Fix remove unit assignments (#136)

* remove units

* remove units from SBML tests

Co-authored-by: Dilan Pathirana <59329744+dilpath@users.noreply.github.com>

tests/test_yaml2sbml/true_sbml_output.xml

@@ -82,20 +82,20 @@
       <compartment id="Compartment" size="1" constant="true"/>
     </listOfCompartments>
     <listOfSpecies>
-      <species id="S1" compartment="Compartment" initialAmount="0.1" substanceUnits="dimensionless" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
-      <species id="S2" compartment="Compartment" initialAmount="1" substanceUnits="dimensionless" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
-      <species id="S3" compartment="Compartment" initialAmount="1" substanceUnits="dimensionless" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
+      <species id="S1" compartment="Compartment" initialAmount="0.1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
+      <species id="S2" compartment="Compartment" initialAmount="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
+      <species id="S3" compartment="Compartment" initialAmount="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
     </listOfSpecies>
     <listOfParameters>
       <parameter id="t" name="t" constant="false"/>
-      <parameter id="c1" name="c1" value="1" units="dimensionless" constant="true"/>
-      <parameter id="Shalve" name="Shalve" value="0.1" units="dimensionless" constant="true"/>
-      <parameter id="Vh" name="Vh" value="0.1" units="dimensionless" constant="true"/>
-      <parameter id="h" name="h" value="0.1" units="dimensionless" constant="true"/>
-      <parameter id="Vmm" name="Vmm" value="0.1" units="dimensionless" constant="true"/>
-      <parameter id="Km" name="Km" value="0.1" units="dimensionless" constant="true"/>
-      <parameter id="v1" name="v1" value="0.1" units="dimensionless" constant="true"/>
-      <parameter id="k4" name="k4" value="0.1" units="dimensionless" constant="true"/>
+      <parameter id="c1" name="c1" value="1" constant="true"/>
+      <parameter id="Shalve" name="Shalve" value="0.1" constant="true"/>
+      <parameter id="Vh" name="Vh" value="0.1" constant="true"/>
+      <parameter id="h" name="h" value="0.1" constant="true"/>
+      <parameter id="Vmm" name="Vmm" value="0.1" constant="true"/>
+      <parameter id="Km" name="Km" value="0.1" constant="true"/>
+      <parameter id="v1" name="v1" value="0.1" constant="true"/>
+      <parameter id="k4" name="k4" value="0.1" constant="true"/>
     </listOfParameters>
     <listOfRules>
       <assignmentRule variable="t">

yaml2sbml/yaml2sbml.py

@@ -268,8 +268,6 @@ def _create_parameter(model: sbml.Model, parameter_id: str, value: str = None):
     """
     Create a parameter and add it to the given SBML model.
 
-    Units are set as dimensionless by default.
-
     Arguments:
         model: the SBML model to which the parameter will be added.
         parameter_id: the parameter ID
@@ -287,8 +285,6 @@ def _create_parameter(model: sbml.Model, parameter_id: str, value: str = None):
     if value is not None:
         k.setValue(float(value))
 
-    k.setUnits('dimensionless')
-
 
 def _read_assignments_block(model: sbml.Model, assignment_list: list):
     """
@@ -327,7 +323,6 @@ def _create_assignment(model: sbml.Model, assignment_id: str, formula: str):
 
     assignment_parameter.setName(assignment_id)
     assignment_parameter.setConstant(False)
-    assignment_parameter.setUnits('dimensionless')
 
     assignment_rule = model.createAssignmentRule()
     assignment_rule.setVariable(assignment_id)
@@ -417,8 +412,6 @@ def _create_species(model: sbml.Model, species_id: str, initial_amount: str):
     """
     Create a species and add it to the SBML model.
 
-    Units are set as dimensionless by default.
-
     Arguments:
         model: the SBML model to which the species will be added.
         species_id: the species ID
@@ -445,8 +438,6 @@ def _create_species(model: sbml.Model, species_id: str, initial_amount: str):
     s.setHasOnlySubstanceUnits(False)
     s.setCompartment('Compartment')
 
-    s.setSubstanceUnits('dimensionless')
-
     return s