Installation

Clone CUBI-TK, create a conda environment and install using pip or uv.

Checkout the repository and create a conda environment:

git clone git@github.com:bihealth/cubi-tk.git
conda env create -n cubi-tk -f environment.yaml
conda activate cubi-tk
cd cubi-tk

Or to update an existing environment use:

conda activate cubi-tk
conda env update -f environment.yaml --prune

Install the package using pip:

pip install -e .

Or using uv:

# if not using conda: `uv python install 3.12`
uv python pin 3.12
uv sync
uv pip install -e .
# alternatively, if you need snappy kickoff:
# GIT_LFS_SKIP_SMUDGE=1 uv pip install -e '.[snappy]'

Run tests

uv run make pytest

Build manual

cd docs_manual
uv run make clean html