Installation

From sources

The sources for tHMM can be downloaded from the Github repo.

You can clone the public repository:

$ git clone https://github.com/meyer-lab/tHMM.git

tHMM is built and its dependencies are managed with uv. Once you have uv installed, set up the environment and install all dependencies with:

$ cd tHMM
$ uv sync

You can then run the test suite:

$ uv run pytest

or use any of the package's modules with:

$ uv run python -c "from lineage.LineageTree import LineageTree"