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Accepting request 880619 from devel:languages:python:numeric

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OBS-URL: https://build.opensuse.org/request/show/880619
OBS-URL: https://build.opensuse.org/package/show/openSUSE:Factory/python-numba?expand=0&rev=28
This commit is contained in:
Dominique Leuenberger 2021-03-24 15:13:57 +00:00 committed by Git OBS Bridge
commit 0efce5cd2d
8 changed files with 257 additions and 55 deletions
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3
numba-0.51.2.tar.gz
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@ -1,3 +0,0 @@
version https://git-lfs.github.com/spec/v1
oid sha256:16bd59572114adbf5f600ea383880d7b2071ae45477e84a24994e089ea390768
size 2059680

3
numba-0.53.0.tar.gz Normal file
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@ -0,0 +1,3 @@
version https://git-lfs.github.com/spec/v1
oid sha256:55c11d7edbba2ba715f2b56f5294cad55cfd87bff98e2627c3047c2d5cc52d16
size 2212284

72
numba-pr6851-llvm-timings.patch Normal file
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@ -0,0 +1,72 @@
diff --git a/numba/misc/llvm_pass_timings.py b/numba/misc/llvm_pass_timings.py
index 205bb3396..b3263dd45 100644
--- a/numba/misc/llvm_pass_timings.py
+++ b/numba/misc/llvm_pass_timings.py
@@ -239,12 +239,14 @@ class ProcessedPassTimings:
missing[k] = 0.0
# parse timings
n = r"\s*((?:[0-9]+\.)?[0-9]+)"
- pat = f"\\s+{n}\\s*\\({n}%\\)" * (len(headers) - 1) + r"\s*(.*)"
+ pat = f"\\s+(?:{n}\\s*\\({n}%\\)|-+)" * (len(headers) - 1)
+ pat += r"\s*(.*)"
for ln in line_iter:
m = re.match(pat, ln)
if m is not None:
raw_data = list(m.groups())
- data = {k: float(v) for k, v in zip(attrs, raw_data)}
+ data = {k: float(v) if v is not None else 0.0
+ for k, v in zip(attrs, raw_data)}
data.update(missing)
pass_name = raw_data[-1]
rec = PassTimingRecord(
diff --git a/numba/tests/test_llvm_pass_timings.py b/numba/tests/test_llvm_pass_timings.py
index a7e9135cd..25b77e2c5 100644
--- a/numba/tests/test_llvm_pass_timings.py
+++ b/numba/tests/test_llvm_pass_timings.py
@@ -5,6 +5,30 @@ from numba.tests.support import TestCase, override_config
from numba.misc import llvm_pass_timings as lpt
+timings_raw1 = """
+===-------------------------------------------------------------------------===
+ ... Pass execution timing report ...
+===-------------------------------------------------------------------------===
+ Total Execution Time: 0.0001 seconds (0.0001 wall clock)
+
+ ---User Time--- --System Time-- --User+System-- ---Wall Time--- --- Name ---
+ 0.0001 ( 90.1%) 0.0001 ( 90.1%) 0.0001 ( 90.1%) 0.0001 ( 90.1%) A1
+ 0.0000 ( 9.9%) 0.0000 ( 9.9%) 0.0000 ( 9.9%) 0.0000 ( 9.9%) A2
+ 0.0001 (100.0%) 0.0001 (100.0%) 0.0001 (100.0%) 0.0001 (100.0%) Total
+
+""" # noqa: E501
+
+timings_raw2 = """
+ Total Execution Time: 0.0001 seconds (0.0001 wall clock)
+
+ ---User Time--- --System Time-- --User+System-- ---Wall Time--- --- Name ---
+ 0.0001 ( 90.1%) ----- 0.0001 ( 90.1%) 0.0001 ( 90.1%) A1
+ 0.0000 ( 9.9%) ----- 0.0000 ( 9.9%) 0.0000 ( 9.9%) A2
+ 0.0001 (100.0%) ----- 0.0001 (100.0%) 0.0001 (100.0%) Total
+
+""" # noqa: E501
+
+
class TestLLVMPassTimings(TestCase):
def test_usage(self):
@@ -61,6 +85,15 @@ class TestLLVMPassTimings(TestCase):
self.assertGreaterEqual(last, cur)
cur = last
+ def test_parse_raw(self):
+ timings1 = lpt.ProcessedPassTimings(timings_raw1)
+ self.assertAlmostEqual(timings1.get_total_time(), 0.0001)
+ self.assertIsInstance(timings1.summary(), str)
+
+ timings2 = lpt.ProcessedPassTimings(timings_raw2)
+ self.assertAlmostEqual(timings2.get_total_time(), 0.0001)
+ self.assertIsInstance(timings2.summary(), str)
+
class TestLLVMPassTimingsDisabled(TestCase):
def test_disabled_behavior(self):

52
packaging-ignore-setuptools-deprecation.patch Normal file
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@ -0,0 +1,52 @@
From 4811aeceb2dde05124697909b87cf4ad2ae07c65 Mon Sep 17 00:00:00 2001
From: Stuart Archibald <stuartarchibald@users.noreply.github.com>
Date: Wed, 17 Mar 2021 12:29:16 +0000
Subject: [PATCH 1/2] Ignore warnings from packaging module when testing import
behaviour.
