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subsample: Don't validate schema in helper functions - #2039

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victorlin merged 1 commit into
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victorlin/subsample-schema-validation
Aug 13, 2026
Merged

subsample: Don't validate schema in helper functions#2039
victorlin merged 1 commit into
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victorlin/subsample-schema-validation

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@victorlin

@victorlin victorlin commented Aug 12, 2026

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Description of proposed changes

This change is primarily intended for pathogen workflows that use the helper functions prior to running augur subsample, commonly during Snakemake's initialization step. Schema is still validated at run time.

We are shifting to a pattern where pathogen workflows define and validate their own schema at workflow start, so the validation in these helper functions is unnecessary duplicate work.

Related issue(s)

Example with measles:

Saved 'config' to 'results/run_config.yaml'.
Validating schema of 'results/run_config.yaml'...                             ← validation already happens here
Saved 'config.subsample.genome/global' to 'results/genome/global/subsample_config.yaml'.
Saved 'config.subsample.N450/global' to 'results/N450/global/subsample_config.yaml'.
Saved 'config.subsample.genome/north-america' to 'results/genome/north-america/subsample_config.yaml'.
host: b1f8e2df1311
Building DAG of jobs...
Validating schema of 'results/genome/global/subsample_config.yaml'...         ← duplicate validation
Validating schema of 'results/N450/global/subsample_config.yaml'...           ← duplicate validation
Validating schema of 'results/genome/north-america/subsample_config.yaml'...  ← duplicate validation

Checklist

  • Automated checks pass failures unrelated
  • 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 Aug 12, 2026
This change is primarily intended for pathogen workflows that use the
helper functions prior to running augur subsample, commonly during
Snakemake's initialization step. Schema is still validated at run time.

We are shifting to a pattern where pathogen workflows define and
validate their own schema at workflow start, so the validation in these
helper functions is unnecessary duplicate work.
@victorlin
victorlin force-pushed the victorlin/subsample-schema-validation branch from 974cd06 to 8752942 Compare August 12, 2026 23:45
@codecov

codecov Bot commented Aug 12, 2026

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Codecov Report

❌ Patch coverage is 75.00000% with 2 lines in your changes missing coverage. Please review.
✅ Project coverage is 73.26%. Comparing base (405c162) to head (8752942).

Files with missing lines Patch % Lines
augur/subsample.py 75.00% 2 Missing ⚠️
Additional details and impacted files
@@           Coverage Diff           @@
##           master    #2039   +/-   ##
=======================================
  Coverage   73.25%   73.26%           
=======================================
  Files          86       86           
  Lines       10766    10765    -1     
  Branches     2099     2099           
=======================================
  Hits         7887     7887           
+ Misses       2504     2503    -1     
  Partials      375      375           

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@victorlin
victorlin merged commit 790fe45 into master Aug 13, 2026
34 of 35 checks passed
@victorlin
victorlin deleted the victorlin/subsample-schema-validation branch August 13, 2026 16:48
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2 participants