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Contributing

We welcome improvements, extensions, bug reports and bug fixes to VAtools!

Bug Reports

To make bug reports most useful, please include:

  • a brief summary of the problem - what did you expect, and what actually happened?
  • precise steps to reproduce the problem, and minimal VCF and annotation files on which the steps can be run, if possible.

Fixes or Feature Additions

Direct pull requests are just fine - fork the repository, create an new branch, then make a PR against this repo.

Before investing time and effort, it is often best to create an issue in the github repository reporting the bug and/or proposing the change, and we'll be happy to discuss the details and feasibility with you.

Running Tests

The test suite uses Python's built-in unittest framework and requires Python 3.10 or newer.

1. Get the code

Clone the repository (or your fork of it) and move into the top-level directory, the one containing setup.py:

git clone https://github.com/griffithlab/VAtools.git
cd VAtools

2. Create an isolated Python environment

This keeps VAtools' dependencies separate from the rest of your system. Use either conda:

conda create -n vatools python=3.12
conda activate vatools

or a virtual environment:

python3 -m venv .venv
source .venv/bin/activate

3. Install VAtools in editable mode

With the environment active, and from the top-level VAtools directory:

pip install -e .

The -e ("editable") flag installs VAtools as a link to your checkout instead of a copy, so changes you make to the code take effect immediately without reinstalling. This step also installs all dependencies, including testfixtures, which the tests need.

4. Run the tests

Still in the top-level directory, run the full suite:

python -m unittest discover -v

To run the tests for a single tool, or a single test, pass its module or test name:

python -m unittest tests.test_vep_annotation_reporter
python -m unittest tests.test_vep_annotation_reporter.VcfExpressionEncoderTests.test_all_vep_fields

Test inputs and expected outputs are in tests/test_data/. Most tests run a tool and compare its output to the expected results in that directory, so if you change a tool's output, you'll have to update the matching expected files too.

The same tests run automatically on GitHub Actions (.github/workflows/tests.yml) for every push and pull request to master, on Python 3.10 through 3.14. Please make sure they pass locally before opening a PR.