Contributing

Contributions are welcome. This fork maintains the Python API and documentation; changes should avoid altering runtime behavior unless required.

Development setup

git clone https://github.com/neoralab/pdbfixer.git
cd pdbfixer
python -m venv .venv
source .venv/bin/activate  # On Windows use: .venv\\Scripts\\activate
pip install -e ".[tests]"

Running tests

pytest

Use pytest -m "not slow" to skip slow or network-heavy tests.

Documentation

pip install -e ".[docs]"
mkdocs serve  # live preview
mkdocs build  # validate build

Pull requests

• Keep changes narrowly scoped and avoid refactoring production code unless necessary for documentation accuracy.
• Update or add examples when API-facing changes are made.
• Ensure new files carry the MIT license header or are clearly covered by the repository LICENSE.