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.
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:
Clone your fork to your local disk, and add the base repository as a remote:
git clone firstname.lastname@example.org:<your Github handle>/molfeat.git cd molfeat git remote add upstream https://github.com/datamol-io/molfeat.git
Create a new branch to hold your development changes:
git checkout -b useful-branch-name
Do not work on the
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 molfeatfirst, before reinstalling it in editable mode with the
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:
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.
molfeat uses Github Actions to:
- Build and test
- Check code formating the code:
- Documentation: build and deploy the documentation on
mainand for every new git tag.
Run tests globally¶
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.