For developers

Installation

Clone the repository using

$ git clone git@github.com:cbg-ethz/covvfit.git

Then, create a new Python environment, e.g., using Micromamba:

$ micromamba create -n covvfit -c conda-forge python=3.11

Install the package in editable mode together with the developer utilities:

$ pip install poetry
$ poetry install --with dev
$ pre-commit install

Testing

We use Pytest to write the unit tests. The unit tests are stored in tests/ directory. After the installation you can verify whether the unit tests are passed by running

$ pytest tests

Documentation

We write the documentation using Mkdocs in the docs/ directory. Apart from tutorials, we generate the API description directly from function docstrings.

Use

$ mkdocs build

to see whether the documentation is built properly. Alternatively, to check the documentation in the interactive mode, use

$ mkdocs serve