STeep

STeep is a set of tools for distilling spatially-resolved transcriptomics (SRT) datasets by removing redundant spots/cells, accelerating downstream applications such as foundation model training and database queries.

Contribution guidelines

Click to expand dev instructions!

Dev environment setup

git clone https://github.com/alam-shahul/steep.git
cd steep
pip install --group=dev -e .
pre-commit install

Among other tools, the above installs the pre-commit command line tool. Once pre-commit is active, every time you commit some changes, it will perform several code-style checks and automatically apply some fixes for you (if there are any issues). When auto-fixes are applied, you need to recommit those changes. Note that this process can require several iterations.

After you are done committing changes and are ready to push the commits to the remote branch, run nox to perform a final quality check. Note that nox is linting only and does not fix the issues for you. You need to address the issues manually based on the instructions provided.

Adding a feature

We use pull requests and squash commits for all new features. Use the following workflow when adding a new feature:

git checkout main # Make sure you're on the main branch
git checkout -b {feature_name}
{add code, add commits}
git push --set-upstream origin {feature_name}

Next, in the GitHub pull request interface, please engage with others to perform code review of your proposed code.

Writing unittests

We use pytest to write unittests. Unittests should always be added for new functionality. New test suites can be added under tests/test_{suite_name}.py.

Run a particular test suite with:

python -m pytest tests/test_{suite_name}.py

Run all tests but the integration test:

python -m pytest -m 'not integration'

Note: to run the integration test, you'll need to specify the Hydra user using a .env file. The contents of the file should be like so:

HYDRA_USER=test

Code style and Nox

We adhere closely to the Google Python styleguide for guidance on standards of code style; please peruse the guide before contributing any code.

Nox is a tool that automates testing in multiple Python environments. Nox can be used to run tests locally as well as remotely, e.g. on GitHub servers when committing code. Please invoke Nox manually as a final quality check to maintain code style.

Run code linting and unittests:

nox

Run code linting only:

nox -e lint