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here is the log from the commit of package python-scikit-umfpack for
openSUSE:Factory checked in at 2023-09-06 19:00:03
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Comparing /work/SRC/openSUSE:Factory/python-scikit-umfpack (Old)
and /work/SRC/openSUSE:Factory/.python-scikit-umfpack.new.1766 (New)
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Package is "python-scikit-umfpack"
Wed Sep 6 19:00:03 2023 rev:7 rq:1109269 version:0.3.3
Changes:
--------
---
/work/SRC/openSUSE:Factory/python-scikit-umfpack/python-scikit-umfpack.changes
2022-04-04 19:26:54.696180121 +0200
+++
/work/SRC/openSUSE:Factory/.python-scikit-umfpack.new.1766/python-scikit-umfpack.changes
2023-09-06 19:04:26.268915008 +0200
@@ -1,0 +2,10 @@
+Thu Aug 31 12:48:22 UTC 2023 - Markéta Machová <mmach...@suse.com>
+
+- update to 0.3.3
+ * use scipy.sparse.linalg function without linsolve namespace
+ * DOC: add citations to README.rst
+- drop merged scikit-umfpack-pr68-scipy-sparse-linalg.patch
+- add numpy125.patch
+- Clean up the SPEC file.
+
+-------------------------------------------------------------------
Old:
----
scikit-umfpack-0.3.2.tar.gz
scikit-umfpack-pr68-scipy-sparse-linalg.patch
New:
----
numpy125.patch
scikit-umfpack-0.3.3.tar.gz
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Other differences:
------------------
++++++ python-scikit-umfpack.spec ++++++
--- /var/tmp/diff_new_pack.BimSim/_old 2023-09-06 19:04:28.020977465 +0200
+++ /var/tmp/diff_new_pack.BimSim/_new 2023-09-06 19:04:28.064979033 +0200
@@ -1,7 +1,7 @@
#
# spec file for package python-scikit-umfpack
#
-# Copyright (c) 2022 SUSE LLC
+# Copyright (c) 2023 SUSE LLC
#
# All modifications and additions to the file contributed by third parties
# remain the property of their copyright owners, unless otherwise agreed
@@ -16,18 +16,17 @@
#
-%{?!python_module:%define python_module() python-%{**} python3-%{**}}
%define oldpython python
Name: python-scikit-umfpack
-Version: 0.3.2
+Version: 0.3.3
Release: 0
Summary: Python interface to UMFPACK sparse direct solver
License: BSD-3-Clause
URL: https://github.com/scikit-umfpack/scikit-umfpack
Source0:
https://files.pythonhosted.org/packages/source/s/scikit-umfpack/scikit-umfpack-%{version}.tar.gz
+# PATCH-FIX-UPSTREAM both patches sent upstream in
https://github.com/scikit-umfpack/scikit-umfpack/pull/87 NumPy 1.25
compatibility fixes
Patch0: do-not-use-numpy-decorators.patch
-# PATCH-FIX-UPSTREAM scikit-umfpack-pr68-scipy-sparse-linalg.patch --
gh#scikit-umfpack/scikit-umfpack68
-Patch1: scikit-umfpack-pr68-scipy-sparse-linalg.patch
+Patch1: numpy125.patch
BuildRequires: %{python_module devel}
BuildRequires: %{python_module numpy-devel >= 1.14.3}
BuildRequires: %{python_module scipy >= 1.0.0rc1}
++++++ do-not-use-numpy-decorators.patch ++++++
--- /var/tmp/diff_new_pack.BimSim/_old 2023-09-06 19:04:28.380990299 +0200
+++ /var/tmp/diff_new_pack.BimSim/_new 2023-09-06 19:04:28.412991439 +0200
@@ -1,7 +1,7 @@
-Index: scikit-umfpack-0.3.2/scikits/umfpack/tests/test_interface.py
