Skip to content

Conversation

@ilan-gold
Copy link
Contributor

@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
@codecov
Copy link

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 36 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

🚀 New features to boost your workflow:
  • ❄️ Test Analytics: Detect flaky tests, report on failures, and find test suite problems.

@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
Copy link
Member

@flying-sheep flying-sheep left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

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×”)

@ilan-gold
Copy link
Contributor Author

@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.
Copy link
Member

@flying-sheep flying-sheep Apr 8, 2025

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

this is still broken:

grafik

Copy link
Member

@flying-sheep flying-sheep left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

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

@ilan-gold ilan-gold merged commit 8466510 into main Apr 9, 2025
14 checks passed
@ilan-gold ilan-gold deleted the ig/zarr_v3_doc branch April 9, 2025 09:27
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment

Projects

None yet

Development

Successfully merging this pull request may close these issues.

2 participants