refactor to enable serilisation, consistent types, update tests

Initial_gen/data/chemsep/chemsep1.xml

@@ -27092,7 +27092,7 @@ edited to remove two compounds (duplicated in chemsep2):
 
 <compound>
 <LibraryIndex name="Index"  value="501" />
-<CompoundID name="Name"  value="Benzene" />
+<CompoundID name="Name"  value="benzene" />
 <StructureFormula name="Structure"  value="-CHCHCHCHCHCH-" />
 <Family name="Family"  value="16" />
 <CriticalTemperature name="Critical temperature"  units="K"  value="562.05" />
@@ -30481,7 +30481,7 @@ edited to remove two compounds (duplicated in chemsep2):
 
 <compound>
 <LibraryIndex name="Index"  value="502" />
-<CompoundID name="Name"  value="Toluene" />
+<CompoundID name="Name"  value="toluene" />
 <StructureFormula name="Structure"  value="(C6H5)CH3" />
 <Family name="Family"  value="16" />
 <CriticalTemperature name="Critical temperature"  units="K"  value="591.75" />

compounds/Compound.py

@@ -3,54 +3,36 @@
 from typing import Dict
 import os
 import json
+from pydantic import BaseModel
 
-
-class Coefficients:
-    # Allows square bracket access
-    def __getitem__(self, name: str) -> any:
-        return self._attributes[name]
-
-    def __setitem__(self, name: str, value: any) -> None:
-        self._attributes[name] = value
-
-    def __init__(self, element: ET.Element):
-        self._attributes = {}
-        for child in element:
-            if child.get('value') is not None:
-                self[child.tag] = convert_string_to_float(child.get('value'))
-
-
-class UnitValuePair:
-    def __init__(self, name, value, unit):
-        self.name = name
-        self.value = convert_string_to_float(value)
-        self.unit = unit
+def convert_string_to_float(string: str) -> float:
+    try:
+        return float(string)
+    except:
+        return string
 
-    def to_dict(self) -> Dict[str, any]:
-        return {
-            'name': self.name,
-            'value': self.value,
-            'unit': self.unit
-        }
+class UnitValuePair(BaseModel):
+    name: str | None
+    value: float | str | None
+    unit: str | None
 
-    def to_json(self) -> str:
-        return json.dumps(self.to_dict())
 
 # Helper functions
 def parse_element(elem: ET.Element):
     try:
-        return UnitValuePair(elem.get('name'), elem.get('value'), elem.get('units'))
+        return UnitValuePair(name=elem.get('name'), value=convert_string_to_float(elem.get('value')), unit=elem.get('units'))
     except:
         return None
 
+Coefficients = Dict[str, float]
 def parse_coeff(element: ET.Element) -> Coefficients:
-    return Coefficients(element)
+    self = {}
+    for child in element:
+        value = child.get('value')
+        if value is not None:
+            self[child.tag] = convert_string_to_float(value)
+    return self
 
-def convert_string_to_float(string: str) -> float:
-    try:
-        return float(string)
-    except:
-        return string
 
 compound_template = {
     'LibraryIndex': parse_element,
@@ -98,45 +80,26 @@ def convert_string_to_float(string: str) -> float:
     'LiquidViscosityRPS': parse_coeff,
 }
 
