add support for variable-length strings #116
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ilia-kats
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Only non-backed reading works currently. This requires JuliaIO/Zarr.jl#116 and JuliaIO/Zarr.jl#117
meggart
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Jun 6, 2023
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Thanks a lot for preparing this PR. It would be really nice to have VLenUTF8 support in here. I think technically the PR would be breaking because dumping a string vector into a zarr array would result into a different representation on disk as before. So I would make sure bunp the minor version in this PR to not forget.
| struct SenMissArray{T,N} <: AbstractArray{Union{T,Missing},N} | ||
| x::Array{T,N} | ||
| senval::T | ||
| end |
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I knwo this was a quite ad-hoc definition of SenMissArray, probably better to keep the sentinel value in a struct field instead of a type parameter. Now that the idea was taken up also here: https://github.com/JuliaData/SentinelArrays.jl it might be an option to just use that implementation. This should not stop this PR from being merged though.
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Pull Request Test Coverage Report for Build 4819746815Warning: 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.
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ilia-kats
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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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This uses the
vlen-utf8filter, which is one of the standard filters included with Python-Zarr.