Release Notes

1.4.0 2026-05-01

Features

• Removed tensorflow and keras and replaced with torch and torchvision.

• The CCI implementation removed string comparisons for LR pairs lists and replaced it with one set of two packed 32 bit integers. Removed deduplication pass (m^2) with a hash lookup (O(n)).

• Added row and polygon annotations.

• Upgrade libraries: numpy >=2.4.0, scanpy >= 1.12.0, scipy >= 1.17.0, added spatialdata, shapely, geopandas.

Bugs

• Fixed exception handling to catch previous exceptions when rethrown.

1.3.0 2026-02-24

Features

• Removed interactive stLearn/embedded web application.

• Removed louvain clustering.

• Renamed methods and classes to follow lowercase standard.

1.2.2 2025-10-20

Features

• Added support for Python 3.11 and 3.12.

• Upgraded scanpy to 1.11 - clustering will be different.

• Added more CCI tests.

Bugs

• Fixed copy-paste error in louvain.py file.

1.1.5 2025-09-17

Features

• Add Leiden clustering wrapper.

• Fix documentation, refactor code in spatial.SME.

1.1.1 2025-07-07

Features

• Support Python 3.10.x

• Added quality checks black, ruff and mypy and fixed appropriate source code.

• Copy parameters now work with the same semantics as scanpy.

• Library upgrades for leidenalg, louvain, numba, numpy, scanpy, and tensorflow.

• datasets.xenium_sge - loads Xenium data (and caches it) similar to scanpy.visium_sge.

Bug fixes

• Xenium TIFF and cell positions are now aligned.

• Consistent with type annotations - mainly missing None annotations.

• pl.cluster_plot - Does not keep colours from previous runs when clustering.

• pl.trajectory.pseudotime_plot - Fix typing of cluster values in .uns[“split_node”].

• Removed datasets.example_bcba - Replaced with wrapper for scanpy.visium_sge.

• Moved spatials directory to spatial, cleaned up pl and tl packages.

0.4.0 2022-02-03

Features

• Upgrade stSME, PSTS and CCI analysis methods.

• Add CCI analysis functions: load_lrs(), grid(), run(), adj_pvals(), run_lr_go(), lr_summary(), lr_diagnostics(), lr_n_spots(), lr_go(), lr_result_plot(), lr_plot(), cci_check(), ccinet_plot(), lr_chord_plot(), lr_cci_map(), cci_map(), lr_plot_interactive(), spatialcci_plot_interactive()

0.3.2 2021-03-29

Features

• Add interactive plotting functions: gene_plot_interactive(), cluster_plot_interactive(), het_plot_interactive()

• Add basic unittest (will add more in the future).

• Add ‘contour’ parameter to use contour plot in gene_plot() and het_plot().

• Add convert_scanpy() to convert object from scanpy to stLearn.

Bug fixes

• Refactor gene_plot()

• Refactor cluster_plot()

• Refactor het_plot()

• Fixed issue with networkx object cannot write h5ad file.