As title.
Fixes #6831
---
numba/tests/test_import.py | 4 +++-
1 file changed, 3 insertions(+), 1 deletion(-)
diff --git a/numba/tests/test_import.py b/numba/tests/test_import.py
index 7cc9082046..a46ad2df6c 100644
--- a/numba/tests/test_import.py
+++ b/numba/tests/test_import.py
@@ -58,7 +58,9 @@ def test_no_accidental_warnings(self):
# checks that importing Numba isn't accidentally triggering warnings due
# to e.g. deprecated use of import locations from Python's stdlib
code = "import numba"
- flags = ["-Werror",]
+ # See: https://github.com/numba/numba/issues/6831
+ # bug in setuptools/packaging causing a deprecation warning
+ flags = ["-Werror", "-Wignore::DeprecationWarning:packaging:"]
self.run_in_subproc(code, flags)
def test_import_star(self):
From 94fc06e77b648b1cb5021cd6d460aa42808a0393 Mon Sep 17 00:00:00 2001
From: Stuart Archibald <stuartarchibald@users.noreply.github.com>
Date: Wed, 17 Mar 2021 16:42:14 +0000
Subject: [PATCH 2/2] Respond to feedback
As title]
---
numba/tests/test_import.py | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/numba/tests/test_import.py b/numba/tests/test_import.py
index a46ad2df6c..a0ca5725eb 100644
--- a/numba/tests/test_import.py
+++ b/numba/tests/test_import.py
@@ -60,7 +60,7 @@ def test_no_accidental_warnings(self):
code = "import numba"
# See: https://github.com/numba/numba/issues/6831
# bug in setuptools/packaging causing a deprecation warning
- flags = ["-Werror", "-Wignore::DeprecationWarning:packaging:"]
+ flags = ["-Werror", "-Wignore::DeprecationWarning:packaging.version:"]
self.run_in_subproc(code, flags)
def test_import_star(self):

85
python-numba.changes
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@ -1,3 +1,88 @@
-------------------------------------------------------------------
Wed Mar 17 16:51:46 UTC 2021 - Ben Greiner <code@bnavigator.de>
- Update to 0.53.0
* Support for Python 3.9
* Function sub-typing
* Initial support for dynamic gufuncs (i.e. from @guvectorize)
* Parallel Accelerator (@njit(parallel=True) now supports
Fortran ordered arrays
* Full release notes at
https://numba.readthedocs.io/en/0.53.0/release-notes.html
- Don't unpin-llvmlite.patch. It really need to be the correct
version.
- Refresh skip-failing-tests.patch
- Add packaging-ignore-setuptools-deprecation.patch
gh#numba/numba#6837
- Add numba-pr6851-llvm-timings.patch gh#numba/numba#6851 in order
to fix 32-bit issues gh#numba/numba#6832
-------------------------------------------------------------------
Wed Feb 17 09:49:48 UTC 2021 - Ben Greiner <code@bnavigator.de>
- Update to 0.52.0
https://numba.readthedocs.io/en/stable/release-notes.html
This release focuses on performance improvements, but also adds
some new features and contains numerous bug fixes and stability
improvements.
Highlights of core performance improvements include:
* Intel kindly sponsored research and development into producing
a new reference count pruning pass. This pass operates at the
LLVM level and can prune a number of common reference counting
patterns. This will improve performance for two primary
reasons:
- There will be less pressure on the atomic locks used to do
the reference counting.
