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Manifest arrays use arrayv3metadata #429

Merged
merged 81 commits into from
Feb 18, 2025
Merged

Manifest arrays use arrayv3metadata #429

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2a01bfa
Added zarray_to_v3metadata and test
abarciauskas-bgse Feb 4, 2025
17fd547
Working on manifest array tests
abarciauskas-bgse Feb 5, 2025
e5666ab
Fix test_manifests/test_array#TestConcat tests
abarciauskas-bgse Feb 5, 2025
5a8cc4c
Passing TestStack tests and add fixture
abarciauskas-bgse Feb 5, 2025
4c0b616
All test_manifests/test_array tests passing
abarciauskas-bgse Feb 6, 2025
ac2f787
Compressors should be list
abarciauskas-bgse Feb 6, 2025
5503c60
Passing dmrpp tests
abarciauskas-bgse Feb 6, 2025
1272051
Merge branch 'main' into manifest-arrays-use-arrayv3metadata
abarciauskas-bgse Feb 6, 2025
1f36755
Passing test_hdf.py tests
abarciauskas-bgse Feb 6, 2025
7098803
Start to work on kerchunk tests
abarciauskas-bgse Feb 6, 2025
ce2284c
Add method to convert array v3 metadata to v2 metadata for kerchunk (…
abarciauskas-bgse Feb 7, 2025
c9853d5
Fix fixtures and mark xfail netcdf3
abarciauskas-bgse Feb 7, 2025
209dae3
Test for convert_v3_to_v2_metadata
abarciauskas-bgse Feb 7, 2025
e7205ef
Deduplicate fixture for array v3 metadata
abarciauskas-bgse Feb 7, 2025
d65e457
Parse filters and compressors from v3 metdata for v2 metadata
abarciauskas-bgse Feb 7, 2025
190c20f
Rewrite extract_codecs
abarciauskas-bgse Feb 7, 2025
47f5ddd
Refactor convert_to_codec_pipeline
abarciauskas-bgse Feb 8, 2025
5d15608
Fix hdf integration tests
abarciauskas-bgse Feb 8, 2025
908bc52
Test for convert_to_codec_pipeline
abarciauskas-bgse Feb 8, 2025
4a8bfdd
Refactor get_codecs and its tests
abarciauskas-bgse Feb 8, 2025
d05cec3
Fix most integration tests and writer tests
abarciauskas-bgse Feb 9, 2025
ff23eeb
Fix xarray tests
abarciauskas-bgse Feb 9, 2025
8560f2d
Working on integration tests
abarciauskas-bgse Feb 9, 2025
97d0a71
Add expected type
abarciauskas-bgse Feb 10, 2025
669ce52
Mark datetime tests xfail
abarciauskas-bgse Feb 10, 2025
b794dab
Upgrade xarray for tests
abarciauskas-bgse Feb 10, 2025
825142d
xfail some unsupported zarr-python 3 data types
abarciauskas-bgse Feb 10, 2025
6684125
Require zarr
abarciauskas-bgse Feb 10, 2025
5e82de4
Remove zarr dep
abarciauskas-bgse Feb 10, 2025
f57b48d
import zarr, explicit dependency
abarciauskas-bgse Feb 10, 2025
b811959
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Feb 10, 2025
8c5139b
Add zarr as a dependency
abarciauskas-bgse Feb 11, 2025
eb2a86c
Merge branch 'manifest-arrays-use-arrayv3metadata' of github.com:zarr…
abarciauskas-bgse Feb 11, 2025
15ac7a7
Merge branch 'main' into manifest-arrays-use-arrayv3metadata
abarciauskas-bgse Feb 11, 2025
5359762
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Feb 11, 2025
c808351
Min numcodecs version
abarciauskas-bgse Feb 12, 2025
bd50167
numcodecs>=0.15.1 in environment and upstream.yml conda env files
abarciauskas-bgse Feb 12, 2025
ed97704
Working on mypy errors
abarciauskas-bgse Feb 12, 2025
a3c190e
Fix mypy errors and tests
abarciauskas-bgse Feb 12, 2025
95886b9
Remove ZArray class
abarciauskas-bgse Feb 12, 2025
a0f72b2
Just return metadata's shape
abarciauskas-bgse Feb 12, 2025
aad511f
Create update metadata function
abarciauskas-bgse Feb 12, 2025
b357b04
Fix typing for update_metadata
abarciauskas-bgse Feb 12, 2025
08e877a
Check for regular chunk grid in manifest instantiation
abarciauskas-bgse Feb 12, 2025
f040459
Remove obsolete codecs code
abarciauskas-bgse Feb 12, 2025
495d660
Fix chunks function and add docstring
abarciauskas-bgse Feb 12, 2025
a262f0b
Remove custom zattrs type
abarciauskas-bgse Feb 12, 2025
bcd68a0
Move some imports and make update_metadata a private method
abarciauskas-bgse Feb 12, 2025
f0ce778
Remove zarr.py
abarciauskas-bgse Feb 12, 2025
0518488