-class Compound:
-
-    def __init__(self, name: str) -> None:
-        """
-        Initializes the Compound object.
-
-        Args:
-            name (str): Name of compound.
-        """
-
-        self._attributes = {}
-        self._parse_xml(name)
-
-    # Allows square bracket access
-    def __getitem__(self, name: str) -> any:
-        return self._attributes[name]
-
-    def __setitem__(self, name: str, value: any) -> None:
-        self._attributes[name] = value
-
-    def _parse_xml(self, name: str):
-        """
-        Parses the XML string and populates the object's attributes.
-
-        Args:
-            xml_string (str): The XML data as a string.
-        """
-
-        with open(os.path.dirname(__file__) + "/data_files/" + name + ".xml", 'r') as file:
-            file = ''.join(file.readlines())
-
-        root = ET.fromstring(file)
-
-        # Iterating over all attributes in the template
-        # and parsing the corresponding XML elements
-        for attr in compound_template:
-            if root.find(attr) is not None:
-                self[attr] = compound_template[attr](root.find(attr))
-            else:
-                self[attr] = None
-
-
+Compound = Dict
+
+def load_compound(name: str) -> Compound:
+    """
+    Parses the XML string and populates the object's attributes.
+
+    Args:
+        xml_string (str): The XML data as a string.
+    """
+    self = {}
+    with open(os.path.dirname(__file__) + "/data_files/" + name.lower() + ".xml", 'r') as file:
+        file = ''.join(file.readlines())
+
+    root = ET.fromstring(file)
+
+    # Iterating over all attributes in the template
+    # and parsing the corresponding XML elements
+    for attr in compound_template:
+        if root.find(attr) is not None:
+            self[attr] = compound_template[attr](root.find(attr))
+        else:
+            self[attr] = None
+    return self

compounds/CompoundDB.py

@@ -1,4 +1,5 @@
-from .Compound import Compound
+from .Compound import load_compound
+from typing import Dict
 import os
 
 # Loads all the compounds, and enables some basic queries for/on the compounds.
@@ -14,9 +15,10 @@
 for file in os.listdir(os.path.dirname(__file__) + "/data_files"):
     if file.endswith(".xml"):
         compound_name = file[:-4]
-        all_compounds[compound_name] = Compound(compound_name)
+        compound = load_compound(compound_name)
+        all_compounds[compound_name] = compound
 
-def get_compound(compound_name: str) -> Compound:
+def get_compound(compound_name: str) -> Dict:
     """
     Returns a Compound object for the given compound name.
 
@@ -26,7 +28,7 @@ def get_compound(compound_name: str) -> Compound:
     Returns:
         Compound: The Compound object.
     """
-    return all_compounds[compound_name]
+    return all_compounds[compound_name.lower()]
 
 def get_compound_names() -> list:
     """

compounds/__init__.py

@@ -1 +1 @@
-from .Compound import Compound
+from .Compound import load_compound

compounds/data_files/benzene.xml

@@ -1,6 +1,6 @@
 <compound>
 <LibraryIndex name="Index"  value="501" />
-<CompoundID name="Name"  value="Benzene" />
+<CompoundID name="Name"  value="benzene" />
 <StructureFormula name="Structure"  value="-CHCHCHCHCHCH-" />
 <Family name="Family"  value="16" />
 <CriticalTemperature name="Critical temperature"  units="K"  value="562.05" />

compounds/data_files/toluene.xml

@@ -1,6 +1,6 @@
 <compound>
 <LibraryIndex name="Index"  value="502" />
-<CompoundID name="Name"  value="Toluene" />
+<CompoundID name="Name"  value="toluene" />
 <StructureFormula name="Structure"  value="(C6H5)CH3" />
 <Family name="Family"  value="16" />
 <CriticalTemperature name="Critical temperature"  units="K"  value="591.75" />

compounds/tests/create_benzene_test.py

@@ -1,7 +1,7 @@
-from ..Compound import Compound
+from ..Compound import load_compound
 
 
 def test_parsing():
-  comp = Compound("Benzene")
+  comp = load_compound("benzene")
   assert comp["AbsEntropy"].value == 269300
   assert comp["AbsEntropy"].unit == "J/kmol/K"

compounds/tests/load_compounddb_test.py

@@ -7,6 +7,6 @@
 
 def test_load_compounds():
     from compounds import CompoundDB as db
-    assert "Benzene" in db.get_compound_names()
-    benzene = db.get_compound("Benzene")
+    assert "benzene" in db.get_compound_names()
+    benzene = db.get_compound("benzene")
     assert benzene["AbsEntropy"].value == 269300

