From 48c269318b5516bb212639df8c8dd3239acb72d6 Mon Sep 17 00:00:00 2001 From: eabdullin Date: Wed, 27 Sep 2023 14:01:44 +0000 Subject: [PATCH] import CS python3.11-scipy-1.10.1-2.el8 --- .gitignore | 2 +- .python3.11-scipy.metadata | 2 +- SOURCES/fix-32bit-test-failures.patch | 93 --------------------------- SOURCES/fix_test_milp_timeout.patch | 53 +++++++++++++++ SPECS/python3.11-scipy.spec | 18 ++++-- 5 files changed, 67 insertions(+), 101 deletions(-) delete mode 100644 SOURCES/fix-32bit-test-failures.patch create mode 100644 SOURCES/fix_test_milp_timeout.patch diff --git a/.gitignore b/.gitignore index 5fdeb12..4501f36 100644 --- a/.gitignore +++ b/.gitignore @@ -1 +1 @@ -SOURCES/scipy-1.10.0.tar.gz +SOURCES/scipy-1.10.1.tar.gz diff --git a/.python3.11-scipy.metadata b/.python3.11-scipy.metadata index 8337583..c0dcbcb 100644 --- a/.python3.11-scipy.metadata +++ b/.python3.11-scipy.metadata @@ -1 +1 @@ -8094557cc6c2d2ec32faf2a9b33ed41b3a8acecc SOURCES/scipy-1.10.0.tar.gz +ff83163396a70276c0441b541befc485b471b27b SOURCES/scipy-1.10.1.tar.gz diff --git a/SOURCES/fix-32bit-test-failures.patch b/SOURCES/fix-32bit-test-failures.patch deleted file mode 100644 index 2f112bc..0000000 --- a/SOURCES/fix-32bit-test-failures.patch +++ /dev/null @@ -1,93 +0,0 @@ -diff --git a/scipy/sparse/linalg/_isolve/tests/test_iterative.py b/scipy/sparse/linalg/_isolve/tests/test_iterative.py -index a782a8d27c2..48fc16b7a00 100644 ---- a/scipy/sparse/linalg/_isolve/tests/test_iterative.py -+++ b/scipy/sparse/linalg/_isolve/tests/test_iterative.py -@@ -409,7 +409,9 @@ def test_atol(solver): - residual = A.dot(x) - b - err = np.linalg.norm(residual) - atol2 = tol * b_norm -- assert_(err <= max(atol, atol2)) -+ # Added 1.00025 fudge factor because of `err` exceeding `atol` just -+ # very slightly on s390x (see gh-17839) -+ assert_(err <= 1.00025 * max(atol, atol2)) - - - @pytest.mark.parametrize("solver", [cg, cgs, bicg, bicgstab, gmres, qmr, minres, lgmres, gcrotmk, tfqmr]) -@@ -452,8 +454,10 @@ def test_zero_rhs(solver): - and sys.version_info[1] == 9, - reason="gh-13019")), - qmr, -- pytest.param(lgmres, marks=pytest.mark.xfail(platform.machine() == 'ppc64le', -- reason="fails on ppc64le")), -+ pytest.param(lgmres, marks=pytest.mark.xfail( -+ platform.machine() not in ['x86_64' 'x86', 'aarch64', 'arm64'], -+ reason="fails on at least ppc64le, ppc64 and riscv64, see gh-17839") -+ ), - pytest.param(cgs, marks=pytest.mark.xfail), - pytest.param(bicg, marks=pytest.mark.xfail), - pytest.param(bicgstab, marks=pytest.mark.xfail), -diff --git a/scipy/special/tests/test_orthogonal.py b/scipy/special/tests/test_orthogonal.py -index a325cb1a9ef..408b03bde2e 100644 ---- a/scipy/special/tests/test_orthogonal.py -+++ b/scipy/special/tests/test_orthogonal.py -@@ -546,7 +546,7 @@ def test_roots_gegenbauer(): - vgq(rootf(170), evalf(170), weightf(170), -1., 