stLearn 1.2.2

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.
• Fixed sphinx documentations errors.

stLearn 1.1.5

What's Changed

• Bump pillow from 11.2.1 to 11.3.0 by @dependabot[bot] in #329
• Add Leiden clustering and update documentation by @newmana in #334

stLearn 1.1.1

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's visium_sge call.

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.

stLearn Nature Communications Release

• This is the official release of the stLearn version used for the work published in Nature Communications.

v0.4.10

Upgrade functions to work with Xenium data

v0.4.8

Bug fix

• Fixed DBSCAN bug
• Added trajectory visualization parameters

v0.4.7

Bug fix

• Added recipe to conda-forge
• Fix the dependencies packages

v0.4.6

Bug fix

• Fix connectomeDB paths

v0.4.5

Bug fix

• Fix dependencies packages
• Fix cci_plot
• Add stlearn-interactive web app