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Hello community,
here is the log from the commit of package python-numcodecs for
openSUSE:Factory checked in at 2023-01-14 00:02:55
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Comparing /work/SRC/openSUSE:Factory/python-numcodecs (Old)
and /work/SRC/openSUSE:Factory/.python-numcodecs.new.32243 (New)
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Package is "python-numcodecs"
Sat Jan 14 00:02:55 2023 rev:4 rq:1058132 version:0.11.0
Changes:
--------
--- /work/SRC/openSUSE:Factory/python-numcodecs/python-numcodecs.changes
2022-04-25 23:36:18.390481951 +0200
+++
/work/SRC/openSUSE:Factory/.python-numcodecs.new.32243/python-numcodecs.changes
2023-01-14 00:03:36.097845065 +0100
@@ -1,0 +2,105 @@
+Thu Jan 12 16:00:40 UTC 2023 - Ben Greiner <c...@bnavigator.de>
+
+- Update to 0.11.0
+ * Speed up isinstance checks of
+ numcodecs.ndarray_like.NDArrayLike,
+ numcodecs.ndarray_like.DType and
+ numcodecs.ndarray_like.FlagsObj. By Andreas Poehlmann, #379.
+ * Remove unnecessary None argument to .get(), it is the default
+ value. By Dimitri Papadopoulos Orfanos, #395.
+ * Apply refurb suggestions. By Dimitri Papadopoulos Orfanos,
+ #372.
+ * Migrate codespell configuration to pyproject.toml and get rid
+ of setup.cfg. By Dimitri Papadopoulos Orfanos #374.
+ * Unvendor cpuinfo. By Dimitri Papadopoulos Orfanos #373.
+ * Drop headers. By John Kirkham, #375.
+ * Remove Python 2 code. By Dimitri Papadopoulos Orfanos #368,
+ #387.
+ * Support Python 3.11. By Dimitri Papadopoulos Orfanos, #369.
+ * Drop Python 3.7. By John Kirkham,, #405 #406.
+ * Test with zfpy 1.0.0. By John Kirkham, #385.
+ * Remove vendored C files and re-generate them on the fly using
+ Cython. Add a pyproject.toml file to define Cython as a build
+ dependency. By Dimitri Papadopoulos Orfanos, #369.
+ * Add tests for all registry classes. By Josh Moore, #349.
+ * Finish pyproject.toml migration. By John Kirkham #382.
+- Add numcodecs-pr417-raggednumpy.patch
+ * gh#zarr-developers/numcodecs#417
+- Refresh unbundle-libs.patch for system blosc supporting snappy
+ * gh#zarr-developers/numcodecs#264
+
+-------------------------------------------------------------------
+Sun Sep 25 20:23:44 UTC 2022 - Arun Persaud <a...@gmx.de>
+
+- specfile:
+ * update copyright year
+ * require python >= 3.7
+
+- update to version 0.10.2:
+ * Fix
+ + Add BitRound (0.10.0) to registry. By Josh Moore, #342.
+
+- changes from version 0.10.1:
+ * Maintenance
+ + Add entrypoints to setup.py. By Josh Moore, #332.
+ + Fix spelling. By Dimitri Papadopoulos Orfanos, #336.
+ + Drop Python 3.6 from tests By Dimitri Papadopoulos Orfanos,
+ #338, #339.
+ + Remove trailing spaces and empty lines. By Dimitri Papadopoulos
+ Orfanos, #341.
+ + Add LGTM.com configuration file By Dimitri Papadopoulos Orfanos,
+ #337.
+
+- changes from version 0.10.0:
+ * Enhancements
+ + Add support of alternative array classes (other than NumPy
+ arrays) By Mads R. B. Kristensen, #305.
+ + Add ability to find codecs via entrypoint numcodecs.codecs. By
+ Martin Durant, #290.
+ + Add bitround codec By Ryan Abernathy and Martin Durant, #298.
+ + Introduce a flat option to ensure_contiguous_ndarray to switch
+ off flatten for ZFPY codec By Haiying Xu, #307.
+ * Bug fixes
+ + Fix a flatten array error for ZFPY, ZFPY codec is supported on
+ Python 3.9 and 3.10 on Linux and MacOS, the docs about ZFPY is
+ also available. By Haiying Xu, John Kirkham, Ryan Abernathey
+ #303.
+ + Codex: make encode and decode @abstractmethods By Mads
+ R. B. Kristensen, #306.
+ + Fix expected result test for Shuffle. By Elliott Sales de
+ Andrade, #282.
+ * Maintenance
+ + Multiple code linting fixes. By Dimitri Papadopoulos Orfanos,
+ #295, #294, #293, and #292.
