https://github.com/bcgsc/pori_graphkb_python

Python adapter package for querying the GraphKB API
https://github.com/bcgsc/pori_graphkb_python

annotation bioinformatics graphdb personalized-medicine pori

Last synced: 10 months ago
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Python adapter package for querying the GraphKB API

• Host: GitHub
• URL: https://github.com/bcgsc/pori_graphkb_python
• Owner: bcgsc
• License: gpl-3.0
• Created: 2020-04-14T23:31:04.000Z (almost 6 years ago)
• Default Branch: master
• Last Pushed: 2024-06-26T20:50:08.000Z (over 1 year ago)
• Last Synced: 2025-04-12T20:46:13.456Z (11 months ago)
• Topics: annotation, bioinformatics, graphdb, personalized-medicine, pori
• Language: Python
• Homepage: https://bcgsc.github.io/pori
• Size: 3.6 MB
• Stars: 7
• Watchers: 5
• Forks: 1
• Open Issues: 3
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

          

# GraphKB (Python)

![build](https://github.com/bcgsc/pori_graphkb_python/workflows/build/badge.svg) [![PyPi](https://img.shields.io/pypi/v/graphkb.svg)](https://pypi.org/project/graphkb) [![codecov](https://codecov.io/gh/bcgsc/pori_graphkb_python/branch/master/graph/badge.svg)](https://codecov.io/gh/bcgsc/pori_graphkb_python) [![PyPI - Downloads](https://img.shields.io/pypi/dm/graphkb)](https://pypistats.org/packages/graphkb) [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.5730523.svg)](https://doi.org/10.5281/zenodo.5730523)

This repository is part of the [platform for oncogenomic reporting and interpretation](https://github.com/bcgsc/pori).

Python adapter package for querying the GraphKB API. See the [user manual](https://bcgsc.github.io/pori/graphkb/scripting/)

- [Getting Started](#getting-started)

  - [Install (For developers)](#install-for-developers)

  - [Run Tests](#run-tests)

- [Generating the Documentation](#generating-the-documentation)

- [Deployment (Publishing)](#deployment-publishing)

## Getting Started

### Install (For developers)

clone this repository

```bash

git clone https://github.com/bcgsc/pori_graphkb_python

cd pori_graphkb_python

```

create a virtual environment

```bash

python3 -m venv venv

source venv/bin/activate

```

install the package and its development dependencies

```bash

pip install -U pip setuptools

pip install -e .[dev]

```

### Run Tests

```bash

pytest tests

```

## Generating the Documentation

User documentation for this repository is hosted in the [central PORI repository](https://github.com/bcgsc/pori/)

## Deployment (Publishing)

Install the deployment dependencies

```bash

pip install .[deploy]

```

Build the distribution files

```bash

python setup.py install sdist bdist_wheel

```

Upload the distibutions to the package server (`-r` is defined in your pypirc)

```bash

twine upload -r bcgsc dist/*

```