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remove out of core median #3379

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remove out of core median #3379

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Intron7
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@Intron7 Intron7 commented Nov 21, 2024

Computing counts per cell for normalize_total leads to better performance.

@Intron7 Intron7 added this to the 1.11.0 milestone Nov 21, 2024
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codecov bot commented Nov 21, 2024

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 75.44%. Comparing base (cce4bd6) to head (b8a6a99).

Additional details and impacted files
@@            Coverage Diff             @@
##             main    #3379      +/-   ##
==========================================
- Coverage   75.44%   75.44%   -0.01%     
==========================================
  Files         113      113              
  Lines       13250    13248       -2     
==========================================
- Hits         9997     9995       -2     
  Misses       3253     3253              
Files with missing lines Coverage Δ
src/scanpy/preprocessing/_normalization.py 81.39% <100.00%> (-0.43%) ⬇️

@flying-sheep
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Fair enough. Can this blow up? I.e. is counts ever big enough that this is a problem?

@flying-sheep flying-sheep modified the milestones: 1.11.0, 1.12.0 Dec 20, 2024
@Intron7
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Intron7 commented Feb 10, 2025

So I did some testing with 1Billion cells. 1Billion cells at 64bit are roughly 8GB. The median costs another 8GB. Thats roughly 16GB. I dont think 16GB of Ram is an issue for someone that analyses 1Billion cells.

@Intron7 Intron7 requested a review from ilan-gold February 10, 2025 15:36
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Why is this for the 1.12 milestone?

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3 participants