musica 0.12.2__cp39-cp39-macosx_15_0_arm64.whl → 0.13.0__cp39-cp39-macosx_15_0_arm64.whl

musica/mechanism_configuration/first_order_loss.py

@@ -1,174 +1,90 @@
-from .utils import _add_other_properties
-from .reactions import ReactionComponentSerializer
+from .utils import _add_other_properties, _remove_empty_keys
 from .species import Species
 from .phase import Phase
 from typing import Optional, Any, Dict, List, Union, Tuple
 from .. import backend
+from .reaction_component import ReactionComponent
+from .ancillary import ReactionType
 
 _backend = backend.get_backend()
-_FirstOrderLoss = _backend._mechanism_configuration._FirstOrderLoss
-_ReactionComponent = _backend._mechanism_configuration._ReactionComponent
-ReactionType = _backend._mechanism_configuration._ReactionType
+FirstOrderLoss = _backend._mechanism_configuration._FirstOrderLoss
 
+original_init = FirstOrderLoss.__init__
 
-class FirstOrderLoss:
+
+@property
+def type(self):
+    return ReactionType.FirstOrderLoss
+
+
+def __init__(
+    self,
+    name: Optional[str] = None,
+    scaling_factor: Optional[float] = None,
+    reactants: Optional[List[Union[Species,
+                                   Tuple[float, Species]]]] = None,
+    gas_phase: Optional[Phase] = None,
+    other_properties: Optional[Dict[str, Any]] = None,
+):
     """
-    A class representing a first-order loss reaction rate constant.
+    Initializes the FirstOrderLoss object with the given parameters.
 
-    Attributes:
+    Args:
         name (str): The name of the first-order loss reaction rate constant.
         scaling_factor (float): The scaling factor for the first-order loss rate constant.
         reactants (List[Union[Species, Tuple[float, Species]]]): A list of reactants involved in the reaction.
         gas_phase (Phase): The gas phase in which the reaction occurs.
         other_properties (Dict[str, Any]): A dictionary of other properties of the first-order loss reaction rate constant.
     """
+    original_init(self)
+
+    self.name = name if name is not None else self.name
+    self.scaling_factor = scaling_factor if scaling_factor is not None else self.scaling_factor
+    self.gas_phase = gas_phase.name if gas_phase is not None else self.gas_phase
+    self.other_properties = other_properties if other_properties is not None else self.other_properties
+    self.reactants = (
+        [
+            (
+                ReactionComponent(r.name)
+                if isinstance(r, Species)
+                else ReactionComponent(r[1].name, r[0])
+            )
+            for r in reactants
+        ]
+        if reactants is not None
+        else self.reactants
+    )
+
+
+def serialize(self) -> Dict:
+    """
+    Serialize the FirstOrderLoss object to a dictionary using only Python-visible data.
 
