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Allow for condition ids to be defined inside array files (SciML problems only)#498

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BSnelling wants to merge 3 commits into
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bes/cond_ids
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Allow for condition ids to be defined inside array files (SciML problems only)#498
BSnelling wants to merge 3 commits into
mainfrom
bes/cond_ids

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@BSnelling

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Condition specific inputs to neural networks can be provided as array files for SciML problems. For these condition specific inputs, condition ids referenced in the experiments table need to be defined in the array files rather than the conditions table. https://petab-sciml.readthedocs.io/latest/format.html#inputs

This PR adds:

  • a check for condition ids in array files to the CheckExperimentConditionsExist validation task
  • a workaround for the array-defined condition ids in _convert_experiment (AMICI's sciml support handles condition specific array inputs elsewhere)

@BSnelling BSnelling requested a review from a team as a code owner June 30, 2026 10:07
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Codecov Report

❌ Patch coverage is 36.36364% with 7 lines in your changes missing coverage. Please review.
✅ Project coverage is 75.11%. Comparing base (9a5eb5b) to head (1e82bc3).

Files with missing lines Patch % Lines
petab/v2/converters.py 0.00% 1 Missing and 2 partials ⚠️
petab/v2/extensions/sciml.py 50.00% 2 Missing and 1 partial ⚠️
petab/v2/lint.py 50.00% 0 Missing and 1 partial ⚠️
Additional details and impacted files
@@            Coverage Diff             @@
##             main     #498      +/-   ##
==========================================
- Coverage   75.22%   75.11%   -0.12%     
==========================================
  Files          64       64              
  Lines        7145     7156      +11     
  Branches     1261     1266       +5     
==========================================
  Hits         5375     5375              
- Misses       1285     1290       +5     
- Partials      485      491       +6     

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2 participants