Troubleshooting

Import Fails With Missing Scanpy

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.

Python Version Mismatch

The package metadata currently requires Python >=3.10,<3.11. Use the repository conda environment when possible.

Notebook Cannot Find The Package

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.

Output Directories Are Missing

For DATASET_class workflows, check the output-related parameters and call make_output_dirs_if_not_exist() before steps that write figures or tables.

Links In Published Docs Go To GitHub

The docs hub deliberately links notebooks, example data, generated tables, and source files to GitHub instead of copying them into the Pages build.