pyvcell 0.3.0__tar.gz → 0.3.2__tar.gz

{pyvcell-0.3.0 → pyvcell-0.3.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: pyvcell
-Version: 0.3.0
+Version: 0.3.2
 Summary: This is the python wrapper for vcell modeling and simulation
 Author: Jim Schaff, Logan Drescher
 Author-email: Jim Schaff <schaff@uchc.edu>, Logan Drescher <drescher@uchc.edu>

{pyvcell-0.3.0 → pyvcell-0.3.2}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "pyvcell"
-version = "0.3.0"
+version = "0.3.2"
 requires-python = ">=3.12,<4.0"
 description = "This is the python wrapper for vcell modeling and simulation"
 repository = "https://github.com/virtualcell/pyvcell"

{pyvcell-0.3.0 → pyvcell-0.3.2}/pyvcell/vcml/models_app.py

@@ -102,6 +102,14 @@ class Simulation(VcmlNode):
             return self.mesh_size[0], self.mesh_size[1], self.mesh_size[2]
 
 
+class AnnotatedFunction(VcmlNode):
+    name: str
+    error_string: str
+    domain: str
+    function_type: str
+    text: str
+
+
 class Application(VcmlNode):
     name: str
     stochastic: bool
@@ -109,6 +117,7 @@ class Application(VcmlNode):
     compartment_mappings: list[CompartmentMapping] = Field(default_factory=list)
     species_mappings: list[SpeciesMapping] = Field(default_factory=list)
     reaction_mappings: list[ReactionMapping] = Field(default_factory=list)
+    output_functions: list[AnnotatedFunction] = Field(default_factory=list)
     simulations: list[Simulation] = Field(default_factory=list)
     application_parameters: list[ApplicationParameter] = Field(default_factory=list)
     math_description: MathDescription | None = None

{pyvcell-0.3.0 → pyvcell-0.3.2}/pyvcell/vcml/vcml_reader.py

@@ -5,6 +5,7 @@ from lxml import etree
 from lxml.etree import _Element
 
 import pyvcell.vcml.models as vc
+import pyvcell.vcml.models_app as vca
 import pyvcell.vcml.models_geometry as vcg
 import pyvcell.vcml.models_math as vcm
 
@@ -219,6 +220,17 @@ class BiomodelVisitor(XMLVisitor):
         node.applications.append(application)
         self.generic_visit_children(element, application)
 
+    def visit_AnnotatedFunction(self, element: _Element, node: vc.Application) -> None:
+        name: str = str(element.get("Name", default="unnamed"))
+        error_string: str = str(element.get("ErrorString", default=""))
+        domain: str = str(element.get("Domain", default="unknown"))
+        function_type: str = str(element.get("FunctionType", default="unknown"))
+        text: str = str(element.text)
+        annotated_function = vca.AnnotatedFunction(
+            name=name, error_string=error_string, domain=domain, function_type=function_type, text=text
+        )
+        node.output_functions.append(annotated_function)
+
     def visit_Simulation(self, element: _Element, node: vc.Application) -> None:
         name: str = element.get("Name", default="unnamed")
         duration: float | None = None

{pyvcell-0.3.0 → pyvcell-0.3.2}/pyvcell/vcml/vcml_writer.py

@@ -17,6 +17,7 @@ from pyvcell.vcml.models import (
     VCMLDocument,
     Version,
 )
+from pyvcell.vcml.models_app import AnnotatedFunction
 from pyvcell.vcml.models_geometry import Geometry, SubVolumeType
 from pyvcell.vcml.models_math import (
     CompartmentSubDomain,
@@ -239,6 +240,21 @@ class VcmlWriter:
             math_description_element = Element("MathDescription", Name="dummy_math_description")
             parent.append(math_description_element)
 
+        # ---- outputFunctions ----
+        output_functions_element = Element("OutputFunctions")
+        parent.append(output_functions_element)
+        annotated_function: AnnotatedFunction
+        for annotated_function in application.output_functions:
+            elem = Element(
+                "AnnotatedFunction",
+                Name=annotated_function.name,
+                ErrorString=annotated_function.error_string,
+                Domain=annotated_function.domain,
+                FunctionType=annotated_function.function_type,
+            )
+            output_functions_element.append(elem)
+            elem.text = str(annotated_function.text)
+
         # ---- simulations -----
         for simulation in application.simulations:
             simulation_element = Element("Simulation", Name=simulation.name)