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CONTRIBUTING.md

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Contributing to NEAT

We welcome contributions to the NEAT project. Before contributing, please review our Code of Conduct.

Issues

To submit issues and enhancement requests, please use the GitHub issues tracker.

Contributing

Currently, the major effort NEAT is focused on bringing the code up to PEP 8 standards, as well as leveraging Biopython and Pandas to speed up analysis. We have plans to increase NEAT's utility for a wider range of genomic situations, such as plants, bacteria, and complex features like cancer.

In general, we follow the "fork-and-pull" Git workflow.

  1. Fork the repo on GitHub
  2. Clone the project to your own machine
  3. Commit changes to your own branch
  4. Push your work back up to your fork
  5. Submit a Pull request so that we can review your changes

Note: Be sure to merge the latest changes before making the pull request. You can increase your chances of a successfull pull request by indicating clearly what branch you are contributing to and making a detailed commit message. It also helps if you open an issue first to let us know you are working on this project.

Running Tests

We use pytest for unit and integration tests.

Recommended setup

conda env create -f environment.yml
conda activate neat
poetry install --with dev

It will also be necessary to gunzip this file:

gunzip data/H1N1.fa.gz

To run all tests, use the following command:

pytest -q tests

It is also possible to run a subset of tests:

pytest -q tests/test_models
pytest -q tests/test_cli/test_basic_cli.py

License

NEAT is licensed under BSD 3-Clause License. Because we also use some of the software from Biopython, we additionally have included the Biopython License Agreement