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Contribute

Welcome to the molfeat community! We appreciate everyone's contribution and welcome all. Apart from code contributions, there are various other ways to support the community. If you would like to get involved, please see the community documentation for more details on how to contribute. However you choose to contribute, please be mindful and respect our code of conduct.

!!! note annotate "Get inspired by community contributions" As we love community contributions, we decided to create a dedicate space in our documentation to highlight and celebrate such contributions. Visit Community Contribitons to learn more!

The rest of this page details the development lifecycle of molfeat.

Setup a dev environment

To contribute, you will first need to setup a dev environment. Follow the steps below:

  1. Fork the repository by clicking on the Fork button on the repository's page. This creates a copy of the code under your GitHub user account.

  2. Clone your fork to your local disk, and add the base repository as a remote:

    git clone [email protected]:<your Github handle>/molfeat.git
cd molfeat
git remote add upstream https://github.com/datamol-io/molfeat.git

  3. Create a new branch to hold your development changes:

    git checkout -b useful-branch-name

    Do not work on the main branch!

  4. Once you have a local copy, setup a development environment and install the dependencies.

    It is strongly recommended that you do so in a new conda environment.

    mamba env create -n molfeat -f env.yml
conda activate molfeat
pip install -e . --no-deps

    If you absolutely cannot use conda/mamba, please use the following pip install command in your virtual environment:

    pip install -e ".[dev]"

    If molfeat was already installed in the virtual environment, remove it with pip uninstall molfeat first, before reinstalling it in editable mode with the -e flag.

  5. Make your changes and modifications on your branch.

    As you work on your code, you should make sure the test suite passes. Run the tests impacted by your changes like this:

    pytest tests/<TEST_TO_RUN>.py

  6. Commit your code, push it to your forked repository and open a pull request with a detailed description of your changes and why they are valuable.

Continuous Integration

molfeat uses Github Actions to:

  • Build and test molfeat.
  • Check code formating the code: black.
  • Documentation: build and deploy the documentation on main and for every new git tag.

Run tests globally

pytest

Build the documentation

You can build and serve the documentation locally with:

# Build and serve the doc
mkdocs serve

Submitting Pull Requests

If you're considering a large code contribution to molfeat, please open an issue first to get early feedback on the idea.

Once you think the code is ready to be reviewed, push it to your fork and open a pull request. We will assign a reviewer to your PR. For a change to be accepted all existing tests will need to pass. We expect additional tests and documentation for any new features.

If you are developing a plugin for molfeat, please refer to the corresponding section Extending molfeat

Adding ETL Notebooks

The ETL (extraction, transformation, and loading) scripts document the process of creating new featurizers, and we make our ETL notebooks open to the community for transparency purposes. As a developer adding new featurizers, please document your process in the etl notebook folder.

By documenting your process in the ETL notebook, you help ensure that the registration of new models can be reviewed by the community and provide greater visibility into the development process. This can help build trust with our users and contributors, and encourage collaboration and feedback.

Releasing a New Version

To release a new version, code maintainers can use the release GitHub action. However, before releasing a new version, it is important to coordinate with the code owners to ensure that the release roadmap is followed and any critical pull requests have been merged.

The release roadmap should be followed to ensure that the new version is stable, functional, and meets the requirements of the release. This includes proper testing, documentation, and ensuring backward compatibility where necessary. By following these guidelines, we can ensure that new versions are released smoothly and efficiently, with clear communication to our users and contributors.