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Contributor Guide

Development Installation

pip install -e .[dev,test]

Style and Pre-Commit

To set up pre-commit:

pre-commit autoupdate
pre-commit install

Then any time you write a commit, it will run ruff, black, mypy, and validate the pyproject.toml. To skip the pre-commit step, use: git commit --no-verify

Ruff, black, and mypy settings are specified in the pyproject.toml. Currently they are not very strict, but this may change in the future.

Testing

To run tests with coverage locally: pytest tests --color=yes --cov --cov-report=term-missing This will also be run automatically when a PR is made to master and a codecov report will be generated telling you if your PR increased or decreased coverage.

Branching and PRs

  • Users that have been added to the CellMap organization and the DaCapo project should be able to develop directly into the CellMap fork of DaCapo. Other users will need to create a fork or ask to be added as a collaborator.
  • For a completely new feature, make a branch off of the main branch of CellMap's fork of DaCapo with a name describing the feature. If you are collaborating on a feature that already has a branch, you can branch off that feature branch.
  • Currently, you should make your PRs into the main branch of CellMap's fork, or the feature branch you branched off of. PRs currently require one maintainer's approval before merging. Once the PR is merged, the feature branch will/should be deleted.
  • main will be regularly published to PyPi when new features are fully implemented and all tests are passing.

Documentation

Documentation is built using Sphinx. To build the documentation locally, run

sphinx-build -M html docs/source docs/build

This will generate the html files in the docs/build/html directory.