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chore: move to zarr#25

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ilan-gold merged 4 commits into
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ig/more_zarr
May 20, 2026
Merged

chore: move to zarr#25
ilan-gold merged 4 commits into
mainfrom
ig/more_zarr

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@ilan-gold
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Turns out most of tutorials are using zarr anyway!

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@ilan-gold ilan-gold requested a review from Zethson May 17, 2026 13:44
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One row per sentence please to make this more reviewable.

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  1. A getting started tutorial should not have warnings like
/var/folders/k9/9wc7lvwj2g34_r74kn6cr0nr0000gn/T/ipykernel_12269/2319192822.py:5: FutureWarning: `__version__` is deprecated, use `importlib.metadata.version('anndata')` instead.
  print(ad.__version__)

and

/var/folders/k9/9wc7lvwj2g34_r74kn6cr0nr0000gn/T/ipykernel_12269/2822107891.py:2: FutureWarning: Automatic reshaping when setting X will be removed in the future.
  adata[:3, 'Gene_1'].X = [0, 0, 0]
/var/folders/k9/9wc7lvwj2g34_r74kn6cr0nr0000gn/T/ipykernel_12269/2822107891.py:2: ImplicitModificationWarning: Setting element `.X` of view, initializing view as actual.
  adata[:3, 'Gene_1'].X = [0, 0, 0]
  1. Maybe we should have a dropdown that explains more details about hdf5 & zarr and when to use what?

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Maybe we should have a dropdown that explains more details about hdf5 & zarr and when to use what?

I added a bit more, but not sure why it should be a dropdown since the info is important. There's so much to say but I tried to wrap it up a bit into the main points - parallelism and async.

@ilan-gold ilan-gold requested a review from Zethson May 18, 2026 17:17
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Nit: This is still on a single line:

Read/Write operations on h5ad and Zarr are supported. One should note that the lazy objects are materialized when this is called. For now, the anndata loaded from file won't be loaded with dask arrays in it. zarr is generally much faster due to the lack of a read-lock.

@ilan-gold ilan-gold merged commit 3ead7c9 into main May 20, 2026
@ilan-gold ilan-gold deleted the ig/more_zarr branch May 20, 2026 15:22
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2 participants