Development
Repository Layout
pyproject.toml: package metadata and install requirements.sctl.yaml: conda environment for the Scanpy stack.src/single_cell_python_tools: package source.Example_notebooks: notebook examples and generated example outputs.docs: canonical Markdown docs for the GitHub Pages docs hub.
Documentation Maintenance
The docs are static Markdown. When public functions, signatures, or exported names change, update the relevant docs page and API Reference in the same change.
The docs hub stages these files into the Sphinx site at build time. Do not copy large notebook outputs or example data into the docs directory.
Public API Notes
Current public names include several legacy spellings. Preserve them in docs and examples unless the package code changes intentionally:
basic_filiteringfilter_cells_by_anotated_QC_gene_plots_depreciated