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merge: Fixes for SQLite version 3.52.0#1969

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victorlin merged 5 commits into
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victorlin/sqlite-errors
Mar 10, 2026
Merged

merge: Fixes for SQLite version 3.52.0#1969
victorlin merged 5 commits into
masterfrom
victorlin/sqlite-errors

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@victorlin victorlin commented Mar 9, 2026

Description of proposed changes

A couple small improvements in error handling.

Related issue(s)

Addresses CI failures due to changes from new SQLite version, first noticed in scheduled run

Checklist

  • Automated checks pass
  • Check if you need to add a changelog message
  • Check if you need to add tests
  • Check if you need to update docs

@victorlin victorlin self-assigned this Mar 9, 2026
@victorlin victorlin force-pushed the victorlin/sqlite-errors branch 2 times, most recently from b920811 to e6c06c3 Compare March 10, 2026 19:43
@victorlin victorlin changed the title merge: Improve error messages from SQLite merge: Fixes for SQLite version 3.52.0 Mar 10, 2026
@victorlin victorlin force-pushed the victorlin/sqlite-errors branch from e6c06c3 to 32d0532 Compare March 10, 2026 20:25
SQLite version 3.52.0 introduced a bug¹ with .once that causes it to send
results to stdout instead of through the pipe.

.output is not affected by the bug, so we use it as a replacement. The
last .output is effectively a no-op, but it's been added to replicate
the behavior with .once.²

¹ https://sqlite.org/forum/forumpost/ea9c546fdf
² https://sqlite.org/cli.html#writing_results_to_a_file
@victorlin victorlin force-pushed the victorlin/sqlite-errors branch from 32d0532 to afb7c26 Compare March 10, 2026 20:52
Instead of always showing raw stderr from the SQLite subprocess, we now
only show it on actual errors, and with a prefix to indicate its origin.
@victorlin victorlin force-pushed the victorlin/sqlite-errors branch 2 times, most recently from f09a285 to be83972 Compare March 10, 2026 23:10
This matches the error message shown with duplicate ids in sequence
files, and avoids needing to match the SQLite error message syntax in
Cram tests.
@victorlin victorlin force-pushed the victorlin/sqlite-errors branch from be83972 to ce65076 Compare March 10, 2026 23:15
@victorlin
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Merging to fix failing tests.

@victorlin victorlin merged commit 6d18cd1 into master Mar 10, 2026
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@victorlin victorlin deleted the victorlin/sqlite-errors branch March 10, 2026 23:36
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codecov Bot commented Mar 11, 2026

Codecov Report

❌ Patch coverage is 88.88889% with 2 lines in your changes missing coverage. Please review.
✅ Project coverage is 74.47%. Comparing base (68db8f5) to head (ce65076).
⚠️ Report is 6 commits behind head on master.

Files with missing lines Patch % Lines
augur/merge.py 85.71% 0 Missing and 2 partials ⚠️
Additional details and impacted files
@@           Coverage Diff           @@
##           master    #1969   +/-   ##
=======================================
  Coverage   74.46%   74.47%           
=======================================
  Files          82       82           
  Lines        9110     9120   +10     
  Branches     1856     1858    +2     
=======================================
+ Hits         6784     6792    +8     
  Misses       2021     2021           
- Partials      305      307    +2     

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