+Index: scikit-umfpack-0.3.3/scikits/umfpack/tests/test_interface.py
===================================================================
---- scikit-umfpack-0.3.2.orig/scikits/umfpack/tests/test_interface.py
-+++ scikit-umfpack-0.3.2/scikits/umfpack/tests/test_interface.py
+--- scikit-umfpack-0.3.3.orig/scikits/umfpack/tests/test_interface.py
++++ scikit-umfpack-0.3.3/scikits/umfpack/tests/test_interface.py
@@ -3,7 +3,7 @@ from __future__ import division, print_f
import warnings
import unittest
@@ -38,10 +38,10 @@
def test_splu_solve_int64(self):
# Prefactorize (with UMFPACK) matrix with int64 indices for solving
with
# multiple rhs
-Index: scikit-umfpack-0.3.2/scikits/umfpack/tests/test_umfpack.py
+Index: scikit-umfpack-0.3.3/scikits/umfpack/tests/test_umfpack.py
===================================================================
---- scikit-umfpack-0.3.2.orig/scikits/umfpack/tests/test_umfpack.py
-+++ scikit-umfpack-0.3.2/scikits/umfpack/tests/test_umfpack.py
+--- scikit-umfpack-0.3.3.orig/scikits/umfpack/tests/test_umfpack.py
++++ scikit-umfpack-0.3.3/scikits/umfpack/tests/test_umfpack.py
@@ -8,7 +8,7 @@ import random
import unittest
import warnings
@@ -50,26 +50,26 @@
+from numpy.testing import assert_array_almost_equal, run_module_suite
from scipy import rand, matrix, diag, eye
- from scipy.sparse import csc_matrix, spdiags, SparseEfficiencyWarning
-@@ -51,7 +51,7 @@ class TestScipySolvers(_DeprecationAccep
- x = linsolve.spsolve(a, b)
+ from scipy.sparse import csc_matrix, linalg, spdiags, SparseEfficiencyWarning
+@@ -50,7 +50,7 @@ class TestScipySolvers(_DeprecationAccep
+ x = linalg.spsolve(a, b)
assert_array_almost_equal(a*x, b)
- @dec.skipif(_is_32bit_platform)
+ @unittest.skipIf(_is_32bit_platform, reason="requires 64 bit platform")
def test_solve_complex_long_umfpack(self):
# Solve with UMFPACK: double precision complex, long indices
- linsolve.use_solver(useUmfpack=True)
-@@ -68,7 +68,7 @@ class TestScipySolvers(_DeprecationAccep
- x = linsolve.spsolve(a, b)
+ linalg.use_solver(useUmfpack=True)
+@@ -67,7 +67,7 @@ class TestScipySolvers(_DeprecationAccep
+ x = linalg.spsolve(a, b)
assert_array_almost_equal(a*x, b)
- @dec.skipif(_is_32bit_platform)
+ @unittest.skipIf(_is_32bit_platform, reason="requires 64 bit platform")
def test_solve_long_umfpack(self):
# Solve with UMFPACK: double precision
- linsolve.use_solver(useUmfpack=True)
-@@ -96,7 +96,7 @@ class TestScipySolvers(_DeprecationAccep
+ linalg.use_solver(useUmfpack=True)
+@@ -95,7 +95,7 @@ class TestScipySolvers(_DeprecationAccep
x2 = solve(self.b2)
assert_array_almost_equal(a*x2, self.b2)
@@ -77,8 +77,8 @@
+ @unittest.skipIf(_is_32bit_platform, reason="requires 64 bit platform")
def test_factorized_long_umfpack(self):
# Prefactorize (with UMFPACK) matrix for solving with multiple rhs
- linsolve.use_solver(useUmfpack=True)
-@@ -151,7 +151,7 @@ class TestFactorization(_DeprecationAcce
+ linalg.use_solver(useUmfpack=True)
+@@ -150,7 +150,7 @@ class TestFactorization(_DeprecationAcce
assert_array_almost_equal(P*R*A*Q,L*U)
