Merge branch 'main' into validate_initial_changes

Author: dweindl

doc/conf.py

@@ -52,6 +52,7 @@
     "numpy": ("https://numpy.org/devdocs/", None),
     "sympy": ("https://docs.sympy.org/latest/", None),
     "python": ("https://docs.python.org/3", None),
+    "pydantic": ("https://docs.pydantic.dev/latest/", None),
 }
 
 # Add any paths that contain templates here, relative to this directory.

petab/__init__.py

@@ -36,7 +36,7 @@ def __getattr__(name):
     return getattr(importlib.import_module("petab.v1"), name)
 
 
-def v1getattr(name, module):
+def _v1getattr(name, module):
     if name not in ("__path__", "__all__"):
         warn(
             f"Accessing `petab.{name}` is deprecated and will be removed in "
@@ -67,7 +67,7 @@ def v1getattr(name, module):
         real_module = importlib.import_module(
             f"petab.v1.{'.'.join(v1_object_parts)}"
         )
-        real_module.__getattr__ = partial(v1getattr, module=real_module)
+        real_module.__getattr__ = partial(_v1getattr, module=real_module)
         sys.modules[module_name] = real_module
     except ModuleNotFoundError:
         pass

petab/v1/models/sbml_model.py

@@ -130,16 +130,18 @@ def from_string(sbml_string, model_id: str = None) -> SbmlModel:
         )
 
     @staticmethod
-    def from_antimony(ant_model: str | Path) -> SbmlModel:
+    def from_antimony(ant_model: str | Path, **kwargs) -> SbmlModel:
         """Create SBML model from an Antimony model.
 
         Requires the `antimony` package (https://github.com/sys-bio/antimony).
 
         :param ant_model: Antimony model as string or path to file.
             Strings are interpreted as Antimony model strings.
+        :param kwargs: Additional keyword arguments passed to
+            :meth:`SbmlModel.from_string`.
         """
         sbml_str = antimony2sbml(ant_model)
-        return SbmlModel.from_string(sbml_str)
+        return SbmlModel.from_string(sbml_str, **kwargs)
 
     def to_antimony(self) -> str:
         """Convert the SBML model to an Antimony string."""

petab/v1/sbml.py

@@ -169,6 +169,7 @@ def write_sbml(sbml_doc: libsbml.SBMLDocument, filename: Path | str) -> None:
         sbml_doc: SBML document containing the SBML model
         filename: Destination file name
     """
+    Path(filename).parent.mkdir(parents=True, exist_ok=True)
     sbml_writer = libsbml.SBMLWriter()
     ret = sbml_writer.writeSBMLToFile(sbml_doc, str(filename))
     if not ret:

petab/v2/core.py

@@ -2035,9 +2035,10 @@ def add_parameter(
     def add_measurement(
         self,
         obs_id: str,
-        experiment_id: str,
+        *,
         time: float,
         measurement: float,
+        experiment_id: str | None = None,
         observable_parameters: Sequence[str | float] | str | float = None,
         noise_parameters: Sequence[str | float] | str | float = None,
     ):

petab/v2/lint.py

@@ -27,6 +27,10 @@
     "ValidationTask",
     "CheckModel",
     "CheckProblemConfig",
+    "CheckMeasuredObservablesDefined",
+    "CheckOverridesMatchPlaceholders",
+    "CheckMeasuredExperimentsDefined",
+    "CheckMeasurementModelId",
     "CheckPosLogMeasurements",
     "CheckValidConditionTargets",
     "CheckUniquePrimaryKeys",
@@ -826,8 +830,39 @@ def run(self, problem: Problem) -> ValidationIssue | None:
         return None
 
 
-# TODO: check that Measurements model IDs match the available ones
-#  https://github.com/PEtab-dev/libpetab-python/issues/392
+class CheckMeasurementModelId(ValidationTask):
+    """Validate model IDs of measurements."""
+
+    def run(self, problem: Problem) -> ValidationIssue | None:
+        messages = []
+        available_models = {m.model_id for m in problem.models}
+
+        for measurement in problem.measurements:
+            if not measurement.model_id:
+                if len(available_models) < 2:
+                    # If there is only one model, it is not required to specify
+                    # the model ID in the measurement table.
+                    continue
+
+                messages.append(
+                    f"Measurement `{measurement}' does not have a model ID, "
+                    "but there are multiple models available. "
+                    "Please specify the model ID in the measurement table."
+                )
+                continue
+
+            if measurement.model_id not in available_models:
+                messages.append(
+                    f"Measurement `{measurement}' has model ID "
+                    f"`{measurement.model_id}' which does not match "
+                    "any of the available models: "
+                    f"{available_models}."
+                )
+
+        if messages:
+            return ValidationError("\n".join(messages))
+
+        return None
 
 
 def get_valid_parameters_for_parameter_table(
@@ -1068,6 +1103,7 @@ def get_placeholders(
     CheckProblemConfig(),
     CheckModel(),
     CheckUniquePrimaryKeys(),
+    CheckMeasurementModelId(),
     CheckMeasuredObservablesDefined(),
     CheckPosLogMeasurements(),
     CheckOverridesMatchPlaceholders(),

pyproject.toml

@@ -65,7 +65,8 @@ doc = [
     # https://github.com/spatialaudio/nbsphinx/issues/687#issuecomment-1339271312
     "ipython>=7.21.0, !=8.7.0",
     "pysb",
-    "antimony>=2.14.0"
+    "antimony>=2.14.0",
+    "sbmlmath>=0.4.0",
 ]
 vis = [
     "matplotlib>=3.6.0",

tests/v2/test_core.py

@@ -389,7 +389,12 @@ def test_problem_from_yaml_multiple_files():
                 problem.experiment_df, Path(tmpdir, f"experiments{i}.tsv")
             )
 
-            problem.add_measurement(f"observable{i}", f"experiment{i}", 1, 1)
+            problem.add_measurement(
+                f"observable{i}",
+                experiment_id=f"experiment{i}",
+                time=1,
+                measurement=1,
+            )
             petab.write_measurement_df(
                 problem.measurement_df, Path(tmpdir, f"measurements{i}.tsv")
             )

tests/v2/test_lint.py

@@ -62,3 +62,30 @@ def test_validate_initial_change_symbols():
     problem.parameter_tables[0].parameters.remove(problem["p2"])
     assert (error := check.run(problem)) is not None
     assert "contains additional symbols: {'p2'}" in error.message
+
+
+def test_invalid_model_id_in_measurements():
+    """Test that measurements with an invalid model ID are caught."""
+    problem = Problem()
+    problem.models.append(SbmlModel.from_antimony("p1 = 1", model_id="model1"))
+    problem.add_observable("obs1", "A")
+    problem.add_measurement("obs1", experiment_id="e1", time=0, measurement=1)
+
+    check = CheckMeasurementModelId()
+
+    # Single model -> model ID is optional
+    assert (error := check.run(problem)) is None, error
+
+    # Two models -> model ID must be set
+    problem.models.append(SbmlModel.from_antimony("p2 = 2", model_id="model2"))
+    assert (error := check.run(problem)) is not None
+    assert "multiple models" in error.message
+
+    # Set model ID to a non-existing model ID
+    problem.measurements[0].model_id = "invalid_model_id"
+    assert (error := check.run(problem)) is not None
+    assert "does not match" in error.message
+
+    # Use a valid model ID
+    problem.measurements[0].model_id = "model1"
+    assert (error := check.run(problem)) is None, error