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(feat): support for zarr-python>=3 #1726

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ilan-gold wants to merge 71 commits intomainscverse/anndata:mainfrom ig/zarr_v3scverse/anndata:ig/zarr_v3Copy head branch name to clipboard

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Commits

Commits on Oct 21, 2024

• (wip): support for new zarr version

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Commits on Nov 18, 2024

• Merge branch 'main' into ig/zarr_v3

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• (chore): create setting for write version

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• (fix): pathing issue

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• (chore): use open_group

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• (fix): another zarr.open

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• (fix): zarr_write_version -> zarr_write_format

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Commits on Dec 5, 2024

• (feat): batched reading for sparse

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• (fix): object codec

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• Merge branch 'main' into ig/zarr_v3

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• (fix): revert compressed vectors

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• (feat): scalar support

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• (fix): open_group for v3

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• (fix): backed sparse copy method

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Commits on Dec 8, 2024

• (fix): add speed-up for zarr by batching indexing

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• (fix): no __len__ on new zarr arrays

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Commits on Jan 9, 2025

• (fix): some v3 fixes

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Commits on Jan 10, 2025

• Merge branch 'main' into ig/zarr_v3

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• Specify mode with kwarg

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• chore: typing fixes

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Commits on Jan 13, 2025

• Merge branch 'ig/zarr_v3' of github.com:scverse/anndata into ig/zarr_v3

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• (fix): more create_dataset args

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Commits on Jan 14, 2025

• Merge branch 'main' into ig/zarr_v3

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• format->version

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• clear properly

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• dynamic format/version

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• Centralize version comparison

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• Fix most create_dataset errors

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• unpin zarr everywhere

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• Almost fix docs

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• (fix): compression test

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• (fix): tracking store

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Commits on Jan 15, 2025

• (fix): as_group mode arg

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• (fix): temporary fix for writing from zarr array

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• (fix): more context issues

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• (fix): no chunks bool arg

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• (fix): return item for array

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• (chore): add issue

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Commits on Jan 16, 2025

• Bump scanpydoc version

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• Merge branch 'main' into ig/zarr_v3

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Commits on Jan 20, 2025

• Merge branch 'main' into ig/zarr_v3

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• (chore): add zarr v2 test

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• (chore): add warning for zarr v2

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• (fix): fix tracking tests for zarr v2

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• (chore): refactor a bit

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Commits on Jan 21, 2025

• (fix): revert zarr v2 test

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• (fix): setting on group test

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Commits on Jan 24, 2025

• (fix): reopening issue

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• (fix): using zip files for backwards compat

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• Merge branch 'main' into ig/zarr_v3

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• (fix): temporary fix for empty

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• (fix): io dispatched keys test

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• (fix): sparse array access tracking

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• (fix): more reopen zarr store

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• [pre-commit.ci] auto fixes from pre-commit.com hooks

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Commits on Jan 27, 2025

• (fix): lazy reading

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• Merge branch 'ig/zarr_v3' of github.com:scverse/anndata into ig/zarr_v3

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Commits on Feb 2, 2025

• Merge branch 'main' into ig/zarr_v3

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Commits on Feb 3, 2025

• (fix): ensure v2 group is made

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• (fix): add visititems

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• (fix): point zarr at main

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• Merge branch 'ig/zarr_v3' of github.com:scverse/anndata into ig/zarr_v3

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• (fix): don't provide VLenUTF8Codec for default string

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• (fix): doctest

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Commits on Feb 4, 2025

• (fix): move off the zarr main branch

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• (fix): pin zarr in benchmarks

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• (feat): zarr v2 handling in tests

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• (fix): warning on zarr.open

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• (fix): create_array instead of create_dataset

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• Merge branch 'main' into ig/zarr_v3

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