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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/andreassag/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
npm install

# Activate the pre-commit git hooks
git config core.hooksPath .githooks

Code style

Python (bin/)

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

ruff check .
ruff format --check .

Nextflow (.nf, .config) & Documentation

Nextflow and config files follow EditorConfig rules and Prettier standards:

npx editorconfig-checker
npx prettier --check .

Pre-commit hooks

Pre-commit git hooks run automatically before each git commit to guarantee clean code and formatting:

Check Tool Purpose
Python Linting ruff check Code style and import order
Python Formatting ruff format Code layout consistency
Line Length & Standards editorconfig-checker Indentation and line endings
Document Formatting prettier Markdown, JSON, and YAML styling

Run all checks manually:

npm run check:all

Testing

Python unit tests

pytest tests/python/ -v

Tests live in tests/python/ and exercise the pure Python functions in bin/.

nf-test (Nextflow pipeline & module tests)

# Run all nf-test suites (integration + local modules)
nf-test test tests/ --verbose

# Run specific local module tests
nf-test test tests/modules/local/summary --verbose
nf-test test tests/modules/local/combgc --verbose
nf-test test tests/modules/local/bigscape --verbose

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