..

Author: dweindl

petab/schemas/petab_schema.v2.0.0.yaml

@@ -29,7 +29,7 @@ properties:
       Identifier of the PEtab problem.
 
       This is optional and has no effect on the PEtab problem itself.
-    pattern: "^[a-zA-Z_]\\w*|^$"
+    pattern: "^[a-zA-Z_]\\w*$"
 
   parameter_files:
     type: array

petab/v2/core.py

@@ -1631,9 +1631,9 @@ def mappings(self) -> list[Mapping]:
         )
 
     @property
-    def id(self) -> str:
+    def id(self) -> str | None:
         """The ID of the PEtab problem if set, ``None`` otherwise."""
-        return self.config.id if self.config else None
+        return self.config.id
 
     @id.setter
     def id(self, value: str):
@@ -2341,7 +2341,7 @@ class ProblemConfig(BaseModel):
     format_version: str = "2.0.0"
 
     #: The problem ID.
-    id: str = ""
+    id: str | None = None
 
     #: The path to the parameter file, relative to ``base_path``.
     # TODO https://github.com/PEtab-dev/PEtab/pull/641:
@@ -2404,6 +2404,9 @@ def to_yaml(self, filename: str | Path):
             data["model_files"][model_id][C.MODEL_LOCATION] = str(
                 data["model_files"][model_id]["location"]
             )
+        if data["id"] is None:
+            # The schema requires a valid id or no id field at all.
+            del data["id"]
 
         write_yaml(data, filename)
 

tests/v2/test_core.py

@@ -707,3 +707,35 @@ def test_petablint_v2(tmpdir):
 
     result = subprocess.run(["petablint", str(Path(tmpdir, "problem.yaml"))])  # noqa: S603,S607
     assert result.returncode == 0
+
+
+def test_problem_id(tmpdir):
+    """Test that the problem ID works as expected."""
+    from jsonschema import ValidationError
+
+    def make_yaml(id_line: str) -> str:
+        return f"""
+        format_version: 2.0.0
+        {id_line}
+        model_files: {{}}
+        parameter_files: []
+        observable_files: []
+        condition_files: []
+        measurement_files: []
+        """
+
+    filepath = Path(tmpdir, "problem.yaml")
+    with open(filepath, "w") as f:
+        f.write(make_yaml("id: my_problem_id"))
+    problem = Problem.from_yaml(filepath)
+    assert problem.id == "my_problem_id"
+
+    with open(filepath, "w") as f:
+        f.write(make_yaml("id: "))
+    with pytest.raises(ValidationError):
+        Problem.from_yaml(filepath)
+
+    with open(filepath, "w") as f:
+        f.write(make_yaml(""))
+    problem = Problem.from_yaml(filepath)
+    assert problem.id is None