musica 0.11.1.4__cp311-cp311-win_amd64.whl → 0.12.0__cp311-cp311-win_amd64.whl

musica/test/test_parser.py

@@ -1,399 +1,6 @@
 import pytest
 from musica.mechanism_configuration import *
-from musica import _ReactionType
-
-
-def validate_species(species):
-    # Define the expected species and their required attributes
-    expected_species = {
-        "A": {"other_properties": {"__absolute tolerance": "1e-30"}},
-        "B": {"tracer_type": "AEROSOL"},
-        "C": {"tracer_type": "THIRD_BODY"},
-        "M": {},
-        "H2O2": {
-            "HLC_298K_mol_m3_Pa": 1.011596348,
-            "HLC_exponential_factor_K": 6340,
-            "diffusion_coefficient_m2_s": 1.46e-05,
-            "N_star": 1.74,
-            "molecular_weight_kg_mol": 0.0340147,
-            "density_kg_m3": 1000.0,
-            "other_properties": {"__absolute tolerance": "1e-10"},
-        },
-        "ethanol": {
-            "diffusion_coefficient_m2_s": 0.95e-05,
-            "N_star": 2.55,
-            "molecular_weight_kg_mol": 0.04607,
-            "other_properties": {"__absolute tolerance": "1e-20"},
-        },
-        "ethanol_aq": {
-            "molecular_weight_kg_mol": 0.04607,
-            "density_kg_m3": 1000.0,
-            "other_properties": {"__absolute tolerance": "1e-20"},
-        },
-        "H2O2_aq": {
-            "molecular_weight_kg_mol": 0.0340147,
-            "density_kg_m3": 1000.0,
-            "other_properties": {"__absolute tolerance": "1e-10"},
-        },
-        "H2O_aq": {
-            "density_kg_m3": 1000.0,
-            "molecular_weight_kg_mol": 0.01801,
-        },
-        "aerosol stuff": {
-            "molecular_weight_kg_mol": 0.5,
-            "density_kg_m3": 1000.0,
-            "other_properties": {"__absolute tolerance": "1e-20"},
-        },
-        "more aerosol stuff": {
-            "molecular_weight_kg_mol": 0.2,
-            "density_kg_m3": 1000.0,
-            "other_properties": {"__absolute tolerance": "1e-20"},
-        },
-    }
-
-    # Create a dictionary for quick lookup of species by name
-    species_dict = {sp.name: sp for sp in species}
-
-    # Validate each expected species
-    for name, attributes in expected_species.items():
-        assert name in species_dict, f"Species '{name}' is missing."
-        for attr, expected_value in attributes.items():
-            assert hasattr(
-                species_dict[name], attr
-            ), f"Attribute '{attr}' is missing for species '{name}'."
-            got_value = getattr(species_dict[name], attr)
-            # Handle special cases for floating-point representation
-            if isinstance(got_value, str) and ".0e" in got_value:
-                got_value = got_value.replace(".0e", "e")
-            elif isinstance(got_value, dict):
-                def replace_in_dict(d):
-                    for key, value in d.items():
-                        if isinstance(value, str) and ".0e" in value:
-                            d[key] = value.replace(".0e", "e")
-                        elif isinstance(value, dict):
-                            replace_in_dict(value)
-                replace_in_dict(got_value)
-            assert got_value == expected_value, (
-                f"Attribute '{attr}' for species '{name}' has value "
-                f"{got_value}, expected {expected_value}."
-            )
-
-
-def validate_phases(phases):
-    # Define the expected phases and their associated species
-    expected_phases = {
-        "gas": ["A", "B", "C", "ethanol"],
-        "aqueous aerosol": ["H2O2_aq", "H2O_aq", "ethanol_aq", "A", "B", "C"],
-        "surface reacting phase": ["aerosol stuff", "more aerosol stuff"],
-        "cloud": ["B", "C"],
-    }
-
-    # Create a dictionary for quick lookup of phases by name
-    phases_dict = {phase.name: phase for phase in phases}
-
-    # Validate each expected phase
-    for name, expected_species in expected_phases.items():
-        assert name in phases_dict, f"Phase '{name}' is missing."
-        assert hasattr(
-            phases_dict[name], "species"
-        ), f"Phase '{name}' does not have a 'species' attribute."
-        phase_species = getattr(phases_dict[name], "species")
-        assert set(phase_species) == set(expected_species), (
-            f"Phase '{name}' has species {phase_species}, "
-            f"expected {expected_species}."
