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Adjust bfio & fsspec versions to avoid bugs #537

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merged 3 commits into from
Oct 30, 2023
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SeanLeRoy
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@SeanLeRoy SeanLeRoy commented Oct 26, 2023

Description

This fixes 2 bugs and a lint issue

fsspec bugfix

The SLDY reader uses the glob() function of fsspec which seems to be buggy after version 2023.9.0, limiting the version until a resolution to the corresponding fsspec issue is reached

bfio bugfix

bfio versions 2.3.1 & 2.3.2 (AKA every version > 2.3.0) seem to leave a file open when it seems they used to automatically close. I didn't catch a change to the API/contract in bfio that suggest that this should happen and to manually close it. Hoping that this will be removed in 2.4.0 hence the weird version selection.

@SeanLeRoy SeanLeRoy force-pushed the bugfix/bfio-2.3.0-issues branch from 67ce3d9 to e0e79a4 Compare October 26, 2023 21:41
@SeanLeRoy SeanLeRoy force-pushed the bugfix/bfio-2.3.0-issues branch from e0e79a4 to 9ffe224 Compare October 26, 2023 22:00
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codecov-commenter commented Oct 26, 2023

Codecov Report

All modified and coverable lines are covered by tests ✅

Comparison is base (942cc53) 89.55% compared to head (9121ab2) 68.23%.

Additional details and impacted files
@@             Coverage Diff             @@
##             main     #537       +/-   ##
===========================================
- Coverage   89.55%   68.23%   -21.33%     
===========================================
  Files          53       53               
  Lines        4662     4662               
===========================================
- Hits         4175     3181      -994     
- Misses        487     1481      +994     
Files Coverage Δ
aicsimageio/readers/nd2_reader.py 90.56% <ø> (ø)

... and 28 files with indirect coverage changes

☔ View full report in Codecov by Sentry.
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@SeanLeRoy SeanLeRoy self-assigned this Oct 26, 2023
@SeanLeRoy SeanLeRoy changed the base branch from bugfix/sldy-fsspec-glob-bug to main October 26, 2023 22:32
@SeanLeRoy SeanLeRoy changed the title Avoid bfio versions 2.3.X except 2.3.0 in hopes of avoid open file issue Adjust bfio & fsspec versions to avoid bugs Oct 26, 2023
@SeanLeRoy SeanLeRoy marked this pull request as ready for review October 26, 2023 22:33
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@BrianWhitneyAI BrianWhitneyAI left a comment

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Nice! is there an issue out for bfio leaving the file open? didnt see one on their github.

@SeanLeRoy SeanLeRoy requested a review from kmitcham October 27, 2023 21:58
@SeanLeRoy SeanLeRoy merged commit c380ce0 into main Oct 30, 2023
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@SeanLeRoy SeanLeRoy deleted the bugfix/bfio-2.3.0-issues branch October 30, 2023 16:25
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4 participants