-    def __init__(
-        self,
-        name: Optional[str] = None,
-        scaling_factor: Optional[float] = None,
-        reactants: Optional[List[Union[Species,
-                                       Tuple[float, Species]]]] = None,
-        gas_phase: Optional[Phase] = None,
-        other_properties: Optional[Dict[str, Any]] = None,
-    ):
-        """
-        Initializes the FirstOrderLoss object with the given parameters.
-
-        Args:
-            name (str): The name of the first-order loss reaction rate constant.
-            scaling_factor (float): The scaling factor for the first-order loss rate constant.
-            reactants (List[Union[Species, Tuple[float, Species]]]): A list of reactants involved in the reaction.
-            gas_phase (Phase): The gas phase in which the reaction occurs.
-            other_properties (Dict[str, Any]): A dictionary of other properties of the first-order loss reaction rate constant.
-        """
-        # Create the internal C++ instance
-        self._instance = _FirstOrderLoss()
-
-        # Set properties if provided
-        if name is not None:
-            self.name = name
-        if scaling_factor is not None:
-            self.scaling_factor = scaling_factor
-        if reactants is not None:
-            self.reactants = reactants
-        if gas_phase is not None:
-            self.gas_phase = gas_phase
-        if other_properties is not None:
-            self.other_properties = other_properties
-
-    @property
-    def name(self) -> str:
-        """Get the name."""
-        return self._instance.name
-
-    @name.setter
-    def name(self, value: str):
-        """Set the name."""
-        self._instance.name = value
-
-    @property
-    def scaling_factor(self) -> float:
-        """Get the scaling factor."""
-        return self._instance.scaling_factor
-
-    @scaling_factor.setter
-    def scaling_factor(self, value: float):
-        """Set the scaling factor."""
-        self._instance.scaling_factor = value
-
-    @property
-    def reactants(self) -> List[Union[Species, Tuple[float, Species]]]:
-        """Get the reactants as Python objects."""
-        # Convert from C++ _ReactionComponent objects to Python Species objects
-        result = []
-        for rc in self._instance.reactants:
-            if hasattr(rc, 'coefficient') and rc.coefficient != 1.0:
-                # Create a tuple with coefficient and species
-                species = Species(name=rc.species_name)
-                result.append((rc.coefficient, species))
-            else:
-                # Just the species
-                species = Species(name=rc.species_name)
-                result.append(species)
-        return result
-
-    @reactants.setter
-    def reactants(self, value: List[Union[Species, Tuple[float, Species]]]):
-        """Set the reactants, converting from Python to C++ objects."""
-        cpp_reactants = []
-        for r in value:
-            if isinstance(r, Species):
-                cpp_reactants.append(_ReactionComponent(r.name))
-            elif isinstance(r, tuple) and len(r) == 2:
-                coefficient, species = r
-                cpp_reactants.append(_ReactionComponent(species.name, coefficient))
-            else:
-                raise ValueError(f"Invalid reactant format: {r}")
-        self._instance.reactants = cpp_reactants
-
-    @property
-    def gas_phase(self) -> str:
-        """Get the gas phase name."""
-        return self._instance.gas_phase
-
-    @gas_phase.setter
-    def gas_phase(self, value: Union[Phase, str]):
-        """Set the gas phase."""
-        if isinstance(value, Phase):
-            self._instance.gas_phase = value.name
-        else:
-            self._instance.gas_phase = value
-
-    @property
-    def other_properties(self) -> Dict[str, Any]:
-        """Get the other properties."""
-        return self._instance.other_properties
-
-    @other_properties.setter
-    def other_properties(self, value: Dict[str, Any]):
-        """Set the other properties."""
-        self._instance.other_properties = value
-
-    @property
-    def type(self):
-        """Get the reaction type."""
-        return ReactionType.FirstOrderLoss
-
-    def serialize(self) -> Dict:
-        """
-        Serialize the FirstOrderLoss object to a dictionary using only Python-visible data.
-
-        Returns:
-            Dict: A dictionary representation of the FirstOrderLoss object.
-        """
-        serialize_dict = {
-            "type": "FIRST_ORDER_LOSS",
-            "name": self.name,
-            "scaling factor": self.scaling_factor,
-            "reactants": ReactionComponentSerializer.serialize_list_reaction_components(self._instance.reactants),
-            "gas phase": self.gas_phase,
-        }
-        _add_other_properties(serialize_dict, self.other_properties)
-        return _remove_empty_keys(serialize_dict)
-
-    @staticmethod
-    def serialize_static(instance) -> Dict:
-        """
-        Static serialize method for compatibility with C++ _FirstOrderLoss objects.
-
-        Args:
-            instance: The _FirstOrderLoss instance to serialize.
-
-        Returns:
-            Dict: A dictionary representation of the FirstOrderLoss object.
-        """
-        serialize_dict = {
-            "type": "FIRST_ORDER_LOSS",
-            "name": instance.name,
-            "scaling factor": instance.scaling_factor,
-            "reactants": ReactionComponentSerializer.serialize_list_reaction_components(instance.reactants),
-            "gas phase": instance.gas_phase,
-        }
-        _add_other_properties(serialize_dict, instance.other_properties)
-        return serialize_dict
+    Returns:
+        Dict: A dictionary representation of the FirstOrderLoss object.
+    """
+    serialize_dict = {
+        "type": "FIRST_ORDER_LOSS",
+        "name": self.name,
+        "scaling factor": self.scaling_factor,
+        "reactants": [r.serialize() for r in self.reactants],
+        "gas phase": self.gas_phase,
+    }
+    _add_other_properties(serialize_dict, self.other_properties)
+    return _remove_empty_keys(serialize_dict)
+
+
+FirstOrderLoss.__doc__ = """
+A class representing a first-order loss reaction rate constant.
+
+Attributes:
+    name (str): The name of the first-order loss reaction rate constant.
+    scaling_factor (float): The scaling factor for the first-order loss rate constant.
+    reactants (List[Union[Species, Tuple[float, Species]]]): A list of reactants involved in the reaction.
+    gas_phase (Phase): The gas phase in which the reaction occurs.
+    other_properties (Dict[str, Any]): A dictionary of other properties of the first-order loss reaction rate constant.
+"""
+
+FirstOrderLoss.__init__ = __init__
+FirstOrderLoss.serialize = serialize
+FirstOrderLoss.type = type

