Biology is the domain-types layer of the sysbioverse ecosystem. It provides biological entities that resolve their own attributes through omnipath-client, together with set-like EntitySet and Namespace objects that bind omics feature spaces to network nodes.
- TODO: replace this with a paragraph that says what the project does and who it is for.
pip install biology- TODO: keep this only once the project is on PyPI; until then point at the repository.
- TODO: Add usage instructions for your project.
import biology
print(biology.__version__)The full documentation is at
https://saezlab.github.io/biology/.
It is built with Material for MkDocs
from the docs/ directory:
mkdocs serveuv venv --python 3.11
uv pip install -e '.[dev,tests,docs]'
pre-commit installruff is the only linter and formatter; it runs on every commit through pre-commit. Tests are run with pytest:
pytestPull requests are welcome. For major changes, please open an issue first to discuss what you would like to change. The contribution guide is at docs/contributing.md.
Please make sure to update tests as appropriate.
BSD 3-Clause License — see the LICENSE file.