This document briefly describes how to contribute to psm_utils.
Before you begin
Not sure where to start? Great contributions to psm_utils include:
Adding support for more file formats.
Adding functionality to the
Improving the performance of existing functions, e.g. parsing peptidoforms or reading and writing PSM files.
Also check out the open issues
that carry the
good first issue or
help wanted labels.
Setup Python 3, and preferably create a virtual environment.
Clone the psm_utils repository.
Use pip in editable mode to setup the development environment:
pip install --editable .[dev,doc]
Run tests with
To work on the documentation and get a live preview, install the requirements
pip install .[doc] sphinx-autobuild --watch ./psm_utils ./docs/source/ ./docs/_build/html/
Then browse to http://localhost:8000 to watch the live preview.
How to contribute
Fork psm_utils on GitHub to make your changes.
Commit and push your changes to your fork.
Ensure that the tests and documentation (both Python docstrings and files in
/docs/source/) have been updated according to your changes. Python docstrings are formatted in the numpydoc style.
Open a pull request with these changes. You pull request message ideally should include:
A description of why the changes should be made.
A description of the implementation of the changes.
A description of how to test the changes.
The pull request should pass all the continuous integration tests which are automatically run by GitHub Actions.
When a new version is ready to be published:
When a new GitHub release is made, the Publish GitHub Action is automatically triggered to build the Python package and publish it to PyPI. Upon a new PyPI release, the Bioconda automations will automatically update the Bioconda package. However, if dependencies are changed, the conda recipe will have to be updated accordingly.