Metadata-Version: 2.1
Name: ga4gh.cat_vrs
Version: 0.1.0
Summary: GA4GH Categorical Variation Representation (Cat-VRS) reference implementation
Author-email: Larry Babb <lbabb@broadinstitute.org>, Alex Wagner <alex.wagner@nationwidechildrens.org>, Daniel Puthawala <daniel.puthawala@nationwidechildrens.org>
License: Apache License
                                   Version 2.0, January 2004
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Project-URL: Homepage, https://github.com/ga4gh/cat-vrs-python
Project-URL: Documentation, https://github.com/ga4gh/cat-vrs-python
Project-URL: Changelog, https://github.com/ga4gh/cat-vrs-python/releases
Project-URL: Source, https://github.com/ga4gh/cat-vrs-python
Project-URL: Bug Tracker, https://github.com/ga4gh/cat-vrs-python/issues
Keywords: bioinformatics,ga4gh,genomics,variation
Classifier: Development Status :: 3 - Alpha
Classifier: Intended Audience :: Developers
Classifier: Intended Audience :: Healthcare Industry
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: Apache Software License
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3.11
Classifier: Programming Language :: Python :: 3.12
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Topic :: Scientific/Engineering :: Medical Science Apps.
Requires-Python: >=3.10
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: ga4gh.vrs ~=2.0.0a12
Requires-Dist: pydantic ==2.*
Provides-Extra: dev
Requires-Dist: pre-commit ; extra == 'dev'
Requires-Dist: ruff ==0.4.9 ; extra == 'dev'
Provides-Extra: tests
Requires-Dist: pytest ; extra == 'tests'
Requires-Dist: pytest-cov ; extra == 'tests'

# cat-vrs-python

GA4GH Categorical Variation Representation Python Implementation

## Information

[![license](https://img.shields.io/badge/license-Apache-green)](https://github.com/ga4gh/cat-vrs-python/blob/main/LICENSE)

## Releases

[![gitHub tag](https://img.shields.io/github/v/tag/ga4gh/cat-vrs-python.svg)](https://github.com/ga4gh/cat-vrs-python/releases) [![pypi](https://img.shields.io/pypi/v/ga4gh.cat_vrs.svg)](https://pypi.org/project/ga4gh.cat_vrs/)

## Development

[![action status](https://github.com/ga4gh/cat-vrs-python/actions/workflows/python-cqa.yaml/badge.svg)](https://github.com/ga4gh/cat-vrs-python/actions/workflows/python-cqa.yaml) [![issues](https://img.shields.io/github/issues-raw/ga4gh/cat-vrs-python.svg)](https://github.com/ga4gh/cat-vrs-python/issues)
[![GitHub Open Pull Requests](https://img.shields.io/github/issues-pr/ga4gh/cat-vrs-python.svg)](https://github.com/ga4gh/cat-vrs-python/pull/) [![GitHub license](https://img.shields.io/github/contributors/ga4gh/cat-vrs-python.svg)](https://github.com/ga4gh/cat-vrs-python/graphs/contributors/) [![GitHub stars](https://img.shields.io/github/stars/ga4gh/cat-vrs-python.svg?style=social&label=Stars)](https://github.com/ga4gh/cat-vrs-python/stargazers) [![GitHub forks](https://img.shields.io/github/forks/ga4gh/cat-vrs-python.svg?style=social&label=Forks)](https://github.com/ga4gh/cat-vrs-python/network)

## Features

- Pydantic implementation of Cat-VRS models

## Known Issues

**You are encouraged to** [browse issues](https://github.com/ga4gh/cat-vrs-python/issues).
All known issues are listed there. Please report any issues you find.

## Developers

This section is intended for developers who contribute to Cat-VRS-Python.

### Installing for development

#### Prerequisites

- Python >= 3.10
  - _Note: Python 3.12 is required for developers contributing to Cat-VRS-Python_

Fork the repo at <https://github.com/ga4gh/cat-vrs-python/>.

Install development dependencies and `pre-commit`:

```shell
git clone --recurse-submodules git@github.com:YOUR_GITHUB_ID/cat-vrs-python.git
cd cat-vrs-python
make devready
source venv/3.12/bin/activate
pre-commit install
```

Check style with `ruff`:

```shell
make format; make lint
```

#### Submodules

cat-vrs-python embeds cat-vrs as a submodule, only for testing purposes. When checking
out cat-vrs-python and switching branches, it is important to make sure that the
submodule tracks cat-vrs-python correctly. The recommended way to do this is
`git config --global submodule.recurse true`. **If you don't set submodule.recurse,
developers and reviewers must be extremely careful to not accidentally upgrade or
downgrade schemas with respect to cat-vrs-python.**

If you already cloned the repo, but forgot to include `--recurse-submodules` you can run:

```shell
git submodule update --init --recursive
```

### Testing

To run tests:

```shell
make test
```

## Security Note (from the GA4GH Security Team)

A stand-alone security review has been performed on the specification itself.
This implementation is offered as-is, and without any security guarantees. It
will need an independent security review before it can be considered ready for
use in security-critical applications. If you integrate this code into your
application it is AT YOUR OWN RISK AND RESPONSIBILITY to arrange for a security
audit.
