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Contributing

This document briefly describes how to contribute to ProteoBench.

Before you begin

If you have an idea for a feature, use case to add or an approach for a bugfix, you are welcome to communicate it with the community by opening a thread in GitHub Discussions or in GitHub Issues.

Not sure where to start? Great contributions to ProteoBench include:

[TODO]

Also check out the open issues that carry the good first issue or help wanted labels.

Development setup

Local installation

Install the package and dependencies with pip:

Change into the directory where you cloned proteobench into, and run:

pip install -e .

Using a virtual environment is recommended.

Unit tests

To run the tests run the command:

We use pytest which also supports unittest if you prefer that.

pytest

Testing the web interface locally

Start the web server locally with:

cd ./webinterface/
streamlit run Home.py

This will launch the Proteobench application in your web browser.

Changes to the code in ./webinterface will trigger a reload of the web server. However, changes in ./proteobench require a full restart of the webserver to be included.

Enabling pre-commit hooks

The project contains a .pre-commit-config.yaml file that defines a set of checks that are run before each commit.

To enable pre-commit checks on your machine install :

pipx install pre-commit

To run all the pre-commit checks on all files, run:

pre-commit run --all-files

To enable automatic pre-commit checks, run:

pre-commit install

running tests, building notebooks and documentation.

You can use nox to run tests build notebooks and build the documentation.

to run test only

nox --session "tests"

nox --session "test_notebooks"

nox --session "docs"

Documentation

To work on the documentation and get a live preview, install the requirements and run sphinx-autobuild:

pip install -e'.[docs]'
sphinx-autobuild  --watch ./proteobench ./docs/ ./docs/_build/html/

Then browse to http://localhost:8000 to watch the live preview.

How to contribute

  • Fork ProteoBench 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.

Release workflow

  • When a new version is ready to be published:

    1. Change the __version__ in proteobench/__init__.py following semantic versioning.
    2. Update the changelog (if not already done) in CHANGELOG.md according to Keep a Changelog.
    3. Merge all final changes with the main branch.
    4. Create a new release on GitHub.

  • 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.