property_packages/modular/builder/base_parser.py

@@ -1,12 +1,13 @@
 from typing import List, Dict
-from compounds.Compound import Compound
+from compounds.Compound import load_compound
 
 class BuildBase:
 
   def __init__(self) -> None:
     pass
-
-  def serialise(compounds: List[Compound]) -> Dict:
+
+  @staticmethod
+  def serialise( compounds: List[Dict]) -> Dict:
     """
     accepts
     - List of compounds

property_packages/modular/builder/common_parsers.py

@@ -1,6 +1,6 @@
 from typing import Any, Dict, List
 from .base_parser import BuildBase
-from compounds.Compound import Compound
+from compounds.Compound import load_compound,Compound
 from pyomo.environ import units as pyunits
 from idaes.models.properties.modular_properties.state_definitions import FTPx
 from idaes.models.properties.modular_properties.phase_equil.bubble_dew import (LogBubbleDew)
@@ -19,7 +19,7 @@
 
 
 class base_units_parser(BuildBase):
-
+    @staticmethod
     def serialise(compounds: List[Compound]) -> Dict[str, Any]:
         return {
             'time': pyunits.s,
@@ -30,11 +30,12 @@ def serialise(compounds: List[Compound]) -> Dict[str, Any]:
         }
 
 class bubble_dew_method_parser(BuildBase):
+    @staticmethod
     def serialise(compounds: List[Compound]) -> Dict[str, Any]:
         return LogBubbleDew
 
 class components_parser(BuildBase):
-
+    @staticmethod
     def serialise(compounds: List[Compound]) -> Dict[str, Any]:
 
         def serialise_component(compound: Compound) -> Dict[str, Any]:
@@ -136,10 +137,12 @@ def serialise_component(compound: Compound) -> Dict[str, Any]:
         return components_output
 
 class phase_equilibrium_state_parser(BuildBase):
+    @staticmethod
     def serialise(compounds: List[Compound]) -> Dict[str, Any]:
         return {("Vap", "Liq"): SmoothVLE} # TODO: Update to Smooth VLE_v2 https://github.com/IDAES/idaes-pse/blob/main/idaes/models/properties/modular_properties/phase_equil/smooth_VLE_2.py
 
 class phases_parser(BuildBase):
+    @staticmethod
     def serialise(compounds: List[Compound]) -> Dict[str, Any]:
         return {
             "Liq": {
@@ -155,14 +158,17 @@ def serialise(compounds: List[Compound]) -> Dict[str, Any]:
         }
 
 class phases_in_equilibrium_parser(BuildBase):
+    @staticmethod
     def serialise(compounds: List[Compound]) -> Dict[str, Any]:
         return [("Vap", "Liq")]
 
 class pressure_ref_parser(BuildBase):
+    @staticmethod
     def serialise(compounds: List[Compound]) -> Dict[str, Any]:
         return (101325, pyunits.Pa)
 
 class state_bounds_parser(BuildBase):
+    @staticmethod
     def serialise(compounds: List[Compound]) -> Dict[str, Any]:
         return {
             "flow_mol": (0, 100, 1000, pyunits.mol / pyunits.s),
@@ -171,15 +177,18 @@ def serialise(compounds: List[Compound]) -> Dict[str, Any]:
         }
 
 class state_definition_parser(BuildBase):
+    @staticmethod
     def serialise(compounds: List[Compound]) -> str:
         return FTPx
 
 class temperature_ref_parser(BuildBase):
+    @staticmethod
     def serialise(compounds: List[Compound]) -> Dict[str, Any]:
         return (298.15, pyunits.K)
 
 
 class pr_kappa_parser(BuildBase):
+    @staticmethod
     def serialise(compounds: List[Compound]) -> Dict[str, Any]:
         kappa_parameters = {}
         for i, compound1 in enumerate(compounds):