Merge branch 'main' into validate_modelid

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/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,
     ):

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")
             )