Releases | Open Source Science

UMAP - release-0.5.9.post2

Full Changelog: https://github.com/lmcinnes/umap/compare/release-0.5.9.post1...release-0.5.9.post2

Scientific Software - Peer-reviewed - Python
Published by lmcinnes 11 months ago

UMAP - release-0.5.9.post1

Full Changelog: https://github.com/lmcinnes/umap/compare/release-0.5.9...release-0.5.9.post1

Scientific Software - Peer-reviewed - Python
Published by lmcinnes 11 months ago

What's Changed

Add the option to exclude raw data from the saved model by @bartbroere in https://github.com/lmcinnes/umap/pull/1126
Umap with Nomic Atlas by @mcembalest in https://github.com/lmcinnes/umap/pull/1202
Migrate the build system to newer methods by @lmcinnes in https://github.com/lmcinnes/umap/pull/1208

New Contributors

@bartbroere made their first contribution in https://github.com/lmcinnes/umap/pull/1126
@mcembalest made their first contribution in https://github.com/lmcinnes/umap/pull/1202

Full Changelog: https://github.com/lmcinnes/umap/compare/release-0.5.8...release-0.5.9

Scientific Software - Peer-reviewed - Python
Published by lmcinnes 11 months ago

What's Changed

Update README.rst by @jc-healy in https://github.com/lmcinnes/umap/pull/1162
[BUG]: Fix feature names for sklearn API by @fraimondo in https://github.com/lmcinnes/umap/pull/1166
Update basic_usage.rst to replace deprecated function. by @rattle99 in https://github.com/lmcinnes/umap/pull/1188
Update requirements by @lmcinnes in https://github.com/lmcinnes/umap/pull/1189

New Contributors

@fraimondo made their first contribution in https://github.com/lmcinnes/umap/pull/1166
@rattle99 made their first contribution in https://github.com/lmcinnes/umap/pull/1188

Full Changelog: https://github.com/lmcinnes/umap/compare/release-0.5.7...release-0.5.8

Scientific Software - Peer-reviewed - Python
Published by lmcinnes about 1 year ago

What's Changed

Update README.rst by @Slyderek in https://github.com/lmcinnes/umap/pull/1111
Allow consistent transform by UMAP by @IntelleKarl in https://github.com/lmcinnes/umap/pull/1129
docs: mention "precomputed" metric as a parameter by @NickCrews in https://github.com/lmcinnes/umap/pull/1137
Fix typo in AlignedUMAP documentation by @milesmcc in https://github.com/lmcinnes/umap/pull/1139
Add pre-release parameter in pipelines by @gclendenning in https://github.com/lmcinnes/umap/pull/1130
Update parametric_umap.py by @AMS-Hippo in https://github.com/lmcinnes/umap/pull/1147
Compile optimizelayouteuclideansingle_epoch once by @kmkolasinski in https://github.com/lmcinnes/umap/pull/1152
Landmarked Re-Trainable Parametric UMAP by @jacobgolding in https://github.com/lmcinnes/umap/pull/1153
Small default functions for landmark-UMAP by @AMS-Hippo in https://github.com/lmcinnes/umap/pull/1156

New Contributors

@Slyderek made their first contribution in https://github.com/lmcinnes/umap/pull/1111
@IntelleKarl made their first contribution in https://github.com/lmcinnes/umap/pull/1129
@NickCrews made their first contribution in https://github.com/lmcinnes/umap/pull/1137
@milesmcc made their first contribution in https://github.com/lmcinnes/umap/pull/1139
@AMS-Hippo made their first contribution in https://github.com/lmcinnes/umap/pull/1147
@kmkolasinski made their first contribution in https://github.com/lmcinnes/umap/pull/1152
@jacobgolding made their first contribution in https://github.com/lmcinnes/umap/pull/1153

Full Changelog: https://github.com/lmcinnes/umap/compare/release-0.5.6...release-0.5.7

Scientific Software - Peer-reviewed - Python
Published by lmcinnes over 1 year ago

What's Changed

Setting random state could still lead to stochastic results by @dannywhuang in https://github.com/lmcinnes/umap/pull/1081
Change release tag structure and switch to real PyPI by @gclendenning in https://github.com/lmcinnes/umap/pull/1085
Add Keras 3 support to ParametricUMAP by @fchollet in https://github.com/lmcinnes/umap/pull/1101
Finish refactoring ParametricUMAP by @fchollet in https://github.com/lmcinnes/umap/pull/1105
Add torch support to ParametricUMAP by @fchollet in https://github.com/lmcinnes/umap/pull/1104
Bit hamming by @lmcinnes in https://github.com/lmcinnes/umap/pull/1107

