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Implement Zarr V3 protocol #898
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64bbbd8
add v3 store classes
grlee77 85b8e23
add TODO comment to meta.py
grlee77 5fee6fb
Merge remote-tracking branch 'upstream/master' into v3-store-part1
grlee77 983d190
fix flake8 errors
grlee77 4057088
Merge remote-tracking branch 'upstream/master' into v3-store-part1
grlee77 9ed6181
follow zarr v3 spec when dealing with extension data types
grlee77 662e310
fixes to v3 dtype handling
grlee77 9950a4d
Merge remote-tracking branch 'upstream/master' into v3-store-part1
grlee77 450c575
flake8 cleanup
grlee77 63a9e3c
remove duplicate lines in Metadata2.encode_array_metadata
grlee77 1a2a1ef
Fix fields in array metadata
grlee77 bcb2d5f
Fix encode/decode of codec metadata
grlee77 9bfeacb
add missing level to Zlib in _decode_codec_metadata
grlee77 23aca42
add extensions entry to v3 array metadata
grlee77 e47035d
dimension_separator should not be in the array metadata for v3
grlee77 7549d5b
update Attributes, adding StoreV3 support
grlee77 765fe7d
add StoreV3 support to core Array object
grlee77 5efc786
update hexdigests
grlee77 6a308c8
handle additional codecs that were not implemented in zarrita
grlee77 f7883fc
fix
grlee77 5040119
fix hexdigests
grlee77 7c3736d
fix indentation
grlee77 d07caed
add StoreV3 support to Group, open_group, etc.
grlee77 00b2cc0
add StoreV3 support to creation routines
grlee77 504913a
Handle dimension_separator appropriately in open_array
grlee77 7142974
TST: add tests for open_array and dimension_separator
grlee77 e4ce79f
only allow Codec not a simple str as compressor during array initiali…
grlee77 8bef4fc
add StoreV3 support to most convenience routines
grlee77 9478ea3
set convenience routines default to zarr_version=None
grlee77 2c21761
adjust test have dimension_separator key was removed from v3 metadata
grlee77 f28d3d3
Merge branch 'v3-store-part1' into v3-store-part6
grlee77 14a3c05
Merge remote-tracking branch 'upstream/master' into v3-store-part6
grlee77 8783f44
add underscores to imported test classes in test_storage_v3.py
grlee77 4bd99dc
Merge branch 'v3-store-part1' into v3-store-part6
grlee77 981c6b9
add underscore to imported TestArrayWithPath in test_core_v3.py
grlee77 fc5c1c1
refactore _valid_keys and add tests
grlee77 83cf345
move KVStoreV3 logic from StoreV3.__eq__ to KVStoreV3.__eq__
grlee77 1dbce4a
expand tests for _ensure_store
grlee77 5391c46
test exception for v2 store input to _get_hierarchy_metadata
grlee77 6feacdb
test exception for init_array with path=None
grlee77 bf244df
remove unneeded checks from Attributes
grlee77 097459b
tests __repr__ of LazyLoader
grlee77 2f15195
test load of individual array
grlee77 235b445
Add simple test case for zarr.tree convenience method
grlee77 0b82bda
add tests for copy_store with a V3 store class
grlee77 ab71ed5
test raising of exception on intialization with mismatched store and …
grlee77 9bcfb24
add key validation on setitem in v3 stores
grlee77 f4bedd6
Fix core V3 tests now that keys are validated on __setitem__
grlee77 95c0a22
pep8 in storage_v3 tests
grlee77 e321c12
flake8 in test_convenience.py
grlee77 2d9058e
pep8
grlee77 63d8d27
fix test_attrs.py
grlee77 8417dc3
Fix SQLLiteStore
grlee77 b9c9ed4
fix failing hierarchy test
grlee77 efb0b38
update ZipStore tests to make sure they all run on V3
grlee77 d2ee391
add default rmdir implementation to all StoreV3 classes
grlee77 6d1ac20
fix test_sync.py
grlee77 e12adac
all rmdir methods for StoreV3 classes need to remove associated metadata
grlee77 d142da1
avoid warning from test_entropy.py
