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Omit empty optional entries in ProblemConfig.to_yaml - #547
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## main #547 +/- ##
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+ Coverage 77.74% 77.77% +0.03%
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dweindl
marked this pull request as ready for review
October 15, 2026 08:51
dilpath
approved these changes
Oct 15, 2026
dilpath
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Looks good. Could also be covered by petab.v2.options but no need I think.
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| # Omit empty optional entries. Required ones are kept even if empty. | ||
| for key in C.PROBLEM_CONFIG_OPTIONAL_KEYS: | ||
| # an empty `id` is invalid and must not be dropped silently |
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Strange that the spec allows "empty" for the optional tables but not for the optional ID?
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Yeah, still some inconsistencies there..
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Agreed |
`ProblemConfig.to_yaml` wrote `condition_files: []`,
`experiment_files: []`, `mapping_files: []` and `extensions: {}` when
these were not set. They are optional in the PEtab v2 schema, so leave
them out. Required entries are still written even when empty, so that a
schema violation stays visible.
This affects `Problem.to_files` and `petab1to2`.
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Add `PROBLEM_CONFIG_REQUIRED_KEYS`, `PROBLEM_CONFIG_OPTIONAL_KEYS` and `PROBLEM_ID`, and use them in `ProblemConfig.to_yaml`. A test checks that the lists match the PEtab v2 schema. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
This was referenced Oct 15, 2026
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ProblemConfig.to_yamlwrotecondition_files: [],experiment_files: [],mapping_files: []andextensions: {}whenever these weren't set. The PEtab v2 schema doesn't require them. They add noise, and they make files written by libpetab differ from files written by hand to the spec. This affects everything that goes throughto_yaml, includingProblem.to_filesandpetab1to2.These four entries are now left out when they're empty. Required entries (
parameter_files,model_files,measurement_files,observable_files) are still written even when empty, so that a schema violation stays visible. Reading problems without these entries already worked, so only the writer changes.The required and optional keys are now available as
petab.v2.C.PROBLEM_CONFIG_REQUIRED_KEYSandpetab.v2.C.PROBLEM_CONFIG_OPTIONAL_KEYS. A test checks that they match the schema.🤖 Drafted with AI assistance (Claude Code)