Add StoreV3 support to creation.py (zarr v3 support part 5) by grlee77 · Pull Request #897 · zarr-developers/zarr-python

grlee77 · 2021-12-01T03:42:17Z

This PR builds on #896 adding v3 support to the high-level array creation routines.

TODO:

Add unit tests and/or doctests in docstrings
Add docstrings and API docs for any new/modified user-facing classes and functions
New/modified features documented in docs/tutorial.rst
Changes documented in docs/release.rst
GitHub Actions have all passed
Test coverage is 100% (Codecov passes)

Define the StoreV3 class and create v3 versions of most existing stores Add a test_storage_v3.py with test classes inheriting from their v2 counterparts. Only a subset of methods involving differences in v3 behavior were overridden.

codecov · 2021-12-01T03:55:35Z

Codecov Report

Merging #897 (2af0045) into master (de7858a) will decrease coverage by 1.34%.
The diff coverage is 93.06%.

❗ Current head 2af0045 differs from pull request most recent head e4ce79f. Consider uploading reports for the commit e4ce79f to get more accurate results

@@ Coverage Diff @@## master #897 +/- ##
==========================================
- Coverage 99.94% 98.59% -1.35% 
==========================================
Files 32 34 +2 Lines 11216 13486 +2270 ==========================================
+ Hits 11210 13297 +2087 - Misses 6 189 +183

Impacted Files	Coverage Δ
zarr/tests/test_core.py	`98.73% <29.41%> (-1.27%)`	⬇️
zarr/tests/test_storage.py	`99.92% <66.66%> (-0.08%)`	⬇️
zarr/_storage/store.py	`85.25% <77.69%> (-14.75%)`	⬇️
zarr/meta.py	`91.92% <81.74%> (-8.08%)`	⬇️
zarr/creation.py	`98.75% <84.61%> (-1.25%)`	⬇️
zarr/storage.py	`97.04% <89.15%> (-2.96%)`	⬇️
zarr/hierarchy.py	`97.90% <92.64%> (-2.10%)`	⬇️
zarr/attrs.py	`97.05% <92.68%> (-2.95%)`	⬇️
zarr/tests/test_hierarchy.py	`98.58% <94.89%> (-1.42%)`	⬇️
zarr/core.py	`99.73% <96.49%> (-0.27%)`	⬇️
... and 9 more

pep8speaks · 2021-12-15T00:53:08Z

Hello @grlee77! Thanks for updating this PR. We checked the lines you've touched for PEP 8 issues, and found:

There are currently no PEP 8 issues detected in this Pull Request. Cheers! 🍻

Comment last updated at 2021-12-17 22:35:47 UTC

zarr_version should not be in the array metadata, only the base store metadata compressor should be absent when there is no compression

classmethods adapted from zarrita code

avoid pytest error about missing fixture fix flake8 error related to zarr_version fixture

update hexdigests

Specifically, we want to be able to infer the dimension_separator from the store if possible

…zation

grlee77 · 2022-03-04T18:33:46Z

closing, these commits along with additional fixes and tests are incorporated in #898

grlee77 · 2021-12-01T03:42:17Z

This PR builds on #896 adding v3 support to the high-level array creation routines.

TODO:

Add unit tests and/or doctests in docstrings
Add docstrings and API docs for any new/modified user-facing classes and functions
New/modified features documented in docs/tutorial.rst
Changes documented in docs/release.rst
GitHub Actions have all passed
Test coverage is 100% (Codecov passes)

Define the StoreV3 class and create v3 versions of most existing stores Add a test_storage_v3.py with test classes inheriting from their v2 counterparts. Only a subset of methods involving differences in v3 behavior were overridden.

codecov · 2021-12-01T03:55:35Z

Codecov Report

Merging #897 (2af0045) into master (de7858a) will decrease coverage by 1.34%.
The diff coverage is 93.06%.

❗ Current head 2af0045 differs from pull request most recent head e4ce79f. Consider uploading reports for the commit e4ce79f to get more accurate results

@@ Coverage Diff @@## master #897 +/- ##
==========================================
- Coverage 99.94% 98.59% -1.35% 
==========================================
Files 32 34 +2 Lines 11216 13486 +2270 ==========================================
+ Hits 11210 13297 +2087 - Misses 6 189 +183

Impacted Files	Coverage Δ
zarr/tests/test_core.py	`98.73% <29.41%> (-1.27%)`	⬇️
zarr/tests/test_storage.py	`99.92% <66.66%> (-0.08%)`	⬇️
zarr/_storage/store.py	`85.25% <77.69%> (-14.75%)`	⬇️
zarr/meta.py	`91.92% <81.74%> (-8.08%)`	⬇️
zarr/creation.py	`98.75% <84.61%> (-1.25%)`	⬇️
zarr/storage.py	`97.04% <89.15%> (-2.96%)`	⬇️
zarr/hierarchy.py	`97.90% <92.64%> (-2.10%)`	⬇️
zarr/attrs.py	`97.05% <92.68%> (-2.95%)`	⬇️
zarr/tests/test_hierarchy.py	`98.58% <94.89%> (-1.42%)`	⬇️
zarr/core.py	`99.73% <96.49%> (-0.27%)`	⬇️
... and 9 more

pep8speaks · 2021-12-15T00:53:08Z

Hello @grlee77! Thanks for updating this PR. We checked the lines you've touched for PEP 8 issues, and found:

There are currently no PEP 8 issues detected in this Pull Request. Cheers! 🍻

Comment last updated at 2021-12-17 22:35:47 UTC

zarr_version should not be in the array metadata, only the base store metadata compressor should be absent when there is no compression

classmethods adapted from zarrita code

avoid pytest error about missing fixture fix flake8 error related to zarr_version fixture

update hexdigests

Specifically, we want to be able to infer the dimension_separator from the store if possible

…zation

grlee77 · 2022-03-04T18:33:46Z

closing, these commits along with additional fixes and tests are incorporated in #898

grlee77 · 2021-12-01T03:42:17Z

This PR builds on #896 adding v3 support to the high-level array creation routines.

