Release Notes¶

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.