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Contributing to Casanovo

First off, thank you for taking the time to contribute.

The following document provides guidelines for contributing to the documentation and the code of Casanovo. No contribution is too small! Even fixing a simple typo in the documentation is immensely helpful.

Contributing to the documentation

We use sphinx generate our documentation and deploy it to this site. Most of the pages on the site are created from simple text files written in the reStructuredText markup language. There are three exceptions to this:

  1. The API and command line documentation are automatically generated from the documentation contained in the code.

  2. The Vignettes are created from Jupyter notebooks.

  3. The Code of Conduct, Release Notes, and this Contributing document are markdown files that live in the root of the Casanovo repository.

Editing most documents

The easiest way to edit a document is by clicking the "Edit on GitHub" like in the top right hand corner of each page. You'll be taken to GitHub where you can click on the pencil to edit the document.

You can then make your changes directly on GitHub. Once you're finished, fill in a description of what you changed and click the "Propose Changes" button.

Alternatively, these documents live in the docs/source directory of the repository and can be edited like code. See Contributing to the code below for more details on contributing this way.

Contributing to the code

We welcome contributions to the source code of Casanovo---particularly ones that address discussed issues.

Contributions to Casanovo follow a standard GitHub contribution workflow:

  1. Create your own fork of the Casanovo repository on GitHub.

  2. Clone your forked Casanovo repository to work on locally.

  3. Create a new branch with a descriptive name for your changes:

git checkout -b fix_x

  1. Make your changes (make sure to read below first).

  2. Add, commit, and push your changes to your forked repository.

  3. On the GitHub page for you forked repository, click "Pull request" to propose adding your changes to Casanovo.

  4. We'll review, discuss, and help you make any revisions that are required. If all goes well, your changes will be added to Casanovo in the next release!

Python code style

The Casanovo project follows the PEP 8 guidelines for Python code style. More specifically, we use black to format code and lint Python code in Casanovo.

We highly recommend setting up a pre-commit hook for black. This will run black on all of the Python source files before the changes can be committed. Because we run black for code linting as part of our tests, setting up this hook can save you from having to revise code formatting. Take the following steps to set up the pre-commit hook:

  1. Verify that black and pre-commit are installed. If not, you can install them with pip or conda:
# Using pip
pip install black pre-commit

# Using conda
conda -c conda-forge black pre-commit
  1. Navigate to your local copy of the Casanovo repository and activate the hook:
pre-commit install

One the hook is installed, black will be run before any commit is made. If a file is changed by black, then you need to git add the file again before finished the commit.