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Contributing

Contributions are welcome. This document describes how to set up a development environment and the conventions the project follows.

Development setup

git clone https://github.com/exterex/clystere.git
cd clystere

# Create a Python virtual environment (Python 3.11+)
python -m venv .venv
source .venv/bin/activate

# Install development tools
pip install pre-commit pytest ruff

# Install and activate the pre-commit hooks
pre-commit install

Code style

Python (bin/)

Python scripts are linted and formatted with Ruff. The target interpreter is Python 3.11.

Nextflow (.nf, .config)

Nextflow files are formatted with Prettier via prettier-plugin-groovy.

Pre-commit hooks

The following hooks run automatically on git commit:

Hook Purpose
ruff Python linting with auto-fix
ruff-format Python formatting
prettier Formatting for Nextflow, JSON, YAML, Markdown
trailing-whitespace Strip trailing whitespace
end-of-file-fixer Ensure files end with a newline
check-yaml Validate YAML syntax
check-json Validate JSON syntax
mixed-line-ending Enforce LF line endings

Run all hooks manually:

pre-commit run --all-files

Testing

Python unit tests

pytest tests/python/ -v

Tests live in tests/python/ and exercise the pure Python functions in bin/. Fixtures are built inline with tmp_path — no external data files needed.

nf-test (Nextflow module tests)

# runs module tests under tests/modules/
nf-test test --profile docker --verbose

# run only heavyweight-module tests in stub mode
nf-test test tests/modules/local/antismash tests/modules/local/deepbgc --verbose

Module tests live under tests/modules/local/**/main.nf.test and include both lightweight script-backed tests and stub-oriented tests for heavyweight tools (antiSMASH/deepBGC). Test fixtures are stored in tests/data/.

Full pipeline test

nextflow run . \
    --input assets/samplesheet.csv \
    --outdir results \
    -profile test,docker

Branching and pull requests

  • main is the stable release branch.
  • Feature branches: feature/<description>
  • Bug/hot fixes: fix/<description>
  • Non-code tasks: chore/<description>
  • Preparing a release: release/<description>
  • Open a pull request against main; CI must be green before merge.

Releases

Releases follow Semantic Versioning. To cut a release:

  1. Update the version in nextflow.config (manifest.version).
  2. Commit with message release: bump version to X.Y.Z.
  3. Push a X.Y.Z tag — the release.yml workflow creates the GitHub Release automatically.
git tag 1.1.0
git push origin 1.1.0