musica/mechanism_configuration/mechanism.py

@@ -0,0 +1,93 @@
+# Copyright (C) 2025 University Corporation for Atmospheric Research
+# SPDX-License-Identifier: Apache-2.0
+#
+# This file is part of the musica Python package.
+# For more information, see the LICENSE file in the top-level directory of this distribution.
+import os
+import json
+import yaml
+from typing import Optional, Any, Dict, List
+from .. import backend
+
+from .species import Species
+from .phase import Phase
+from .reactions import Reactions
+from .ancillary import Version
+
+_backend = backend.get_backend()
+Mechanism = _backend._mechanism_configuration._Mechanism
+
+original_init = Mechanism.__init__
+
+
+def export(self, file_path: str) -> None:
+    directory, file = os.path.split(file_path)
+    if directory:
+        os.makedirs(directory, exist_ok=True)
+
+    dictionary = self.serialize()
+
+    _, file_ext = os.path.splitext(file)
+    file_ext = file_ext.lower()
+    if file_ext in ['.yaml', '.yml']:
+        with open(file_path, 'w') as file:
+            yaml.dump(dictionary, file)
+    elif '.json' == file_ext:
+        json_str = json.dumps(dictionary, indent=4)
+        with open(file_path, 'w') as file:
+            file.write(json_str)
+    else:
+        raise ValueError(
+            'Allowable write formats are .json, .yaml, and .yml')
+
+
+def __init__(
+    self,
+    name: Optional[str] = None,
+    reactions: Optional[List[Any]] = None,
+    species: Optional[List[Species]] = None,
+    phases: Optional[List[Phase]] = None,
+    version: Optional[Version] = None,
+):
+    """
+    Initializes the Mechanism object with the given parameters.
+
+    Args:
+        name (str): The name of the mechanism.
+        reactions (List[]): A list of reactions in the mechanism.
+        species (List[Species]): A list of species in the mechanism.
+        phases (List[Phase]): A list of phases in the mechanism.
+        version (Version): The version of the mechanism.
+    """
+    original_init(self)
+    self.name = name
+    self.species = species if species is not None else []
+    self.phases = phases if phases is not None else []
+    self.reactions = Reactions(reactions=reactions if reactions is not None else [])
+    self.version = version if version is not None else Version()
+
+
+def serialize(self) -> Dict:
+    return {
+        "name": self.name,
+        "reactions": [r.serialize() for r in self.reactions],
+        "species": [s.serialize() for s in self.species],
+        "phases": [p.serialize() for p in self.phases],
+        "version": self.version.to_string(),
+    }
+
+
+Mechanism.__doc__ = """
+    A class representing a chemical mechanism.
+
+    Attributes:
+        name (str): The name of the mechanism.
+        reactions (List[Reaction]): A list of reactions in the mechanism.
+        species (List[Species]): A list of species in the mechanism.
+        phases (List[Phase]): A list of phases in the mechanism.
+        version (Version): The version of the mechanism.
+    """
+
+Mechanism.__init__ = __init__
+Mechanism.serialize = serialize
+Mechanism.export = export

musica/mechanism_configuration/phase.py

@@ -1,47 +1,58 @@
-from typing import Optional, Any, Dict, List
+from typing import Optional, Any, Dict, List, Union
 from .. import backend
 from .species import Species
+from .phase_species import PhaseSpecies
 from .utils import _add_other_properties, _remove_empty_keys
 
