Contributing

PyDESeq2 is a living project and any contributions are welcome! The project is hosted on Github.

You can help us by adding a star to the PyDESeq2 repository on github or talk about our repository on the social media or on your blog or article.

We also kindly ask you to follow the Python code of conduct.

If you find any bugs in the code please report them to the issue tracker.

How can I contribute?

Submitting a bug or asking for a new feature

First, check if the issue which you are facing or the feature you would like to have added is not already described in the issue tracker. If this is the case you can give a thumb up to that issue / feature. If there are multiple thumbs ups to a given issue it makes us prioritize it higher. You can also add a comment if you think there is something you would like to add to what have been said.

If the issue / feature is not yet described make sure to give precise details on how you reached that issue (if possible giving code snippets) or precisely describe how the new feature should function. If it’s an issue you should also mention which version of pydeseq2 you are using. You can check this by running the following python code:

import pydeseq2
pydeseq2.__version__

Contributing to the code

Thanks for willing to help us out with the development of PyDESeq2.

If you are contributing to an existing issue, add in the comment of that issue that you plan to contribute on it to avoid duplicate work. Once you start working on your pull request, link it to the issue by adding #{issue_number} in your comment.

1. To contribute, you will first need to fork the Github repository using the fork button in github. This will create a copy of pydeseq2 on your github account (you must be logged in to github).

  1. clone the pydeseq2 version from your account:

git clone git@github.com:<your-github-username>/pydeseq2.git
cd pydeseq2

We recommend using conda environment, run:

conda env create -n pydeseq2-dev python=3.9
conda activate pydeseq2-dev

and then install pydeseq2 in the development mode. This will also install all the required dependencies.

pip install -e ."[dev]"
pre-commit install

The pre-commit tool will automatically run black and isort, and check flake8 compatibility

  1. Add the upstream remote:

git remote add upstream git@github.com:owkin/pydeseq2.git

  1. Ensure that the origin and upstream are configured correctly by running:

git remote -v

you should see something like this:

origin  git@github.com:<your-github-username>/pydeseq2.git (fetch)
origin  git@github.com:<your-github-username>/pydeseq2.git (push)
upstream        git@github.com:owkin/pydeseq2.git (fetch)
upstream        git@github.com:owkin/pydeseq2.git (push)

You are now all set and ready to start on your pull request (PR).

  1. Synchronize your branch with the upstream repository:

git checkout main
git fetch upstream
git merge upstream/main --rebase

  1. Create a new branch where you will add your contributions:

git checkout -b my_new_branch

You can now make the changes committing to your new branch. Each time you commit, the pre-commit will check for style in your code.

  1. Once you are ready to submit your PR, first make sure that all the changes you have made are pushed into your github account:

git push -u origin my_feature

  1. Now create a pull request from your fork by following those guidelines. Ensure that the description of your PR is sufficient to understand what you are doing in the code. The core developers of pydeseq2 will receive a message that your PR is ready for reviews.

  2. You will need to respond to all the comments before your PR can be merged. Thanks for your contribution.

Improving the documentation

If you wish to contribute to the documentation you need to follow the same guidelines as for the code PR (Contributing to the code) and additionally install the dependencies required for building the documentation. Once you have your environment for development ready, navigate to docs directory and install required libraries

cd docs
pip install -r requirements.txt

After you make the changes in the documentation you can check if it builds correctly by running (in the docs directory):

make clean html

If the build was correct you can now view the new document in the docs/build/html directory.

PR reviews and answering questions on issues

You can also help us by reviewing an existing PR or by answering questions posed on the issue board issue tracker.

Thanks again and happy contributing!