flepimop2

The next generation of the flexible epidemic modeling pipeline.

Local Development

1. Clone the repository

git clone git@github.com: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.