Metadata-Version: 2.3
Name: cg
Version: 75.2.1
Summary: Clinical Genomics command center
Requires-Python: >=3.9,<3.13
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 3.11
Classifier: Programming Language :: Python :: Implementation :: CPython
Provides-Extra: coveralls
Provides-Extra: mock
Provides-Extra: pre-commit
Provides-Extra: pytest
Provides-Extra: pytest-cov
Provides-Extra: pytest-freezegun
Provides-Extra: pytest-httpserver
Provides-Extra: pytest-mock
Provides-Extra: pytest-xdist
Provides-Extra: ruff
Requires-Dist: CacheControl
Requires-Dist: Flask
Requires-Dist: Flask-Admin
Requires-Dist: Flask-CORS
Requires-Dist: Flask-Dance
Requires-Dist: Flask-WTF
Requires-Dist: Jinja2
Requires-Dist: MarkupSafe
Requires-Dist: PyMySQL
Requires-Dist: PyYAML
Requires-Dist: SQLAlchemy
Requires-Dist: WTForms (==3.0.0)
Requires-Dist: alembic
Requires-Dist: blinker
Requires-Dist: cachetools
Requires-Dist: click
Requires-Dist: coloredlogs
Requires-Dist: coveralls ; extra == "coveralls"
Requires-Dist: cryptography
Requires-Dist: email-validator (>=2.2.0)
Requires-Dist: genologics
Requires-Dist: google-auth
Requires-Dist: gunicorn
Requires-Dist: housekeeper (>=4.11.3)
Requires-Dist: lxml
Requires-Dist: marshmallow
Requires-Dist: mock ; extra == "mock"
Requires-Dist: openpyxl
Requires-Dist: packaging
Requires-Dist: pandas
Requires-Dist: paramiko
Requires-Dist: petname
Requires-Dist: pre-commit ; extra == "pre-commit"
Requires-Dist: psutil
Requires-Dist: pydantic (==2.7.4)
Requires-Dist: pydantic-settings (>=2.3.3)
Requires-Dist: pytest ; extra == "pytest"
Requires-Dist: pytest-cov ; extra == "pytest-cov"
Requires-Dist: pytest-freezegun ; extra == "pytest-freezegun"
Requires-Dist: pytest-httpserver ; extra == "pytest-httpserver"
Requires-Dist: pytest-mock ; extra == "pytest-mock"
Requires-Dist: pytest-xdist ; extra == "pytest-xdist"
Requires-Dist: python-dateutil
Requires-Dist: requests
Requires-Dist: rich-click (>=1.8.4)
Requires-Dist: ruff ; extra == "ruff"
Requires-Dist: tabulate
Requires-Dist: typing_extensions
Requires-Dist: urllib3
Requires-Dist: werkzeug
Description-Content-Type: text/markdown

# cg
![Build Status - Github][gh-actions-badge]
[![Coverage Status][coveralls-image]][coveralls-url]
[![GitHub issues-closed][closed-issues-img]][closed-issues-url]
[![Average time to resolve an issue][ismaintained-resolve-img]][ismaintained-resolve-url]
[![Percentage of issues still open][ismaintained-open-rate-img]][ismaintained-open-rate-url]
[![CodeFactor][codefactor-badge]][codefactor-url]
[![Code style: black][black-image]][black-url]


`cg` stands for _Clinical Genomics_; a clinical sequencing platform under [SciLifeLab][scilife]

In this context, `cg` provides the interface between these tools to facilitate automation and other necessary cross-talk. It also exposes some APIs:

- HTTP REST for powering the web portal: [clinical.scilifelab.se][portal]
- CLI for interactions on the command line

### Contributing

Please check out our [guide for contributing to cg](CONTRIBUTING.md)

## Installation

Cg written in Python 3.9+ and is available on the [Python Package Index][pypi] (PyPI).

```bash
pip install cg
```

If you would like to install the latest development version, use [poetry](https://python-poetry.org/docs/).

```bash
git clone https://github.com/Clinical-Genomics/cg
cd cg
poetry install
```

For development, use `poetry install --all-extras` to install development dependencies.


[portal]: https://clinical.scilifelab.se/
[trailblazer]: https://github.com/Clinical-Genomics/trailblazer
[housekeeper]: https://github.com/Clinical-Genomics/housekeeper
[genotype]: https://github.com/Clinical-Genomics/genotype
[scilife]: https://www.scilifelab.se/
[pypi]: https://pypi.org/


[black]: https://black.readthedocs.io/en/stable/

<!-- badges -->

[coveralls-url]: https://coveralls.io/github/Clinical-Genomics/cg
[coveralls-image]: https://coveralls.io/repos/github/Clinical-Genomics/cg/badge.svg?branch=master

[gh-actions-badge]: https://github.com/Clinical-Genomics/cg/workflows/Tests%20and%20coveralls/badge.svg
[closed-issues-img]: https://img.shields.io/github/issues-closed/Clinical-Genomics/cg.svg
[closed-issues-url]: https://GitHub.com/Clinical-Genomics/cg/issues?q=is%3Aissue+is%3Aclosed
[ismaintained-resolve-img]: http://isitmaintained.com/badge/resolution/Clinical-Genomics/cg.svg
[ismaintained-resolve-url]: http://isitmaintained.com/project/Clinical-Genomics/cg
[ismaintained-open-rate-img]: http://isitmaintained.com/badge/open/Clinical-Genomics/cg.svg
[ismaintained-open-rate-url]: http://isitmaintained.com/project/Clinical-Genomics/cg
[codefactor-badge]: https://www.codefactor.io/repository/github/clinical-genomics/cg/badge
[codefactor-url]: https://www.codefactor.io/repository/github/clinical-genomics/cg
[black-image]: https://img.shields.io/badge/code%20style-black-000000.svg
[black-url]: https://github.com/psf/black

