Cumulus Library Study Template

This project aims to give you a forkable repository you can use for creating clinical studies with Cumulus Library, along with some examples of how to create tables

How do I get started?

Here's what we recommend:

• Pick a name for your study (e.g. your-study) This name is how it will appear in the Cumulus dashboard. You will also need a package name - cumulus-library-your-study is what we usually chose. Just make sure it's a unique python package name. You'll use dashes in the package name in pyproject.toml, and underscores elsewhere

• Rename the cumulus_library_template folder to match your package name

• Change this line in .github/workflows/ci.yaml:

  python -m pytest --cov-report xml --cov=cumulus_library_template tests

  to point to your new package name

• Follow the comment instructions in pyproject.toml and manifest.toml to set up these files to work with Cumulus Library.

• When invoking with cumulus-library, use the --study_dir flag to point to the directory containing the manifest.toml, or use the CUMULUS_LIBRARY_STUDY_DIR env var to a filepath which contains your study directory. The --study-dir flag will check subdirectories for you.

We also suggest the following:

• Install the dev dependencies with pip install [.dev]
• Run pre-commit install to install the pre-commit hooks, which will auto run linters before you push a commit
• We have CI actions for running linters and unit tests as validation in github, which will run with no additional configuration

The example study includes some sample files that will build a functioning study, which you can use as a reference for starting. For more information, see the Example docs