Contributing to PyEnsembl¶

PyEnsembl is open source software under the Apache 2.0 license, and we welcome contributions. Contributed code is assumed to use the same license.

Filing issues¶

Check the open issues first, then open a new issue for a bug or feature request. Include your PyEnsembl and Python versions. If the problem involves a particular gene, transcript or locus, name it and the release, e.g. "Missing transcript sequence for BRCA1-002 in Ensembl release 74".

Pull requests¶

Start a new feature with an issue explaining its scope and rationale, and reference the issue in the PR, e.g. "Closes #123".
Follow PEP 8; ./lint.sh runs ruff.
Accompany new code with unit tests.
Support Python 3.9 and later.
Bump the version in pyensembl/version.py in every PR, including documentation-only changes.

Development setup¶

git clone https://github.com/openvax/pyensembl.git
cd pyensembl
pip install -e '.[dev]'
./lint.sh
./test.sh

The dev extra installs pytest, pytest-cov, ruff and build. Most tests need Ensembl data installed first; .github/workflows/tests.yml lists the releases CI installs. Tests use exactly those releases, so other genomes in your cache do not change what they check.

Species assembly ranges are checked against Ensembl's archive. After raising MAX_ENSEMBL_RELEASE, recheck every assembly boundary on the live FTP servers:

PYENSEMBL_NETWORK_TESTS=1 ./test.sh tests/test_species_assemblies.py

Timed benchmarks are opt-in because wall-clock limits depend on the machine and its load. Run them on an otherwise idle machine:

PYENSEMBL_BENCHMARKS=1 ./test.sh tests/test_timings.py -s

Documentation¶

Follow the documentation style guide, then build and check the site:

pip install -e '.[dev,docs]'
./docs.sh  # strict build plus link, anchor and API checks
python scripts/check_docs_examples.py  # needs human release 93

Preview with mkdocs serve and review changed pages at desktop and narrow widths.

Releasing¶

Maintainers merge through a PR and publish from a clean main; see releasing.