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Fix v2.ProblemConfig.extension type #403

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Merged
m-philipps merged 1 commit into from
Jul 14, 2025
Merged

Fix v2.ProblemConfig.extension type #403

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2 changes: 1 addition & 1 deletion petab/v2/petab1to2.py
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Original file line number Diff line number Diff line change
Expand Up @@ -280,7 +280,7 @@ def _update_yaml(yaml_config: dict) -> dict:
yaml_config[v2.C.FORMAT_VERSION] = "2.0.0"

# Add extensions
yaml_config[v2.C.EXTENSIONS] = []
yaml_config[v2.C.EXTENSIONS] = {}

# Move models and set IDs (filename for now)
for problem in yaml_config[v2.C.PROBLEMS]:
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9 changes: 4 additions & 5 deletions petab/v2/problem.py
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Original file line number Diff line number Diff line change
Expand Up @@ -846,7 +846,7 @@ def validate(

validation_results = ValidationResultList()
if self.config.extensions:
extensions = ",".join(e.name for e in self.config.extensions)
extensions = ",".join(self.config.extensions.keys())
validation_results.append(
ValidationIssue(
ValidationIssueSeverity.WARNING,
Expand Down Expand Up @@ -1116,7 +1116,7 @@ def model_dump(self, **kwargs) -> dict[str, Any]:
>>> p += core.Parameter(id="par", lb=0, ub=1)
>>> pprint(p.model_dump())
{'conditions': [],
'config': {'extensions': [],
'config': {'extensions': {},
'format_version': '2.0.0',
'parameter_file': None,
'problems': []},
Expand Down Expand Up @@ -1168,7 +1168,6 @@ class SubProblem(BaseModel):
class ExtensionConfig(BaseModel):
"""The configuration of a PEtab extension."""

name: str
version: str
config: dict

Expand All @@ -1194,8 +1193,8 @@ class ProblemConfig(BaseModel):
parameter_file: str | AnyUrl | None = None
#: The list of problems in the configuration.
problems: list[SubProblem] = []
#: Extensiions used by the problem.
extensions: list[ExtensionConfig] = []
#: Extensions used by the problem.
extensions: dict[str, ExtensionConfig] = {}

def to_yaml(self, filename: str | Path):
"""Write the configuration to a YAML file.
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