Contributing

Development Setup

git clone https://github.com/AxelRolov/cdr_bench.git
cd cdr_bench
uv sync --group dev   # Install with dev dependencies (includes JupyterLab)
uv sync --group docs  # Install documentation dependencies

Running Tests

pytest tests/

Test configuration is in tests/test_configs/test_run_benchmarking.toml. Sample test data is in tests/test_datasets/.

Building Documentation

mkdocs serve          # Live preview at http://localhost:8000
mkdocs build --strict # Build static site to site/

Code Conventions

• Docstrings: Google style (Args/Returns blocks)
• Type hints: On public function signatures
• Imports: Absolute imports from project root (from src.cdr_bench.module import X)
• Data format: HDF5 for all data storage (via h5py)
• Config format: TOML for all configuration files

Project Structure

• src/cdr_bench/ -- Core library code
• scripts/ -- Executable pipeline scripts
• bench_configs/ -- TOML configuration files
• tests/ -- Test suite
• notebooks/ -- Jupyter notebooks for exploration
• datasets/ -- Sample ChEMBL datasets
• results/ -- Benchmark results
• docs/ -- Documentation source (MkDocs)