-- altair 5.0+
-- statsmodels 0.14+
-
-### R Environment
-- **R**: 4.0+ (system installation required)
-- **R Packages**: ggplot2, mgcv
-- **Python-R Bridge**: rpy2 3.5+
-
-### Other Key Dependencies
-- Jinja2 with jinja2-highlight for templating
-- selenium 4.15+ with geckodriver for browser automation
-- markdown for text processing
-
-**Configuration Files:**
-- `pyproject.toml`: Modern Python project metadata and dependencies
-- `requirements.txt`: Pin-free dependency list
-- `setup_r.sh`: R package installation script
+Python dependencies are declared in `pyproject.toml` and locked in `uv.lock` (committed). Key libraries: pandas, matplotlib, seaborn, plotnine, plotly (+kaleido), altair (+vl-convert-python), statsmodels, rpy2, Jinja2 with jinja2-highlight.
+
+R (system install) with ggplot2 and mgcv, installed by `setup_r.sh`.
 
 ## CI/CD
 
-The project uses **GitHub Actions** for continuous integration and deployment (migrated from Travis CI).
-
-### Workflow (.github/workflows/deploy.yml)
-
-**On Every Push:**
-1. Setup R 4.3 using r-lib/setup-r action
-2. Install R packages (ggplot2, mgcv)
-3. Setup Python 3.11
-4. Install uv and Python dependencies
-5. Setup Firefox and geckodriver for selenium
-6. Run pytest tests with xvfb (virtual display)
-7. Execute notebook and render site
-8. Deploy to Netlify:
-   - **master branch**: Production deployment
-   - **Other branches**: Preview deployments
-
-**Required Secrets:**
-- `NETLIFY_AUTH_TOKEN`: Netlify authentication token
-- `NETLIFY_SITE_ID`: Netlify site identifier
-
-**Environment Variables:**
-- `R_HOME`: Set to R installation path (e.g., `/opt/R/4.3.3/lib/R` on GitHub runners)
-
-### Legacy CI Files
-- `.travis.yml`: Old Travis CI config (deprecated)
-- `.travis/`: Old CI scripts (mostly deprecated)
-- `.travis/authenticate_plotly.py`: No longer needed with plotly v5+
+GitHub Actions (`.github/workflows/deploy.yml`) on every push:
+
+1. Setup R (r-lib/actions, RSPM binary packages) and install ggplot2/mgcv
+2. Install uv (astral-sh/setup-uv with caching) and `uv sync`
+3. `uv run kaleido_get_chrome`
+4. Run pytest
+5. Execute notebook and render site
+6. Deploy to Netlify: production on master pushes, preview otherwise
+
+**Required Secrets:** `NETLIFY_AUTH_TOKEN`, `NETLIFY_SITE_ID`

Makefile

@@ -1,20 +1,14 @@
 GIT_COMMIT=$(shell git log -1 --pretty=format:"%h")
 OUTPUTDIR=web
 
-S3_BUCKET=pythonplot.com
-
 all: render
 
-deploy: render s3_upload
-
 clean:
 	rm -f Examples.*.ipynb
 	rm -f *.pyc
 	rm -f  .Rhistory
 	rm -f .setup_done
 
-travis: render
-
 .setup_done:
 	@echo "Setting up development environment..."
 	@echo "1. Installing Python dependencies with uv..."
@@ -38,19 +32,10 @@ qrender: .setup_done
 render: .setup_done run_nb
 	uv run python render.py "Examples.$(GIT_COMMIT).ipynb"
 
-s3_upload:
-	s3cmd sync $(OUTPUTDIR)/ s3://$(S3_BUCKET) --acl-public --delete-removed --guess-mime-type --no-mime-magic --no-preserve
-
 run_nb: .setup_done
 	uv run jupyter nbconvert --to notebook --execute "Examples.ipynb" --output "Examples.$(GIT_COMMIT).ipynb"
 
 dev_environment: setup
 	@echo "Development environment ready!"
-	@echo ""
-	@echo "Note: This project now uses uv instead of conda."
-	@echo "R must be installed separately on your system."
-
-cloudfront_invalidate:
-	python .travis/invalidate_cloudfront.py
 
-.PHONY: all deploy qrender render s3_upload run_nb travis clean cloudfront_invalidate test dev_environment setup
+.PHONY: all qrender render run_nb clean test dev_environment setup