Skip to content

CONTRIBUTING.md

Latest commit

 

History

History
59 lines (40 loc) · 3.16 KB

CONTRIBUTING.md

File metadata and controls

59 lines (40 loc) · 3.16 KB
Raw

Contributing to PocketDock

Thanks for your interest in PocketDock! Bug reports, feature ideas, and pull requests are all welcome.

Getting set up

The fastest way to get a working dev environment is Docker — docker compose up --build brings up the full stack (web, Celery worker, Redis) along with P2Rank and AutoDock Vina.

For a native install (RDKit/OpenMM via conda + external Vina/P2Rank binaries), see the Local development section in Getting Started.

Reporting bugs and requesting features

Open a GitHub Issue. For bugs, please include:

  • PocketDock version (commit hash or release tag)
  • How you're running it (Docker / native)
  • The exact input that triggered the problem (PDB + SDF if you can share them)
  • The full traceback from the Celery worker logs (docker compose logs celery)

Submitting a pull request

  1. Fork the repo and create a feature branch off main (e.g. fix/box-padding-edge-case, feat/refinement-amber99sb).
  2. Make your change. Keep PRs focused — one logical change per PR is much easier to review than a sweeping refactor.
  3. Add or update tests in docking/tests/. The project uses pytest + pytest-django, and there's an existing fixture directory at docking/tests/fixtures/ with small PDB/SDF inputs you can reuse.
  4. Run the test suite locally: 
    pytest
  5. Run the linter and formatter: 
    ruff check .
ruff format .
    The CI lint workflow (.github/workflows/lint.yml) enforces these on every PR.
  6. Push and open a PR against main. In the description, explain why (the problem you're solving), not just what (the diff already shows that). Link related issues with Fixes #123.

Code style

  • Python 3.11+. Type hints are welcome but not required everywhere — focus on public APIs and tricky logic.
  • Follow the existing module layout: domain logic in docking/tasks.py (the docking pipeline), thin views in docking/views.py, models in docking/models.py.
  • ruff handles formatting and most lint rules — config is in pyproject.toml. Don't fight it.

Adding a new dependency

  • Pure-Python / pip-installable: add it to requirements.txt with a pinned upper bound.
  • Needs a system library or wheel from conda-forge (RDKit, OpenMM, Gemmi, PDBFixer): add a mamba install line to the Dockerfile and the conda install command in docs/getting-started.md. Also update requirements.txt if the package is pip-importable so editors don't flag it as missing.

Scope of contributions

PocketDock is an integration of well-established tools (P2Rank, AutoDock Vina, RDKit, OpenMM). Pull requests that:

  • ✅ Fix bugs in the integration layer
  • ✅ Improve the UI / results presentation
  • ✅ Add new scoring/refinement options that wrap an established method
  • ✅ Improve docs, examples, and tests

are all welcome. Contributions that re-implement physics or scoring methods from scratch are out of scope — we prefer to call into well-validated upstream libraries.