Contributing to MERlin

Contributions to MERlin can either be submitted by opening an issue to raise concerns or offer suggestions or by opening a pull request to offer improvements to the code base.

Opening a pull request

A pull request allows code to be proposed to be incorporated into MERlin. To receive feedback on work in progress, mark the pull request with WIP in the subject line. To open a pull request:

  1. Fork the repository to your github account and clone it locally.

  2. Create a new branch for your edits.

  3. Make your desired edits to the code.

  4. Run the tests to ensure MERlin is still functional. Write new tests to cover your new contribution as necessary.

#. Submit a pull request from your edited branch to the latest vx.y.z (for example v0.1.4) branch of the MERlin repository representing the version of the next release. Be sure to reference any relevant issues and request at least one reviewer. Periodically the vx.y.z branch will be merged with the master branch.

Code formatting

Code contributions should follow the PEP 8 style guide with the exception that variable names should be mixedCase instead of words separated by underscores. Comments should follow the Google docstring style.

Running the tests

All contributions to MERlin must maintain the integrity of the tests. Before submitting a pull request, please ensure that all tests pass. Tests are implemented using the pytest framework. The tests are in the test directory and they can be run by executing pytest in the root MERlin directory. To facilitate efficient debugging, tests that take more than few seconds are marked with `slowtest` and can be excluded from the run using the command:

pytest -v  test

Generating documentation

Documentation for MERlin is generated using Sphinx. The API documentation can be generated with the command from the root MERlin directory:

sphinx-apidoc -f -o ./docs/_modules .