flepimop2 0.1.0

The flexible epidemic modeling pipeline

flepimop2

The next generation of the flexible epidemic modeling pipeline.

Local Development

1. Clone the repository

git clone [e-mail]:ACCIDDA/flepimop2.git
cd flepimop2

2. Create a virtual environment and install dependencies using uv. To create a .venv with the package installed:

uv sync --dev

This will create a virtual environment and install the package along with development dependencies (mypy, pytest, ruff).

3. Run default checks using just. To run the default development tasks:

just

This will run:

• ruff format - Format code.
• ruff check --fix - Lint and auto-fix issues.
• pytest --doctest-modules - Run tests including doctests.
• mypy --strict - Type check with strict settings.
• yamllint --strict - Lint YAML files.

4. CI runs on pull requests to main and tests against Python 3.11, 3.12, 3.13, and 3.14. The CI checks are defined in just ci and include:

• ruff format --check - Verify code formatting (no auto-fix).
• ruff check --no-fix - Lint without modifications.
• pytest --doctest-modules - Run test suite.
• mypy --strict - Type checking.

To run the same checks locally that run in CI (say for diagnosing CI failures):

just ci

There is a separate CI check which will run just yamllint and just docs to check YAML file formatting and that the documentation builds successfully.

Funding Acknowledgement

This project was made possible by the Insight Net cooperative agreement CDC-RFA-FT-23-0069 from the CDC’s Center for Forecasting and Outbreak Analytics. Its contents are solely the responsibility of the authors and do not necessarily represent the official views of the Centers for Disease Control and Prevention.