Changelog

All notable changes to PySingleCellNet should be listed here. The definition of 'notable' is dynamic.

[Unreleased]

TO FIX

tl.score_gene_sets should add scores, one matrix to .obsm and not as columsn to .obs

Added

• requirements.txt and environment.yml for reproducible environment setup
• Installation instructions in docs/install.md for pip and conda workflows
• Test suite (tests/) covering classifier, clustering, categorize, utils, and plotting
• tests/generate_test_data.py to create small h5ad fixtures from full datasets
• CLAUDE.md for AI-assisted development guidelines

Changed

• tl.cluster_subclusters layer should be None instead of counts
• Completed Google-style docstrings (Args/Returns/Raises) across all public functions for mkdocs auto-extraction

Fixed

• tl.cluster_subclusters calls sc.pp.pca with mask_var instead of use_highly_variable

[0.1.3] - 2025-09-15

Changed

• replace cl with tl
• moved functions to more fitting files, like unused ones to utils.misc.py
• do not export unused functions

Added

• tl.discover_cell_cliques labels cells by consensus cluster labels, kind of
• tl.clustering_quality_vs_nn_summary computes metrics of clustering quality
• tl.cluster_alot
• tl.cluster_subcluster
• resurrected gene clustering functions
• notebook tutorial on cell clustering

Fixed

• filter_anndata_slots to handle .uns and dependencies across slots
• classify_anndata bug that prevented writing h5ad. see https://github.com/CahanLab/PySingleCellNet/issues/13

Removed

• ut.mito_rib_heme
• lots of stuff that is old or has been moved to other packages like STUF

[0.1.2] - 2025-08-05

Removed

• stale functions in old/

[0.1.1] - 2025-08-04

Fixed

• Wrestled pyproject.toml into shape

Removed

• stale functions in old/

[0.1.0] - 2025-08-04

Added

• new versioning system

Fixed

• typos in docs