Sync from SUSE:ALP:Source:Standard:1.0 python-numcodecs revision 755e4dda643d95f723d966ef7404d273

2024-01-05 10:02:32 +01:00 · 2024-01-05 10:02:32 +01:00 · f5d904f396
commit f5d904f396
7 changed files with 537 additions and 0 deletions
--- a/.gitattributes
+++ b/.gitattributes
@ -0,0 +1,23 @@
+## Default LFS
+*.7z filter=lfs diff=lfs merge=lfs -text
+*.bsp filter=lfs diff=lfs merge=lfs -text
+*.bz2 filter=lfs diff=lfs merge=lfs -text
+*.gem filter=lfs diff=lfs merge=lfs -text
+*.gz filter=lfs diff=lfs merge=lfs -text
+*.jar filter=lfs diff=lfs merge=lfs -text
+*.lz filter=lfs diff=lfs merge=lfs -text
+*.lzma filter=lfs diff=lfs merge=lfs -text
+*.obscpio filter=lfs diff=lfs merge=lfs -text
+*.oxt filter=lfs diff=lfs merge=lfs -text
+*.pdf filter=lfs diff=lfs merge=lfs -text
+*.png filter=lfs diff=lfs merge=lfs -text
+*.rpm filter=lfs diff=lfs merge=lfs -text
+*.tbz filter=lfs diff=lfs merge=lfs -text
+*.tbz2 filter=lfs diff=lfs merge=lfs -text
+*.tgz filter=lfs diff=lfs merge=lfs -text
+*.ttf filter=lfs diff=lfs merge=lfs -text
+*.txz filter=lfs diff=lfs merge=lfs -text
+*.whl filter=lfs diff=lfs merge=lfs -text
+*.xz filter=lfs diff=lfs merge=lfs -text
+*.zip filter=lfs diff=lfs merge=lfs -text
+*.zst filter=lfs diff=lfs merge=lfs -text
--- a/move-from-entrypoints.patch
+++ b/move-from-entrypoints.patch
@ -0,0 +1,95 @@
+From af20af8210384371f91f30251fc78a35ffd0c072 Mon Sep 17 00:00:00 2001
+From: Steve Kowalik <steven@wedontsleep.org>
+Date: Wed, 9 Aug 2023 15:15:52 +1000
+Subject: [PATCH] Remove use of entrypoints
+
+Since Python 3.8, the standard library has included functionality to
+query entry points directly using importlib.metadata. Since the API has
+changed for the better with Python 3.10, we need to support both ways of
+using it.
+---
+ numcodecs/registry.py               | 14 +++++++++-----
+ numcodecs/tests/test_entrypoints.py |  2 --
+ pyproject.toml                      |  7 ++++++-
+ 3 files changed, 15 insertions(+), 8 deletions(-)
+
+diff --git a/numcodecs/registry.py b/numcodecs/registry.py
+index 532e9967..a4dff6d7 100644
+--- a/numcodecs/registry.py
+++ b/numcodecs/registry.py
+@@ -1,7 +1,7 @@
+ """The registry module provides some simple convenience functions to enable
+ applications to dynamically register and look-up codec classes."""
+from importlib.metadata import entry_points
+ import logging
+-from contextlib import suppress
+ 
+ logger = logging.getLogger("numcodecs")
+ codec_registry = {}
+@@ -9,13 +9,17 @@
+ 
+ 
+ def run_entrypoints():
+-    import entrypoints
+     entries.clear()
+-    entries.update(entrypoints.get_group_named("numcodecs.codecs"))
+    eps = entry_points()
+    if hasattr(eps, 'select'):
+        # If entry_points() has a select method, use that. Python 3.10+
+        entries.update(eps.select(group="numcodecs.codecs"))
+    else:
+        # Otherwise, fallback to using get
+        entries.update(eps.get("numcodecs.codecs", []))
+ 
+ 
+-with suppress(ImportError):
+-    run_entrypoints()
+run_entrypoints()
+ 
+ 
+ def get_codec(config):
+diff --git a/numcodecs/tests/test_entrypoints.py b/numcodecs/tests/test_entrypoints.py
+index 81af635d..0d017f2d 100644
+--- a/numcodecs/tests/test_entrypoints.py
+++ b/numcodecs/tests/test_entrypoints.py
+@@ -7,7 +7,6 @@
+ 
+ 
+ here = os.path.abspath(os.path.dirname(__file__))
+-pytest.importorskip("entrypoints")
+ 
+ 
+ @pytest.fixture()
+@@ -20,7 +19,6 @@ def set_path():
+     numcodecs.registry.codec_registry.pop("test")
+ 
+ 
+-@pytest.mark.xfail(reason="FIXME: not working in wheels build")
+ def test_entrypoint_codec(set_path):
+     cls = numcodecs.registry.get_codec({"id": "test"})
+     assert cls.codec_id == "test"
+diff --git a/pyproject.toml b/pyproject.toml
+index a2b50e32..147f9b54 100644
+--- a/pyproject.toml
+++ b/pyproject.toml
+@@ -15,7 +15,6 @@ in data storage and communication applications.
