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Adrian Schröter 2024-05-03 23:36:20 +02:00
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## 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
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*.pdf filter=lfs diff=lfs merge=lfs -text
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*.tbz2 filter=lfs diff=lfs merge=lfs -text
*.tgz filter=lfs diff=lfs merge=lfs -text
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*.zip filter=lfs diff=lfs merge=lfs -text
*.zst filter=lfs diff=lfs merge=lfs -text

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-------------------------------------------------------------------
Fri Jan 19 14:52:05 UTC 2024 - Daniel Garcia <daniel.garcia@suse.com>
- skip broken tests in s390x, gh#zarr-developers/zarr-python#1375
bsc#1218611
-------------------------------------------------------------------
Wed Dec 27 16:02:56 UTC 2023 - Dirk Müller <dmueller@suse.com>
- 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 <mmachova@suse.com>
- 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 <dmueller@suse.com>
- set python311 context for SLE15
-------------------------------------------------------------------
Sun Oct 9 19:15:50 UTC 2022 - Arun Persaud <arun@gmx.de>
- 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 <arun@gmx.de>
- update to version 2.13.2:
* Fix test failure on conda-forge builds (again). By :user:`Josh
Moore <joshmoore>`; see zarr-feedstock#65.
-------------------------------------------------------------------
Tue Sep 27 17:21:04 UTC 2022 - Arun Persaud <arun@gmx.de>
- 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 <arun@gmx.de>
- 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 <arun@gmx.de>
- 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 <mcepl@suse.com>
- 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 <mcepl@suse.com>
- 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 <code@bnavigator.de>
- 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 <code@bnavigator.de>
- 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 <code@bnavigator.de>
- 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 <code@bnavigator.de>
- Initial specfile for v2.6.1
- required by dask

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#
# 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

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