@@ -87,7 +87,7 @@
def test_complex_int64_lu(self):
# Getting factors of complex matrix with long indices
umfpack = um.UmfpackContext("zl")
-@@ -192,7 +192,7 @@ class TestFactorization(_DeprecationAcce
+@@ -191,7 +191,7 @@ class TestFactorization(_DeprecationAcce
assert_array_almost_equal(P*R*A*Q,L*U)
++++++ numpy125.patch ++++++
Index: scikit-umfpack-0.3.3/scikits/umfpack/tests/test_interface.py
===================================================================
--- scikit-umfpack-0.3.3.orig/scikits/umfpack/tests/test_interface.py
+++ scikit-umfpack-0.3.3/scikits/umfpack/tests/test_interface.py
@@ -3,7 +3,7 @@ from __future__ import division, print_f
import warnings
import unittest
-from numpy.testing import assert_allclose, run_module_suite
+from numpy.testing import assert_allclose
from numpy.linalg import norm as dense_norm
from scipy.sparse import csc_matrix, spdiags, SparseEfficiencyWarning
@@ -133,4 +133,4 @@ class TestSolvers(unittest.TestCase):
assert_allclose(A2, A.A, atol=1e-13)
if __name__ == "__main__":
- run_module_suite()
+ unittest.main()
Index: scikit-umfpack-0.3.3/scikits/umfpack/tests/test_umfpack.py
===================================================================
--- scikit-umfpack-0.3.3.orig/scikits/umfpack/tests/test_umfpack.py
+++ scikit-umfpack-0.3.3/scikits/umfpack/tests/test_umfpack.py
@@ -8,7 +8,7 @@ import random
import unittest
import warnings
-from numpy.testing import assert_array_almost_equal, run_module_suite
+from numpy.testing import assert_array_almost_equal
from scipy import rand, matrix, diag, eye
from scipy.sparse import csc_matrix, linalg, spdiags, SparseEfficiencyWarning
@@ -239,4 +239,4 @@ class TestFactorization(_DeprecationAcce
if __name__ == "__main__":
- run_module_suite()
+ unittest.main()
Index: scikit-umfpack-0.3.3/scikits/umfpack/__init__.py
===================================================================
--- scikit-umfpack-0.3.3.orig/scikits/umfpack/__init__.py
+++ scikit-umfpack-0.3.3/scikits/umfpack/__init__.py
@@ -22,5 +22,3 @@ if __doc__ is not None:
del _umfpack_doc, _interface_doc
__all__ = [s for s in dir() if not s.startswith('_')]
-from numpy.testing import Tester
-test = Tester().test
++++++ scikit-umfpack-0.3.2.tar.gz -> scikit-umfpack-0.3.3.tar.gz ++++++
diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn'
'--exclude=.svnignore' old/scikit-umfpack-0.3.2/PKG-INFO
new/scikit-umfpack-0.3.3/PKG-INFO
--- old/scikit-umfpack-0.3.2/PKG-INFO 2018-10-12 21:09:08.000000000 +0200
+++ new/scikit-umfpack-0.3.3/PKG-INFO 2022-08-04 22:45:51.000000000 +0200
@@ -1,6 +1,6 @@
Metadata-Version: 1.1
Name: scikit-umfpack
-Version: 0.3.2
+Version: 0.3.3
Summary: Python interface to UMFPACK sparse direct solver.
Home-page: https://scikit-umfpack.github.io/scikit-umfpack
Author: Robert Cimrman
@@ -10,8 +10,8 @@
Description: scikit-umfpack
==============
- scikit-umfpack provides wrapper of UMFPACK sparse direct solver to
- SciPy.
+ `scikit-umfpack <https://scikit-umfpack.github.io/scikit-umfpack>`_
provides
+ wrapper of UMFPACK sparse direct solver to SciPy.
