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Fix shape inference for X=None #1121

Merged
merged 19 commits into from Sep 8, 2023
Merged

Fix shape inference for X=None #1121

merged 19 commits into from Sep 8, 2023

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flying-sheep
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@flying-sheep flying-sheep commented Sep 5, 2023

TODO:

  • Views (basically just check that .X = None doesn't change other view behavior, a[idx].X doesn't do anything weird, and copying views still works)
    unclear if that’s covered @ivirshup can you clarify the scope of this?
  • Figure out inference of AnnData shape when X is None

Later:

  • Backed mode
  • Concatenation
  • IO tests
  • Specialized writers like to_csvs
  • Raw

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codecov bot commented Sep 5, 2023

Codecov Report

Merging #1121 (e1c19c1) into main (2c8759d) will decrease coverage by 2.07%.
The diff coverage is 97.14%.

Additional details and impacted files
@@            Coverage Diff             @@
##             main    #1121      +/-   ##
==========================================
- Coverage   84.75%   82.68%   -2.07%     
==========================================
  Files          36       36              
  Lines        5149     5153       +4     
==========================================
- Hits         4364     4261     -103     
- Misses        785      892     +107     
Flag Coverage Δ
gpu-tests ?

Flags with carried forward coverage won't be shown. Click here to find out more.

Files Changed Coverage Δ
anndata/_core/anndata.py 83.60% <96.96%> (+0.80%) ⬆️
anndata/_core/raw.py 79.28% <100.00%> (-4.17%) ⬇️

... and 6 files with indirect coverage changes

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@flying-sheep flying-sheep added this to the 0.10.0 milestone Sep 5, 2023
@flying-sheep flying-sheep marked this pull request as draft September 5, 2023 15:40
@flying-sheep flying-sheep changed the title Finish up X=None support Improve X=None support Sep 7, 2023
@ivirshup ivirshup marked this pull request as ready for review September 7, 2023 09:50
@flying-sheep flying-sheep changed the title Improve X=None support Fix shape inference for X=None Sep 7, 2023
@flying-sheep flying-sheep self-assigned this Sep 7, 2023
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@ivirshup ivirshup left a comment

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Mostly minor changes, otherwise good.

For the subsetting + views, I think I was concerned about aligned mappings + raw with various kinds of subsetting.

anndata/_core/anndata.py Outdated Show resolved Hide resolved
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@ivirshup ivirshup merged commit 88dd129 into main Sep 8, 2023
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@ivirshup ivirshup deleted the add-x-none-tests branch September 8, 2023 11:27
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2 participants