vrsatile-pydantic

Translation of the GA4GH VRS and VRSATILE schemas to a Pydantic data model

The ga4gh/vrsatile/pydantic repo depends on VRS and VRSATILE models, and therefore each ga4gh.vrsatile.pydantic package on PyPI uses a particular version of VRS and VRSATILE. The correspondences between the packages may be summarized as:

Installation

vrsatile-pydantic is available via PyPI:

pip install ga4gh.vrsatile.pydantic

Developer Instructions

Following are sections include instructions specifically for developers.

Installation

For a development install, we recommend using Pipenv. See the pipenv docs for direction on installing pipenv in your compute environment.

Once installed, clone the repo and initialize the environment:

git clone https://github.com/ga4gh/vrsatile-pydantic
cd vrsatile-pydantic
pipenv shell
pipenv update
pipenv install --dev

Init coding style tests

Code style is managed by flake8 and checked prior to commit.

We use pre-commit to run conformance tests.

This ensures:

• Check code style
• Check for added large files
• Detect AWS Credentials
• Detect Private Key

Before first commit run:

pre-commit install

Running unit tests

Running unit tests is as easy as pytest.

pipenv run pytest tests