 _backend = backend.get_backend()
-_Phase = _backend._mechanism_configuration._Phase
+Phase = _backend._mechanism_configuration._Phase
+Phase.__doc__ = """
+    A class representing a phase in a chemical mechanism.
+
+    Attributes:
+        name (str): The name of the phase.
+        species (List[Species]): A list of species in the phase.
+        other_properties (Dict[str, Any]): A dictionary of other properties of the phase.
+    """
 
+original_init = Phase.__init__
 
-class Phase(_Phase):
+
+def init(
+    self,
+    name: Optional[str] = None,
+    species: Optional[Union[List[Species], List[PhaseSpecies]]] = None,
+    other_properties: Optional[Dict[str, Any]] = None,
+):
     """
-    A class representing a phase in a chemical mechanism.
+    Initializes the Phase object with the given parameters.
 
-    Attributes:
+    Args:
         name (str): The name of the phase.
         species (List[Species]): A list of species in the phase.
         other_properties (Dict[str, Any]): A dictionary of other properties of the phase.
     """
+    original_init(self)
+    self.name = name if name is not None else self.name
+    converted_species = []
+    if species is not None:
+        for s in species:
+            if isinstance(s, PhaseSpecies):
+                converted_species.append(s)
+            elif isinstance(s, Species):
+                converted_species.append(PhaseSpecies(name=s.name))
+    self.species = converted_species
+    self.other_properties = other_properties if other_properties is not None else self.other_properties
+
+
+def serialize(instance):
+    serialize_dict = {
+        "name": instance.name,
+        "species": [s.serialize() for s in instance.species],
+    }
+    _add_other_properties(serialize_dict, instance.other_properties)
+    return _remove_empty_keys(serialize_dict)
+
 
-    def __init__(
-        self,
-        name: Optional[str] = None,
-        species: Optional[List[Species]] = None,
-        other_properties: Optional[Dict[str, Any]] = None,
-    ):
-        """
-        Initializes the Phase object with the given parameters.
-
-        Args:
-            name (str): The name of the phase.
-            species (List[Species]): A list of species in the phase.
-            other_properties (Dict[str, Any]): A dictionary of other properties of the phase.
-        """
-        super().__init__()
-        self.name = name if name is not None else self.name
-        self.species = [
-            s.name for s in species] if species is not None else self.species
-        self.other_properties = other_properties if other_properties is not None else self.other_properties
-
-    @staticmethod
-    def serialize(instance):
-        serialize_dict = {
-            "name": instance.name,
-            "species": instance.species,
-        }
-        _add_other_properties(serialize_dict, instance.other_properties)
-        return _remove_empty_keys(serialize_dict)
+Phase.__init__ = init
+Phase.serialize = serialize

