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Merged
meggart merged 3 commits into from
Jun 6, 2023
Merged

add support for 0-dimensional arrays/scalars #117

meggart merged 3 commits into from
Jun 6, 2023

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@ilia-kats
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@ilia-kats ilia-kats commented Apr 28, 2023

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ilia-kats added a commit to scverse/Muon.jl that referenced this pull request Apr 28, 2023
@ilia-kats
add basic Zarr support
735cd1a 
Only non-backed reading works currently. This requires
JuliaIO/Zarr.jl#116 and
JuliaIO/Zarr.jl#117
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nhz2 commented May 1, 2023

A few questions.

Why is the single chunk named "0" for 0-dimensional arrays? Is that part of the Zarr spec somewhere?

Also, could the scalar value be stored Base64 encoded in the array fill value, and then not have any chunks?

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ilia-kats commented May 1, 2023

I have to admit the spec is somewhat ambiguous with regard to zero-dimensional arrays, but the Python reference implementation has hardcoded chunk 0, but otherwise treats zero-dimensional arrays as any other array, so I don't think the value is ever stored in the fill value.

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@joshmoore joshmoore mentioned this pull request May 2, 2023
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LGTM

@meggart meggart merged commit 26f7ed0 into JuliaIO:master Jun 6, 2023
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meggart commented Jun 6, 2023

Thanks a lot and sorry for taking so long to review. Make sure to ping me next time if there is no reaction.

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coveralls commented May 20, 2024

Pull Request Test Coverage Report for Build 4853403590

Warning: This coverage report may be inaccurate.

This pull request's base commit is no longer the HEAD commit of its target branch. This means it includes changes from outside the original pull request, including, potentially, unrelated coverage changes.

Details

  • 7 of 9 (77.78%) changed or added relevant lines in 3 files are covered.
  • 10 unchanged lines in 2 files lost coverage.
  • Overall coverage increased (+0.07%) to 86.461%
Changes Missing Coverage Covered Lines Changed/Added Lines %
src/Compressors.jl 4 6 66.67%
Files with Coverage Reduction New Missed Lines %
src/Compressors.jl 3 91.07%
src/metadata.jl 7 78.89%
Totals Coverage Status
Change from base Build 4698045635: 0.07%
Covered Lines: 728
Relevant Lines: 842
💛 - Coveralls

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coveralls commented May 20, 2024

Pull Request Test Coverage Report for Build 4853403590

Warning: This coverage report may be inaccurate.

This pull request's base commit is no longer the HEAD commit of its target branch. This means it includes changes from outside the original pull request, including, potentially, unrelated coverage changes.

Details

  • 7 of 9 (77.78%) changed or added relevant lines in 3 files are covered.
  • 10 unchanged lines in 2 files lost coverage.
  • Overall coverage increased (+0.07%) to 86.461%
Changes Missing Coverage Covered Lines Changed/Added Lines %
src/Compressors.jl 4 6 66.67%
Files with Coverage Reduction New Missed Lines %
src/Compressors.jl 3 91.07%
src/metadata.jl 7 78.89%
Totals Coverage Status
Change from base Build 4698045635: 0.07%
Covered Lines: 728
Relevant Lines: 842
💛 - Coveralls

ilia-kats added a commit to scverse/Muon.jl that referenced this pull request Aug 26, 2025
@ilia-kats
Implement support for Zarr read/write
92c546d 
Squashed commit of the following:

commit 649aa0a
Author: Ilia Kats <ilia-kats@gmx.net>
Date:   Tue Aug 26 15:11:46 2025 +0200

    enable unit tests for Zarr and make them pass

commit 8ed25ed
Author: Ilia Kats <ilia-kats@gmx.net>
Date:   Mon Aug 25 18:17:58 2025 +0200

    make tests pass again

commit 17bb1b2
Author: Ilia Kats <ilia-kats@gmx.net>
Date:   Mon Aug 25 16:09:11 2025 +0200

    update JuliaFormatter config and reformat everything

commit a702865
Author: Ilia Kats <ilia-kats@gmx.net>
Date:   Mon Aug 25 16:07:06 2025 +0200

    implement support for writing Zarr files

commit db9abf9
Merge: ef4d948 eefb2c6
Author: Ilia Kats <ilia-kats@gmx.net>
Date:   Fri Aug 22 15:20:40 2025 +0200

    Merge branch 'main' into zarr

commit ef4d948
Author: Ilia Kats <ilia-kats@gmx.net>
Date:   Fri Apr 28 15:00:31 2023 +0200

    split reading into separate functions for hdf5 and zarr

commit 22bde93
Author: Ilia Kats <ilia-kats@gmx.net>
Date:   Fri Apr 28 14:19:33 2023 +0200

    Zarr for mudata, some bugfixes for backed storage

commit c61faba
Author: Ilia Kats <ilia-kats@gmx.net>
Date:   Fri Apr 28 13:35:12 2023 +0200

    initial Zarr-backed AnnData support

commit 735cd1a
Author: Ilia Kats <ilia-kats@gmx.net>
Date:   Fri Apr 28 10:09:29 2023 +0200

    add basic Zarr support

    Only non-backed reading works currently. This requires
    JuliaIO/Zarr.jl#116 and
    JuliaIO/Zarr.jl#117
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@meggart meggart meggart approved these changes

@nhz2 nhz2 nhz2 approved these changes

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