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Parallelize umap with process pools #221

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Parallelize umap with process pools #221

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mtauraso
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  • We use a process pool to do the transform
  • We use another process pool to do writing of inference data out (also impacts infer verb)
  • Some of the loudest warnings from the umap package have been supressed

@mtauraso
Parallelize umap with process pools
a9098ee 
- We use a process pool to do the transform
- We use another process pool to do writing of inference data out (also impacts infer verb)
- Some of the loudest warnings from the umap package have been supressed
@mtauraso mtauraso linked an issue Feb 18, 2025 that may be closed by this pull request
Optimize UMAP Creation #213
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codecov bot commented Feb 18, 2025

Codecov Report

Attention: Patch coverage is 19.23077% with 21 lines in your changes missing coverage. Please review.

Project coverage is 37.86%. Comparing base (f9ea911) to head (a9098ee).

Files with missing lines Patch % Lines
src/fibad/verbs/umap.py 19.04% 17 Missing ⚠️
src/fibad/data_sets/inference_dataset.py 20.00% 4 Missing ⚠️
Additional details and impacted files 
@@            Coverage Diff             @@
##             main     #221      +/-   ##
==========================================
- Coverage   37.92%   37.86%   -0.06%     
==========================================
  Files          30       30              
  Lines        2418     2435      +17     
==========================================
+ Hits          917      922       +5     
- Misses       1501     1513      +12

☔ View full report in Codecov by Sentry.
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Before [f9ea911] After [20e432d] Ratio Benchmark (Parameter)
3.41±1s 1.17±0.8s ~0.34 benchmarks.time_computation
3.03k 2.38k 0.79 benchmarks.mem_list

Click here to view all benchmarks.

aritraghsh09
aritraghsh09 approved these changes Feb 19, 2025
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Looks good to me! No comments!

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@aritraghsh09 aritraghsh09 aritraghsh09 approved these changes

@drewoldag drewoldag Awaiting requested review from drewoldag

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Optimize UMAP Creation
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@mtauraso @aritraghsh09