single_cell_python_tools imports the Scanpy stack. If import fails with
ModuleNotFoundError: No module named 'scanpy', create and activate the conda
environment from sctl.yaml, or install the dependencies listed
in pyproject.toml.
The package metadata currently requires Python >=3.10,<3.11. Use the
repository conda environment when possible.
Install the package in editable mode:
pip install -e .For path-based notebook work, add the parent directory that contains the package
repository to sys.path before importing single_cell_python_tools.
For DATASET_class workflows, check the output-related parameters and call
make_output_dirs_if_not_exist() before steps that write figures or tables.
The docs hub deliberately links notebooks, example data, generated tables, and source files to GitHub instead of copying them into the Pages build.