Merged update from upstream sources

This is an automated DistroBaker update from upstream sources.
If you do not know what this is about or would like to opt out,
contact the OSCI team.

Source: https://src.fedoraproject.org/rpms/scipy.git#0a4506f8b7780273ea7ee7c4f72219024045aed7

.gitignore

@@ -33,3 +33,5 @@ scipy-0.7.2.tar.gz
 /scipy-1.5.3.tar.gz
 /scipy-1.5.4.tar.gz
 /scipy-1.6.0.tar.gz
+/scipy-1.6.1.tar.gz
+/scipy-1.6.2.tar.gz

scipy.spec

@@ -14,8 +14,8 @@
 
 Summary:    Scientific Tools for Python
 Name:       scipy
-Version:    1.6.0
-Release:    3%{?dist}
+Version:    1.6.2
+Release:    1%{?dist}
 
 # BSD -- whole package except:
 # Boost -- scipy/special/cephes/scipy_iv.c
@@ -24,9 +24,6 @@ License:    BSD and Boost and Public Domain
 Url:        http://www.scipy.org/scipylib/index.html
 Source0:    https://github.com/scipy/scipy/releases/download/v%{version}/scipy-%{version}.tar.gz
 
-# https://github.com/scipy/scipy/pull/13387
-Patch0:     wavfile.patch
-
 BuildRequires: fftw-devel, suitesparse-devel
 BuildRequires: %{blaslib}-devel
 BuildRequires: gcc-gfortran, swig, gcc-c++
@@ -128,6 +125,25 @@ for PY in %{python3_version}; do
   %endif
 done
 
+# FIXME: shared objects built from Fortran sources contain RPATH, find a way to prevent that
+# scipy/integrate/_odepack
+# scipy/integrate/_quadpack
+# scipy/integrate/_test_odeint_banded
+# scipy/integrate/lsoda
+# scipy/integrate/vode
+# scipy/linalg/_fblas
+# scipy/linalg/_flapack
+# scipy/linalg/_flinalg
+# scipy/linalg/_interpolative
+# scipy/linalg/cython_blas
+# scipy/linalg/cython_lapack
+# scipy/odr/__odrpack
+# scipy/optimize/_lbfgsb
+# scipy/sparse/linalg/eigen/arpack/_arpack
+# scipy/sparse/linalg/isolve/_iterative
+# scipy/special/_ufuncs
+# scipy/special/cython_special
+
 %install
 %py3_install
 # Some files got ambiguous python shebangs, we fix them after everything else is done
@@ -177,6 +193,14 @@ popd
 %endif
 
 %changelog
+* Thu Mar 25 2021 Nikola Forró <nforro@redhat.com> - 1.6.2-1
+- New upstream release 1.6.2
+  resolves: #1942896
+
+* Thu Feb 18 2021 Nikola Forró <nforro@redhat.com> - 1.6.1-1
+- New upstream release 1.6.1
+  resolves: #1929994
+
 * Wed Feb 03 2021 Nikola Forró <nforro@redhat.com> - 1.6.0-3
 - Increase test timeout on s390x
 

skip-certain-tests-on-32-bit-arches.patch

@@ -1,47 +0,0 @@
-From ea0a77cf8761a8b8636b93314139ed0fc0a9d1db Mon Sep 17 00:00:00 2001
-From: =?UTF-8?q?Nikola=20Forr=C3=B3?= <nforro@redhat.com>
-Date: Wed, 30 Sep 2020 11:44:25 +0200
-Subject: [PATCH] TST: make a couple of tests expected to fail on 32-bit
- architectures
-MIME-Version: 1.0
-Content-Type: text/plain; charset=UTF-8
-Content-Transfer-Encoding: 8bit
-
-In TestConstructUtils.test_concatenate_int32_overflow
-and test_nnz_overflow, on a 32-bit architecture, in case
-check_free_memory() passes, ValueError is raised on an attempt
-to create a numpy array too large for a 32-bit architecture.
-
-Signed-off-by: Nikola Forró <nforro@redhat.com>
----
- scipy/sparse/tests/test_construct.py   | 1 +
- scipy/sparse/tests/test_sparsetools.py | 1 +
- 2 files changed, 2 insertions(+)
-
-diff --git a/scipy/sparse/tests/test_construct.py b/scipy/sparse/tests/test_construct.py
-index 3a882c6cc..5a2b92667 100644
---- a/scipy/sparse/tests/test_construct.py
-+++ b/scipy/sparse/tests/test_construct.py
-@@ -378,6 +378,7 @@ class TestConstructUtils(object):
-         excinfo.match(r'Got blocks\[0,1\]\.shape\[0\] == 1, expected 2')
- 
-     @pytest.mark.slow
-+    @pytest.mark.xfail_on_32bit("Can't create large array for test")
-     def test_concatenate_int32_overflow(self):
-         """ test for indptr overflow when concatenating matrices """
-         check_free_memory(30000)
-diff --git a/scipy/sparse/tests/test_sparsetools.py b/scipy/sparse/tests/test_sparsetools.py
-index 0c208ef44..e95df1ba0 100644
---- a/scipy/sparse/tests/test_sparsetools.py
-+++ b/scipy/sparse/tests/test_sparsetools.py
-@@ -61,6 +61,7 @@ def test_regression_std_vector_dtypes():
- 
- 
- @pytest.mark.slow
-+@pytest.mark.xfail_on_32bit("Can't create large array for test")
- def test_nnz_overflow():
-     # Regression test for gh-7230 / gh-7871, checking that coo_todense
-     # with nnz > int32max doesn't overflow.
--- 
-2.26.2
-

