Update dependency umap-learn to v0.5.5

[renovate]

This PR contains the following updates:

Package	Change	Age	Adoption	Passing	Confidence
umap-learn	==0.5.3 -> ==0.5.5

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Release Notes

lmcinnes/umap (umap-learn)

v0.5.5

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v0.5.4: Patch release 0.5.4

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What's Changed

• Add numerically stable cross entropy loss by @​jgraving in https://github.com/lmcinnes/umap/pull/856
• Fix AlignedUMAP.update by @​hndgzkn in https://github.com/lmcinnes/umap/pull/861
• Fixed numerical issue in make_epochs_per_sample by @​GregDemand in https://github.com/lmcinnes/umap/pull/875
• Fix in1d() return type issue by @​GregDemand in https://github.com/lmcinnes/umap/pull/877
• Fix use of relation_dicts in expand_relations by @​GregDemand in https://github.com/lmcinnes/umap/pull/880
• Fix indexing issue with relations array by @​GregDemand in https://github.com/lmcinnes/umap/pull/882
• Added uniqueness flag to intersect1d by @​SkBlaz in https://github.com/lmcinnes/umap/pull/896
• Fix typos in docstrings by @​sky-2002 in https://github.com/lmcinnes/umap/pull/903
• consistency between install_requires and requirements.txt by @​jlmelville in https://github.com/lmcinnes/umap/pull/908
• Search index is optional for precomputed_knn by @​jlmelville in https://github.com/lmcinnes/umap/pull/909
• Fix doc build (a bit) by @​jlmelville in https://github.com/lmcinnes/umap/pull/910
• Fix the doc build by @​jlmelville in https://github.com/lmcinnes/umap/pull/913
• PCA initialization option by @​jlmelville in https://github.com/lmcinnes/umap/pull/911
• Allow points to be passed to umap.plot.points by @​dribnet in https://github.com/lmcinnes/umap/pull/912
• feature: add ability to specify tools to interactive charts so richer exploration with images and other content is possible by @​suneeta-mall in https://github.com/lmcinnes/umap/pull/858
• tighten test_umap_trustworthiness_random_init bound by @​austereantelope in https://github.com/lmcinnes/umap/pull/850
• tighten test_umap_sparse_trustworthiness bound by @​austereantelope in https://github.com/lmcinnes/umap/pull/851
• Get intermediate results at different epochs by @​matthieuheitz in https://github.com/lmcinnes/umap/pull/696
• Update penguins doc by @​jlmelville in https://github.com/lmcinnes/umap/pull/914
• ignore force approximation with precomputed knn by @​jlmelville in https://github.com/lmcinnes/umap/pull/927
• Update deprecated matplotlib colormap registry by @​yannikschaelte in https://github.com/lmcinnes/umap/pull/929
• Esm metagenomic atlas to Interactive Visualizations by @​BioGeek in https://github.com/lmcinnes/umap/pull/936
• get_feature_names_out for UMAP + tests by @​CarloLepelaars in https://github.com/lmcinnes/umap/pull/939
• Updated densMAP citation in README by @​hhcho in https://github.com/lmcinnes/umap/pull/945
• sklearn parwise distances doesn't support np.matrix anymore by @​lmcinnes in https://github.com/lmcinnes/umap/pull/946
• Minor performance improvements by @​rohan-shah-nearmap in https://github.com/lmcinnes/umap/pull/948
• Anticipate stricter asarray handling in numpy by @​lmcinnes in https://github.com/lmcinnes/umap/pull/952
• Aligned umap issues by @​GregDemand in https://github.com/lmcinnes/umap/pull/958
• Update densmap_demo.rst by @​aizardar in https://github.com/lmcinnes/umap/pull/973
• Allow UMAP to accept data with nan or inf values by @​SamKlier in https://github.com/lmcinnes/umap/pull/977
• new spectral initialization option: a truncated SVD-warmed lobpcg by @​jlmelville in https://github.com/lmcinnes/umap/pull/924
• fix: fix numpy.int and numpy.float deprecation to be compatible with numpy >= 1.20.0 by @​TTTPOB in https://github.com/lmcinnes/umap/pull/1010
• Docs | Add missing space in precomputed_k-nn.rst by @​Odessit007 in https://github.com/lmcinnes/umap/pull/1014
• Docs | Fix typo in supervised.rst by @​Odessit007 in https://github.com/lmcinnes/umap/pull/1013
• Update README.rst by @​dsblank in https://github.com/lmcinnes/umap/pull/1016
• Fix docstring formatting of init parameter of UMAP class by @​felixdivo in https://github.com/lmcinnes/umap/pull/1019
• Plotting Fix: fixing capitalization for Bokeh plotting for version 3.1.1 compatibility by @​msakarvadia in https://github.com/lmcinnes/umap/pull/1023
• Issue warning if setting n_jobs and random_state by @​crypdick in https://github.com/lmcinnes/umap/pull/1002
• docs : Fix formatting in UMAP class documentation by @​Hamza-nabil in https://github.com/lmcinnes/umap/pull/992
• docs: minor typos fix by @​0xTiger in https://github.com/lmcinnes/umap/pull/983
• [TYPO] Update precomputed_k-nn.rst by @​cakiki in https://github.com/lmcinnes/umap/pull/922
• Bug fix round pre0.5.4 by @​lmcinnes in https://github.com/lmcinnes/umap/pull/1038
• Fix unit tests by @​hamelin in https://github.com/lmcinnes/umap/pull/1031
• fix relations_dictionary problems which prevents from correctly updating aligned_umap by @​hndgzkn in https://github.com/lmcinnes/umap/pull/863
• Drop requirements.txt, embrace setup.py for deps by @​hamelin in https://github.com/lmcinnes/umap/pull/1044
• Fix unit tests involving spectral initialization by @​hamelin in https://github.com/lmcinnes/umap/pull/1043
• Drop dependency on TBB on non-Intel deployments by @​hamelin in https://github.com/lmcinnes/umap/pull/1045
• Add azure devops pipeline to push to PyPI by @​gclendenning in https://github.com/lmcinnes/umap/pull/1053