TODO:

Add unit tests and/or doctests in docstrings
Add docstrings and API docs for any new/modified user-facing classes and functions
New/modified features documented in docs/tutorial.rst
Changes documented in docs/release.rst
GitHub Actions have all passed
Test coverage is 100% (Codecov passes)

Define the StoreV3 class and create v3 versions of most existing stores Add a test_storage_v3.py with test classes inheriting from their v2 counterparts. Only a subset of methods involving differences in v3 behavior were overridden.

codecov · 2021-12-01T03:55:35Z

Codecov Report

Merging #897 (2af0045) into master (de7858a) will decrease coverage by 1.34%.
The diff coverage is 93.06%.

❗ Current head 2af0045 differs from pull request most recent head e4ce79f. Consider uploading reports for the commit e4ce79f to get more accurate results

@@ Coverage Diff @@## master #897 +/- ##
==========================================
- Coverage 99.94% 98.59% -1.35% 
==========================================
Files 32 34 +2 Lines 11216 13486 +2270 ==========================================
+ Hits 11210 13297 +2087 - Misses 6 189 +183

Impacted Files	Coverage Δ
zarr/tests/test_core.py	`98.73% <29.41%> (-1.27%)`	⬇️
zarr/tests/test_storage.py	`99.92% <66.66%> (-0.08%)`	⬇️
zarr/_storage/store.py	`85.25% <77.69%> (-14.75%)`	⬇️
zarr/meta.py	`91.92% <81.74%> (-8.08%)`	⬇️
zarr/creation.py	`98.75% <84.61%> (-1.25%)`	⬇️
zarr/storage.py	`97.04% <89.15%> (-2.96%)`	⬇️
zarr/hierarchy.py	`97.90% <92.64%> (-2.10%)`	⬇️
zarr/attrs.py	`97.05% <92.68%> (-2.95%)`	⬇️
zarr/tests/test_hierarchy.py	`98.58% <94.89%> (-1.42%)`	⬇️
zarr/core.py	`99.73% <96.49%> (-0.27%)`	⬇️
... and 9 more

pep8speaks · 2021-12-15T00:53:08Z

Hello @grlee77! Thanks for updating this PR. We checked the lines you've touched for PEP 8 issues, and found:

There are currently no PEP 8 issues detected in this Pull Request. Cheers! 🍻

Comment last updated at 2021-12-17 22:35:47 UTC

zarr_version should not be in the array metadata, only the base store metadata compressor should be absent when there is no compression

classmethods adapted from zarrita code

avoid pytest error about missing fixture fix flake8 error related to zarr_version fixture

update hexdigests

Specifically, we want to be able to infer the dimension_separator from the store if possible

…zation

grlee77 · 2022-03-04T18:33:46Z

closing, these commits along with additional fixes and tests are incorporated in #898

grlee77 · 2021-12-01T03:42:17Z

This PR builds on #896 adding v3 support to the high-level array creation routines.

TODO:

Add unit tests and/or doctests in docstrings
Add docstrings and API docs for any new/modified user-facing classes and functions
New/modified features documented in docs/tutorial.rst
Changes documented in docs/release.rst
GitHub Actions have all passed
Test coverage is 100% (Codecov passes)

Define the StoreV3 class and create v3 versions of most existing stores Add a test_storage_v3.py with test classes inheriting from their v2 counterparts. Only a subset of methods involving differences in v3 behavior were overridden.

codecov · 2021-12-01T03:55:35Z

Codecov Report

Merging #897 (2af0045) into master (de7858a) will decrease coverage by 1.34%.
The diff coverage is 93.06%.

❗ Current head 2af0045 differs from pull request most recent head e4ce79f. Consider uploading reports for the commit e4ce79f to get more accurate results

@@ Coverage Diff @@## master #897 +/- ##
==========================================
- Coverage 99.94% 98.59% -1.35% 
==========================================
Files 32 34 +2 Lines 11216 13486 +2270 ==========================================
+ Hits 11210 13297 +2087 - Misses 6 189 +183

Impacted Files	Coverage Δ
zarr/tests/test_core.py	`98.73% <29.41%> (-1.27%)`	⬇️
zarr/tests/test_storage.py	`99.92% <66.66%> (-0.08%)`	⬇️
zarr/_storage/store.py	`85.25% <77.69%> (-14.75%)`	⬇️
zarr/meta.py	`91.92% <81.74%> (-8.08%)`	⬇️
zarr/creation.py	`98.75% <84.61%> (-1.25%)`	⬇️
zarr/storage.py	`97.04% <89.15%> (-2.96%)`	⬇️
zarr/hierarchy.py	`97.90% <92.64%> (-2.10%)`	⬇️
zarr/attrs.py	`97.05% <92.68%> (-2.95%)`	⬇️
zarr/tests/test_hierarchy.py	`98.58% <94.89%> (-1.42%)`	⬇️
zarr/core.py	`99.73% <96.49%> (-0.27%)`	⬇️
... and 9 more

pep8speaks · 2021-12-15T00:53:08Z

Hello @grlee77! Thanks for updating this PR. We checked the lines you've touched for PEP 8 issues, and found:

There are currently no PEP 8 issues detected in this Pull Request. Cheers! 🍻

Comment last updated at 2021-12-17 22:35:47 UTC

zarr_version should not be in the array metadata, only the base store metadata compressor should be absent when there is no compression

classmethods adapted from zarrita code

avoid pytest error about missing fixture fix flake8 error related to zarr_version fixture

update hexdigests

Specifically, we want to be able to infer the dimension_separator from the store if possible

…zation

grlee77 · 2022-03-04T18:33:46Z

closing, these commits along with additional fixes and tests are incorporated in #898

grlee77 · 2021-12-01T03:42:17Z

This PR builds on #896 adding v3 support to the high-level array creation routines.