skip-factorial-float-tests-on-py310.patch

@@ -1,40 +0,0 @@
-From eabd8ea25fe291665f37fd069a1c574cd30d12cc Mon Sep 17 00:00:00 2001
-From: Victor Stinner <vstinner@python.org>
-Date: Wed, 25 Nov 2020 11:41:15 +0100
-Subject: [PATCH] GH-13122: Skip factorial() float tests on Python 3.10
-
-special.factorial() argument should be an array of integers.
-On Python 3.10, math.factorial() reject float.
-On Python 3.9, a DeprecationWarning is emitted.
-A numpy array casts all integers to float if the array contains a
-single NaN.
----
- scipy/special/tests/test_basic.py | 8 ++++++++
- 1 file changed, 8 insertions(+)
-
-diff --git a/scipy/special/tests/test_basic.py b/scipy/special/tests/test_basic.py
-index 9b7260e8435..e2ae29812a5 100644
---- a/scipy/special/tests/test_basic.py
-+++ b/scipy/special/tests/test_basic.py
-@@ -19,6 +19,7 @@
- 
- import itertools
- import platform
-+import sys
- 
- import numpy as np
- from numpy import (array, isnan, r_, arange, finfo, pi, sin, cos, tan, exp,
-@@ -1822,6 +1823,13 @@ def test_nan_inputs(self, x, exact):
-         result = special.factorial(x, exact=exact)
-         assert_(np.isnan(result))
- 
-+    # GH-13122: special.factorial() argument should be an array of integers.
-+    # On Python 3.10, math.factorial() reject float.
-+    # On Python 3.9, a DeprecationWarning is emitted.
-+    # A numpy array casts all integers to float if the array contains a
-+    # single NaN.
-+    @pytest.mark.skipif(sys.version_info >= (3, 10),
-+                        reason="Python 3.10+ math.factorial() requires int")
-     def test_mixed_nan_inputs(self):
-         x = np.array([np.nan, 1, 2, 3, np.nan])
-         with suppress_warnings() as sup:

sources

@@ -1 +1 @@
-SHA512 (scipy-1.6.0.tar.gz) = 995ffaf56b713cdd4bdb98d8525b892e9ad84a511878b43213cb71a67f34d87c111da36cf1e0b044c75c0d5af64bfde4ad0f3e9c5e71cae2dbf053251f37064e
+SHA512 (scipy-1.6.2.tar.gz) = 18b03f32e8343c5a6c6148ac0bfd4b5f2cc9ff5f74d5d41761ae9e773d6af8774c7b09a3fcc47122864eccce1dbbc17e9325819885d3fc3ab2baf98e7d3befa4

wavfile.patch

@@ -1,36 +0,0 @@
-commit 09d753f0ae71441906f5cee7a44b2d2b80212082
-Author: Nikola Forró <nforro@redhat.com>
-Date:   Thu Jan 14 14:34:14 2021 +0100
-
-    ENH: Support big-endian platforms and big-endian WAVs
-    
-    PR #12287 added support for reading arbitrary-bit-depth WAVs, but
-    the code doesn't consider big-endian WAVs, and doesn't work as expected
-    on big-endian platforms due to the use of native-byte-order data-types.
-    This change fixes that.
-    
-    There is also a simple test case that compares euqivalent RIFX
-    (big-endian) and RIFF (little-endian) files to verify the data read
-    are the same.
-
-diff --git a/scipy/io/wavfile.py b/scipy/io/wavfile.py
-index 9b5845d6b..951f8d201 100644
---- a/scipy/io/wavfile.py
-+++ b/scipy/io/wavfile.py
-@@ -458,10 +458,13 @@ def _read_data_chunk(fid, format_tag, channels, bit_depth, is_big_endian,
- 
-         if dtype == 'V1':
-             # Rearrange raw bytes into smallest compatible numpy dtype
--            dt = numpy.int32 if bytes_per_sample == 3 else numpy.int64
--            a = numpy.zeros((len(data) // bytes_per_sample, dt().itemsize),
-+            dt = f'{fmt}i4' if bytes_per_sample == 3 else f'{fmt}i8'
-+            a = numpy.zeros((len(data) // bytes_per_sample, numpy.dtype(dt).itemsize),
-                             dtype='V1')
--            a[:, -bytes_per_sample:] = data.reshape((-1, bytes_per_sample))
-+            if is_big_endian:
-+                a[:, :bytes_per_sample] = data.reshape((-1, bytes_per_sample))
-+            else:
-+                a[:, -bytes_per_sample:] = data.reshape((-1, bytes_per_sample))
-             data = a.view(dt).reshape(a.shape[:-1])
-     else:
-         if bytes_per_sample in {1, 2, 4, 8}: