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Contributing

Contributions are welcome! Please open an issue to discuss significant changes before opening a PR.

Prerequisites

  • Pixi — manages all environments and dependencies
  • Git

Install Pixi, then clone and set up:

git clone https://github.com/BioVisionCenter/ngio
cd ngio
pixi install

Development

Work in the dev environment, which includes linters, type checker, and test dependencies:

pixi shell -e dev        # activate shell
# or prefix individual commands:
pixi run -e dev <cmd>

Running tests

pixi run -e test pytest           # single run (Python 3.11)
pixi run -e test13 pytest         # a specific Python version: test11, test12, test13, test14

Coverage is reported automatically. Pull requests run a reduced matrix — Linux on Python 3.11 and 3.13 — while main and tags run the full one: test11–test14 across Linux, macOS, and Windows.

Linting and formatting

pixi run -e dev lint              # run all hooks on all files

This runs Ruff (lint + format), typos (spell check), YAML/TOML validation, and notebook output stripping. Hooks also run automatically on git commit.

Commit conventions

Please follow Conventional Commits — this is not enforced by a hook (yet), but helps maintain a clean history and enables automated changelog generation.

Examples:

feat: add support for multiscale labels
fix: correct axis order in NgffImage
docs: update contributing guide

Opening a pull request

  1. Fork the repo and create a branch from main.
  2. Make your changes with tests where relevant.
  3. Run pixi run -e dev lint and ensure all checks pass.
  4. Open a PR against main with a clear description of what and why.

CI runs the linters and the test matrix automatically.

Releasing (maintainers only)

Versions are derived from git tags via hatch-vcs. Use the Pixi bump tasks in the dev environment:

pixi run -e dev bump-patch    # 1.0.0 → 1.0.1
pixi run -e dev bump-minor    # 1.0.0 → 1.1.0
pixi run -e dev bump-major    # 1.0.0 → 2.0.0
pixi run -e dev bump-alpha    # → 1.1.0a1  (pre-release)

Append -- --dry-run to preview without creating a tag. Once tagged, CI builds and publishes to PyPI automatically.