TODO:

Add unit tests and/or doctests in docstrings
Add docstrings and API docs for any new/modified user-facing classes and functions
New/modified features documented in docs/tutorial.rst
Changes documented in docs/release.rst
GitHub Actions have all passed
Test coverage is 100% (Codecov passes)

Define the StoreV3 class and create v3 versions of most existing stores Add a test_storage_v3.py with test classes inheriting from their v2 counterparts. Only a subset of methods involving differences in v3 behavior were overridden.

codecov · 2021-12-01T03:55:35Z

Codecov Report

Merging #897 (2af0045) into master (de7858a) will decrease coverage by 1.34%.
The diff coverage is 93.06%.

❗ Current head 2af0045 differs from pull request most recent head e4ce79f. Consider uploading reports for the commit e4ce79f to get more accurate results

@@ Coverage Diff @@## master #897 +/- ##
==========================================
- Coverage 99.94% 98.59% -1.35% 
==========================================
Files 32 34 +2 Lines 11216 13486 +2270 ==========================================
+ Hits 11210 13297 +2087 - Misses 6 189 +183

Impacted Files	Coverage Δ
zarr/tests/test_core.py	`98.73% <29.41%> (-1.27%)`	⬇️
zarr/tests/test_storage.py	`99.92% <66.66%> (-0.08%)`	⬇️
zarr/_storage/store.py	`85.25% <77.69%> (-14.75%)`	⬇️
zarr/meta.py	`91.92% <81.74%> (-8.08%)`	⬇️
zarr/creation.py	`98.75% <84.61%> (-1.25%)`	⬇️
zarr/storage.py	`97.04% <89.15%> (-2.96%)`	⬇️
zarr/hierarchy.py	`97.90% <92.64%> (-2.10%)`	⬇️
zarr/attrs.py	`97.05% <92.68%> (-2.95%)`	⬇️
zarr/tests/test_hierarchy.py	`98.58% <94.89%> (-1.42%)`	⬇️
zarr/core.py	`99.73% <96.49%> (-0.27%)`	⬇️
... and 9 more

pep8speaks · 2021-12-15T00:53:08Z

Hello @grlee77! Thanks for updating this PR. We checked the lines you've touched for PEP 8 issues, and found:

There are currently no PEP 8 issues detected in this Pull Request. Cheers! 🍻

Comment last updated at 2021-12-17 22:35:47 UTC

zarr_version should not be in the array metadata, only the base store metadata compressor should be absent when there is no compression

classmethods adapted from zarrita code

avoid pytest error about missing fixture fix flake8 error related to zarr_version fixture

update hexdigests

Specifically, we want to be able to infer the dimension_separator from the store if possible

…zation

grlee77 · 2022-03-04T18:33:46Z

closing, these commits along with additional fixes and tests are incorporated in #898

grlee77 · 2021-12-01T03:42:17Z

This PR builds on #896 adding v3 support to the high-level array creation routines.

TODO:

Add unit tests and/or doctests in docstrings
Add docstrings and API docs for any new/modified user-facing classes and functions
New/modified features documented in docs/tutorial.rst
Changes documented in docs/release.rst
GitHub Actions have all passed
Test coverage is 100% (Codecov passes)

Define the StoreV3 class and create v3 versions of most existing stores Add a test_storage_v3.py with test classes inheriting from their v2 counterparts. Only a subset of methods involving differences in v3 behavior were overridden.

codecov · 2021-12-01T03:55:35Z

Codecov Report

Merging #897 (2af0045) into master (de7858a) will decrease coverage by 1.34%.
The diff coverage is 93.06%.

❗ Current head 2af0045 differs from pull request most recent head e4ce79f. Consider uploading reports for the commit e4ce79f to get more accurate results

@@ Coverage Diff @@## master #897 +/- ##
==========================================
- Coverage 99.94% 98.59% -1.35% 
==========================================
Files 32 34 +2 Lines 11216 13486 +2270 ==========================================
+ Hits 11210 13297 +2087 - Misses 6 189 +183

Impacted Files	Coverage Δ
zarr/tests/test_core.py	`98.73% <29.41%> (-1.27%)`	⬇️
zarr/tests/test_storage.py	`99.92% <66.66%> (-0.08%)`	⬇️
zarr/_storage/store.py	`85.25% <77.69%> (-14.75%)`	⬇️
zarr/meta.py	`91.92% <81.74%> (-8.08%)`	⬇️
zarr/creation.py	`98.75% <84.61%> (-1.25%)`	⬇️
zarr/storage.py	`97.04% <89.15%> (-2.96%)`	⬇️
zarr/hierarchy.py	`97.90% <92.64%> (-2.10%)`	⬇️
zarr/attrs.py	`97.05% <92.68%> (-2.95%)`	⬇️
zarr/tests/test_hierarchy.py	`98.58% <94.89%> (-1.42%)`	⬇️
zarr/core.py	`99.73% <96.49%> (-0.27%)`	⬇️
... and 9 more

pep8speaks · 2021-12-15T00:53:08Z

Hello @grlee77! Thanks for updating this PR. We checked the lines you've touched for PEP 8 issues, and found:

There are currently no PEP 8 issues detected in this Pull Request. Cheers! 🍻

Comment last updated at 2021-12-17 22:35:47 UTC

zarr_version should not be in the array metadata, only the base store metadata compressor should be absent when there is no compression

classmethods adapted from zarrita code

avoid pytest error about missing fixture fix flake8 error related to zarr_version fixture

update hexdigests

Specifically, we want to be able to infer the dimension_separator from the store if possible

…zation

grlee77 · 2022-03-04T18:33:46Z

closing, these commits along with additional fixes and tests are incorporated in #898

grlee77 · 2021-12-01T03:42:17Z

This PR builds on #896 adding v3 support to the high-level array creation routines.