- Removal of reference counting operations permits more
inlining and the optimisation passes can in general do more
with what is present.
(Siu Kwan Lam).
* Intel also sponsored work to improve the performance of the
numba.typed.List container, particularly in the case of
__getitem__ and iteration (Stuart Archibald).
* Superword-level parallelism vectorization is now switched on
and the optimisation pipeline has been lightly analysed and
tuned so as to be able to vectorize more and more often
(Stuart Archibald).
Highlights of core feature changes include:
* The inspect_cfg method on the JIT dispatcher object has been
significantly enhanced and now includes highlighted output and
interleaved line markers and Python source (Stuart Archibald).
* The BSD operating system is now unofficially supported (Stuart
Archibald).
* Numerous features/functionality improvements to NumPy support,
including support for:
- np.asfarray (Guilherme Leobas)
- “subtyping” in record arrays (Lucio Fernandez-Arjona)
- np.split and np.array_split (Isaac Virshup)
- operator.contains with ndarray (@mugoh).
- np.asarray_chkfinite (Rishabh Varshney).
- NumPy 1.19 (Stuart Archibald).
- the ndarray allocators, empty, ones and zeros, accepting a
dtype specified as a string literal (Stuart Archibald).
* Booleans are now supported as literal types (Alexey Kozlov).
* On the CUDA target:
* CUDA 9.0 is now the minimum supported version (Graham Markall).
* Support for Unified Memory has been added (Max Katz).
* Kernel launch overhead is reduced (Graham Markall).
* Cudasim support for mapped array, memcopies and memset has
been * added (Mike Williams).
* Access has been wired in to all libdevice functions (Graham
Markall).
* Additional CUDA atomic operations have been added (Michae
Collison).
* Additional math library functions (frexp, ldexp, isfinite)
(Zhihao * Yuan).
* Support for power on complex numbers (Graham Markall).
Deprecations to note:
* There are no new deprecations. However, note that
“compatibility” mode, which was added some 40 releases ago to
help transition from 0.11 to 0.12+, has been removed! Also,
the shim to permit the import of jitclass from Numba’s top
level namespace has now been removed as per the deprecation
schedule.
- NEP 29: Skip python36 build. Python 3.6 is dropped by NumPy 1.20
-------------------------------------------------------------------
Mon Nov 2 16:34:48 UTC 2020 - Marketa Calabkova <mcalabkova@suse.com>

66
python-numba.spec
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@ -1,7 +1,7 @@
#
# spec file for package python-numba
# spec file for package python-numba-test
#
# Copyright (c) 2020 SUSE LLC
# Copyright (c) 2021 SUSE LLC
#
# All modifications and additions to the file contributed by third parties
# remain the property of their copyright owners, unless otherwise agreed
@ -18,6 +18,8 @@
%{?!python_module:%define python_module() python-%{**} python3-%{**}}
%define skip_python2 1
# NEP 29: python36-numpy and -scipy no longer in TW
%define skip_python36 1
%global flavor @BUILD_FLAVOR@%{nil}
%if "%{flavor}" == "test"
%define psuffix -test
@ -27,16 +29,20 @@
%bcond_with test
%endif
Name: python-numba%{psuffix}
Version: 0.51.2
Version: 0.53.0
Release: 0
Summary: NumPy-aware optimizing compiler for Python using LLVM
License: BSD-2-Clause
URL: https://github.com/numba/numba
URL: https://numba.pydata.org/
Source: https://files.pythonhosted.org/packages/source/n/numba/numba-%{version}.tar.gz
Patch0: skip-failing-tests.patch
# PATCH-FIX-UPSTREAM fix-max-name-size.patch -- fix for gh#numba/numba#3876 -- from gh#numba/numba#4373
Patch1: fix-max-name-size.patch
Patch2: unpin-llvmlite.patch
