Metadata-Version: 2.1
Name: ipr
Version: 1.0.0
Summary: UNKNOWN
Home-page: UNKNOWN
Author: graphkb
Author-email: graphkb@bcgsc.ca
Maintainer: graphkb
Maintainer-email: graphkb@bcgsc.ca
License: UNKNOWN
Description: 
        # IPR
        
        ![build](https://github.com/bcgsc/pori_ipr_python/workflows/build/badge.svg) [![PyPi](https://img.shields.io/pypi/v/ipr.svg)](https://pypi.org/project/ipr) [![codecov](https://codecov.io/gh/bcgsc/pori_ipr_python/branch/master/graph/badge.svg)](https://codecov.io/gh/bcgsc/pori_ipr_python)
        
        This python tool takes in variant inputs as tab-delimited files and annotates them using GraphKB.
        The resulting output is uploaded to IPR as a report. Additional report content such as images and
        metadata can be passed to be included in the report upload.
        
        
        ## Getting Started
        
        ### Install (For developers)
        
        clone this repository
        
        ```
        git clone https://github.com/bcgsc/pori_ipr_python.git
        cd pori_ipr_python
        ```
        
        create a virtual environment
        
        ```
        python3 -m venv venv
        source venv/bin/activate
        ```
        
        install the package and its development dependencies
        
        ```
        pip install -e .[dev]
        ```
        
        Run the tests
        
        ```
        pytest tests
        ```
        
        ## Generating the Documentation
        
        This documentation is generated using [mkdocs](https://www.mkdocs.org), [mkdocs-material](https://pypi.org/project/mkdocs-material), and [markdown_refdocs](https://pypi.org/project/markdown-refdocs).
        
        First install the documentation dependencies
        
        ```bash
        pip install .[doc]
        ```
        
        Then generate the user manual files
        
        ```bash
        markdown_refdocs ipr -o docs/reference
        mkdocs build
        ```
        
        There should now be static html files under `build-docs`. To view the files, serve the folder using
        the built-in python http server
        
        ```bash
        python3 -m http.server -d build-docs
        ```
        
Platform: UNKNOWN
Requires-Python: >=3.6
Description-Content-Type: text/markdown
Provides-Extra: dev
Provides-Extra: deploy
Provides-Extra: test
Provides-Extra: doc
