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CONTRIBUTING.md

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How to contribute

We welcome contributions to ImmuneDB, whether small or large. For non-developers, reporting bugs and adding to documentation are both valuable ways to assist. Developers can help by submitting pull requests for open issues or implementing new features.

Reporting Bugs

When reporting a bug make sure to include details about the environment being used and any error messages.

Submitting Pull Requests

Pull requests can be submitted for ImmuneDB by anyone. Before submitting a pull request, you should make sure they pass local tests by running:

    $ pip install coverage nose requests
    $ ./tests/run.sh

The environment variable DB_ADMIN_PASS should be set to your MySQL root password. To regression test Baseline's selection pressure calculations, the BASELINE_PATH must be set to the path of Baseline_Main.r.

For new features, please add tests as necessary. To change the regression test reference database, when running the tests, set the GENERATE environment variable. Please verify that the changes to the files in tests/data/regression/ accurately represent your intentions.

Further, pull requests should be PEP8 compliant. To check your code for compliance, you should get no style warning after running:

    $ pip install pycodestyle flake8
    $ pycodestyle immunedb
    $ flake8 immunedb

After completing these steps, please submit a pull request. Tests will be run on Travis. After they pass, we'll consider merging your changes or discuss further modifications.