New Contributors

• @​jgraving made their first contribution in https://github.com/lmcinnes/umap/pull/856
• @​hndgzkn made their first contribution in https://github.com/lmcinnes/umap/pull/861
• @​GregDemand made their first contribution in https://github.com/lmcinnes/umap/pull/875
• @​SkBlaz made their first contribution in https://github.com/lmcinnes/umap/pull/896
• @​sky-2002 made their first contribution in https://github.com/lmcinnes/umap/pull/903
• @​dribnet made their first contribution in https://github.com/lmcinnes/umap/pull/912
• @​suneeta-mall made their first contribution in https://github.com/lmcinnes/umap/pull/858
• @​matthieuheitz made their first contribution in https://github.com/lmcinnes/umap/pull/696
• @​yannikschaelte made their first contribution in https://github.com/lmcinnes/umap/pull/929
• @​BioGeek made their first contribution in https://github.com/lmcinnes/umap/pull/936
• @​CarloLepelaars made their first contribution in https://github.com/lmcinnes/umap/pull/939
• @​rohan-shah-nearmap made their first contribution in https://github.com/lmcinnes/umap/pull/948
• @​aizardar made their first contribution in https://github.com/lmcinnes/umap/pull/973
• @​SamKlier made their first contribution in https://github.com/lmcinnes/umap/pull/977
• @​TTTPOB made their first contribution in https://github.com/lmcinnes/umap/pull/1010
• @​Odessit007 made their first contribution in https://github.com/lmcinnes/umap/pull/1014
• @​dsblank made their first contribution in https://github.com/lmcinnes/umap/pull/1016
• @​msakarvadia made their first contribution in https://github.com/lmcinnes/umap/pull/1023
• @​crypdick made their first contribution in https://github.com/lmcinnes/umap/pull/1002
• @​Hamza-nabil made their first contribution in https://github.com/lmcinnes/umap/pull/992
• @​0xTiger made their first contribution in https://github.com/lmcinnes/umap/pull/983
• @​cakiki made their first contribution in https://github.com/lmcinnes/umap/pull/922
• @​hamelin made their first contribution in https://github.com/lmcinnes/umap/pull/1031
• @​gclendenning made their first contribution in https://github.com/lmcinnes/umap/pull/1053

Full Changelog: lmcinnes/umap@0.5.3...0.5.4

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