+ + Drop Python 3.6 By Josh Moore, #318.
+ + Fix macOS Python 3.10 By John Kirkham, #311.
+ + chore: bump cibuildwheel version, use action By Henry Schreiner,
+ #309.
+ + Specify language as âenâ instead of None. By John Kirkham, #329.
+ + Move master to main. By John Kirkham, #322.
+ + Drop fastparquet benchmark. By John Kirkham, #321.
+ + Trim wheel builds. By John Kirkham, #320.
+
+- changes from version 0.9.1:
+ * Fix inaccurate docstrings for Blosc. By James Webber, #287.
+
+- changes from version 0.9.0:
+ * c-blosc upgrade 1.18.1 -> 1.21.0. Warning: this temporarily
+ removes support for snappy compression! By kindjacket, #283.
+ * Fix an ImportError with Blosc on Android. By Daniel Jewell, #284.
+
+- changes from version 0.8.1:
+ * Fix an ImportError with Blosc on Android. By Daniel Jewell, #284.
+
+- changes from version 0.8.0:
+ * The numcodecs.zfpy.ZFPY codec is now supported on Python 3.8 if
+ zfpy==0.5.5 is installed. By haiying xu, #229.
+ * Add support for byte Shuffle filter By Paul Branson and Martin
+ Durant #273.
+ * Update Windows + Mac CI to run all tests. By Jackson Maxfield
+ Brown, #276. Help from Oleg Höfling, #273.
+ * Update cpuinfo to 8.0.0. By Florian Jetter, #280.
+ * Drop out-of-date manual release docs. By John Kirkham, #272.
+ * Add support for Python 3.9 and Update GitHub Actions.
+
+-------------------------------------------------------------------
Old:
----
numcodecs-0.7.3.tar.gz
New:
----
numcodecs-0.11.0.tar.gz
numcodecs-pr417-raggednumpy.patch
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Other differences:
------------------
++++++ python-numcodecs.spec ++++++
--- /var/tmp/diff_new_pack.AtU9gQ/_old 2023-01-14 00:03:37.933855759 +0100
+++ /var/tmp/diff_new_pack.AtU9gQ/_new 2023-01-14 00:03:37.977856015 +0100
@@ -1,7 +1,7 @@
#
# spec file for package python-numcodecs
#
-# Copyright (c) 2021 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
@@ -16,21 +16,24 @@
#
-%{?!python_module:%define python_module() python-%{**} python3-%{**}}
-%define skip_python2 1
-%define skip_python36 1
Name: python-numcodecs
-Version: 0.7.3
+Version: 0.11.0
Release: 0
Summary: Buffer compression and transformation codecs
License: MIT
URL: https://github.com/zarr-developers/numcodecs
Source:
https://files.pythonhosted.org/packages/source/n/numcodecs/numcodecs-%{version}.tar.gz
-# PATCH-FEATURE-UPSTREAM unbundle-libs.patch -- unbundle system libs
+# PATCH-FEATURE-UPSTREAM unbundle-libs.patch -- unbundle system libs
gh#zarr-developers/numcodecs#264
Patch0: unbundle-libs.patch
+# PATCH-FIX-UPSTREAM numcodecs-pr417-raggednumpy.patch
gh#zarr-developers/numcodecs#417
+Patch1: numcodecs-pr417-raggednumpy.patch
BuildRequires: %{python_module Cython}
-BuildRequires: %{python_module setuptools > 18.0}
-BuildRequires: %{python_module setuptools_scm > 1.5.4}
+BuildRequires: %{python_module base >= 3.8}
+BuildRequires: %{python_module pip}
+BuildRequires: %{python_module py-cpuinfo}
+BuildRequires: %{python_module setuptools > 64}
+BuildRequires: %{python_module setuptools_scm > 6.2}
+BuildRequires: %{python_module wheel}
BuildRequires: blosc-devel
BuildRequires: cmake
BuildRequires: fdupes
@@ -40,10 +43,14 @@
BuildRequires: pkgconfig(liblz4)
BuildRequires: pkgconfig(libzstd)
BuildRequires: pkgconfig(zlib)
+Requires: python-entrypoints
Requires: python-numpy >= 1.7
Suggests: python-msgpack
+Suggests: python-zfpy >= 1
# SECTION test requirements
BuildRequires: %{python_module numpy >= 1.7}
+BuildRequires: %{python_module entrypoints}
+BuildRequires: %{python_module msgpack}
BuildRequires: %{python_module pytest}
# /SECTION
%python_subpackages
@@ -56,22 +63,23 @@
%autosetup -p1 -n numcodecs-%{version}
# use system libraries instead of bundled ones
rm -r c-blosc
+sed -i 's/--cov=numcodecs --cov-report xml//' pyproject.toml
%build
export CFLAGS="%{optflags}"
export DISABLE_NUMCODECS_AVX2=1
-%python_build
+%pyproject_wheel