Patch0: fix-max-name-size.patch
# PATCH-FIX-UPSTREAM packaging-ignore-setuptools-deprecation.patch -- gh#numba/numba#6837
Patch1: https://github.com/numba/numba/pull/6837.patch#/packaging-ignore-setuptools-deprecation.patch
# PATCH-FIX-USPTREAM ignore empty system time column on llvm timings -- gh#numba/numba#6851
Patch2: numba-pr6851-llvm-timings.patch
# PATCH-FIX-OPENSUSE skip tests failing due to OBS specifics
Patch3: skip-failing-tests.patch
BuildRequires: %{python_module devel}
BuildRequires: %{python_module numpy-devel >= 1.15}
BuildRequires: %{python_module setuptools}
@ -44,11 +50,12 @@ BuildRequires: fdupes
BuildRequires: gcc-c++
BuildRequires: python-rpm-macros
BuildRequires: tbb-devel
Requires: python-llvmlite >= 0.33
Requires: python-llvmlite < 0.37
Requires: python-llvmlite >= 0.36
Requires: python-numpy >= 1.15
Requires: python-scipy >= 0.16
Requires(post): update-alternatives
Requires(preun): update-alternatives
Requires(preun):update-alternatives
Recommends: python-Jinja2
Recommends: python-Pygments
Recommends: python-cffi
@ -59,10 +66,10 @@ BuildRequires: %{python_module PyYAML}
BuildRequires: %{python_module Pygments}
BuildRequires: %{python_module cffi}
BuildRequires: %{python_module ipython}
BuildRequires: %{python_module llvmlite >= 0.33}
BuildRequires: %{python_module numba >= %{version}}
BuildRequires: %{python_module numba-devel >= %{version}}
BuildRequires: %{python_module pip}
BuildRequires: %{python_module psutil}
BuildRequires: %{python_module pytest}
BuildRequires: %{python_module scipy >= 0.16}
BuildRequires: %{python_module tbb}
@ -99,19 +106,20 @@ This package contains files for developing applications using numba.
%setup -q -n numba-%{version}
%autopatch -p1
# due to new numpy version tests now fail
# Remove this with version update! (>0.48.0)
# Incompatilbe numpy versions (?)
# Check these with every version update! (Last check 0.53)
# https://github.com/numba/numba/issues/5251
# https://numba.discourse.group/t/helping-test-numba-0-53-0-rc/519/34
rm numba/tests/test_np_functions.py
rm numba/tests/test_ufuncs.py
rm numba/tests/test_array_manipulation.py
rm numba/tests/test_array_reductions.py
# https://github.com/numba/numba/issues/5179
rm numba/tests/test_hashing.py
# timeouts randomly in OBS
rm numba/tests/test_typedlist.py
# as we reduced the amount of tests:
sed -i -e 's:5000:3000:' numba/tests/test_runtests.py
# if we reduced the amount of tests too much:
#sed -i -e '/check_testsuite_size/ s/5000/3000/' numba/tests/test_runtests.py
# our setup imports distutils. Not sure why, but should not be a problem.
sed -i -e "/def test_laziness/,/def/ {/'distutils',/ d}" numba/tests/test_import.py
sed -i -e '1{/env python/ d}' numba/misc/appdirs.py
%build
export CFLAGS="%{optflags} -fPIC"
@ -120,7 +128,12 @@ export CFLAGS="%{optflags} -fPIC"
%install
%if !%{with test}
%python_install
%python_expand %fdupes %{buildroot}%{$python_sitearch}
%{python_expand #
%fdupes %{buildroot}%{$python_sitearch}
find %{buildroot}%{$python_sitearch} -name '*.[ch]' > devel-files0-%{$python_bin_suffix}.files
sed 's|^%{buildroot}||' devel-files0-%{$python_bin_suffix}.files > devel-files-%{$python_bin_suffix}.files
sed 's|^%{buildroot}|%%exclude |' devel-files0-%{$python_bin_suffix}.files > devel-files-exclude-%{$python_bin_suffix}.files
}
%python_clone -a %{buildroot}%{_bindir}/numba
%python_clone -a %{buildroot}%{_bindir}/pycc
@ -130,7 +143,7 @@ export CFLAGS="%{optflags} -fPIC"
%if %{with test}
mv numba numba_temp
export NUMBA_PARALLEL_DIAGNOSTICS=1
%{python_expand export PYTHONPATH=%{$python_sitearch}
%{python_expand # test the installed package
%{_bindir}/numba-%{$python_bin_suffix} -s
