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Contributing to TreeTime

Thank you for your interest in contributing to TreeTime. We welcome pull-requests that fix bugs or implement new features.

Bugs

If you come across a bug or unexpected behavior, please file an issue.

Testing

Upon pushing a commit, GitHub Actions runs tests across supported Python versions and lint checks. Tests use data from the neherlab/treetime_examples repository.

Releasing

Steps

  1. Add a # Unreleased heading at the top of changelog.md followed by bullet points describing the changes. Commit to master (directly or via PR).
  2. Run the release script from the repo root: 
    ./release 0.x.y
  3. Review the diff shown by the script, then confirm to push.
  4. Watch CI complete at https://github.com/neherlab/treetime/actions. On success, the GitHub Release and the PyPI package are created automatically.

How it works

The release script:

  • Validates the working tree: clean, on master, up-to-date with origin, tag absent, # Unreleased present in changelog.
  • Bumps the version in treetime/__init__.py.
  • Renames the # Unreleased heading to # 0.x.y in changelog.md.
  • Commits (chore: release 0.x.y) and creates tag v0.x.y.
  • Pushes the commit and tag after confirmation.

The tag push triggers the release CI workflow, which:

  • Runs the full test matrix and lint.

  • Extracts the changelog section using scripts/extract-release-notes and creates a GitHub Release.

  • Builds and publishes the package to PyPI using the PYPI_API_TOKEN repository secret.

    To verify the secret is present:

    gh secret list

Coding conventions (loosly adhered to)

  • indentation: 4 spaces
  • docstrings: numpy style
  • variable names: snake_case