v0.2.5

What's Changed

Added

• Added batch_size parameter to Kernel.compute_neighbors() for backend-agnostic batching
• Added subset parameter to plot_confusion_matrix() for filtering cells
• Added Python 3.14 support

Changed

• Default postfixes now include underscore: _pred and _conf instead of pred and conf
• Switched from MathJax to KaTeX for documentation math rendering
• Updated GitHub Actions to latest versions (checkout v5, setup-uv v7)
• Updated test matrix to Python 3.11/3.14

Fixed

• Fixed PackageNotFoundError when checking rapids availability in conda environments
• Fixed stale k-NN state when compute_neighbors() fails
• Fixed plot_confusion_matrix() handling of NaN values, mismatched categories, and float categories
• Fixed importlib.resources.files() compatibility with Python 3.14

Full Changelog: v0.2.4...v0.2.5

v0.2.4

What's Changed

• Deprecate py310 and add instructions by @Marius1311 in #55
• Update template to v0.6.0 by @scverse-bot in #54

New Contributors

• @scverse-bot made their first contribution in #54

Full Changelog: v0.2.3...v0.2.4

v0.2.3

What's Changed

• Improve return probabilities option by @Marius1311 in #49
• Library size adjustments by @Marius1311 in #50
• Make minmax normalization of presence scores optional to allow smoothing before processing. by @le-ander in #51

New Contributors

• @le-ander made their first contribution in #51

Full Changelog: v0.2.2...v0.2.3

v0.2.2

What's Changed

• Fix logging and tutorials by @Marius1311 in #43
• Prettify the README a bit. by @Marius1311 in #44
• Enable subsetting categories by @Marius1311 in #46
• Fix hvg mask to joint_pca by @Marius1311 in #48

Full Changelog: v0.2.1...v0.2.2

v0.2.1

What's Changed

• Decrease docstring duplication by @Marius1311 in #41
• Update Changelog by @Marius1311 in #42

Full Changelog: v0.2.0...v0.2.1

v0.2.0

What's Changed

• Add Zenodo link by @Marius1311 in #33
• Implement umap approach to estimate connectivities in self-mapping mode by @Marius1311 in #34
• Implement the Mapping Operator by @Marius1311 in #35
• Refactor the neighbor classes and fix symmetrization by @Marius1311 in #36
• Add tutorial on data smoothing by @Marius1311 in #37
• Add a tutorial on same-modality query to reference mapping by @Marius1311 in #38
• Return the mapping probabilities by @Marius1311 in #39
• Update the changelog by @Marius1311 in #40

Full Changelog: v0.1.4...v0.2.0

v0.1.4

What's Changed

• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #7
• Introduce embedding mixin class by @Marius1311 in #27
• Enhanced numerical obs mapping support and method consistency by @Marius1311 in #30
• Update to the docs by @Marius1311 in #32

New Contributors

• @pre-commit-ci made their first contribution in #7

Full Changelog: v0.1.3...v0.1.4

v0.1.3

What's Changed

• Work with pre-computed objects for imputed values and k-NN graphs by @Marius1311 in #21
• Implement simple kernel with equal weight for all neighbors by @Marius1311 in #22
• Add niche identification tutorial by @Marius1311 in #23

Full Changelog: v0.1.2...v0.1.3

v0.1.2

What's Changed

• Extend tests & update the README by @Marius1311 in #15
• Implement presence scores and allow evaluation per group by @Marius1311 in #16
• Set up docs by @Marius1311 in #17
• Fix rendering of the docs by @Marius1311 in #18
• Write a tutorial by @Marius1311 in #19

Full Changelog: v0.1.1...v0.1.2

v0.1.1

What's Changed

• Fix/versioning by @Marius1311 in #5

Full Changelog: v0.1.0...v0.1.1