From fec790dd513758b83272b6e86c9308bcf5070058436bc7c2d1588ca4aceac6b3 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Adrian=20Schr=C3=B6ter?= Date: Fri, 3 May 2024 23:36:20 +0200 Subject: [PATCH] Sync from SUSE:SLFO:Main python-zarr revision 9f0ec741ee293492eff4a6dd06a22886 --- .gitattributes | 23 +++ python-zarr.changes | 340 ++++++++++++++++++++++++++++++++++++++++++++ python-zarr.spec | 96 +++++++++++++ zarr-2.16.1.tar.gz | 3 + 4 files changed, 462 insertions(+) create mode 100644 .gitattributes create mode 100644 python-zarr.changes create mode 100644 python-zarr.spec create mode 100644 zarr-2.16.1.tar.gz diff --git a/.gitattributes b/.gitattributes new file mode 100644 index 0000000..9b03811 --- /dev/null +++ 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 diff --git a/python-zarr.changes b/python-zarr.changes new file mode 100644 index 0000000..93a9d0c --- /dev/null +++ b/python-zarr.changes @@ -0,0 +1,340 @@ +------------------------------------------------------------------- +Fri Jan 19 14:52:05 UTC 2024 - Daniel Garcia + +- skip broken tests in s390x, gh#zarr-developers/zarr-python#1375 + bsc#1218611 + +------------------------------------------------------------------- +Wed Dec 27 16:02:56 UTC 2023 - Dirk Müller + +- update to 2.16.1: + * Require ``setuptools_scm`` version ``1.5.4``\+ + * Add ``docs`` requirements to ``pyproject.toml`` + * Fixed caching issue in ``LRUStoreCache``. + +------------------------------------------------------------------- +Tue Aug 1 13:24:34 UTC 2023 - Markéta Machová + +- update to version 2.16 + * Migrate to pyproject.toml and remove redundant infrastructure. + * Require setuptools 64.0.0+ + * Bump to NumPy 1.20+ in environment.yml. + * More maintenance changes, special thanks to Outreachy participants + for contributing to most of the maintenance PRs. + * Improve Zarr V3 support, adding partial store read/write and + storage transformers. + * N5 nows supports Blosc. Remove warnings emitted when using N5Store + or N5FSStore with a blosc-compressed array. + * Implement more extensive fallback of getitem/setitem for + orthogonal indexing. + * Getitems supports meta_array. + * Allow for partial codec specification in V3 array metadata. + * Implemented blockwise (chunk blocks) indexing to zarr.Array. + +------------------------------------------------------------------- +Thu Jul 27 09:47:45 UTC 2023 - Dirk Müller + +- set python311 context for SLE15 + +------------------------------------------------------------------- +Sun Oct 9 19:15:50 UTC 2022 - Arun Persaud + +- update to version 2.13.3: + * Improve performance of slice selections with steps by omitting + chunks with no relevant data. By Richard Shaw #843. + +------------------------------------------------------------------- +Wed Sep 28 13:11:03 UTC 2022 - Arun Persaud + +- update to version 2.13.2: + * Fix test failure on conda-forge builds (again). By :user:`Josh + Moore `; see zarr-feedstock#65. + +------------------------------------------------------------------- +Tue Sep 27 17:21:04 UTC 2022 - Arun Persaud + +- update to version 2.13.1: + * Fix test failure on conda-forge builds. By Josh Moore; see + zarr-feedstock#65. + +------------------------------------------------------------------- +Sun Sep 25 20:17:30 UTC 2022 - Arun Persaud + +- specfile: + * requrie python >= 3.8 + +- update to version 2.13.0: + * Major changes + + Support of alternative array classes by introducing a new + argument, meta_array, that specifies the type/class of the + underlying array. The meta_array argument can be any class + instance that can be used as the like argument in NumPy (see NEP + 35). enabling support for CuPy through, for example, the + creation of a CuPy CPU compressor. By Mads R. B. Kristensen + #934. + + Remove support for Python 3.7 in concert with NumPy + dependency. By Davis Bennett #1067. + + Zarr v3: add support for the default root path rather than + requiring that all API users pass an explicit path. By Gregory + R. Lee #1085, #1142. + * Bug fixes + + Remove/relax erroneous “meta” path check (regression). By + Gregory R. Lee #1123. + + Cast all attribute keys to strings (and issue deprecation + warning). By Mattia Almansi #1066. + + Fix bug in N5 storage that prevented arrays located in the root + of the hierarchy from bearing the n5 keyword. Along with fixing + this bug, new tests were added for N5 routines that had + previously been excluded from testing, and type annotations were + added to the N5 codebase. By Davis Bennett #1092. + + Fix