"Translation of the GA4GH VRS and VRSATILE Schemas to a Pydantic data model"
Project description
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:
| ga4gh.vrsatile.pydantic branch | ga4gh.vrsatile.pydantic version | VRS version | VRSATILE version |
|---|---|---|---|
| vrs-1.2 (no longer being updated) | 0.0.X | 1.2.X | main |
| metaschema-update | 0.1.X | metaschema-update | metaschema-update |
| main | 0.2.X | 1.3.X | main |
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
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