TODO:

Add unit tests and/or doctests in docstrings
Add docstrings and API docs for any new/modified user-facing classes and functions
New/modified features documented in docs/tutorial.rst
Changes documented in docs/release.rst
GitHub Actions have all passed
Test coverage is 100% (Codecov passes)

Define the StoreV3 class and create v3 versions of most existing stores Add a test_storage_v3.py with test classes inheriting from their v2 counterparts. Only a subset of methods involving differences in v3 behavior were overridden.

codecov · 2021-12-01T03:55:35Z

Codecov Report

Merging #897 (2af0045) into master (de7858a) will decrease coverage by 1.34%.
The diff coverage is 93.06%.

❗ Current head 2af0045 differs from pull request most recent head e4ce79f. Consider uploading reports for the commit e4ce79f to get more accurate results

@@ Coverage Diff @@## master #897 +/- ##
==========================================
- Coverage 99.94% 98.59% -1.35% 
==========================================
Files 32 34 +2 Lines 11216 13486 +2270 ==========================================
+ Hits 11210 13297 +2087 - Misses 6 189 +183

Impacted Files	Coverage Δ
zarr/tests/test_core.py	`98.73% <29.41%> (-1.27%)`	⬇️
zarr/tests/test_storage.py	`99.92% <66.66%> (-0.08%)`	⬇️
zarr/_storage/store.py	`85.25% <77.69%> (-14.75%)`	⬇️
zarr/meta.py	`91.92% <81.74%> (-8.08%)`	⬇️
zarr/creation.py	`98.75% <84.61%> (-1.25%)`	⬇️
zarr/storage.py	`97.04% <89.15%> (-2.96%)`	⬇️
zarr/hierarchy.py	`97.90% <92.64%> (-2.10%)`	⬇️
zarr/attrs.py	`97.05% <92.68%> (-2.95%)`	⬇️
zarr/tests/test_hierarchy.py	`98.58% <94.89%> (-1.42%)`	⬇️
zarr/core.py	`99.73% <96.49%> (-0.27%)`	⬇️
... and 9 more

pep8speaks · 2021-12-15T00:53:08Z

Hello @grlee77! Thanks for updating this PR. We checked the lines you've touched for PEP 8 issues, and found:

There are currently no PEP 8 issues detected in this Pull Request. Cheers! 🍻

Comment last updated at 2021-12-17 22:35:47 UTC

zarr_version should not be in the array metadata, only the base store metadata compressor should be absent when there is no compression

classmethods adapted from zarrita code

avoid pytest error about missing fixture fix flake8 error related to zarr_version fixture

update hexdigests

Specifically, we want to be able to infer the dimension_separator from the store if possible

…zation

grlee77 · 2022-03-04T18:33:46Z

closing, these commits along with additional fixes and tests are incorporated in #898

grlee77 · 2021-12-01T03:42:17Z

This PR builds on #896 adding v3 support to the high-level array creation routines.

TODO:

Add unit tests and/or doctests in docstrings
Add docstrings and API docs for any new/modified user-facing classes and functions
New/modified features documented in docs/tutorial.rst
Changes documented in docs/release.rst
GitHub Actions have all passed
Test coverage is 100% (Codecov passes)

Define the StoreV3 class and create v3 versions of most existing stores Add a test_storage_v3.py with test classes inheriting from their v2 counterparts. Only a subset of methods involving differences in v3 behavior were overridden.

codecov · 2021-12-01T03:55:35Z

Codecov Report

Merging #897 (2af0045) into master (de7858a) will decrease coverage by 1.34%.
The diff coverage is 93.06%.

❗ Current head 2af0045 differs from pull request most recent head e4ce79f. Consider uploading reports for the commit e4ce79f to get more accurate results

@@ Coverage Diff @@## master #897 +/- ##
==========================================
- Coverage 99.94% 98.59% -1.35% 
==========================================
Files 32 34 +2 Lines 11216 13486 +2270 ==========================================
+ Hits 11210 13297 +2087 - Misses 6 189 +183

Impacted Files	Coverage Δ
zarr/tests/test_core.py	`98.73% <29.41%> (-1.27%)`	⬇️
zarr/tests/test_storage.py	`99.92% <66.66%> (-0.08%)`	⬇️
zarr/_storage/store.py	`85.25% <77.69%> (-14.75%)`	⬇️
zarr/meta.py	`91.92% <81.74%> (-8.08%)`	⬇️
zarr/creation.py	`98.75% <84.61%> (-1.25%)`	⬇️
zarr/storage.py	`97.04% <89.15%> (-2.96%)`	⬇️
zarr/hierarchy.py	`97.90% <92.64%> (-2.10%)`	⬇️
zarr/attrs.py	`97.05% <92.68%> (-2.95%)`	⬇️
zarr/tests/test_hierarchy.py	`98.58% <94.89%> (-1.42%)`	⬇️
zarr/core.py	`99.73% <96.49%> (-0.27%)`	⬇️
... and 9 more

pep8speaks · 2021-12-15T00:53:08Z

Hello @grlee77! Thanks for updating this PR. We checked the lines you've touched for PEP 8 issues, and found:

There are currently no PEP 8 issues detected in this Pull Request. Cheers! 🍻

Comment last updated at 2021-12-17 22:35:47 UTC

zarr_version should not be in the array metadata, only the base store metadata compressor should be absent when there is no compression

classmethods adapted from zarrita code

avoid pytest error about missing fixture fix flake8 error related to zarr_version fixture

update hexdigests

Specifically, we want to be able to infer the dimension_separator from the store if possible

