文件列表:

docs/
releases/
src/debio/
tests/
.bumpversion.cfg
.readthedocs.yml
LICENSE
MANIFEST.in
pyproject.toml
setup.cfg
tox.ini

DeBiO

A community-curated, decentralized biomedical ontology. ## Installation The most recent release can be installed from [PyPI](https://pypi.org/project/debio/) with: ```bash $ pip install debio ``` The most recent code and data can be installed directly from GitHub with: ```bash $ pip install git+https://github.com/biopragmatics/debio.git ``` ## Contributing Contributions, whether filing an issue, making a pull request, or forking, are appreciated. See [CONTRIBUTING.md](https://github.com/biopragmatics/debio/blob/master/.github/CONTRIBUTING.md) for more information on getting involved. ## Attribution ### License The code in this package is licensed under the MIT License. ### Cookiecutter This package was created with [@audreyfeldroy](https://github.com/audreyfeldroy)'s [cookiecutter](https://github.com/cookiecutter/cookiecutter) package using [@cthoyt](https://github.com/cthoyt)'s [cookiecutter-snekpack](https://github.com/cthoyt/cookiecutter-snekpack) template. ## For Developers

See developer instructions

The final section of the README is for if you want to get involved by making a code contribution. ### Development Installation To install in development mode, use the following: ```bash $ git clone git+https://github.com/biopragmatics/debio.git $ cd debio $ pip install -e . ``` ### Testing After cloning the repository and installing `tox` with `pip install tox`, the unit tests in the `tests/` folder can be run reproducibly with: ```shell $ tox ``` Additionally, these tests are automatically re-run with each commit in a [GitHub Action](https://github.com/biopragmatics/debio/actions?query=workflow%3ATests). ### Building the Documentation The documentation can be built locally using the following: ```shell $ git clone git+https://github.com/biopragmatics/debio.git $ cd debio $ tox -e docs $ open docs/build/html/index.html ``` The documentation automatically installs the package as well as the `docs` extra specified in the [`setup.cfg`](setup.cfg). `sphinx` plugins like `texext` can be added there. Additionally, they need to be added to the `extensions` list in [`docs/source/conf.py`](docs/source/conf.py). ### 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: ```shell $ tox -e finish ``` This script does the following: 1. Uses [Bump2Version](https://github.com/c4urself/bump2version) to switch the version number in the `setup.cfg`, `src/debio/version.py`, and [`docs/source/conf.py`](docs/source/conf.py) to not have the `-dev` suffix 2. Packages the code in both a tar archive and a wheel using [`build`](https://github.com/pypa/build) 3. Uploads to PyPI using [`twine`](https://github.com/pypa/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.

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