Patch release 0.5.4

What's Changed

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

New Contributors

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

Full Changelog: 0.5.3...0.5.4