New Contributors

@dannywhuang made their first contribution in https://github.com/lmcinnes/umap/pull/1081
@fchollet made their first contribution in https://github.com/lmcinnes/umap/pull/1101

Full Changelog: https://github.com/lmcinnes/umap/compare/release-0.5.5...release-0.5.6

Scientific Software - Peer-reviewed - Python
Published by lmcinnes about 2 years ago

What's Changed

fix interactive plot if hover_data but no tools is provided by @timoleistner in https://github.com/lmcinnes/umap/pull/1058
Fixed bug causing digits data bokeh plot in tutorial to break by @Liqs-v2 in https://github.com/lmcinnes/umap/pull/1067
Make tbb requirement optional by @mithaler in https://github.com/lmcinnes/umap/pull/1066
Fix pkg_resources deprecation warning by @laclouis5 in https://github.com/lmcinnes/umap/pull/1072

New Contributors

@timoleistner made their first contribution in https://github.com/lmcinnes/umap/pull/1058
@Liqs-v2 made their first contribution in https://github.com/lmcinnes/umap/pull/1067
@mithaler made their first contribution in https://github.com/lmcinnes/umap/pull/1066
@laclouis5 made their first contribution in https://github.com/lmcinnes/umap/pull/1072

Full Changelog: https://github.com/lmcinnes/umap/compare/0.5.4...release-0.5.5

Scientific Software - Peer-reviewed - Python
Published by lmcinnes over 2 years ago

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 makeepochsper_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 relationdicts in expandrelations 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 testumaptrustworthinessrandominit bound by @austereantelope in https://github.com/lmcinnes/umap/pull/850
tighten testumapsparse_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 njobs and randomstate 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 relationsdictionary problems which prevents from correctly updating alignedumap 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: https://github.com/lmcinnes/umap/compare/0.5.3...0.5.4

Scientific Software - Peer-reviewed - Python
Published by lmcinnes over 2 years ago

What's Changed

Use labels in AlignedUMAP if provided by @gclen in https://github.com/lmcinnes/umap/pull/802
Properly escape invalid escape sequences. by @brilee in https://github.com/lmcinnes/umap/pull/807
Update parametric_umap.rst by @timsainb in https://github.com/lmcinnes/umap/pull/811
homtopically -> homotopically by @faisito in https://github.com/lmcinnes/umap/pull/820
covert -> convert by @faisito in https://github.com/lmcinnes/umap/pull/819
super minor grammar by @faisito in https://github.com/lmcinnes/umap/pull/818
Add Mutual-NN Description by @adalmia96 in https://github.com/lmcinnes/umap/pull/822
Loss needs to be handled independently now as well by @lmcinnes in https://github.com/lmcinnes/umap/pull/808
Fix header for Mutual NN Doc by @adalmia96 in https://github.com/lmcinnes/umap/pull/823
Add missing links for graph layout methods by @jlmelville in https://github.com/lmcinnes/umap/pull/829
tighten testumaptrustworthinessfastapprox bound by @austereantelope in https://github.com/lmcinnes/umap/pull/832

New Contributors

@brilee made their first contribution in https://github.com/lmcinnes/umap/pull/807
@faisito made their first contribution in https://github.com/lmcinnes/umap/pull/820
@adalmia96 made their first contribution in https://github.com/lmcinnes/umap/pull/822
@austereantelope made their first contribution in https://github.com/lmcinnes/umap/pull/832

Full Changelog: https://github.com/lmcinnes/umap/compare/0.5.2...0.5.3

Scientific Software - Peer-reviewed - Python
Published by lmcinnes about 4 years ago

UMAP - 0.5.2

Various bug fixes for transform, update, etc. Support for passing pre-defined knn-graphs as input.

Scientific Software - Peer-reviewed - Python
Published by lmcinnes over 4 years ago

UMAP - 0.5.1

A few minor fixes, including a bug fix against the upcoming numba 0.53

Scientific Software - Peer-reviewed - Python
Published by lmcinnes over 5 years ago

UMAP - Major release 0.5

Adds support for ParametricUMAP, DensMAP, AlignedUMAP and more.

Scientific Software - Peer-reviewed - Python
Published by lmcinnes over 5 years ago

UMAP - Minor patch release

Fix some issues with the latest scipy sparse lil_matrix handling.

Scientific Software - Peer-reviewed - Python
Published by lmcinnes almost 6 years ago