1., 5, atol=1e-13) - vgq(rootf(170), evalf(170), weightf(170), -1., 1., 25, atol=1e-12) - vgq(rootf(170), evalf(170), weightf(170), -1., 1., 100, atol=1e-11) -- vgq(rootf(170.5), evalf(170.5), weightf(170.5), -1., 1., 5, atol=1e-13) -+ vgq(rootf(170.5), evalf(170.5), weightf(170.5), -1., 1., 5, atol=1.25e-13) - vgq(rootf(170.5), evalf(170.5), weightf(170.5), -1., 1., 25, atol=1e-12) - vgq(rootf(170.5), evalf(170.5), weightf(170.5), -1., 1., 100, atol=1e-11) - -diff --git a/scipy/stats/tests/test_distributions.py b/scipy/stats/tests/test_distributions.py -index eceeafdffe0..139b0537174 100644 ---- a/scipy/stats/tests/test_distributions.py -+++ b/scipy/stats/tests/test_distributions.py -@@ -4254,7 +4254,7 @@ def test_pdf_nolan_samples( - ], - # for small alpha very slightly reduced accuracy - [ -- 'piecewise', 5e-11, lambda r: ( -+ 'piecewise', 2.5e-10, lambda r: ( - np.isin(r['pct'], pct_range) & - np.isin(r['alpha'], alpha_range) & - np.isin(r['beta'], beta_range) & -@@ -4358,7 +4358,7 @@ def test_cdf_nolan_samples( - tests = [ - # piecewise generally good accuracy - [ -- 'piecewise', 1e-12, lambda r: ( -+ 'piecewise', 2e-12, lambda r: ( - np.isin(r['pct'], pct_range) & - np.isin(r['alpha'], alpha_range) & - np.isin(r['beta'], beta_range) & -@@ -4480,6 +4480,14 @@ def test_location_scale( - ): - """Tests for pdf and cdf where loc, scale are different from 0, 1 - """ -+ -+ uname = platform.uname() -+ is_linux_32 = uname.system == 'Linux' and "32bit" in platform.architecture()[0] -+ # Test seems to be unstable (see gh-17839 for a bug report on Debian -+ # i386), so skip it. -+ if is_linux_32 and case == 'pdf': -+ pytest.skip("Test unstable on some platforms; see gh-17839, 17859") -+ - data = nolan_loc_scale_sample_data - # We only test against piecewise as location/scale transforms - # are same for other methods. -diff --git a/scipy/stats/tests/test_mstats_basic.py b/scipy/stats/tests/test_mstats_basic.py -index cd53c7b7914..76cbfd8c253 100644 ---- a/scipy/stats/tests/test_mstats_basic.py -+++ b/scipy/stats/tests/test_mstats_basic.py -@@ -1768,8 +1768,8 @@ def test_skewtest_2D_WithMask(self): - r = stats.skewtest(x) - rm = stats.mstats.skewtest(xm) - -- assert_allclose(r[0][0], rm[0][0], rtol=2e-15) -- assert_allclose(r[0][1], rm[0][1], rtol=1e-15) -+ assert_allclose(r[0][0], rm[0][0], rtol=1e-14) -+ assert_allclose(r[0][1], rm[0][1], rtol=1e-14) - - def test_normaltest(self): - with np.errstate(over='raise'), suppress_warnings() as sup: diff --git a/SOURCES/fix_test_milp_timeout.patch b/SOURCES/fix_test_milp_timeout.patch new file mode 100644 index 0000000..83a3e90 --- /dev/null +++ b/SOURCES/fix_test_milp_timeout.patch @@ -0,0 +1,53 @@ +From 9b068e5a68d9efd9c2403e9499b2c381b6c1d3a6 Mon Sep 17 00:00:00 2001 +From: Matt Haberland +Date: Fri, 21 Apr 2023 07:07:41 -0700 +Subject: [PATCH 1/2] MAINT: optimize: fix