+ """
+ readme =  "README.rst"
+ dependencies = [
+-    "entrypoints",
+     "numpy>=1.7",
+ ]
+ requires-python = ">=3.8"
+@@ -71,6 +70,12 @@ package-dir = {"" = "."}
+ packages = ["numcodecs", "numcodecs.tests"]
+ zip-safe = false
+ 
+[tool.setuptools.package-data]
+numcodecs = [
+    "tests/package_with_entrypoint/__init__.py",
+    "tests/package_with_entrypoint-0.1.dist-info/entry_points.txt"
+]
+
+ [tool.setuptools_scm]
+ version_scheme = "guess-next-dev"
+ local_scheme = "dirty-tag"
--- a/numcodecs-0.11.0.tar.gz
+++ b/numcodecs-0.11.0.tar.gz
--- a/numcodecs-pr417-raggednumpy.patch
+++ b/numcodecs-pr417-raggednumpy.patch
@ -0,0 +1,151 @@
+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():
--- a/python-numcodecs.changes
+++ b/python-numcodecs.changes
@ -0,0 +1,131 @@
+-------------------------------------------------------------------
+Mon Aug 28 02:21:23 UTC 2023 - Steve Kowalik <steven.kowalik@suse.com>
+
+- Add patch move-from-entrypoints.patch:
+  * Drop requirements on entrypoints, use importlib.metadata.
+
+-------------------------------------------------------------------
+Thu Jan 12 16:00:40 UTC 2023 - Ben Greiner <code@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 <arun@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 ‘en’ 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.
+
+-------------------------------------------------------------------
+Mon Apr 25 11:13:12 UTC 2022 - Bernhard Wiedemann <bwiedemann@suse.com>
+
+- Disable AVX2 to make package build reproducible (boo#1198818)
+
+-------------------------------------------------------------------
+Sat Apr 17 14:41:47 UTC 2021 - Ben Greiner <code@bnavigator.de>
+
+- Update to v0.7.3
+  * Add support for Python 3.9
+- Disable python36 build (NumPy not available, NEP 29)
+
+-------------------------------------------------------------------
+Mon Dec 28 12:24:07 UTC 2020 - Benjamin Greiner <code@bnavigator.de>
+
+- initial specfile for v0.7.2
+- use and link against system provided blosc, zstd, lz4
+  * unbundle-libs.patch
+  * gh#zarr-developers/numcodecs#264
+- required by zarr, which is required by dask
--- a/python-numcodecs.spec
+++ b/python-numcodecs.spec
@ -0,0 +1,86 @@
+#
+# spec file for package python-numcodecs
+#
+# 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
+# upon. The license for this file, and modifications and additions to the
+# file, is the same license as for the pristine package itself (unless the
+# license for the pristine package is not an Open Source License, in which
+# case the license is the MIT License). An "Open Source License" is a
+# license that conforms to the Open Source Definition (Version 1.9)
+# published by the Open Source Initiative.
+
+# Please submit bugfixes or comments via https://bugs.opensuse.org/
+#
+
+
+Name:           python-numcodecs
+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 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
+# PATCH-FIX-UPSTREAM gh#zarr-developers/numcodecs#442
+Patch2:         move-from-entrypoints.patch
+BuildRequires:  %{python_module Cython}
+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
+BuildRequires:  gcc-c++
+BuildRequires:  pkgconfig
+BuildRequires:  python-rpm-macros
+BuildRequires:  pkgconfig(liblz4)
+BuildRequires:  pkgconfig(libzstd)
+BuildRequires:  pkgconfig(zlib)
+Requires:       python-numpy >= 1.7
+Suggests:       python-msgpack
+Suggests:       python-zfpy >= 1
+# SECTION test requirements
+BuildRequires:  %{python_module numpy >= 1.7}
+BuildRequires:  %{python_module msgpack}
+BuildRequires:  %{python_module pytest}
+# /SECTION
+%python_subpackages
+
+%description
+A Python package providing buffer compression and transformation codecs for use
+in data storage and communication applications.
+
+%prep
+%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
+%pyproject_wheel
+
+%install
+%pyproject_install
+%python_expand %fdupes %{buildroot}%{$python_sitearch}
+
+%check
+%pytest_arch --pyargs numcodecs -rsfE
+
+%files %{python_files}
+%doc README.rst
+%license LICENSE.txt
+%{python_sitearch}/numcodecs
+%{python_sitearch}/numcodecs-%{version}*-info
+
+%changelog
--- a/unbundle-libs.patch
+++ b/unbundle-libs.patch
@ -0,0 +1,48 @@
+Index: numcodecs-0.11.0/setup.py
+===================================================================
+--- 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,
+                  libraries=[] if blosc_sources else ['blosc'],
+                   define_macros=define_macros,
+                   extra_compile_args=extra_compile_args,
+                   ),
+@@ -138,6 +139,7 @@ def zstd_extension():
+         Extension('numcodecs.zstd',
+                   sources=sources + zstd_sources,
+                   include_dirs=include_dirs,
+                  libraries=[] if zstd_sources else ['zstd'],
+                   define_macros=define_macros,
+                   extra_compile_args=extra_compile_args,
+                   ),
+@@ -165,6 +167,7 @@ def lz4_extension():
+         Extension('numcodecs.lz4',
+                   sources=sources + lz4_sources,
+                   include_dirs=include_dirs,
+                  libraries=[] if lz4_sources else ['lz4'],
+                   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)