Python package for inference and analysis of mutation trees and copy number trees.
import pyggdrasil as yg
To build package and maintain dependencies we use Poetry. In particular, it's good to install it and become familiar with its basic functionalities by reading the documentation.
To set up the environment (together with development tools) run:
$ poetry install --with dev
$ poetry run pre-commit install
Then, you will be able to run tests:
$ poetry run pytest
... or check the types:
$ poetry run pyright
Alternatively, you may prefer to work with the right Python environment using:
$ poetry shell
$ pytest
The code quality checks run during on GitHub can be seen in .github/workflows/test.yml
.
We are using:
- Ruff to lint the code.
- Black to format the code.
- Pyright to check the types.
- Pytest to run the unit tests.
- Interrogate to check the documentation.
We use Feature Branch Workflow, in which modifications of the code should happen via small pull requests.
We recommend submitting small pull requests and starting with drafts outlining proposed changes.
- The package code is in
src/pyggdrasil/
and is partitioned into subpackages. - The unit tests are in
tests/
and the structure of this directory should reflect the one of the package. - Experimental workflows are in
workflows/
, with a description of how to set up the environment inworkflows/README.md