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Add id field to v2.ProblemConfig #442

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Merged
dweindl merged 2 commits into from
Oct 2, 2025
Merged

Add id field to v2.ProblemConfig #442

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Add `id` field to `v2.ProblemConfig`
dweindl Sep 24, 2025
511c6d4
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dweindl Oct 1, 2025
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8 changes: 8 additions & 0 deletions petab/schemas/petab_schema.v2.0.0.yaml
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Expand Up @@ -23,6 +23,14 @@ properties:
- type: integer
description: Version of the PEtab format

id:
type: string
description: |
Identifier of the PEtab problem.

This is optional and has no effect on the PEtab problem itself.
pattern: "^[a-zA-Z_]\\w*|^$"

parameter_files:
type: array
description: |
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16 changes: 16 additions & 0 deletions petab/v2/core.py
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Expand Up @@ -1630,6 +1630,18 @@ def mappings(self) -> list[Mapping]:
chain.from_iterable(mt.mappings for mt in self.mapping_tables)
)

@property
def id(self) -> str:
"""The ID of the PEtab problem if set, ``None`` otherwise."""
return self.config.id if self.config else None
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@dilpath dilpath Sep 29, 2025

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Suggested change
@property
def id(self) -> str:
"""The ID of the PEtab problem if set, ``None`` otherwise."""
return self.config.id if self.config else None
@property
def id(self) -> str | None:
"""The ID of the PEtab problem if set, ``None`` otherwise."""
return self.config.id if self.config else None

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@dweindl dweindl Sep 30, 2025

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Ah, yeah, I was undecided whether we should go for None or '' if no ID is set. I think always having a string could be more convenient. Any preference?

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@dilpath dilpath Sep 30, 2025

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Hm, I think the Pythonic way would be to use None, because it's the absence of an ID. Also the "no ID" case is a special case that will always need to be handled, e.g. to avoid writing a file name .yaml to disc. Maybe using None then makes it easier to detect errors since the special case is more explicit. No strong opinion though.

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@dweindl dweindl Sep 30, 2025

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Memo to self: The yaml schema may need updating. If we distinguish empty strings and null/None, the former should raise a validation error whereas the latter should not.


@id.setter
def id(self, value: str):
"""Set the ID of the PEtab problem."""
if self.config is None:
self.config = ProblemConfig(format_version="2.0.0")
self.config.id = value

def get_optimization_parameters(self) -> list[str]:
"""
Get the list of optimization parameter IDs from parameter table.
Expand Down Expand Up @@ -2327,6 +2339,10 @@ class ProblemConfig(BaseModel):
)
#: The PEtab format version.
format_version: str = "2.0.0"

#: The problem ID.
id: str = ""

#: The path to the parameter file, relative to ``base_path``.
# TODO https://github.com/PEtab-dev/PEtab/pull/641:
# rename to parameter_files in yaml for consistency with other files?
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