…zation

grlee77 · 2022-03-04T18:33:46Z

closing, these commits along with additional fixes and tests are incorporated in #898

grlee77 added 5 commits November 17, 2021 13:30

add v3 store classes
64bbbd8
Define the StoreV3 class and create v3 versions of most existing stores Add a test_storage_v3.py with test classes inheriting from their v2 counterparts. Only a subset of methods involving differences in v3 behavior were overridden.

add TODO comment to meta.py
85b8e23

Merge remote-tracking branch 'upstream/master' into v3-store-part1
5fee6fb

fix flake8 errors
983d190

Merge remote-tracking branch 'upstream/master' into v3-store-part1
4057088

grlee77 mentioned this pull request Dec 1, 2021
Implement Zarr V3 protocol #898
Merged
6 tasks

grlee77 added 3 commits December 14, 2021 19:15

follow zarr v3 spec when dealing with extension data types
9ed6181

fixes to v3 dtype handling
662e310

Merge remote-tracking branch 'upstream/master' into v3-store-part1
9950a4d

grlee77 force-pushed the v3-store-part5 branch from 2af0045 to dd7d237Compare December 15, 2021 00:52

flake8 cleanup
450c575

grlee77 force-pushed the v3-store-part5 branch from dd7d237 to 8e3c443Compare December 15, 2021 14:48

remove duplicate lines in Metadata2.encode_array_metadata
63a9e3c

grlee77 force-pushed the v3-store-part5 branch from 8e3c443 to b0eaa37Compare December 16, 2021 20:43

grlee77 added 14 commits December 16, 2021 22:24

Fix fields in array metadata
1a2a1ef
zarr_version should not be in the array metadata, only the base store metadata compressor should be absent when there is no compression

Fix encode/decode of codec metadata
bcb2d5f
classmethods adapted from zarrita code

add missing level to Zlib in _decode_codec_metadata
9bfeacb

add extensions entry to v3 array metadata
23aca42

dimension_separator should not be in the array metadata for v3
e47035d

update Attributes, adding StoreV3 support
7549d5b
avoid pytest error about missing fixture fix flake8 error related to zarr_version fixture

add StoreV3 support to core Array object
765fe7d

update hexdigests
5efc786

handle additional codecs that were not implemented in zarrita
6a308c8
update hexdigests

fix
f7883fc

fix hexdigests
5040119

fix indentation
7c3736d

add StoreV3 support to Group, open_group, etc.
d07caed

add StoreV3 support to creation routines
00b2cc0

grlee77 added 3 commits December 17, 2021 17:06

Handle dimension_separator appropriately in open_array
504913a
Specifically, we want to be able to infer the dimension_separator from the store if possible

TST: add tests for open_array and dimension_separator
7142974

only allow Codec not a simple str as compressor during array initiali…
e4ce79f
…zation

grlee77 force-pushed the v3-store-part5 branch from b0eaa37 to e4ce79fCompare December 17, 2021 22:35

grlee77 closed this Mar 4, 2022

grlee77 added 5 commits November 17, 2021 13:30

add v3 store classes
64bbbd8
Define the StoreV3 class and create v3 versions of most existing stores Add a test_storage_v3.py with test classes inheriting from their v2 counterparts. Only a subset of methods involving differences in v3 behavior were overridden.

add TODO comment to meta.py
85b8e23

Merge remote-tracking branch 'upstream/master' into v3-store-part1
5fee6fb

fix flake8 errors
983d190

Merge remote-tracking branch 'upstream/master' into v3-store-part1
4057088

grlee77 mentioned this pull request Dec 1, 2021
Implement Zarr V3 protocol #898
Merged
6 tasks

grlee77 added 3 commits December 14, 2021 19:15

follow zarr v3 spec when dealing with extension data types
9ed6181

fixes to v3 dtype handling
662e310

Merge remote-tracking branch 'upstream/master' into v3-store-part1
9950a4d

grlee77 force-pushed the v3-store-part5 branch from 2af0045 to dd7d237Compare December 15, 2021 00:52

flake8 cleanup
450c575

grlee77 force-pushed the v3-store-part5 branch from dd7d237 to 8e3c443Compare December 15, 2021 14:48

remove duplicate lines in Metadata2.encode_array_metadata
63a9e3c

grlee77 force-pushed the v3-store-part5 branch from 8e3c443 to b0eaa37Compare December 16, 2021 20:43

grlee77 added 14 commits December 16, 2021 22:24

Fix fields in array metadata
1a2a1ef
zarr_version should not be in the array metadata, only the base store metadata compressor should be absent when there is no compression

Fix encode/decode of codec metadata
bcb2d5f
classmethods adapted from zarrita code

add missing level to Zlib in _decode_codec_metadata
9bfeacb

add extensions entry to v3 array metadata
23aca42

dimension_separator should not be in the array metadata for v3
e47035d

update Attributes, adding StoreV3 support
7549d5b
avoid pytest error about missing fixture fix flake8 error related to zarr_version fixture

add StoreV3 support to core Array object
765fe7d

update hexdigests
5efc786

handle additional codecs that were not implemented in zarrita
6a308c8
update hexdigests

fix
f7883fc

fix hexdigests
5040119

fix indentation
7c3736d

add StoreV3 support to Group, open_group, etc.
d07caed

add StoreV3 support to creation routines
00b2cc0

grlee77 added 3 commits December 17, 2021 17:06

Handle dimension_separator appropriately in open_array
504913a
Specifically, we want to be able to infer the dimension_separator from the store if possible

