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- update to 1.0.2:

Browse Source 
* build wheels for Python 3.12 (#255)
  * update minimum Python version to 3.9
  * add numpy 2.x support

OBS-URL: https://build.opensuse.org/package/show/devel:languages:python:numeric/python-openTSNE?expand=0&rev=15
This commit is contained in:
Dirk Mueller 2024-11-14 09:02:41 +00:00 committed by Git OBS Bridge
commit 6fad603649
7 changed files with 221 additions and 0 deletions
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## Default LFS
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.osc

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version https://git-lfs.github.com/spec/v1
oid sha256:525b3e33716b67c577a3c4567627ab6388ea61d5dd0b230c87e434f3c7268e1d
size 22107255

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version https://git-lfs.github.com/spec/v1
oid sha256:41d34d969b26649a1f3a3778a1b874b690bfbe71536c0d436fe35318bf3aedae
size 22107860

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Author: Bernhard M. Wiedemann <bwiedemann suse de>
Date: 2021-04-01
Do not build code using instructions because they are available on a random build worker.
Instead we pin the CPU type to a reasonable compromise
to allow people to run it on >50% of systems,
but also to use CPU instructions available since 10+ years
to speed up processing.
Index: openTSNE-1.0.1/setup.py
===================================================================
--- openTSNE-1.0.1.orig/setup.py
+++ openTSNE-1.0.1/setup.py
@@ -155,9 +155,9 @@ class CythonBuildExt(build_ext):
# package is being built locally, this is desired
if not ("AZURE_BUILD" in os.environ or "CONDA_BUILD" in os.environ):
if platform.machine() == "ppc64le":
- extra_compile_args += ["-mcpu=native"]
+ extra_compile_args += ["-mcpu=power8"]
if platform.machine() == "x86_64":
- extra_compile_args += ["-march=native"]
+ extra_compile_args += ["-march=corei7"]
# We will disable openmp flags if the compiler doesn't support it. This
# is only really an issue with OSX clang

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-------------------------------------------------------------------
Thu Nov 14 09:02:21 UTC 2024 - Dirk Müller <dmueller@suse.com>
- update to 1.0.2:
* build wheels for Python 3.12 (#255)
* update minimum Python version to 3.9
* add numpy 2.x support
-------------------------------------------------------------------
Tue Sep 3 09:44:28 UTC 2024 - Andreas Schwab <schwab@suse.de>
- TestTSNECorrectnessUsingPrecomputedDistanceMatrix fails almost everywhere
-------------------------------------------------------------------
Fri Mar 22 20:48:51 UTC 2024 - Dirk Müller <dmueller@suse.com>
- update to 1.0.1:
* setup.py maintenance
* drop Python 3.6 support
* correctly implement dof parameter in exact BH implementation
- drop get-numpy-include.patch (upstream)
-------------------------------------------------------------------
Thu Sep 14 13:26:03 UTC 2023 - Markéta Machová <mmachova@suse.com>
- Update to 1.0.0
* Given the longtime stability of openTSNE, it is only fitting
that we release a v1.0.0.
* Various documentation fixes
* Include Python 3.11 in the test and build matrix
* Uniform affinity kernel now supports mean and max mode
- add get-numpy-include.patch
-------------------------------------------------------------------
Sun Mar 20 19:38:50 UTC 2022 - Ben Greiner <code@bnavigator.de>
- Update to 0.6.2
* By default, we now use the MultiscaleMixture affinity model,
enabling us to pass in a list of perplexities instead of a
single perplexity value. This is fully backwards compatible.
* Previously, perplexity values would be changed according to the
dataset. E.g. we pass in perplexity=100 with N=150. Then
TSNE.perplexity would be equal to 50. Instead, keep this value
as is and add an effective_perplexity_ attribute (following the
convention from scikit-learn, which puts in the corrected
perplexity values.
* Fix bug where interpolation grid was being prepared even when
using BH optimization during transform.
* Enable calling .transform with precomputed distances. In this
case, the data matrix will be assumed to be a distance matrix.
* Fix potential problem with clang-13, which actually does
optimization with infinities using the -ffast-math flag
- Enable python310 build
- Skip a test in 32bit failing due to rounding errors
-------------------------------------------------------------------
Fri Feb 4 16:10:13 UTC 2022 - Ben Greiner <code@bnavigator.de>
- Update to 0.6.1
* Remove affinites from TSNE construction, allow custom
affinities and initialization in .fit method. This improves the
API when dealing with non-tabular data. This is not backwards
compatible.
* Add metric="precomputed". This includes the addition of
openTSNE.nearest_neighbors.PrecomputedDistanceMatrix and
openTSNE.nearest_neighbors.PrecomputedNeighbors.
* Add knn_index parameter to openTSNE.affinity classes.
* Add (less-than-ideal) workaround for pickling Annoy objects.
* Extend the range of recommended FFTW boxes up to 1000.
* Remove deprecated openTSNE.nearest_neighbors.BallTree.
* Remove deprecated openTSNE.callbacks.ErrorLogger.
* Remove deprecated TSNE.neighbors_method property.
* Add and set as default negative_gradient_method="auto".
- Skip building on python310: gh#pavlin-policar/openTSNE#205
-------------------------------------------------------------------
Thu Apr 1 07:36:31 UTC 2021 - Bernhard Wiedemann <bwiedemann@suse.com>
- Add python-openTSNE-disable-CPU-autodetection.patch (boo#1100677)
-------------------------------------------------------------------
Fri Jan 29 19:18:18 UTC 2021 - Ben Greiner <code@bnavigator.de>
- initial specfile for version 0.5.1
- replaces python-fastTSNE
- The pytest_arch macro needs the "Cepl-Strangelove-Parameter"
(= specify --import-mode)

