From 00f091d0cf4547a38722224bbe7e7a8003580933 Mon Sep 17 00:00:00 2001 From: DistroBaker Date: Mon, 29 Mar 2021 18:40:18 +0000 Subject: [PATCH] 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 | 2 + scipy.spec | 34 +++++++++++++--- skip-certain-tests-on-32-bit-arches.patch | 47 ----------------------- skip-factorial-float-tests-on-py310.patch | 40 ------------------- sources | 2 +- wavfile.patch | 36 ----------------- 6 files changed, 32 insertions(+), 129 deletions(-) delete mode 100644 skip-certain-tests-on-32-bit-arches.patch delete mode 100644 skip-factorial-float-tests-on-py310.patch delete mode 100644 wavfile.patch diff --git a/.gitignore b/.gitignore index ab0e569..1ad3344 100644 --- a/.gitignore +++ b/.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 diff --git a/scipy.spec b/scipy.spec index 8b09372..0ceab6d 100644 --- a/scipy.spec +++ b/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 - 1.6.2-1 +- New upstream release 1.6.2 + resolves: #1942896 + +* Thu Feb 18 2021 Nikola Forró - 1.6.1-1 +- New upstream release 1.6.1 + resolves: #1929994 + * Wed Feb 03 2021 Nikola Forró - 1.6.0-3 - Increase test timeout on s390x diff --git a/skip-certain-tests-on-32-bit-arches.patch b/skip-certain-tests-on-32-bit-arches.patch deleted file mode 100644 index f7ca46d..0000000 --- a/skip-certain-tests-on-32-bit-arches.patch +++ /dev/null @@ -1,47 +0,0 @@ -From ea0a77cf8761a8b8636b93314139ed0fc0a9d1db Mon Sep 17 00:00:00 2001 -From: =?UTF-8?q?Nikola=20Forr=C3=B3?= -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 ---- - 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 - diff --git a/skip-factorial-float-tests-on-py310.patch b/skip-factorial-float-tests-on-py310.patch deleted file mode 100644 index 46a8b78..0000000 --- a/skip-factorial-float-tests-on-py310.patch +++ /dev/null @@ -1,40 +0,0 @@ -From eabd8ea25fe291665f37fd069a1c574cd30d12cc Mon Sep 17 00:00:00 2001 -From: Victor Stinner -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: diff --git a/sources b/sources index 3250601..8f533f5 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (scipy-1.6.0.tar.gz) = 995ffaf56b713cdd4bdb98d8525b892e9ad84a511878b43213cb71a67f34d87c111da36cf1e0b044c75c0d5af64bfde4ad0f3e9c5e71cae2dbf053251f37064e +SHA512 (scipy-1.6.2.tar.gz) = 18b03f32e8343c5a6c6148ac0bfd4b5f2cc9ff5f74d5d41761ae9e773d6af8774c7b09a3fcc47122864eccce1dbbc17e9325819885d3fc3ab2baf98e7d3befa4 diff --git a/wavfile.patch b/wavfile.patch deleted file mode 100644 index 06258c5..0000000 --- a/wavfile.patch +++ /dev/null @@ -1,36 +0,0 @@ -commit 09d753f0ae71441906f5cee7a44b2d2b80212082 -Author: Nikola Forró -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}: