y0-bio

Biological applications for y0.

💪 Getting Started

Check that your BEL graph is identifiable under a causal query:

import pybel
from y0.dsl import P, Variable
from y0.identify import is_identifiable
from y0_bio.resources import BEL_EXAMPLE
from y0_bio.io.bel import bel_to_nxmg
bel_graph = pybel.load(BEL_EXAMPLE)
nxmg = bel_to_nxmg(bel_graph)
assert is_identifiable(
    nxmg,
    P(Variable('Severe Acute Respiratory Syndrome') @ Variable('angiotensin II')),
)

⬇️ Installation

The most recent release can be installed from PyPI with:

$ pip install y0_bio

The most recent code and data can be installed directly from GitHub with:

$ pip install git+https://github.com/y0-causal-inference/y0-bio.git

To install in development mode, use the following:

$ git clone git+https://github.com/y0-causal-inference/y0-bio.git
$ cd y0-bio
$ pip install -e .

⚖️ License

The code in this package is licensed under the MIT License.

🙏 Contributing

Contributions, whether filing an issue, making a pull request, or forking, are appreciated. See CONTRIBUTING.rst for more information on getting involved.

🍪 Cookiecutter Acknowledgement

This package was created with @audreyr's cookiecutter package using @cthoyt's cookiecutter-python-package template.

🛠️ Development

The final section of the README is for if you want to get involved by making a code contribution.

❓ Testing

After cloning the repository and installing tox with pip install tox, the unit tests in the tests/ folder can be run reproducibly with:

$ tox

Additionally, these tests are automatically re-run with each commit in a GitHub Action.

📦 Making a Release

After installing the package in development mode and installing tox with pip install tox, the commands for making a new release are contained within the finish environment in tox.ini. Run the following from the shell:

$ tox -e finish

This script does the following:

1. Uses BumpVersion to switch the version number in the setup.cfg and src/y0_bio/version.py to not have the -dev suffix
2. Packages the code in both a tar archive and a wheel
3. Uploads to PyPI using twine. Be sure to have a .pypirc file configured to avoid the need for manual input at this step
4. Push to GitHub. You'll need to make a release going with the commit where the version was bumped.
5. Bump the version to the next patch. If you made big changes and want to bump the version by minor, you can use tox -e bumpversion minor after.