bug in LRUEStoreCache in which the current size wasn’t reset + on invalidation. By BGCMHou and Josh Moore #1076, #1077. + + Remove erroneous check that disallowed array keys starting with + “meta”. By Gregory R. Lee #1105. + * Documentation + + Typo fixes to close quotes. By Pavithra Eswaramoorthy + + Added copy button to documentation. By Altay Sansal #1124. + * Maintenance + + Simplify release docs. By Josh Moore #1119. + + Pin werkzeug to prevent test hangs. By Davis Bennett #1098. + + Fix a few DeepSource.io alerts By Dimitri Papadopoulos Orfanos + #1080. + + Fix URLs. By Dimitri Papadopoulos Orfanos, #1074. + + Fix spelling. By Dimitri Papadopoulos Orfanos, #1073. + + Update GitHub issue templates with YAML format. By Saransh + Chopra #1079. + + Remove option to return None from _ensure_store. By Greggory Lee + #1068. + + Fix a typo of “integers”. By Richard Scott #1056. + +------------------------------------------------------------------- +Sun Aug 21 15:21:17 UTC 2022 - Arun Persaud + +- specfile: + * update copyright year + +- update to version 2.12.0: + * Enhancements + + Add support for reading and writing Zarr V3. The new + zarr._store.v3 package has the necessary classes and functions + for evaluating Zarr V3. Since the format is not yet finalized, + the classes and functions are not automatically imported into + the regular zarr name space. Setting the + ZARR_V3_EXPERIMENTAL_API environment variable will activate + them. By Greggory Lee; #898, #1006, and #1007 as well as by Josh + Moore #1032. + + Create FSStore from an existing fsspec filesystem. If you have + created an fsspec filesystem outside of Zarr, you can now pass + it as a keyword argument to FSStore. By Ryan Abernathey; #911. + + Add numpy encoder class for json.dumps By Eric Prestat; #933. + + Appending performance improvement to Zarr arrays, e.g., when + writing to S3. By hailiangzhang; #1014. + + Add number encoder for json.dumps to support numpy intergers in + chunks arguments. By Eric Prestat #697. + * Bug fixes + + Fix bug that made it impossible to create an FSStore on + unlistable filesystems (e.g. some HTTP servers). By Ryan + Abernathey; #993. + * Documentation + + Update resize doc to clarify surprising behavior. By + hailiangzhang; #1022. + * Maintenance + + Added Pre-commit configuration, incl. Yaml Check. By Shivank + Chaudhary; #1015, #1016. + + Fix URL to renamed file in Blosc repo. By Andrew Thomas #1028. + + Activate Py 3.10 builds. By Josh Moore #1027. + + Make all unignored zarr warnings errors. By Josh Moore #1021. + +- changes from version 2.11.3: + * Bug fixes + + Fix missing case to fully revert change to default + write_empty_chunks. By Tom White; #1005. + +- changes from version 2.11.2: + * Bug fixes + + Changes the default value of write_empty_chunks to True to + prevent unanticipated data losses when the data types do not + have a proper default value when empty chunks are read back + in. By Vyas Ramasubramani; #965, #1001. + +- changes from version 2.11.1: + * Bug fixes + + Fix bug where indexing with a scalar numpy value returned a + single-value array. By Ben Jeffery #967. + + Removed clobber argument from normalize_store_arg. This enables + to change data within a opened consolidated group using mode + “r+” (i.e region write). By Tobias Kölling #975. + +- changes from version 2.11.0: + * Enhancements + + Sparse changes with performance impact! One of the advantages of + the Zarr format is that it is sparse, which means that chunks + with no data (more precisely, with data equal to the fill value, + which is usually 0) don’t need to be written to disk at + all. They will simply be assumed to be empty at read + time. However, until this release, the Zarr library would write + these empty chunks to disk anyway. This changes in this version: + a small performance penalty at write time leads to significant + speedups at read time and in filesystem operations in the case + of sparse arrays. To revert to the old behavior, pass the + argument write_empty_chunks=True to the array creation + function. By Juan Nunez-Iglesias; #853 and Davis Bennett; #738. + + Fancy indexing. Zarr arrays now support NumPy-style fancy + indexing with arrays of integer coordinates. This is equivalent + to using zarr.Array.vindex. Mixing slices and integer arrays is + not supported. By Juan Nunez-Iglesias; #725. + + New base class. This release of Zarr Python introduces a new + BaseStore class that all provided store classes implemented in + Zarr Python now inherit from. This