Development

Development

Setup

git clone https://github.com/duceppemo/BACoN && cd BACoN
conda env create -f environment.yml && conda activate BACoN
pip install -e ".[test]"
pre-commit install

Code

Module	Contents
bacon/cli.py	command line
bacon/pipeline.py	the steps, checkpoints, summary and provenance
bacon/samples.py	finding samples (file, folder, sample sheet)
bacon/steps.py	baiting, filtering, assembly
bacon/compare.py	SKA2, Parsnp, distances, trees
bacon/newick.py	Newick parsing, midpoint rooting, SVG drawing
bacon/seqio.py	fasta/fastq reading and writing
bacon/tools.py	running external programs and logging their output

BACoN uses the Python standard library only (python-isal is used when installed). External programs are run with bacon.tools.run, which logs the command and the program's messages and raises an error with the end of the log when a program fails.

Tests

ruff check .
pytest --cov=bacon

The tests replace the external programs by small stub scripts (tests/test_pipeline.py), so they run in seconds, without conda, and test the pipeline logic: resuming, parameter changes, failures, provenance. The real programs are exercised by the example and the validation:

bash example/run_example.sh                   # seconds; checks SNP distances against the truth
bash validation/run_validation.sh /tmp/val    # a few minutes; scores every assembler and SNP method

Continuous integration (.github/workflows/ci.yml) runs ruff, the tests on Python 3.10 to 3.13 (and macOS), and the example in the conda environment.

Adding or replacing a program

A program is added or replaces another only if it is maintained, installs with the others from bioconda, and does at least as well in the validation. Add it to environment.yml, recipe/meta.yaml and bacon/tools.py (PACKAGES), with a stub in tests/test_pipeline.py, then run the validation and record the results in a new dated folder under validation/results/ (never rewrite an old record).

Documentation

The wiki is maintained in docs/wiki/ and published to the GitHub wiki by .github/workflows/wiki.yml on every push to main that changes it. Do not edit the wiki on GitHub: the next publication overwrites it.

Releases

1. Update version in pyproject.toml, __version__ in bacon/__init__.py, CITATION.cff (version and date) and CHANGELOG.md.
2. Commit, tag vX.Y.Z and push the tag: .github/workflows/release.yml checks the versions, builds the package and creates the GitHub release with the changelog section.
3. Update recipe/meta.yaml (version, sha256 of the tag's tarball) and the bioconda-recipes pull request.