%install
-%python_install
+%pyproject_install
%python_expand %fdupes %{buildroot}%{$python_sitearch}
%check
-%pytest_arch
+%pytest_arch --pyargs numcodecs -rsfE
%files %{python_files}
%doc README.rst
-%license LICENSE
+%license LICENSE.txt
%{python_sitearch}/numcodecs
%{python_sitearch}/numcodecs-%{version}*-info
++++++ numcodecs-0.7.3.tar.gz -> numcodecs-0.11.0.tar.gz ++++++
++++ 198771 lines of diff (skipped)
++++++ numcodecs-pr417-raggednumpy.patch ++++++
diff --git a/numcodecs/json.py b/numcodecs/json.py
index 670f223..b803a77 100644
--- a/numcodecs/json.py
+++ b/numcodecs/json.py
@@ -54,7 +54,10 @@ class JSON(Codec):
self._decoder = _json.JSONDecoder(**self._decoder_config)
def encode(self, buf):
- buf = np.asarray(buf)
+ try:
+ buf = np.asarray(buf)
+ except ValueError:
+ buf = np.asarray(buf, dtype=object)
items = buf.tolist()
items.extend((buf.dtype.str, buf.shape))
return self._encoder.encode(items).encode(self._text_encoding)
diff --git a/numcodecs/msgpacks.py b/numcodecs/msgpacks.py
index 026f583..6556498 100644
--- a/numcodecs/msgpacks.py
+++ b/numcodecs/msgpacks.py
@@ -52,7 +52,10 @@ class MsgPack(Codec):
self.raw = raw
def encode(self, buf):
- buf = np.asarray(buf)
+ try:
+ buf = np.asarray(buf)
+ except ValueError:
+ buf = np.asarray(buf, dtype=object)
items = buf.tolist()
items.extend((buf.dtype.str, buf.shape))
return msgpack.packb(items, use_bin_type=self.use_bin_type,
diff --git a/numcodecs/tests/test_json.py b/numcodecs/tests/test_json.py
index 7e8fcd6..8dac2b4 100644
--- a/numcodecs/tests/test_json.py
+++ b/numcodecs/tests/test_json.py
@@ -2,7 +2,7 @@ import itertools
import numpy as np
-
+import pytest
from numcodecs.json import JSON
from numcodecs.tests.common import (check_config, check_repr,
check_encode_decode_array,
@@ -53,21 +53,23 @@ def test_backwards_compatibility():
check_backwards_compatibility(JSON.codec_id, arrays, codecs)
-def test_non_numpy_inputs():
+@pytest.mark.parametrize(
+ "input_data, dtype",
+ [
+ ([0, 1], None),
+ ([[0, 1], [2, 3]], None),
+ ([[0], [1], [2, 3]], object),
+ ([[[0, 0]], [[1, 1]], [[2, 3]]], None),
+ (["1"], None),
+ (["11", "11"], None),
+ (["11", "1", "1"], None),
+ ([{}], None),
+ ([{"key": "value"}, ["list", "of", "strings"]], object),
+ ]
+)
+def test_non_numpy_inputs(input_data, dtype):
# numpy will infer a range of different shapes and dtypes for these inputs.
# Make sure that round-tripping through encode preserves this.
- data = [
- [0, 1],
- [[0, 1], [2, 3]],
- [[0], [1], [2, 3]],
- [[[0, 0]], [[1, 1]], [[2, 3]]],
- ["1"],
- ["11", "11"],
- ["11", "1", "1"],
- [{}],
- [{"key": "value"}, ["list", "of", "strings"]],
- ]
- for input_data in data:
- for codec in codecs:
- output_data = codec.decode(codec.encode(input_data))
- assert np.array_equal(np.array(input_data), output_data)
+ for codec in codecs:
+ output_data = codec.decode(codec.encode(input_data))
+ assert np.array_equal(np.array(input_data, dtype=dtype), output_data)
diff --git a/numcodecs/tests/test_msgpacks.py b/numcodecs/tests/test_msgpacks.py
index 6aeadcf..d76aa12 100644
--- a/numcodecs/tests/test_msgpacks.py
+++ b/numcodecs/tests/test_msgpacks.py
@@ -2,6 +2,7 @@ import unittest
import numpy as np
+import pytest
try:
@@ -52,30 +53,32 @@ def test_backwards_compatibility():
check_backwards_compatibility(codec.codec_id, arrays, [codec])
-def test_non_numpy_inputs():
+@pytest.mark.parametrize(
+ "input_data, dtype",
+ [
+ ([0, 1], None),
+ ([[0, 1], [2, 3]], None),
+ ([[0], [1], [2, 3]], object),
+ ([[[0, 0]], [[1, 1]], [[2, 3]]], None),
+ (["1"], None),
+ (["11", "11"], None),
+ (["11", "1", "1"], None),
+ ([{}], None),
+ ([{"key": "value"}, ["list", "of", "strings"]], object),
+ ([b"1"], None),
+ ([b"11", b"11"], None),
+ ([b"11", b"1", b"1"], None),
+ ([{b"key": b"value"}, [b"list", b"of", b"strings"]], object),
+ ]
+)
+def test_non_numpy_inputs(input_data, dtype):
codec = MsgPack()
