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spateo-release

Spatiotemporal modeling of spatial transcriptomics

Spateo Development Process

  • Follow feature-staging-main review process
    • create a specific branch for new feature
    • implement and test on your branch; add unit tests
    • create pull request
    • discuss with lab members and merge into the main branch once all checks pass
  • Follow python Google code style

Code quality

  • File and function docstrings should be written in Google style
  • We use black to automatically format code in a standardized format. To ensure that any code changes are up to standard, use pre-commit as such.
# Run the following two lines ONCE.
pip install pre-commit
pre-commit install

Then, all future commits will call black automatically to format the code. Any code that does not follow the standard will cause a check to fail.

Unit testing

Unit-tests should be written for most functions. To run unit tests, simply run the following.

# Install ONCE.
pip install -r dev-requirements.txt

# Run test
make test

Any failing tests will cause a check to fail.