is done as part of + refactoring to enable future support of the Zarr version 3 + spec. Existing third-party stores that are a MutableMapping + (e.g. dict) can be converted to a new-style key/value store + inheriting from BaseStore by passing them as the argument to the + new zarr.storage.KVStore class. For backwards compatibility, + various higher-level array creation and convenience functions + still accept plain Python dicts or other mutable mappings for + the store argument, but will internally convert these to a + KVStore. By Greggory Lee; #839, #789, and #950. + + Allow to assign array fill_values and update metadata + accordingly. By Ryan Abernathey, #662. + + Allow to update array fill_values By Matthias Bussonnier #665. + * Bug fixes + + Fix bug where the checksum of zipfiles is wrong By Oren Watson + #930. + + Fix consolidate_metadata with FSStore. By Joe Hamman #916. + + Unguarded next inside generator. By Dimitri Papadopoulos Orfanos + #889. + * Documentation + + Update docs creation of dev env. By Ray Bell #921. + + Update docs to use python -m pytest. By Ray Bell #923. + + Fix versionadded tag in zarr.core.Array docstring. By Juan + Nunez-Iglesias #852. + + Doctest seem to be stricter now, updating tostring() to + tobytes(). By John Kirkham #907. + + Minor doc fix. By Mads R. B. Kristensen #937. + * Maintenance + + Upgrade MongoDB in test env. By Joe Hamman #939. + + Pass dimension_separator on fixture generation. By Josh Moore + #858. + + Activate Python 3.9 in GitHub Actions. By Josh Moore #859. + + Drop shortcut fsspec[s3] for dependency. By Josh Moore #920. + + and a swath of code-linting improvements by Dimitri Papadopoulos + Orfanos: + o Unnecessary comprehension (#899) + o Unnecessary None provided as default (#900) + o use an if expression instead of and/or (#888) + o Remove unnecessary literal (#891) + o Decorate a few method with @staticmethod (#885) + o Drop unneeded return (#884) + o Drop explicit object inheritance from class-es (#886) + o Unnecessary comprehension (#883) + o Codespell configuration (#882) + o Fix typos found by codespell (#880) + o Proper C-style formatting for integer (#913) + o Add LGTM.com / DeepSource.io configuration files (#909) + +- changes from version 2.10.3: + * Bug fixes + + N5 keywords now emit UserWarning instead of raising a + ValueError. By Boaz Mohar; #860. + + blocks_to_decompress not used in read_part function. By Boaz + Mohar; #861. + + defines blocksize for array, updates hexdigest values. By Andrew + Fulton; #867. + + Fix test failure on Debian and conda-forge builds. By Josh + Moore; #871. + +- changes from version 2.10.2: + * Bug fixes + + Fix NestedDirectoryStore datasets without dimension_separator + metadata. By Josh Moore; #850. + +- changes from version 2.10.1: + * Bug fixes + + Fix regression by setting normalize_keys=False in fsstore + constructor. By Davis Bennett; #842. + +- changes from version 2.10.0: + * Enhancements + + Add N5FSStore. By Davis Bennett; #793. + * Bug fixes + + Ignore None dim_separators in save_array. By Josh Moore; #831. + +------------------------------------------------------------------- +Wed Sep 1 09:34:16 UTC 2021 - Matej Cepl + +- Update to 2.9.5: + - Fix FSStore.listdir behavior for nested directories (replaces + now unnecessary skip-825-TestFSStore-test_create.patch). + - Fix structured arrays that contain objects (which replaces + zarr-pr802-fsspec-2021-07.patch). + +------------------------------------------------------------------- +Sat Aug 28 08:54:39 UTC 2021 - Matej Cepl + +- Update to 2.9.3: + - Mark the fact that some tests that require fsspec, without + compromising the code coverage score. By Ben Williams; #823. + - Only inspect alternate node type if desired isn’t + present. By Trevor Manz; #696. + - Correct conda-forge deployment of Zarr by fixing some Zarr + tests. By Ben Williams; #821. +- Add skip-825-TestFSStore-test_create.patch + (gh#zarr-developers/zarr-python#825). + +------------------------------------------------------------------- +Mon Aug 23 16:51:52 UTC 2021 - Ben Greiner + +- Update to version 2.9.0 + * This release of Zarr Python is the first release of Zarr to not + support Python 3.6. + * Update ABSStore for compatibility with newer azure.storage. + blob. + * Pathlib support. + * Fix dimension_separator support. + * Extract ABSStore to zarr._storage.absstore. + * TST: add missing assert in test_hexdigest. +- Add zarr-pr802-fsspec-2021-07.patch + * gh#zarr-developers/zarr-python#802 + * gh#zarr-developers/zarr-python#812 + +------------------------------------------------------------------- +Fri Jul 16 15:07:21 UTC 2021 - Ben Greiner + +- Update to v2.8.3 + * FSStore: default to normalize_keys=False +- Release 2.8.2 + * Add section on rechunking to tutorial + * Expand FSStore tests and fix implementation issues + * Updated ipytree warning for jlab3 + * Update Python classifiers (Zarr is stable!) +- Release 2.8.1 + * raise an error if create_dataset’s dimension_separator is + inconsistent +- Release 2.8.0 + * V2 Specification Update + * Introduce optional dimension_separator .zarray key for nested + chunks. +- Release 2.7.1 + * Update Array to respect FSStore’s key_separator (#718) +- Release 2.7.0 + * Start stop for iterator (islice()) + * Add capability to partially read and decompress chunks + * Make DirectoryStore __setitem__ resilient against antivirus + file locking + * Compare test data’s content generally + * Fix dtype usage in zarr/meta.py + * Fix FSStore key_seperator usage + * Simplify text handling in DB Store + +------------------------------------------------------------------- +Wed Feb 17 21:08:29 UTC 2021 - Ben Greiner + +- Requires numpy: NEP 29, NumPy 1.20 in TW dropped Python 3.6 + support. Skip python36 build. + +------------------------------------------------------------------- +Mon Dec 28 12:16:28 UTC 2020 - Benjamin Greiner + +- Initial specfile for v2.6.1 +- required by dask diff --git a/python-zarr.spec b/python-zarr.spec new file mode 100644 index 0000000..d798095 --- /dev/null +++ b/python-zarr.spec @@ -0,0 +1,96 @@ +# +# spec file for package python-zarr +# +# Copyright (c) 2024 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/ +# + + +%{?sle15_python_module_pythons} +Name: python-zarr +Version: 2.16.1 +Release: 0 +Summary: An implementation of chunked, compressed, N-dimensional arrays for Python +License: MIT +URL: https://github.com/zarr-developers/zarr-python +Source: https://files.pythonhosted.org/packages/source/z/zarr/zarr-%{version}.tar.gz +BuildRequires: %{python_module pip} +BuildRequires: %{python_module setuptools >= 64.0.0} +BuildRequires: %{python_module setuptools_scm > 1.5.4} +BuildRequires: %{python_module wheel} +BuildRequires: fdupes +BuildRequires: python-rpm-macros +# Needs full python stdlib, base is not enough +Requires: python >= 3.8 +Requires: python-asciitree +Requires: python-fasteners +Requires: python-numcodecs >= 0.6.4 +Requires: python-numpy >= 1.20 +Suggests: python-dbm +Suggests: python-fsspec >= 0.8.4 +Suggests: python-ipytree +Suggests: python-msgpack +Suggests: python-notebook +BuildArch: noarch +# SECTION test requirements +BuildRequires: %{python_module asciitree} +BuildRequires: %{python_module dbm} +BuildRequires: %{python_module fasteners} +BuildRequires: %{python_module fsspec >= 0.8.4} +BuildRequires: %{python_module msgpack} +BuildRequires: %{python_module numcodecs >= 0.6.4} +BuildRequires: %{python_module numpy >= 1.20} +BuildRequires: %{python_module pytest} +# Needs full python stdlib, base is not enough +BuildRequires: %{pythons} >= 3.8 +# /SECTION +%python_subpackages + +%description +An implementation of chunked, compressed, N-dimensional arrays for Python. + +%prep +%autosetup -p1 -n zarr-%{version} + +%build +export SETUPTOOLS_SCM_PRETEND_VERSION=%{version} +%pyproject_wheel + +%install +export SETUPTOOLS_SCM_PRETEND_VERSION=%{version} +%pyproject_install +%python_expand %fdupes %{buildroot}%{$python_sitelib} + +%check +# avoid broken tests in s390x, gh#zarr-developers/zarr-python#1375 +%if "%_arch" == "s390x" +donttest="test_hexdigest or test_nbytes_stored" +donttest+=" or test_array_1d or test_array_1d_fill_value or test_array_1d_selections" +donttest+=" or test_array_2d or test_array_2d_edge_case or test_array_order" +donttest+=" or test_resize_2d or test_append_2d or test_append_2d_axis" +donttest+=" or test_np_ufuncs or test_iter or test_islice or test_non_cont" +donttest+=" or test_read_nitems_less_than_blocksize_from_multiple_chunks" +donttest+=" or test_read_from_all_blocks" +donttest+=" or test_format_compatibility" +%pytest -k "not ($donttest)" +%else +%pytest +%endif + +%files %{python_files} +%doc README.md +%license LICENSE.txt +%{python_sitelib}/zarr +%{python_sitelib}/zarr-%{version}*-info + +%changelog diff --git a/zarr-2.16.1.tar.gz b/zarr-2.16.1.tar.gz new file mode 100644 index 0000000..fdda426 --- /dev/null +++ b/zarr-2.16.1.tar.gz @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:4276cf4b4a653431042cd53ff2282bc4d292a6842411e88529964504fb073286 +size 3597771