musica/mechanism_configuration/phase_species.py

@@ -0,0 +1,58 @@
+from typing import Optional, Any, Dict
+from .. import backend
+from .utils import _add_other_properties, _remove_empty_keys
+
+_backend = backend.get_backend()
+PhaseSpecies = _backend._mechanism_configuration._PhaseSpecies
+original_init = PhaseSpecies.__init__
+
+
+def __init__(
+    self,
+    name: Optional[str] = None,
+    diffusion_coefficient_m2_s: Optional[float] = None,
+    other_properties: Optional[Dict[str, Any]] = None,
+):
+    """
+    Initializes the PhaseSpecies object with the given parameters.
+
+    Args:
+        name (str): The name of the species.
+        diffusion_coefficient_m2_s (float): Diffusion coefficient [m2 s-1]
+        other_properties (Dict[str, Any]): A dictionary of other properties of the species.
+    """
+    original_init(self)
+    self.name = name if name is not None else self.name
+    self.diffusion_coefficient_m2_s = diffusion_coefficient_m2_s if diffusion_coefficient_m2_s is not None else self.diffusion_coefficient_m2_s
+    self.other_properties = other_properties if other_properties is not None else self.other_properties
+
+
+def serialize(self) -> Dict:
+    serialize_dict = {
+        "name": self.name,
+        "diffusion coefficient [m2 s-1]": self.diffusion_coefficient_m2_s,
+    }
+    _add_other_properties(serialize_dict, self.other_properties)
+    return _remove_empty_keys(serialize_dict)
+
+
+def equals(self, other):
+    return self.name == other.name and self.diffusion_coefficient_m2_s == other.diffusion_coefficient_m2_s
+
+
+PhaseSpecies.__doc__ = """
+    Represents a chemical species within a specific phase of a mechanism,
+    including phase-specific properties such as diffusion coefficients.
+
+    This class is distinct from a regular Species class in that it models
+    properties relevant to the species' behavior in a particular phase
+    (e.g., gas, liquid, or solid), such as the diffusion coefficient.
+
+    Attributes:
+        name (str): The name of the species.
+        diffusion_coefficient_m2_s (float): Diffusion coefficient in the phase [m2 s-1].
+        other_properties (Dict[str, Any]): A dictionary of other phase-specific properties of the species.
+    """
+PhaseSpecies.__init__ = __init__
+PhaseSpecies.serialize = serialize
+PhaseSpecies.__eq__ = equals

musica/mechanism_configuration/photolysis.py

@@ -1,20 +1,35 @@
 from .utils import _add_other_properties
-from .reactions import ReactionComponentSerializer
 from .species import Species
 from .phase import Phase
 from typing import Optional, Any, Dict, List, Union, Tuple
 from .. import backend
+from .reaction_component import ReactionComponent
+from .ancillary import ReactionType
 
 _backend = backend.get_backend()
-_Photolysis = _backend._mechanism_configuration._Photolysis
-_ReactionComponent = _backend._mechanism_configuration._ReactionComponent
+Photolysis = _backend._mechanism_configuration._Photolysis
 
+original_init = Photolysis.__init__
 
-class Photolysis(_Photolysis):
+
+@property
+def type(self):
+    return ReactionType.Photolysis
+
+
+def __init__(
+    self,
+    name: Optional[str] = None,
+    scaling_factor: Optional[float] = None,
+    reactants: Optional[List[Union[Species, Tuple[float, Species]]]] = None,
+    products: Optional[List[Union[Species, Tuple[float, Species]]]] = None,
+    gas_phase: Optional[Phase] = None,
+    other_properties: Optional[Dict[str, Any]] = None,
+):
     """
-    A class representing a photolysis reaction rate constant.
+    Initializes the Photolysis object with the given parameters.
 
-    Attributes:
+    Args:
         name (str): The name of the photolysis reaction rate constant.
         scaling_factor (float): The scaling factor for the photolysis rate constant.
         reactants (List[Union[Species, Tuple[float, Species]]]): A list of reactants involved in the reaction.
@@ -22,67 +37,62 @@ class Photolysis(_Photolysis):
         gas_phase (Phase): The gas phase in which the reaction occurs.
         other_properties (Dict[str, Any]): A dictionary of other properties of the photolysis reaction rate constant.
     """
+    original_init(self)
+    self.name = name if name is not None else self.name
+    self.scaling_factor = scaling_factor if scaling_factor is not None else self.scaling_factor
+    self.reactants = (
+        [
+            (
+                ReactionComponent(r.name)
+                if isinstance(r, Species)
+                else ReactionComponent(r[1].name, r[0])
+            )
+            for r in reactants
+        ]
+        if reactants is not None
+        else self.reactants
+    )
+    self.products = (
+        [
+            (
+                ReactionComponent(p.name)
+                if isinstance(p, Species)
+                else ReactionComponent(p[1].name, p[0])
+            )
+            for p in products
+        ]
+        if products is not None
+        else self.products
+    )
+    self.gas_phase = gas_phase.name if gas_phase is not None else self.gas_phase
+    self.other_properties = other_properties if other_properties is not None else self.other_properties
+
+
+def serialize(self) -> Dict:
+    serialize_dict = {
+        "type": "PHOTOLYSIS",
+        "name": self.name,
+        "scaling factor": self.scaling_factor,
+        "reactants": [r.serialize() for r in self.reactants],
+        "products": [r.serialize() for r in self.products],
+        "gas phase": self.gas_phase,
+    }
+    _add_other_properties(serialize_dict, self.other_properties)
+    return serialize_dict
+
 