Usage:
@@ -23,9 +23,25 @@
Installing scikits.umfpack also enables using UMFPACK solver via some
of
the scipy.sparse.linalg functions, for SciPy >= 0.14.0. Note you will
- need to have installed UMFPACK before hand. UMFPACK is parse of
+ need to have installed UMFPACK before hand. UMFPACK is a part of
`SuiteSparse <http://faculty.cse.tamu.edu/davis/suitesparse.html>`__.
+ References
+ ----------
+
+ .. [1] T. A. Davis, Algorithm 832: UMFPACK - an unsymmetric-pattern
+ multifrontal method with a column pre-ordering strategy, ACM
Trans. on
+ Mathematical Software, 30(2), 2004, pp. 196--199.
+ https://dl.acm.org/doi/abs/10.1145/992200.992206
+ .. [2] P. Amestoy, T. A. Davis, and I. S. Duff, Algorithm 837: An
approximate
+ minimum degree ordering algorithm, ACM Trans. on Mathematical
Software,
+ 30(3), 2004, pp. 381--388.
+ https://dl.acm.org/doi/abs/10.1145/1024074.1024081
+ .. [3] T. A. Davis, J. R. Gilbert, S. Larimore, E. Ng, Algorithm 836:
COLAMD,
+ an approximate column minimum degree ordering algorithm, ACM
Trans. on
+ Mathematical Software, 30(3), 2004, pp. 377--380.
+ https://doi.org/10.1145/1024074.1024080
+
Dependencies
============
diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn'
'--exclude=.svnignore' old/scikit-umfpack-0.3.2/README.rst
new/scikit-umfpack-0.3.3/README.rst
--- old/scikit-umfpack-0.3.2/README.rst 2018-10-12 08:58:49.000000000 +0200
+++ new/scikit-umfpack-0.3.3/README.rst 2022-04-10 19:16:15.000000000 +0200
@@ -1,8 +1,8 @@
scikit-umfpack
==============
-scikit-umfpack provides wrapper of UMFPACK sparse direct solver to
-SciPy.
+`scikit-umfpack <https://scikit-umfpack.github.io/scikit-umfpack>`_ provides
+wrapper of UMFPACK sparse direct solver to SciPy.
Usage:
@@ -14,9 +14,25 @@
Installing scikits.umfpack also enables using UMFPACK solver via some of
the scipy.sparse.linalg functions, for SciPy >= 0.14.0. Note you will
-need to have installed UMFPACK before hand. UMFPACK is parse of
+need to have installed UMFPACK before hand. UMFPACK is a part of
`SuiteSparse <http://faculty.cse.tamu.edu/davis/suitesparse.html>`__.
+References
+----------
+
+.. [1] T. A. Davis, Algorithm 832: UMFPACK - an unsymmetric-pattern
+ multifrontal method with a column pre-ordering strategy, ACM Trans. on
+ Mathematical Software, 30(2), 2004, pp. 196--199.
+ https://dl.acm.org/doi/abs/10.1145/992200.992206
+.. [2] P. Amestoy, T. A. Davis, and I. S. Duff, Algorithm 837: An approximate
+ minimum degree ordering algorithm, ACM Trans. on Mathematical Software,
+ 30(3), 2004, pp. 381--388.
+ https://dl.acm.org/doi/abs/10.1145/1024074.1024081
+.. [3] T. A. Davis, J. R. Gilbert, S. Larimore, E. Ng, Algorithm 836: COLAMD,
+ an approximate column minimum degree ordering algorithm, ACM Trans. on
+ Mathematical Software, 30(3), 2004, pp. 377--380.
