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Merged
merged 39 commits into from
Apr 9, 2025
Merged

(feat): zarr v3 guide #1948

merged 39 commits into from
Apr 9, 2025

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ilan-gold
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@ilan-gold ilan-gold commented Mar 31, 2025

  • Closes #
  • Tests added
  • Release note added (or unnecessary)

Rendered

@ilan-gold ilan-gold changed the title (feat): zarr v3 guid (feat): zarr v3 guide Mar 31, 2025
@ilan-gold ilan-gold added this to the 0.12.0 milestone Mar 31, 2025
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codecov bot commented Mar 31, 2025

Codecov Report

Attention: Patch coverage is 75.00000% with 2 lines in your changes missing coverage. Please review.

Project coverage is 84.79%. Comparing base (6d9eb08) to head (1f25a0d).
Report is 1 commits behind head on main.

Files with missing lines Patch % Lines
src/anndata/_io/specs/methods.py 75.00% 2 Missing ⚠️
Additional details and impacted files
@@             Coverage Diff             @@
##             main    #1948       +/-   ##
===========================================
+ Coverage   24.85%   84.79%   +59.93%     
===========================================
  Files          46       47        +1     
  Lines        6904     6918       +14     
===========================================
+ Hits         1716     5866     +4150     
+ Misses       5188     1052     -4136     
Files with missing lines Coverage Δ
src/anndata/_io/specs/methods.py 89.34% <75.00%> (+78.39%) ⬆️

... and 46 files with indirect coverage changes

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@ilan-gold ilan-gold marked this pull request as ready for review March 31, 2025 14:53
@ilan-gold ilan-gold requested a review from flying-sheep April 1, 2025 09:16
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Hi, the text is mostly great, nicely structured! I commented on the few cases where I got confused.

First of all it’s always nice when a PR is about 1-2 docs pages to provide links in your initial PR comment (“PR body”? I never know how to refer to that text box).

Something like

### [Rendered](https://icb-anndata--1948.com.readthedocs.build/en/1948/zarr-v3.html)

Please start using one sentence per line in markup documents, that way I can actually comment on what I want to comment on instead of one giant paragraph. I did it myself this time so I could comment.

Please also use typography:

  • En-dashes: “–” (very easy to type on your MacBook: Alt/option+-)
  • Times symbol: “×” (avoids confusion between AnnData.X and factors like “2×”)

Co-authored-by: Philipp A. <flying-sheep@web.de>
ilan-gold and others added 2 commits April 4, 2025 18:28
Co-authored-by: Philipp A. <flying-sheep@web.de>
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@flying-sheep I update the notebook a bit to use the new public data url and also added a note about obstore among some other minor cleanups.

@ilan-gold ilan-gold requested a review from flying-sheep April 7, 2025 13:33
@ilan-gold ilan-gold requested a review from flying-sheep April 8, 2025 12:54

Local data generally poses a different set of challenges.
First, write speeds can be somewhat slow and second, the creation of many small files on a file system can slow down a filesystem.
For the "many small files" problem, `zarr` has introduced `{ref} sharding <zarr:user-guide-sharding>` in the v3 file format.
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@flying-sheep flying-sheep Apr 8, 2025

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this is still broken:

grafik

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looks good apart from the broken syntax, please fix that before merging

@ilan-gold ilan-gold merged commit 8466510 into main Apr 9, 2025
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@ilan-gold ilan-gold deleted the ig/zarr_v3_doc branch April 9, 2025 09:27
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2 participants