TST: add tests for open_array and dimension_separator
7142974

only allow Codec not a simple str as compressor during array initiali…
e4ce79f
…zation

grlee77 force-pushed the v3-store-part5 branch from b0eaa37 to e4ce79fCompare December 17, 2021 22:35

grlee77 closed this Mar 4, 2022

grlee77 added 5 commits November 17, 2021 13:30

add v3 store classes
64bbbd8
Define the StoreV3 class and create v3 versions of most existing stores Add a test_storage_v3.py with test classes inheriting from their v2 counterparts. Only a subset of methods involving differences in v3 behavior were overridden.

add TODO comment to meta.py
85b8e23

Merge remote-tracking branch 'upstream/master' into v3-store-part1
5fee6fb

fix flake8 errors
983d190

Merge remote-tracking branch 'upstream/master' into v3-store-part1
4057088

grlee77 mentioned this pull request Dec 1, 2021
Implement Zarr V3 protocol #898
Merged
6 tasks

grlee77 added 3 commits December 14, 2021 19:15

follow zarr v3 spec when dealing with extension data types
9ed6181

fixes to v3 dtype handling
662e310

Merge remote-tracking branch 'upstream/master' into v3-store-part1
9950a4d

grlee77 force-pushed the v3-store-part5 branch from 2af0045 to dd7d237Compare December 15, 2021 00:52

flake8 cleanup
450c575

grlee77 force-pushed the v3-store-part5 branch from dd7d237 to 8e3c443Compare December 15, 2021 14:48

remove duplicate lines in Metadata2.encode_array_metadata
63a9e3c

grlee77 force-pushed the v3-store-part5 branch from 8e3c443 to b0eaa37Compare December 16, 2021 20:43

grlee77 added 14 commits December 16, 2021 22:24

Fix fields in array metadata
1a2a1ef
zarr_version should not be in the array metadata, only the base store metadata compressor should be absent when there is no compression

Fix encode/decode of codec metadata
bcb2d5f
classmethods adapted from zarrita code

add missing level to Zlib in _decode_codec_metadata
9bfeacb

add extensions entry to v3 array metadata
23aca42

dimension_separator should not be in the array metadata for v3
e47035d

update Attributes, adding StoreV3 support
7549d5b
avoid pytest error about missing fixture fix flake8 error related to zarr_version fixture

add StoreV3 support to core Array object
765fe7d

update hexdigests
5efc786

handle additional codecs that were not implemented in zarrita
6a308c8
update hexdigests

fix
f7883fc

fix hexdigests
5040119

fix indentation
7c3736d

add StoreV3 support to Group, open_group, etc.
d07caed

add StoreV3 support to creation routines
00b2cc0

grlee77 added 3 commits December 17, 2021 17:06

Handle dimension_separator appropriately in open_array
504913a
Specifically, we want to be able to infer the dimension_separator from the store if possible

TST: add tests for open_array and dimension_separator
7142974

only allow Codec not a simple str as compressor during array initiali…
e4ce79f
…zation

grlee77 force-pushed the v3-store-part5 branch from b0eaa37 to e4ce79fCompare December 17, 2021 22:35

grlee77 closed this Mar 4, 2022

grlee77 added 5 commits November 17, 2021 13:30

add v3 store classes
64bbbd8
Define the StoreV3 class and create v3 versions of most existing stores Add a test_storage_v3.py with test classes inheriting from their v2 counterparts. Only a subset of methods involving differences in v3 behavior were overridden.

add TODO comment to meta.py
85b8e23

Merge remote-tracking branch 'upstream/master' into v3-store-part1
5fee6fb

fix flake8 errors
983d190

Merge remote-tracking branch 'upstream/master' into v3-store-part1
4057088

grlee77 mentioned this pull request Dec 1, 2021
Implement Zarr V3 protocol #898
Merged
6 tasks

grlee77 added 3 commits December 14, 2021 19:15

follow zarr v3 spec when dealing with extension data types
9ed6181

fixes to v3 dtype handling
662e310

Merge remote-tracking branch 'upstream/master' into v3-store-part1
9950a4d

grlee77 force-pushed the v3-store-part5 branch from 2af0045 to dd7d237Compare December 15, 2021 00:52

flake8 cleanup
450c575

grlee77 force-pushed the v3-store-part5 branch from dd7d237 to 8e3c443Compare December 15, 2021 14:48

remove duplicate lines in Metadata2.encode_array_metadata
63a9e3c

grlee77 force-pushed the v3-store-part5 branch from 8e3c443 to b0eaa37Compare December 16, 2021 20:43

grlee77 added 14 commits December 16, 2021 22:24

Fix fields in array metadata
1a2a1ef
zarr_version should not be in the array metadata, only the base store metadata compressor should be absent when there is no compression

Fix encode/decode of codec metadata
bcb2d5f
classmethods adapted from zarrita code

add missing level to Zlib in _decode_codec_metadata
9bfeacb

add extensions entry to v3 array metadata
23aca42

dimension_separator should not be in the array metadata for v3
e47035d

update Attributes, adding StoreV3 support
7549d5b
avoid pytest error about missing fixture fix flake8 error related to zarr_version fixture

add StoreV3 support to core Array object
765fe7d

update hexdigests
5efc786

handle additional codecs that were not implemented in zarrita
6a308c8
update hexdigests

fix
f7883fc

fix hexdigests
5040119

fix indentation
7c3736d

add StoreV3 support to Group, open_group, etc.
d07caed

add StoreV3 support to creation routines
00b2cc0

grlee77 added 3 commits December 17, 2021 17:06

Handle dimension_separator appropriately in open_array
504913a
Specifically, we want to be able to infer the dimension_separator from the store if possible