# numpy will infer a range of different shapes and dtypes for these inputs.
# Make sure that round-tripping through encode preserves this.
- data = [
- [0, 1],
- [[0, 1], [2, 3]],
- [[0], [1], [2, 3]],
- [[[0, 0]], [[1, 1]], [[2, 3]]],
- ["1"],
- ["11", "11"],
- ["11", "1", "1"],
- [{}],
- [{"key": "value"}, ["list", "of", "strings"]],
- [b"1"],
- [b"11", b"11"],
- [b"11", b"1", b"1"],
- [{b"key": b"value"}, [b"list", b"of", b"strings"]],
- ]
- for input_data in data:
- actual = codec.decode(codec.encode(input_data))
- expect = np.array(input_data)
- assert expect.shape == actual.shape
- assert np.array_equal(expect, actual)
+ actual = codec.decode(codec.encode(input_data))
+ expect = np.array(input_data, dtype=dtype)
+ assert expect.shape == actual.shape
+ assert np.array_equal(expect, actual)
def test_encode_decode_shape_dtype_preserved():
++++++ unbundle-libs.patch ++++++
--- /var/tmp/diff_new_pack.AtU9gQ/_old 2023-01-14 00:03:38.801860815 +0100
+++ /var/tmp/diff_new_pack.AtU9gQ/_new 2023-01-14 00:03:38.805860839 +0100
@@ -1,8 +1,8 @@
-Index: numcodecs-0.7.2/setup.py
+Index: numcodecs-0.11.0/setup.py
===================================================================
---- numcodecs-0.7.2.orig/setup.py
-+++ numcodecs-0.7.2/setup.py
-@@ -112,6 +112,7 @@ def blosc_extension():
+--- numcodecs-0.11.0.orig/setup.py
++++ numcodecs-0.11.0/setup.py
+@@ -104,6 +104,7 @@ def blosc_extension():
Extension('numcodecs.blosc',
sources=sources + blosc_sources,
include_dirs=include_dirs,
@@ -10,7 +10,7 @@
define_macros=define_macros,
extra_compile_args=extra_compile_args,
),
-@@ -152,6 +153,7 @@ def zstd_extension():
+@@ -138,6 +139,7 @@ def zstd_extension():
Extension('numcodecs.zstd',
sources=sources + zstd_sources,
include_dirs=include_dirs,
@@ -18,7 +18,7 @@
define_macros=define_macros,
extra_compile_args=extra_compile_args,
),
-@@ -185,6 +187,7 @@ def lz4_extension():
+@@ -165,6 +167,7 @@ def lz4_extension():
Extension('numcodecs.lz4',
sources=sources + lz4_sources,
include_dirs=include_dirs,
@@ -26,4 +26,24 @@
define_macros=define_macros,
extra_compile_args=extra_compile_args,
),
+Index: numcodecs-0.11.0/numcodecs/tests/test_blosc.py
+===================================================================
+--- numcodecs-0.11.0.orig/numcodecs/tests/test_blosc.py
++++ numcodecs-0.11.0/numcodecs/tests/test_blosc.py
+@@ -155,10 +155,11 @@ def test_compress_complib(use_threads):
+ }
+ blosc.use_threads = use_threads
+ for cname in blosc.list_compressors():
+- enc = blosc.compress(arr, cname.encode(), 1, Blosc.NOSHUFFLE)
+- complib = blosc.cbuffer_complib(enc)
+- expected_complib = expected_complibs[cname]
+- assert complib == expected_complib
++ if cname in expected_complibs:
++ enc = blosc.compress(arr, cname.encode(), 1, Blosc.NOSHUFFLE)
++ complib = blosc.cbuffer_complib(enc)
++ expected_complib = expected_complibs[cname]
++ assert complib == expected_complib
+ with pytest.raises(ValueError):
+ # capitalized cname
+ blosc.compress(arr, b'LZ4', 1)