Add zarr to other ci env files
abarciauskas-bgse Feb 13, 2025
0712979
Fixture array_v3_metadata uses array_v3_metadata_dict
abarciauskas-bgse Feb 13, 2025
c40915d
No need for union type for CodecPipeline
abarciauskas-bgse Feb 13, 2025
cdaca53
Use type alias
abarciauskas-bgse Feb 13, 2025
2415e07
Add comment
abarciauskas-bgse Feb 13, 2025
9366d69
Update virtualizarr/manifests/array_api.py
abarciauskas-bgse Feb 13, 2025
d590cfc
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Feb 13, 2025
6394207
Revised copy_and_replace_metadata to be in utils and called correctly
abarciauskas-bgse Feb 13, 2025
ea9fd56
Update virtualizarr/translators/kerchunk.py
abarciauskas-bgse Feb 13, 2025
0ee2b48
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Feb 13, 2025
86d1de5
Refactor create v3 array metadata
abarciauskas-bgse Feb 13, 2025
fe8305f
Rename to create_v3_array_metadata
abarciauskas-bgse Feb 13, 2025
0f5b32d
Fix some codecs fixtures
abarciauskas-bgse Feb 13, 2025
97bc7cd
Use global vars and simple fixture for creating codec pipelines
abarciauskas-bgse Feb 13, 2025
b5a1dc6
Remove redundant create_codec_pipeline fixture
abarciauskas-bgse Feb 13, 2025
12c6260
Fix docstring
abarciauskas-bgse Feb 13, 2025
4b555b6
Use create_v3_array_metadata in from_kerchunk_refs
abarciauskas-bgse Feb 13, 2025
c245b0a
Add links to zarr-python 3.0 issues for big endian, datetime and time…
abarciauskas-bgse Feb 14, 2025
23ac776
Reorganize conftest
abarciauskas-bgse Feb 14, 2025
402af7f
Remove obsolete comment
abarciauskas-bgse Feb 15, 2025
3e2e8ec
Rename function numcodec_config_to_configurable
abarciauskas-bgse Feb 15, 2025
92293a6
Fix parameters in docstring for convert_to_codec_pipeline
abarciauskas-bgse Feb 15, 2025
eccc215
Revert change to pytest mark skipif for astropy
abarciauskas-bgse Feb 15, 2025
8fa72b2
Remove commented arguments
abarciauskas-bgse Feb 15, 2025
f747681
Add classes to test_codecs and make zarr_array a fixture
abarciauskas-bgse Feb 15, 2025
ba2e467
Add tests for extract_codecs
abarciauskas-bgse Feb 16, 2025
68695c9
Add test for get_codec_config
abarciauskas-bgse Feb 16, 2025
f22bf96
Remove obsolete comment
abarciauskas-bgse Feb 17, 2025
8af37a0
Add test for copy_and_replace_metadata
abarciauskas-bgse Feb 17, 2025
d4946ab
Add release notes
abarciauskas-bgse Feb 17, 2025
2c43c61
Attempt to fix rst links
abarciauskas-bgse Feb 17, 2025
05cd57a
Move convert_v3_to_v2_metadata to utils
abarciauskas-bgse Feb 18, 2025
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5 changes: 3 additions & 2 deletions ci/environment.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -14,7 +14,7 @@ dependencies:
- packaging
- universal_pathlib
- hdf5plugin
- numcodecs
- numcodecs>=0.15.1
- icechunk>=0.1.1
# Testing
- codecov[toml]
Expand All @@ -36,5 +36,6 @@ dependencies:
# for opening FITS files
- astropy
- pip
- zarr>=3.0.2
- pip:
- imagecodecs-numcodecs==2024.6.1
- imagecodecs-numcodecs==2024.6.1
5 changes: 3 additions & 2 deletions ci/min-deps.yml
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Expand Up @@ -6,9 +6,9 @@ dependencies:
- h5py
- hdf5
- netcdf4
- xarray>=2024.10.0
- xarray>=2025.1.1
- numpy>=2.0.0
- numcodecs
- numcodecs>=0.15.1
- packaging
- ujson
- universal_pathlib
Expand All @@ -23,3 +23,4 @@ dependencies:
- pytest
- pooch
- fsspec
- zarr>=3.0.2
3 changes: 2 additions & 1 deletion ci/upstream.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -13,7 +13,7 @@ dependencies:
- ujson
- universal_pathlib
- hdf5plugin
- numcodecs
- numcodecs>=0.15.1
- imagecodecs>=2024.6.1
# Testing
- codecov[toml]
Expand All @@ -28,6 +28,7 @@ dependencies:
- pooch
- fsspec
- pip
- zarr>=3.0.2
- pip:
- git+https://github.com/earth-mover/icechunk.git@main#subdirectory=icechunk-python # Installs zarr-python v3.0.0 as dependency
- git+https://github.com/fsspec/kerchunk.git@main
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