Merge pull request #32 from virtualcell/app-params

parse vcml application parameters

Author: jcschaff

.gitignore

@@ -178,3 +178,7 @@ test_output_1/
 examples/test_output/SimID_*
 /examples/notebooks/*.py
 /examples/solver_output/zarr/
+
+examples/notebooks/workspace/
+
+examples/scripts/workspace/

README.md

@@ -77,4 +77,4 @@ coming soon.
 
 ### Geometry import example
 
-[![Open in Colab ](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/drive/14L3WaV42PEu7NvAQdil7i8mEL4WTPF9h?usp=sharing)
+[![Open in Colab ](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/drive/14L3WaV42PEu7NvAQdil7i8mEL4WTPF9h?usp=sharing)

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "pyvcell"
-version = "0.1.18"
+version = "0.1.19"
 description = "This is the python wrapper for vcell modeling and simulation"
 authors = ["Jim Schaff <[email protected]>"]
 repository = "https://github.com/virtualcell/pyvcell"

pyvcell/vcml/models.py

@@ -32,6 +32,10 @@ class Parameter(VcmlNode):
     unit: str
 
 
+class ApplicationParameter(Parameter):
+    pass
+
+
 class ModelParameter(Parameter):
     pass
 
@@ -370,6 +374,7 @@ class Application(VcmlNode):
     species_mappings: list[SpeciesMapping] = Field(default_factory=list)
     reaction_mappings: list[ReactionMapping] = Field(default_factory=list)
     simulations: list[Simulation] = Field(default_factory=list)
+    application_parameters: list[ApplicationParameter] = Field(default_factory=list)
 
     def __repr__(self) -> str:
         return f"Application(name={self.name}, geometry={self.geometry}, sims={self.simulation_names})"

pyvcell/vcml/vcml_reader.py

@@ -144,7 +144,7 @@ def visit_Parameter(self, element: _Element, node: vc.Model | vc.Kinetics) -> No
         name: str = element.get("Name", default="unnamed")
         role = element.get("Role", default="user defined")
         unit = element.get("Unit", default="tbd")
-        parameter: vc.ModelParameter | vc.KineticsParameter
+        parameter: vc.ModelParameter | vc.KineticsParameter | vc.ApplicationParameter
         if strip_namespace(parent.tag) == "ModelParameters":
             model: vc.Model = node  # type: ignore[assignment]
             model_parameter = vc.ModelParameter(name=name, value=value, role=role, unit=unit)
@@ -161,6 +161,11 @@ def visit_Parameter(self, element: _Element, node: vc.Model | vc.Kinetics) -> No
             )
             kinetics.kinetics_parameters.append(kinetics_parameter)
             parameter = kinetics_parameter
+        elif strip_namespace(parent.tag) == "ApplicationParameters":
+            application: vc.Application = node  # type: ignore[assignment]
+            application_parameter = vc.ApplicationParameter(name=name, value=value, role=role, unit=unit)
+            application.application_parameters.append(application_parameter)
+            parameter = application_parameter
         else:
             raise ValueError("Unexpected parent tag")
         self.generic_visit(element, parameter)

pyvcell/vcml/vcml_writer.py

@@ -119,6 +119,14 @@ def write_application(self, application: Application, parent: _Element) -> None:
         parent.append(geometry_element)
         self.write_geometry(application.geometry, geometry_element)
 
+        # ---- application parameters -----
+        application_parameters_element = Element("ApplicationParameters")
+        parent.append(application_parameters_element)
+        for parameter in application.application_parameters:
+            parameter_element = Element("Parameter", Name=parameter.name, Role=parameter.role, Unit=parameter.unit)
+            parameter_element.text = str(parameter.value)
+            application_parameters_element.append(parameter_element)
+
         # ---- geometry context -----
         geometry_context_element = Element("GeometryContext")
         parent.append(geometry_context_element)

tests/_internal/api/vcell_client/test_publication_api.py

@@ -49,4 +49,4 @@ def test_get_publications() -> None:
         mathmodel_refs=[],
         var_date=date(year=2024, month=11, day=26),
     )
-    assert pubs[0] == example_pub
+    assert example_pub in pubs