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Add semantic dimension identifier to concat API #1244

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merged 29 commits into from
Jun 3, 2024
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@flying-sheep flying-sheep commented Nov 28, 2023

Follows the consensus axis/axis_name

@flying-sheep flying-sheep changed the title Concat API needs dim Concat API lacks semantic dimension identifier Nov 28, 2023
@flying-sheep flying-sheep changed the title Concat API lacks semantic dimension identifier Add semantic dimension identifier to concat API Nov 28, 2023
@flying-sheep flying-sheep marked this pull request as draft November 28, 2023 10:39
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codecov bot commented Nov 28, 2023

Codecov Report

Attention: Patch coverage is 97.36842% with 1 line in your changes missing coverage. Please review.

Project coverage is 84.34%. Comparing base (1bff5fb) to head (f346188).
Report is 59 commits behind head on main.

Files with missing lines Patch % Lines
src/anndata/experimental/merge.py 93.75% 1 Missing ⚠️
Additional details and impacted files
@@            Coverage Diff             @@
##             main    #1244      +/-   ##
==========================================
+ Coverage   84.27%   84.34%   +0.06%     
==========================================
  Files          35       35              
  Lines        5693     5685       -8     
==========================================
- Hits         4798     4795       -3     
+ Misses        895      890       -5     
Files with missing lines Coverage Δ
src/anndata/_core/aligned_mapping.py 91.96% <100.00%> (ø)
src/anndata/_core/anndata.py 84.96% <100.00%> (ø)
src/anndata/_core/merge.py 84.17% <100.00%> (+0.64%) ⬆️
src/anndata/utils.py 84.21% <100.00%> (ø)
src/anndata/experimental/merge.py 91.37% <93.75%> (ø)

@flying-sheep flying-sheep added this to the 0.10.4 milestone Nov 28, 2023
@flying-sheep flying-sheep marked this pull request as ready for review November 29, 2023 11:26
@flying-sheep flying-sheep self-assigned this Dec 7, 2023
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@ivirshup ivirshup left a comment

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I commented on the original issue, but basically would like to discuss this.

To me, you are proposing that we do a broad API change of introducing a keyword argument dim which is analogous to axis, but refers to the axes as "obs", "var" instead of 0, 1. I would like to at least discuss the implications of this, especially considering that we allow names to be set dynamically on the dimensions. Let's do this on the issue.

I also would not consider this a bug fix as it introduces a new element to the API.

@flying-sheep flying-sheep modified the milestones: 0.10.4, 0.10.5 Jan 4, 2024
@ivirshup ivirshup modified the milestones: 0.10.5, 0.11.0 Jan 23, 2024
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@flying-sheep flying-sheep requested a review from ivirshup January 23, 2024 12:55
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A couple points.

It would also be good to address the missing coverage on the added code.

  • axis_size may be able to just get deleted
  • dim_len could probably get deleted (was it used somewhere?), or it should get a deprecation test

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@flying-sheep flying-sheep requested a review from ivirshup February 2, 2024 14:20
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all done, including the axis_size and dim_len parts

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@flying-sheep could you merge main on this one?

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done!

@flying-sheep flying-sheep enabled auto-merge (squash) June 3, 2024 09:12
@flying-sheep flying-sheep merged commit 90c76dd into main Jun 3, 2024
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@flying-sheep flying-sheep deleted the fix-concat-api branch June 3, 2024 09:31
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Concat API lacks semantic dimension identifier
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