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Collect minor spec inconsistencies and clean-ups for the next PEtab version #681
Description
This issue collects small inconsistencies and clean-ups in the PEtab v2 specification. None of them warrant a change on their own, but they could be handled in the next version. Please add further items as comments.
- Empty values for optional problem YAML entries: The optional file lists (
condition_files,experiment_files,mapping_files) andextensionsmay be present but empty ([],{}). The optionalidcan't be empty (id: ""andid:fail the schema); it can only be left out. It's worth deciding whether empty values should be valid for all optional entries or for none, and whether the specification should recommend leaving out unused optional entries. (Came up in Omit empty optional entries inProblemConfig.to_yamllibpetab-python#547.)
🤖 Drafted with AI assistance (Claude Code)
Activity
dweindl commentedon Oct 15, 2026
Conditionally empty columns in the parameter table:
lowerBound,upperBoundandnominalValueare typed[NUMERIC], i.e., neitherOPTIONALnorNULL, and are not bracketed in the table overview. Their descriptions, however, allow empty values depending onestimate("Optional, ifestimate==false" / "Optional, unlessestimate==false"). This leaves open (a) whether the columns may be omitted if they would be empty in every row (e.g.,nominalValueif all parameters are estimated), and (b) whether individual cells may be empty, which would correspond toNULL. By contrast,observableParametersandnoiseParametersexplicitly state when the column may be omitted. Also, the general remark "Fields enclosed in "[]" are optional and may be left empty" mixes optional columns and empty cells, which theOPTIONAL/NULLnotation distinguishes. (Came up in PEtab-dev/libpetab-python#543.)🤖 Drafted with AI assistance (Claude Code)
dweindl commentedon Oct 15, 2026
Redundant name annotations: Human-readable names can be provided both via
parameterNamein the parameter table (andobservableNamein the observable table) and via thenamecolumn of the mapping table. WithpetabEntityId == modelEntityId(explicitly allowed "for annotations"), or an emptymodelEntityId("annotations only"), a parameter can get a name from both tables, and it's not specified which one takes precedence if they differ. Options would be to dropparameterName/observableNamein favor of the mapping table, to restrict mapping table names to entities without a name column, or to define a precedence. (Came up in PEtab-dev/libpetab-python#543.)🤖 Drafted with AI assistance (Claude Code)