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index: Allow FileNotFoundError to be handled at the top level #1646

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merged 2 commits into from
Sep 30, 2024

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@victorlin victorlin commented Sep 25, 2024

Description of proposed changes

The removed error handling is flawed: it assumes that FileNotFoundError can only come from a missing input file (--sequences). The reality is that FileNotFoundError can also come from a missing output directory (--output). The top-level exception handler parses the filepath from the error directly, which is accurate.

Related issue(s)

Fixes #1644

Checklist

  • Automated checks pass (except unrelated docs build)
  • Check if you need to add a changelog message
  • Check if you need to add tests tested locally that this works. I don't think adding a test is necessary in this case
  • Check if you need to update docs

@victorlin victorlin self-assigned this Sep 25, 2024
@victorlin victorlin force-pushed the victorlin/fix-augur-index-FileNotFoundError branch from 6bd9983 to c2a1c64 Compare September 25, 2024 23:56
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A test would be nice…

@victorlin victorlin changed the title Allow FileNotFoundError to be handled at the top level index: Allow FileNotFoundError to be handled at the top level Sep 26, 2024
The removed error handling is flawed: it assumes that FileNotFoundError
can only come from a missing input file (--sequences). The reality is
that FileNotFoundError can also come from a missing output directory
(--output). The top-level exception handler parses the filepath from the
error directly, which is accurate.
@victorlin victorlin force-pushed the victorlin/fix-augur-index-FileNotFoundError branch from c2a1c64 to 296a6c6 Compare September 26, 2024 23:23
@victorlin victorlin mentioned this pull request Sep 26, 2024
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Updated tests in force-push.

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codecov bot commented Sep 26, 2024

Codecov Report

Attention: Patch coverage is 0% with 4 lines in your changes missing coverage. Please review.

Project coverage is 71.17%. Comparing base (bf05db8) to head (296a6c6).
Report is 3 commits behind head on master.

Files with missing lines Patch % Lines
augur/index.py 0.00% 4 Missing ⚠️
Additional details and impacted files
@@            Coverage Diff             @@
##           master    #1646      +/-   ##
==========================================
+ Coverage   71.14%   71.17%   +0.03%     
==========================================
  Files          79       79              
  Lines        8273     8268       -5     
  Branches     2010     2010              
==========================================
- Hits         5886     5885       -1     
+ Misses       2099     2095       -4     
  Partials      288      288              

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@victorlin victorlin merged commit 18fe343 into master Sep 30, 2024
29 of 30 checks passed
@victorlin victorlin deleted the victorlin/fix-augur-index-FileNotFoundError branch September 30, 2024 17:51
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Successfully merging this pull request may close these issues.

Augur index may always report sequence file is missing even if output dir is missing?
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