TST: add tests for open_array and dimension_separator
7142974

only allow Codec not a simple str as compressor during array initiali…
e4ce79f
…zation

grlee77 force-pushed the v3-store-part5 branch from b0eaa37 to e4ce79fCompare December 17, 2021 22:35

grlee77 closed this Mar 4, 2022

grlee77 added 5 commits November 17, 2021 13:30

add v3 store classes
64bbbd8
Define the StoreV3 class and create v3 versions of most existing stores Add a test_storage_v3.py with test classes inheriting from their v2 counterparts. Only a subset of methods involving differences in v3 behavior were overridden.

add TODO comment to meta.py
85b8e23

Merge remote-tracking branch 'upstream/master' into v3-store-part1
5fee6fb

fix flake8 errors
983d190

Merge remote-tracking branch 'upstream/master' into v3-store-part1
4057088

grlee77 mentioned this pull request Dec 1, 2021
Implement Zarr V3 protocol #898
Merged
6 tasks

grlee77 added 3 commits December 14, 2021 19:15

follow zarr v3 spec when dealing with extension data types
9ed6181

fixes to v3 dtype handling
662e310

Merge remote-tracking branch 'upstream/master' into v3-store-part1
9950a4d

grlee77 force-pushed the v3-store-part5 branch from 2af0045 to dd7d237Compare December 15, 2021 00:52

flake8 cleanup
450c575

grlee77 force-pushed the v3-store-part5 branch from dd7d237 to 8e3c443Compare December 15, 2021 14:48

remove duplicate lines in Metadata2.encode_array_metadata
63a9e3c

grlee77 force-pushed the v3-store-part5 branch from 8e3c443 to b0eaa37Compare December 16, 2021 20:43

grlee77 added 14 commits December 16, 2021 22:24

Fix fields in array metadata
1a2a1ef
zarr_version should not be in the array metadata, only the base store metadata compressor should be absent when there is no compression

Fix encode/decode of codec metadata
bcb2d5f
classmethods adapted from zarrita code

add missing level to Zlib in _decode_codec_metadata
9bfeacb

add extensions entry to v3 array metadata
23aca42

dimension_separator should not be in the array metadata for v3
e47035d

update Attributes, adding StoreV3 support
7549d5b
avoid pytest error about missing fixture fix flake8 error related to zarr_version fixture

add StoreV3 support to core Array object
765fe7d

update hexdigests
5efc786

handle additional codecs that were not implemented in zarrita
6a308c8
update hexdigests

fix
f7883fc

fix hexdigests
5040119

fix indentation
7c3736d

add StoreV3 support to Group, open_group, etc.
d07caed

add StoreV3 support to creation routines
00b2cc0

grlee77 added 3 commits December 17, 2021 17:06

Handle dimension_separator appropriately in open_array
504913a
Specifically, we want to be able to infer the dimension_separator from the store if possible

TST: add tests for open_array and dimension_separator
7142974

only allow Codec not a simple str as compressor during array initiali…
e4ce79f
…zation

grlee77 force-pushed the v3-store-part5 branch from b0eaa37 to e4ce79fCompare December 17, 2021 22:35

grlee77 closed this Mar 4, 2022

grlee77 added 5 commits November 17, 2021 13:30

add v3 store classes
64bbbd8
Define the StoreV3 class and create v3 versions of most existing stores Add a test_storage_v3.py with test classes inheriting from their v2 counterparts. Only a subset of methods involving differences in v3 behavior were overridden.

add TODO comment to meta.py
85b8e23

Merge remote-tracking branch 'upstream/master' into v3-store-part1
5fee6fb

fix flake8 errors
983d190

Merge remote-tracking branch 'upstream/master' into v3-store-part1
4057088

grlee77 mentioned this pull request Dec 1, 2021
Implement Zarr V3 protocol #898
Merged
6 tasks

grlee77 added 3 commits December 14, 2021 19:15

follow zarr v3 spec when dealing with extension data types
9ed6181

fixes to v3 dtype handling
662e310

Merge remote-tracking branch 'upstream/master' into v3-store-part1
9950a4d

grlee77 force-pushed the v3-store-part5 branch from 2af0045 to dd7d237Compare December 15, 2021 00:52

flake8 cleanup
450c575

grlee77 force-pushed the v3-store-part5 branch from dd7d237 to 8e3c443Compare December 15, 2021 14:48

remove duplicate lines in Metadata2.encode_array_metadata
63a9e3c

grlee77 force-pushed the v3-store-part5 branch from 8e3c443 to b0eaa37Compare December 16, 2021 20:43

grlee77 added 14 commits December 16, 2021 22:24

Fix fields in array metadata
1a2a1ef
zarr_version should not be in the array metadata, only the base store metadata compressor should be absent when there is no compression

Fix encode/decode of codec metadata
bcb2d5f
classmethods adapted from zarrita code

add missing level to Zlib in _decode_codec_metadata
9bfeacb

add extensions entry to v3 array metadata
23aca42

dimension_separator should not be in the array metadata for v3
e47035d

update Attributes, adding StoreV3 support
7549d5b
avoid pytest error about missing fixture fix flake8 error related to zarr_version fixture

add StoreV3 support to core Array object
765fe7d

update hexdigests
5efc786

handle additional codecs that were not implemented in zarrita
6a308c8
update hexdigests

fix
f7883fc

fix hexdigests
5040119

fix indentation
7c3736d

add StoreV3 support to Group, open_group, etc.
d07caed

add StoreV3 support to creation routines
00b2cc0

grlee77 added 3 commits December 17, 2021 17:06

Handle dimension_separator appropriately in open_array
504913a
Specifically, we want to be able to infer the dimension_separator from the store if possible