test_milp_timeout + +--- + scipy/optimize/tests/test_milp.py | 4 +--- + 1 file changed, 1 insertion(+), 3 deletions(-) + +diff --git a/scipy/optimize/tests/test_milp.py b/scipy/optimize/tests/test_milp.py +index 51996642..1f60fce3 100644 +--- a/scipy/optimize/tests/test_milp.py ++++ b/scipy/optimize/tests/test_milp.py +@@ -279,9 +279,7 @@ _msg_iter = "Iteration limit reached. (HiGHS Status 14:" + + @pytest.mark.skipif(np.intp(0).itemsize < 8, + reason="Unhandled 32-bit GCC FP bug") +-@pytest.mark.slow +-@pytest.mark.timeout(360) +-@pytest.mark.parametrize(["options", "msg"], [({"time_limit": 10}, _msg_time), ++@pytest.mark.parametrize(["options", "msg"], [({"time_limit": 0.1}, _msg_time), + ({"node_limit": 1}, _msg_iter)]) + def test_milp_timeout_16545(options, msg): + # Ensure solution is not thrown away if MILP solver times out +-- +2.40.0 + + +From 024568a4f4292e7b22643f40ae61d33d273cf674 Mon Sep 17 00:00:00 2001 +From: Matt Haberland +Date: Sat, 22 Apr 2023 15:43:07 -0700 +Subject: [PATCH 2/2] Update scipy/optimize/tests/test_milp.py + +[skip ci] +--- + scipy/optimize/tests/test_milp.py | 1 + + 1 file changed, 1 insertion(+) + +diff --git a/scipy/optimize/tests/test_milp.py b/scipy/optimize/tests/test_milp.py +index 1f60fce3..42dae29a 100644 +--- a/scipy/optimize/tests/test_milp.py ++++ b/scipy/optimize/tests/test_milp.py +@@ -279,6 +279,7 @@ _msg_iter = "Iteration limit reached. (HiGHS Status 14:" + + @pytest.mark.skipif(np.intp(0).itemsize < 8, + reason="Unhandled 32-bit GCC FP bug") ++@pytest.mark.slow + @pytest.mark.parametrize(["options", "msg"], [({"time_limit": 0.1}, _msg_time), + ({"node_limit": 1}, _msg_iter)]) + def test_milp_timeout_16545(options, msg): +-- +2.40.0 + diff --git a/SPECS/python3.11-scipy.spec b/SPECS/python3.11-scipy.spec index c83a980..3294596 100644 --- a/SPECS/python3.11-scipy.spec +++ b/SPECS/python3.11-scipy.spec @@ -21,8 +21,8 @@ Summary: Scientific Tools for Python Name: python%{python3_pkgversion}-scipy -Version: 1.10.0 -Release: 1%{?dist} +Version: 1.10.1 +Release: 2%{?dist} # BSD -- whole package except: # Boost -- scipy/special/cephes/scipy_iv.c @@ -31,10 +31,10 @@ 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 -# Fix some test failures on 32 bits -# https://github.com/scipy/scipy/pull/17859 -# https://github.com/scipy/scipy/pull/17931 -Patch0: fix-32bit-test-failures.patch + +# Fix test_milp_timeout failure +# Resolved upstream: https://github.com/scipy/scipy/pull/18339 +Patch0: fix_test_milp_timeout.patch BuildRequires: fftw-devel, suitesparse-devel BuildRequires: %{blaslib}-devel @@ -243,6 +243,12 @@ popd %{python3_sitearch}/*.egg-info %changelog +* Wed May 10 2023 Charalampos Stratakis - 1.10.1-2 +- Fix test_milp_timeout failure + +* Tue May 02 2023 Ryan Erickson - 1.10.1-1 +- Update to 1.10.1 + * Sun Feb 19 2023 Charalampos Stratakis - 1.10.0-1 - Update to 1.10.0