Installation

The package targets Python >=3.10,<3.11 and depends on the Scanpy single-cell analysis stack. The repository includes both a conda environment file and a standard editable Python package setup.

Conda Environment

From the repository root:

conda env remove -n sctl
conda env create -f sctl.yaml
conda activate sctl

The conda environment installs the package in editable mode through the pip section of sctl.yaml.

Editable Install

If the Scanpy stack is already available in your active environment:

pip install -e .

Verify Import

python -c "import single_cell_python_tools as sctl; print(sctl.__all__)"

The package import requires dependencies such as scanpy, anndata, gseapy, leidenalg, and bbknn to be installed.