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Expose number of jobs to organize #1341

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CodyCBakerPhD
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@CodyCBakerPhD CodyCBakerPhD commented Oct 31, 2023

Recent usage of the DANDI API in the NWB GUIDE revealed a sporadic joblib issue that results in segmentation faults - no clue what actually causes it for some users, but the best solution we have for now is to just expose job usage directly

Where should tests for this go?

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codecov bot commented Oct 31, 2023

Codecov Report

All modified and coverable lines are covered by tests ✅

Comparison is base (e99ee62) 88.88% compared to head (579d108) 89.03%.

Additional details and impacted files
@@            Coverage Diff             @@
##           master    #1341      +/-   ##
==========================================
+ Coverage   88.88%   89.03%   +0.14%     
==========================================
  Files          76       76              
  Lines       10240    10243       +3     
==========================================
+ Hits         9102     9120      +18     
+ Misses       1138     1123      -15     
Flag Coverage Δ
unittests 89.03% <100.00%> (+0.14%) ⬆️

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Files Coverage Δ
dandi/cli/cmd_organize.py 100.00% <100.00%> (ø)
dandi/organize.py 85.29% <100.00%> (+1.71%) ⬆️
dandi/tests/test_organize.py 95.53% <100.00%> (+0.02%) ⬆️

... and 5 files with indirect coverage changes

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@yarikoptic
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more info on segfault? I usually try to run those through valgrind to get a sense where/why might be happening although IIRC it was tricky with python stuff.

re tests - just make one of the invocations in dandi/tests/test_organize.py with jobs=1 to cover that codepath, not sure if we should sweat too much on really testing beyond smoke test on that aspect

@CodyCBakerPhD
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CodyCBakerPhD commented Nov 1, 2023

more info on segfault? I usually try to run those through valgrind to get a sense where/why might be happening although IIRC it was tricky with python stuff.

Sadly no. It was just something random that occurred in certain user environments during first round of alpha testing - the local traceback led back to joblib called by DANDI organize - we've been unable to reproduce it generally - so the best workaround we can think on is to disable joblib usage in those situations

Co-authored-by: Yaroslav Halchenko <[email protected]>
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@CodyCBakerPhD CodyCBakerPhD marked this pull request as ready for review November 1, 2023 18:40
@yarikoptic yarikoptic added the minor Increment the minor version when merged label Nov 1, 2023
@yarikoptic yarikoptic merged commit c567c8b into dandi:master Nov 1, 2023
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@CodyCBakerPhD CodyCBakerPhD deleted the expose_number_of_jobs_to_organize branch November 2, 2023 02:38
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github-actions bot commented Nov 8, 2023

🚀 PR was released in 0.58.0 🚀

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