-    def __init__(
-        self,
-        name: Optional[str] = None,
-        scaling_factor: Optional[float] = None,
-        reactants: Optional[List[Union[Species,
-                                       Tuple[float, Species]]]] = None,
-        products: Optional[List[Union[Species, Tuple[float, Species]]]] = None,
-        gas_phase: Optional[Phase] = None,
-        other_properties: Optional[Dict[str, Any]] = None,
-    ):
-        """
-        Initializes the Photolysis object with the given parameters.
+Photolysis.__doc__ = """
+A class representing a photolysis reaction rate constant.
 
-        Args:
-            name (str): The name of the photolysis reaction rate constant.
-            scaling_factor (float): The scaling factor for the photolysis rate constant.
-            reactants (List[Union[Species, Tuple[float, Species]]]): A list of reactants involved in the reaction.
-            products (List[Union[Species, Tuple[float, Species]]]): A list of products formed in the reaction.
-            gas_phase (Phase): The gas phase in which the reaction occurs.
-            other_properties (Dict[str, Any]): A dictionary of other properties of the photolysis reaction rate constant.
-        """
-        super().__init__()
-        self.name = name if name is not None else self.name
-        self.scaling_factor = scaling_factor if scaling_factor is not None else self.scaling_factor
-        self.reactants = (
-            [
-                (
-                    _ReactionComponent(r.name)
-                    if isinstance(r, Species)
-                    else _ReactionComponent(r[1].name, r[0])
-                )
-                for r in reactants
-            ]
-            if reactants is not None
-            else self.reactants
-        )
-        self.products = (
-            [
-                (
-                    _ReactionComponent(p.name)
-                    if isinstance(p, Species)
-                    else _ReactionComponent(p[1].name, p[0])
-                )
-                for p in products
-            ]
-            if products is not None
-            else self.products
-        )
-        self.gas_phase = gas_phase.name if gas_phase is not None else self.gas_phase
-        self.other_properties = other_properties if other_properties is not None else self.other_properties
+Attributes:
+    name (str): The name of the photolysis reaction rate constant.
+    scaling_factor (float): The scaling factor for the photolysis rate constant.
+    reactants (List[Union[Species, Tuple[float, Species]]]): A list of reactants involved in the reaction.
+    products (List[Union[Species, Tuple[float, Species]]]): A list of products formed in the reaction.
+    gas_phase (Phase): The gas phase in which the reaction occurs.
+    other_properties (Dict[str, Any]): A dictionary of other properties of the photolysis reaction rate constant.
+"""
 
-    @staticmethod
-    def serialize(instance) -> Dict:
-        serialize_dict = {
-            "type": "PHOTOLYSIS",
-            "name": instance.name,
-            "scaling factor": instance.scaling_factor,
-            "reactants": ReactionComponentSerializer.serialize_list_reaction_components(instance.reactants),
-            "products": ReactionComponentSerializer.serialize_list_reaction_components(instance.products),
-            "gas phase": instance.gas_phase,
-        }
-        _add_other_properties(serialize_dict, instance.other_properties)
-        return serialize_dict
+Photolysis.__init__ = __init__
+Photolysis.serialize = serialize
+Photolysis.type = type