$python -m numba.runtests -v -b --exclude-tags='long_running' -m %{_smp_build_ncpus} -- numba.tests
}
@ -144,23 +157,16 @@ mv numba_temp numba
%preun
%python_uninstall_alternative numba
%files %{python_files}
%files %{python_files} -f devel-files-exclude-%{python_bin_suffix}.files
%license LICENSE
%doc CHANGE_LOG README.rst
%python_alternative %{_bindir}/numba
%python_alternative %{_bindir}/pycc
%{python_sitearch}/numba/
%{python_sitearch}/numba-%{version}-py*.egg-info
%exclude %{python_sitearch}/numba/*.c
%exclude %{python_sitearch}/numba/*.h
%exclude %{python_sitearch}/numba/*/*.c
%exclude %{python_sitearch}/numba/*/*.h
%files %{python_files devel}
%{python_sitearch}/numba/*.c
%{python_sitearch}/numba/*.h
%{python_sitearch}/numba/*/*.c
%{python_sitearch}/numba/*/*.h
%files %{python_files devel} -f devel-files-%{python_bin_suffix}.files
%license LICENSE
%endif
%changelog

18
skip-failing-tests.patch
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@ -1,8 +1,8 @@
Index: numba-0.49.0/numba/tests/test_parfors.py
Index: numba-0.53.0/numba/tests/test_parfors.py
===================================================================
--- numba-0.49.0.orig/numba/tests/test_parfors.py
+++ numba-0.49.0/numba/tests/test_parfors.py
@@ -1505,7 +1505,7 @@ class TestParfors(TestParforsBase):
--- numba-0.53.0.orig/numba/tests/test_parfors.py
+++ numba-0.53.0/numba/tests/test_parfors.py
@@ -1649,7 +1649,7 @@ class TestParfors(TestParforsBase):
msg = ("The reshape API may only include one negative argument.")
self.assertIn(msg, str(raised.exception))
@ -11,7 +11,7 @@ Index: numba-0.49.0/numba/tests/test_parfors.py
def test_ndarray_fill(self):
def test_impl(x):
x.fill(7.0)
@@ -2541,7 +2541,7 @@ class TestParforsVectorizer(TestPrangeBa
@@ -2842,7 +2842,7 @@ class TestParforsVectorizer(TestPrangeBa
# to check vsqrtpd operates on zmm
match_vsqrtpd_on_zmm = re.compile('\n\s+vsqrtpd\s+.*zmm.*\n')
@ -20,7 +20,7 @@ Index: numba-0.49.0/numba/tests/test_parfors.py
def test_vectorizer_fastmath_asm(self):
""" This checks that if fastmath is set and the underlying hardware
is suitable, and the function supplied is amenable to fastmath based
@@ -2584,7 +2584,7 @@ class TestParforsVectorizer(TestPrangeBa
@@ -2885,7 +2885,7 @@ class TestParforsVectorizer(TestPrangeBa
# check no zmm addressing is present
self.assertTrue('zmm' not in v)
@ -29,10 +29,10 @@ Index: numba-0.49.0/numba/tests/test_parfors.py
def test_unsigned_refusal_to_vectorize(self):
""" This checks that if fastmath is set and the underlying hardware
is suitable, and the function supplied is amenable to fastmath based
Index: numba-0.49.0/numba/tests/test_parfors_passes.py
Index: numba-0.53.0/numba/tests/test_parfors_passes.py
===================================================================
--- numba-0.49.0.orig/numba/tests/test_parfors_passes.py
+++ numba-0.49.0/numba/tests/test_parfors_passes.py
--- numba-0.53.0.orig/numba/tests/test_parfors_passes.py
+++ numba-0.53.0/numba/tests/test_parfors_passes.py
@@ -512,6 +512,7 @@ class TestConvertLoopPass(BaseTest):
str(raises.exception),
)

13
unpin-llvmlite.patch
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@ -1,13 +0,0 @@
Index: numba-0.51.2/setup.py
===================================================================
--- numba-0.51.2.orig/setup.py
+++ numba-0.51.2/setup.py
@@ -300,7 +300,7 @@ packages = find_packages(include=["numba
build_requires = ['numpy >={}'.format(min_numpy_build_version)]
install_requires = [
- 'llvmlite >={},<{}'.format(min_llvmlite_version, max_llvmlite_version),
+ 'llvmlite >={}'.format(min_llvmlite_version),
'numpy >={}'.format(min_numpy_run_version),
'setuptools',
]