Add id field to v2.ProblemConfig (#442)

* Update schema
* v2.Problem.id
* v2.ProblemConfig.id

Related to PEtab-dev/PEtab#646.
Closes #441.

Author: dweindl

petab/schemas/petab_schema.v2.0.0.yaml

@@ -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: |

petab/v2/core.py

@@ -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 | None:
+        """The ID of the PEtab problem if set, ``None`` otherwise."""
+        return self.config.id
+
+    @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.
@@ -2327,6 +2339,10 @@ class ProblemConfig(BaseModel):
     )
     #: The PEtab format version.
     format_version: str = "2.0.0"
+
+    #: The problem ID.
+    id: str | None = None
+
     #: 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?
@@ -2388,6 +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