Metadata-Version: 2.1
Name: pyphetools
Version: 0.2.13
Summary: Generate and work with GA4GH phenopackets
Author-email: Peter Robinson <peter.robinson@jax.org>
License: MIT License
        
        Copyright (c) 2023, The Monarch Initiative
        
        Permission is hereby granted, free of charge, to any person obtaining a copy
        of this software and associated documentation files (the "Software"), to deal
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Project-URL: homepage, https://github.com/monarch-initiative/pyphetools
Project-URL: repository, https://github.com/monarch-initiative/pyphetools.git
Project-URL: documentation, https://github.com/monarch-initiative/pyphetools
Project-URL: bugtracker, https://github.com/monarch-initiative/pyphetools/issues
Keywords: Global Alliance for Genomics and Health,GA4GH Phenopacket Schema,Human Phenotype Ontology,GA4GH,HPO
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python :: 3
Requires-Python: >=3.5
Description-Content-Type: text/markdown
License-File: LICENSE

# pyphetools
Python Phenopacket Tools

This package currently is designed to test how to use the Python version of the phenopackets package together with pandas to create phenopackets from typical supplemental tables.

Development goals include making builder code similar to the Java package to create valid phenopackets and to perform JSON Schema-based validation.


## Setup

For initial development, we will use notebooks mainly. Do the following to get set up. Note that now
we are using phenopackets version 2.0.2. openpyxl is needed to read Excel files.


```
python3 -m venv venv
source venv/bin/activate
pip install -r requirements.txt
pip install jupyter
python -m ipykernel install --name "venv" --display-name "venv"
cd notebooks
jupyter-notebook
```

We have installed the package in the Python Package Index (pypi) at [pyphentools](https://pypi.org/project/pyphetools/).

### Updating package in PyPI
Make sure the build and twine packages are installed.
```
python3 -m pip install --upgrade build
python3 -m pip install --upgrade twine
```
Update the version number in the pyproject.toml file
Build and install
```
python3 -m build
python3 -m twine upload dist/*
```
