From e7af5306863e8def22547ae807c65ee8f7ac1d6a Mon Sep 17 00:00:00 2001
From: Daniel Weindl <daniel.weindl@uni-bonn.de>
Date: Wed, 24 Sep 2025 16:30:50 +0200
Subject: [PATCH 1/2] Add `id` field to `v2.ProblemConfig`

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

Related to PEtab-dev/PEtab#646.
Closes #441.
---
 petab/schemas/petab_schema.v2.0.0.yaml |  8 ++++++++
 petab/v2/core.py                       | 16 ++++++++++++++++
 2 files changed, 24 insertions(+)

diff --git a/petab/schemas/petab_schema.v2.0.0.yaml b/petab/schemas/petab_schema.v2.0.0.yaml
index 7f1b7443..6e7f9e0d 100644
--- a/petab/schemas/petab_schema.v2.0.0.yaml
+++ b/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: |
diff --git a/petab/v2/core.py b/petab/v2/core.py
index 0f55ea8e..ef5c724b 100644
--- a/petab/v2/core.py
+++ b/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:
+        """The ID of the PEtab problem if set, ``None`` otherwise."""
+        return self.config.id if self.config else None
+
+    @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 = ""
+
     #: 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?

From 511c6d424ea25869c53d5b060367a4948d5ddd93 Mon Sep 17 00:00:00 2001
From: Daniel Weindl <daniel.weindl@uni-bonn.de>
Date: Wed, 1 Oct 2025 16:49:16 +0200
Subject: [PATCH 2/2] ..

---
 petab/schemas/petab_schema.v2.0.0.yaml |  2 +-
 petab/v2/core.py                       |  9 +++++---
 tests/v2/test_core.py                  | 32 ++++++++++++++++++++++++++
 3 files changed, 39 insertions(+), 4 deletions(-)

diff --git a/petab/schemas/petab_schema.v2.0.0.yaml b/petab/schemas/petab_schema.v2.0.0.yaml
index 6e7f9e0d..1a285070 100644
--- a/petab/schemas/petab_schema.v2.0.0.yaml
+++ b/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
diff --git a/petab/v2/core.py b/petab/v2/core.py
index ef5c724b..b331c713 100644
--- a/petab/v2/core.py
+++ b/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)
 
diff --git a/tests/v2/test_core.py b/tests/v2/test_core.py
index 0a9e2429..e38f31f1 100644
--- a/tests/v2/test_core.py
+++ b/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