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Switch to python multithreading #1544

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merged 1 commit into from
Sep 18, 2019
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@ttung ttung commented Sep 10, 2019

smFISH notebook is ~2% faster. Didn't benchmark anything else though.

Test plan: passes unit tests, used the -alltest magic branch name introduced in #1543
Depends on: #1541, #1542, #1543
Fixes #834, #1268

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codecov-io commented Sep 10, 2019

Codecov Report

Merging #1544 into tonytung-preserve-float-range will decrease coverage by 0.48%.
The diff coverage is 100%.

Impacted file tree graph

@@                        Coverage Diff                        @@
##           tonytung-preserve-float-range    #1544      +/-   ##
=================================================================
- Coverage                          87.67%   87.18%   -0.49%     
=================================================================
  Files                                140      138       -2     
  Lines                               5045     5002      -43     
=================================================================
- Hits                                4423     4361      -62     
- Misses                               622      641      +19
Impacted Files Coverage Δ
...re/spots/DetectPixels/combine_adjacent_features.py 98.18% <100%> (+13.63%) ⬆️
starfish/core/imagestack/imagestack.py 94.42% <100%> (-0.07%) ⬇️
starfish/core/imagestack/_mp_dataarray.py 0% <0%> (-100%) ⬇️
starfish/core/image/Filter/clip.py 100% <0%> (+3.84%) ⬆️
starfish/core/image/Filter/match_histograms.py 97.05% <0%> (+8.82%) ⬆️
starfish/core/image/Filter/linear_unmixing.py 100% <0%> (+26.92%) ⬆️

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@ttung ttung force-pushed the tonytung-multithreading-alltest branch 2 times, most recently from 201b3ea to 4efb2bb Compare September 11, 2019 00:02
@ttung ttung force-pushed the tonytung-multithreading-alltest branch 2 times, most recently from e1eb7ab to e6a4628 Compare September 13, 2019 17:24
@ttung ttung force-pushed the tonytung-multithreading-base branch from 3481dd9 to e24ba6a Compare September 16, 2019 19:16
@ttung ttung force-pushed the tonytung-multithreading-alltest branch from e6a4628 to 63cd24b Compare September 16, 2019 19:16
@ttung ttung force-pushed the tonytung-multithreading-base branch from e24ba6a to fc04b93 Compare September 16, 2019 20:51
@ttung ttung force-pushed the tonytung-multithreading-alltest branch 3 times, most recently from f0ded2b to 439fa64 Compare September 16, 2019 20:57
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everything is so much simpler!

@ttung ttung force-pushed the tonytung-multithreading-alltest branch from 439fa64 to f1e9fb8 Compare September 17, 2019 00:40
@ttung ttung force-pushed the tonytung-multithreading-base branch from 55271fe to d8cfa4c Compare September 18, 2019 17:56
@ttung ttung force-pushed the tonytung-multithreading-alltest branch 3 times, most recently from 87eb91b to b6138c1 Compare September 18, 2019 18:57
@ttung ttung changed the base branch from tonytung-multithreading-base to tonytung-preserve-float-range September 18, 2019 19:00
@ttung ttung force-pushed the tonytung-multithreading-alltest branch from b6138c1 to 6f8d1f5 Compare September 18, 2019 19:01
smFISH notebook is ~2% faster.  Didn't benchmark anything else though.

Test plan: passes unit tests, used the -alltest magic branch name introduced in #1543
Depends on: #1541, #1542, #1543
Fixes #834
@ttung ttung force-pushed the tonytung-multithreading-alltest branch from 6f8d1f5 to c87706c Compare September 18, 2019 21:24
@ttung ttung changed the base branch from tonytung-preserve-float-range to master September 18, 2019 21:25
@ttung ttung merged commit 9f64c76 into master Sep 18, 2019
@ttung ttung deleted the tonytung-multithreading-alltest branch September 18, 2019 22:51
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ImageStack multiprocessing problematic on Windows
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