TST: add tests for open_array and dimension_separator
7142974

only allow Codec not a simple str as compressor during array initiali…
e4ce79f
…zation

grlee77 force-pushed the v3-store-part5 branch from b0eaa37 to e4ce79fCompare December 17, 2021 22:35

grlee77 closed this Mar 4, 2022

grlee77 added 5 commits November 17, 2021 13:30

add v3 store classes
64bbbd8
Define the StoreV3 class and create v3 versions of most existing stores Add a test_storage_v3.py with test classes inheriting from their v2 counterparts. Only a subset of methods involving differences in v3 behavior were overridden.

add TODO comment to meta.py
85b8e23

Merge remote-tracking branch 'upstream/master' into v3-store-part1
5fee6fb

fix flake8 errors
983d190

Merge remote-tracking branch 'upstream/master' into v3-store-part1
4057088

grlee77 mentioned this pull request Dec 1, 2021
Implement Zarr V3 protocol #898
Merged
6 tasks

grlee77 added 3 commits December 14, 2021 19:15

follow zarr v3 spec when dealing with extension data types
9ed6181

fixes to v3 dtype handling
662e310

Merge remote-tracking branch 'upstream/master' into v3-store-part1
9950a4d

grlee77 force-pushed the v3-store-part5 branch from 2af0045 to dd7d237Compare December 15, 2021 00:52

flake8 cleanup
450c575

grlee77 force-pushed the v3-store-part5 branch from dd7d237 to 8e3c443Compare December 15, 2021 14:48

remove duplicate lines in Metadata2.encode_array_metadata
63a9e3c

grlee77 force-pushed the v3-store-part5 branch from 8e3c443 to b0eaa37Compare December 16, 2021 20:43

grlee77 added 14 commits December 16, 2021 22:24

Fix fields in array metadata
1a2a1ef
zarr_version should not be in the array metadata, only the base store metadata compressor should be absent when there is no compression

Fix encode/decode of codec metadata
bcb2d5f
classmethods adapted from zarrita code

add missing level to Zlib in _decode_codec_metadata
9bfeacb

add extensions entry to v3 array metadata
23aca42

dimension_separator should not be in the array metadata for v3
e47035d

update Attributes, adding StoreV3 support
7549d5b
avoid pytest error about missing fixture fix flake8 error related to zarr_version fixture

add StoreV3 support to core Array object
765fe7d

update hexdigests
5efc786

handle additional codecs that were not implemented in zarrita
6a308c8
update hexdigests

fix
f7883fc

fix hexdigests
5040119

fix indentation
7c3736d

add StoreV3 support to Group, open_group, etc.
d07caed

add StoreV3 support to creation routines
00b2cc0

grlee77 added 3 commits December 17, 2021 17:06

Handle dimension_separator appropriately in open_array
504913a
Specifically, we want to be able to infer the dimension_separator from the store if possible

TST: add tests for open_array and dimension_separator
7142974

only allow Codec not a simple str as compressor during array initiali…
e4ce79f
…zation

grlee77 force-pushed the v3-store-part5 branch from b0eaa37 to e4ce79fCompare December 17, 2021 22:35

grlee77 closed this Mar 4, 2022

grlee77 added 5 commits November 17, 2021 13:30

add v3 store classes
64bbbd8
Define the StoreV3 class and create v3 versions of most existing stores Add a test_storage_v3.py with test classes inheriting from their v2 counterparts. Only a subset of methods involving differences in v3 behavior were overridden.

add TODO comment to meta.py
85b8e23

Merge remote-tracking branch 'upstream/master' into v3-store-part1
5fee6fb

fix flake8 errors
983d190

Merge remote-tracking branch 'upstream/master' into v3-store-part1
4057088

grlee77 mentioned this pull request Dec 1, 2021
Implement Zarr V3 protocol #898
Merged
6 tasks

grlee77 added 3 commits December 14, 2021 19:15

follow zarr v3 spec when dealing with extension data types
9ed6181

fixes to v3 dtype handling
662e310

Merge remote-tracking branch 'upstream/master' into v3-store-part1
9950a4d

grlee77 force-pushed the v3-store-part5 branch from 2af0045 to dd7d237Compare December 15, 2021 00:52

flake8 cleanup
450c575

grlee77 force-pushed the v3-store-part5 branch from dd7d237 to 8e3c443Compare December 15, 2021 14:48

remove duplicate lines in Metadata2.encode_array_metadata
63a9e3c

grlee77 force-pushed the v3-store-part5 branch from 8e3c443 to b0eaa37Compare December 16, 2021 20:43

grlee77 added 14 commits December 16, 2021 22:24

Fix fields in array metadata
1a2a1ef
zarr_version should not be in the array metadata, only the base store metadata compressor should be absent when there is no compression

Fix encode/decode of codec metadata
bcb2d5f
classmethods adapted from zarrita code

add missing level to Zlib in _decode_codec_metadata
9bfeacb

add extensions entry to v3 array metadata
23aca42

dimension_separator should not be in the array metadata for v3
e47035d

update Attributes, adding StoreV3 support
7549d5b
avoid pytest error about missing fixture fix flake8 error related to zarr_version fixture

add StoreV3 support to core Array object
765fe7d

update hexdigests
5efc786

handle additional codecs that were not implemented in zarrita
6a308c8
update hexdigests

fix
f7883fc

fix hexdigests
5040119

fix indentation
7c3736d

add StoreV3 support to Group, open_group, etc.
d07caed

add StoreV3 support to creation routines
00b2cc0

grlee77 added 3 commits December 17, 2021 17:06

Handle dimension_separator appropriately in open_array
504913a
Specifically, we want to be able to infer the dimension_separator from the store if possible

TST: add tests for open_array and dimension_separator
7142974

only allow Codec not a simple str as compressor during array initiali…
e4ce79f
…zation

grlee77 force-pushed the v3-store-part5 branch from b0eaa37 to e4ce79fCompare December 17, 2021 22:35

grlee77 closed this Mar 4, 2022

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