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#
# spec file for package python-openTSNE
#
# Copyright (c) 2024 SUSE LLC
#
# All modifications and additions to the file contributed by third parties
# remain the property of their copyright owners, unless otherwise agreed
# upon. The license for this file, and modifications and additions to the
# file, is the same license as for the pristine package itself (unless the
# license for the pristine package is not an Open Source License, in which
# case the license is the MIT License). An "Open Source License" is a
# license that conforms to the Open Source Definition (Version 1.9)
# published by the Open Source Initiative.
# Please submit bugfixes or comments via https://bugs.opensuse.org/
#
%{?sle15_python_module_pythons}
Name: python-openTSNE
Version: 1.0.2
Release: 0
Summary: Extensible, parallel implementations of t-SNE
License: BSD-3-Clause
URL: https://github.com/pavlin-policar/openTSNE
# tests are not packaged in the PyPI sdist, use GitHub instead
Source: %{url}/archive/v%{version}.tar.gz#/openTSNE-%{version}-gh.tar.gz
Patch0: python-openTSNE-disable-CPU-autodetection.patch
BuildRequires: %{python_module Cython}
BuildRequires: %{python_module devel >= 3.7}
BuildRequires: %{python_module numpy-devel >= 1.16.6}
BuildRequires: %{python_module scikit-learn >= 0.20}
BuildRequires: %{python_module scipy}
BuildRequires: %{python_module setuptools}
BuildRequires: c++_compiler
BuildRequires: fdupes
BuildRequires: fftw3-devel
BuildRequires: python-rpm-macros
# SECTION test requirements
BuildRequires: %{python_module pytest}
# /SECTION
Requires: python-numpy >= 1.16.6
Requires: python-scikit-learn >= 0.20
Requires: python-scipy
Suggests: python-hnswlib
Suggests: python-pynndescent
Provides: python-fastTSNE = %{version}
Obsoletes: python-fastTSNE < %{version}
%python_subpackages
%description
Extensible, parallel implementations of t-SNE
%prep
%autosetup -p1 -n openTSNE-%{version}
%build
export CFLAGS="%{optflags}"
%python_build
%install
%python_install
%python_expand %fdupes %{buildroot}%{$python_sitearch}
%check
%ifarch %ix86 %arm32 aarch64 riscv64 s390x
# precision errors
%define donttest -k "not TestTSNECorrectnessUsingPrecomputedDistanceMatrix"
%endif
%pytest_arch --import-mode append %{?donttest}
%files %{python_files}
%doc README.rst
%license LICENSE
%{python_sitearch}/openTSNE
%{python_sitearch}/openTSNE-%{version}*-info
%changelog