grlee77 2c8098e
pep8 fixes
grlee77 ae2145a
greatly reduce code duplication in test_storage_v3.py
grlee77 9fa4bdc
remove redundant test_hexdigest methods
grlee77 3291890
move test_core_v3.py functions back into test_core.py
grlee77 1850d88
typing fixes for mypy
grlee77 7524764
can assume self.keys() exists since BaseStore inherits from MutableMa…
grlee77 4824143
refactor rmdir methods for v3 and improve coverage
grlee77 19fcbee
improve coverage of core.py
grlee77 81d1c9a
improve coverage of convenience.py
grlee77 b0a963a
expend info tests
grlee77 2b79be1
Expand tests of Array.view
grlee77 02d9535
improve coverage of creation.py
grlee77 f2dbf7b
improve coverage of hierarchy.py
grlee77 f3378b8
improve coverage of meta.py
grlee77 c86802a
pep8
grlee77 20338c4
skip FSStoreV3 test when fsspec not installed
grlee77 70ea4a5
test raising of PermissionError for setter on views
grlee77 f2982d0
remove redundant check (_normalize_store_arg will already raise here)
grlee77 9bc92c5
improve coverage and fix bugs in normalize_store_arg
grlee77 82be4c9
improve coverage of storage.py
grlee77 8bea4b6
pep8
grlee77 ce64fab
fix StoreV3 tests
grlee77 9de3849
Merge remote-tracking branch 'upstream/master' into v3-store-part6
grlee77 b5a691b
fix duplicate zarr_fsstore entry
grlee77 47e4354
fix rename
grlee77 2415d85
remove debug statements
grlee77 98120df
fix typo
grlee77 a99519c
skip unavailable NumPy dtypes
grlee77 bd613bf
pep8
grlee77 eec4a3e
mypy fixes
grlee77 5970c69
remove redundant check (already done above)
grlee77 77f6fee
remove KeyError check. list_prefix only returns keys that exist
grlee77 f2b3ed8
coverage fixes
grlee77 05fbb2f
Merge remote-tracking branch 'upstream/master' into v3-store-part6
grlee77 347b67d
implemented ConsolidatedMetadataStoreV3
grlee77 0f2d583
expand ConsolidatedMetadataStoreV3 tests
grlee77 0c39bd4
remove debug statement
grlee77 993493b
fix tests: restore clobber=True
grlee77 a08d4f7
test error path in consolidate_metadata
grlee77 43dfa29
add pragma: no cover for lines in test_meta.py that will only be visi…
grlee77 41b052f
flake8 fixes
grlee77 8af6131
flake8
grlee77 001510b
ENH: add ABSStoreV3
grlee77 92f4b80
flake8
grlee77 aa64b7e
Merge remote-tracking branch 'upstream/master' into v3-store-part6
grlee77 c358506
fix ABSStore.rmdir test coverage
grlee77 133ee26
always use / in path
grlee77 652960f
Merge remote-tracking branch 'upstream/master' into v3-store-part6
grlee77 34f6747
remove remaining use of clobber argument in new tests
grlee77 9f56e82
remove NestedDirectoryStoreV3
grlee77 88405a8
flake8
grlee77 87b9543
Merge remote-tracking branch 'upstream/master' into v3-store-part6
grlee77 69e5a12
remove rmdir_abs: rmdir method of ABSStore parent class in ABSStoreV3
grlee77 58c8c20
define meta_root and data_root variables
grlee77 5e1ed7f
move _valid_key_characters to be a StoreV3 class field
grlee77 3593cad
make _get_hierarchy_metadata strictly require 'zarr.json'
grlee77 f036215
ignore type checks for _get_metadata_suffix
grlee77 6f08185
Merge remote-tracking branch 'upstream/master' into v3-store-part6
grlee77 353058d
remove unneeded if/else in Array and Hierarchy class __init__
grlee77 2ec2b2d
remove unused import
grlee77 2b82967
define DEFAULT_ZARR_VERSION so we can later more easily change from 2…
grlee77 7aa5dff
add test_get_hierarchy_metadata to test the v3 _get_hierarchy_metadat…
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Why is this not a method on the store?
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Not sure why I did it that way. I can make this
ABSStore.rmdir
and just call it from there inABSStoreV3.rmdir