+ https://doi.org/10.1145/1024074.1024080
+
Dependencies
============
diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn'
'--exclude=.svnignore'
old/scikit-umfpack-0.3.2/scikits/umfpack/tests/test_umfpack.py
new/scikit-umfpack-0.3.3/scikits/umfpack/tests/test_umfpack.py
--- old/scikit-umfpack-0.3.2/scikits/umfpack/tests/test_umfpack.py
2017-10-16 14:06:56.000000000 +0200
+++ new/scikit-umfpack-0.3.3/scikits/umfpack/tests/test_umfpack.py
2022-04-08 11:17:24.000000000 +0200
@@ -11,8 +11,7 @@
from numpy.testing import assert_array_almost_equal, run_module_suite, dec
from scipy import rand, matrix, diag, eye
-from scipy.sparse import csc_matrix, spdiags, SparseEfficiencyWarning
-from scipy.sparse.linalg import linsolve
+from scipy.sparse import csc_matrix, linalg, spdiags, SparseEfficiencyWarning
import numpy as np
import scikits.umfpack as um
@@ -45,51 +44,51 @@
def test_solve_complex_umfpack(self):
# Solve with UMFPACK: double precision complex
- linsolve.use_solver(useUmfpack=True)
+ linalg.use_solver(useUmfpack=True)
a = self.a.astype('D')
b = self.b
- x = linsolve.spsolve(a, b)
+ x = linalg.spsolve(a, b)
assert_array_almost_equal(a*x, b)
@dec.skipif(_is_32bit_platform)
def test_solve_complex_long_umfpack(self):
# Solve with UMFPACK: double precision complex, long indices
- linsolve.use_solver(useUmfpack=True)
+ linalg.use_solver(useUmfpack=True)
a = _to_int64(self.a.astype('D'))
b = self.b
- x = linsolve.spsolve(a, b)
+ x = linalg.spsolve(a, b)
assert_array_almost_equal(a*x, b)
def test_solve_umfpack(self):
# Solve with UMFPACK: double precision
- linsolve.use_solver(useUmfpack=True)
+ linalg.use_solver(useUmfpack=True)
a = self.a.astype('d')
b = self.b
- x = linsolve.spsolve(a, b)
+ x = linalg.spsolve(a, b)
assert_array_almost_equal(a*x, b)
@dec.skipif(_is_32bit_platform)
def test_solve_long_umfpack(self):
# Solve with UMFPACK: double precision
- linsolve.use_solver(useUmfpack=True)
+ linalg.use_solver(useUmfpack=True)
a = _to_int64(self.a.astype('d'))
b = self.b
- x = linsolve.spsolve(a, b)
+ x = linalg.spsolve(a, b)
assert_array_almost_equal(a*x, b)
def test_solve_sparse_rhs(self):
# Solve with UMFPACK: double precision, sparse rhs
- linsolve.use_solver(useUmfpack=True)
+ linalg.use_solver(useUmfpack=True)
a = self.a.astype('d')
b = csc_matrix(self.b).T
- x = linsolve.spsolve(a, b)
+ x = linalg.spsolve(a, b)
assert_array_almost_equal(a*x, self.b)
def test_factorized_umfpack(self):
# Prefactorize (with UMFPACK) matrix for solving with multiple rhs
- linsolve.use_solver(useUmfpack=True)
+ linalg.use_solver(useUmfpack=True)
a = self.a.astype('d')
- solve = linsolve.factorized(a)
+ solve = linalg.factorized(a)
x1 = solve(self.b)
assert_array_almost_equal(a*x1, self.b)
@@ -99,9 +98,9 @@
@dec.skipif(_is_32bit_platform)
def test_factorized_long_umfpack(self):
# Prefactorize (with UMFPACK) matrix for solving with multiple rhs
- linsolve.use_solver(useUmfpack=True)
+ linalg.use_solver(useUmfpack=True)
a = _to_int64(self.a.astype('d'))
- solve = linsolve.factorized(a)
+ solve = linalg.factorized(a)
x1 = solve(self.b)
assert_array_almost_equal(a*x1, self.b)
@@ -110,9 +109,9 @@
def test_factorized_without_umfpack(self):
# Prefactorize matrix for solving with multiple rhs
- linsolve.use_solver(useUmfpack=False)
+ linalg.use_solver(useUmfpack=False)
a = self.a.astype('d')
- solve = linsolve.factorized(a)
+ solve = linalg.factorized(a)
x1 = solve(self.b)
assert_array_almost_equal(a*x1, self.b)
diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn'
'--exclude=.svnignore' old/scikit-umfpack-0.3.2/scikits/umfpack/umfpack.py
new/scikit-umfpack-0.3.3/scikits/umfpack/umfpack.py
--- old/scikit-umfpack-0.3.2/scikits/umfpack/umfpack.py 2017-10-16
14:06:56.000000000 +0200
+++ new/scikit-umfpack-0.3.3/scikits/umfpack/umfpack.py 2022-04-10
19:16:15.000000000 +0200
@@ -13,6 +13,21 @@
Use 'print UmfpackContext().funs' to see all UMFPACK library functions the
module exposes, if you need something not covered by the examples below.
