- Removed interactive stLearn/embedded web application.
- Removed louvain clustering - replaced with leiden.
API and Bug Fixes: * Fix import on MutableVertexPartition to use leidenalg.VertexPartition. * Switch default flavour in leiden to use igraph (and its required parameters). * Renamed methods and classes to follow lowercase standard.
- Added support for Python 3.11 and 3.12.
- Upgraded scanpy to 1.11 - clustering will be different.
- Added more CCI tests.
API and Bug Fixes:
- Fixed copy-paste error in louvain.py file.
- Add Leiden clustering wrapper.
- Fix documentation, refactor code in spatial.SME.
- 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.
API and 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.