+References
+----------
+
+[1] T. A. Davis, Algorithm 832: UMFPACK - an unsymmetric-pattern
+ multifrontal method with a column pre-ordering strategy, ACM Trans. on
+ Mathematical Software, 30(2), 2004, pp. 196--199.
+ https://dl.acm.org/doi/abs/10.1145/992200.992206
+[2] P. Amestoy, T. A. Davis, and I. S. Duff, Algorithm 837: An approximate
+ minimum degree ordering algorithm, ACM Trans. on Mathematical Software,
+ 30(3), 2004, pp. 381--388.
+ https://dl.acm.org/doi/abs/10.1145/1024074.1024081
+[3] T. A. Davis, J. R. Gilbert, S. Larimore, E. Ng, Algorithm 836: COLAMD,
+ an approximate column minimum degree ordering algorithm, ACM Trans. on
+ Mathematical Software, 30(3), 2004, pp. 377--380.
+ https://doi.org/10.1145/1024074.1024080
Module contents
---------------
@@ -116,7 +131,7 @@
"""
# Interface to the UMFPACK library.
-#
+#
# Author: Robert Cimrman
from __future__ import division, print_function, absolute_import
@@ -394,7 +409,7 @@
Parameters
----------
family : {'di', 'dl', 'zi', 'zl'}
- Family of UMFPACK functions
+ Family of UMFPACK functions
maxCond : float, optional
If estimated condition number is greater than maxCond,
a warning is issued (default: 1e12)
diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn'
'--exclude=.svnignore' old/scikit-umfpack-0.3.2/scikits/umfpack/version.py
new/scikit-umfpack-0.3.3/scikits/umfpack/version.py
--- old/scikit-umfpack-0.3.2/scikits/umfpack/version.py 2018-10-12
21:09:07.000000000 +0200
+++ new/scikit-umfpack-0.3.3/scikits/umfpack/version.py 2022-08-04
22:45:49.000000000 +0200
@@ -1,8 +1,8 @@
# THIS FILE IS GENERATED FROM scikit-umfpack SETUP.PY
-short_version = '0.3.2'
-version = '0.3.2'
-full_version = '0.3.2'
-git_revision = 'a2102ef92f4dd060138e72bb5d7c444f8ec49cbc'
+short_version = '0.3.3'
+version = '0.3.3'
+full_version = '0.3.3'
+git_revision = '05b2a4c2cebb7d3f0ceaabb34d3fd6722549df0b'
release = True
if not release:
diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn'
'--exclude=.svnignore' old/scikit-umfpack-0.3.2/setup.py
new/scikit-umfpack-0.3.3/setup.py
--- old/scikit-umfpack-0.3.2/setup.py 2018-10-12 21:08:01.000000000 +0200
+++ new/scikit-umfpack-0.3.3/setup.py 2022-08-04 22:45:41.000000000 +0200
@@ -10,7 +10,7 @@
URL = 'https://scikit-umfpack.github.io/scikit-umfpack'
LICENSE = 'BSD'
DOWNLOAD_URL = URL
-VERSION = '0.3.2'
+VERSION = '0.3.3'
ISRELEASED = True
import sys