-        )
-
-
-def extract_components(components):
-    return [
-        {"species name": component.species_name, "coefficient": component.coefficient}
-        for component in components
-    ]
-
-
-def validate_arrhenius(reactions):
-    assert reactions[0].type == ReactionType.Arrhenius
-    assert extract_components(reactions[0].reactants) == [
-        {"species name": "B", "coefficient": 1}
-    ]
-    assert extract_components(reactions[0].products) == [
-        {"species name": "C", "coefficient": 1}
-    ]
-    assert reactions[0].A == 32.1
-    assert reactions[0].B == -2.3
-    assert reactions[0].C == 102.3
-    assert reactions[0].D == 63.4
-    assert reactions[0].E == -1.3
-    assert reactions[0].name == "my arrhenius"
-    assert reactions[0].other_properties == {}
-    assert reactions[1].type == ReactionType.Arrhenius
-    assert extract_components(reactions[1].reactants) == [
-        {"species name": "A", "coefficient": 1}
-    ]
-    assert extract_components(reactions[1].products) == [
-        {"species name": "B", "coefficient": 1.2}
-    ]
-    assert reactions[1].A == 29.3
-    assert reactions[1].B == -1.5
-    assert reactions[1].C == -101.2 / 1.380649e-23
-    assert reactions[1].D == 82.6
-    assert reactions[1].E == -0.98
-    assert reactions[1].name == "my other arrhenius"
-    assert reactions[1].other_properties == {}
-
-
-def validate_henrys_law(reactions):
-    assert reactions[0].type == ReactionType.HenrysLaw
-    assert reactions[0].gas_phase == "gas"
-    assert extract_components([reactions[0].gas_phase_species]) == [
-        {"species name": "H2O2", "coefficient": 1}
-    ]
-    assert reactions[0].aerosol_phase == "aqueous aerosol"
-    assert extract_components([reactions[0].aerosol_phase_species]) == [
-        {"species name": "H2O2_aq", "coefficient": 1}
-    ]
-    assert reactions[0].aerosol_phase_water == "H2O_aq"
-    assert reactions[0].name == "my henry's law"
-
-
-def validate_simpol_phase_transfer(reactions):
-    assert reactions[0].type == ReactionType.SimpolPhaseTransfer
-    assert reactions[0].gas_phase == "gas"
-    assert extract_components([reactions[0].gas_phase_species]) == [
-        {"species name": "ethanol", "coefficient": 1}
-    ]
-    assert reactions[0].aerosol_phase == "aqueous aerosol"
-    assert extract_components([reactions[0].aerosol_phase_species]) == [
-        {"species name": "ethanol_aq", "coefficient": 1}
-    ]
-    assert reactions[0].B == [-1.97e03, 2.91e00, 1.96e-03, -4.96e-01]
-    assert reactions[0].name == "my simpol"
-
-
-def validate_aqueous_equilibrium(reactions):
-    assert reactions[0].type == ReactionType.AqueousEquilibrium
-    assert reactions[0].aerosol_phase == "aqueous aerosol"
-    assert reactions[0].aerosol_phase_water == "H2O_aq"
-    assert reactions[0].A == 1.14e-2
-    assert reactions[0].C == 2300.0
-    assert reactions[0].k_reverse == 0.32
-    assert extract_components(reactions[0].reactants) == [
-        {"species name": "A", "coefficient": 2}
-    ]
-    assert extract_components(reactions[0].products) == [
-        {"species name": "B", "coefficient": 1},
-        {"species name": "C", "coefficient": 1},
-    ]
-    assert reactions[0].name == "my aqueous eq"
-
-
-def validate_condensed_phase_arrhenius(reactions):
-    for reaction in reactions:
-        assert reaction.type == ReactionType.CondensedPhaseArrhenius
-        assert reaction.aerosol_phase == "aqueous aerosol"
-        assert reaction.aerosol_phase_water == "H2O_aq"
-        assert reaction.A == 123.45
-        assert reaction.B == 1.3
-        assert reaction.D == 300.0
-        assert reaction.E == 0.6e-5
-        assert extract_components(reaction.reactants) == [
-            {"species name": "H2O2_aq", "coefficient": 1},
-            {"species name": "H2O_aq", "coefficient": 1},
-        ]
-        assert extract_components(reaction.products) == [
-            {"species name": "ethanol_aq", "coefficient": 1}
-        ]
-    assert reactions[0].name == "my condensed arrhenius"
-    assert reactions[0].C == -123.45 / 1.380649e-23
-    assert reactions[1].name == "my other condensed arrhenius"
-    assert reactions[1].C == 123.45
-
-
-def validate_condensed_phase_photolysis(reactions):
-    assert reactions[0].type == ReactionType.CondensedPhasePhotolysis
-    assert reactions[0].aerosol_phase == "aqueous aerosol"
-    assert reactions[0].aerosol_phase_water == "H2O_aq"
-    assert extract_components(reactions[0].reactants) == [
-        {"species name": "H2O2_aq", "coefficient": 1}
-    ]
-    assert extract_components(reactions[0].products) == [
-        {"species name": "ethanol_aq", "coefficient": 1}
-    ]
-    assert reactions[0].scaling_factor == 12.3
-    assert reactions[0].name == "condensed photo B"
-
-
-def validate_emission(reactions):
-    assert reactions[0].type == ReactionType.Emission
-    assert reactions[0].gas_phase == "gas"
-    assert extract_components(reactions[0].products) == [
-        {"species name": "B", "coefficient": 1}
-    ]
-    assert reactions[0].scaling_factor == 12.3
-    assert reactions[0].name == "my emission"
-
-
-def validate_first_order_loss(reactions):
-    assert reactions[0].type == ReactionType.FirstOrderLoss
-    assert reactions[0].gas_phase == "gas"
-    assert extract_components(reactions[0].reactants) == [
-        {"species name": "C", "coefficient": 1}
-    ]
-    assert reactions[0].scaling_factor == 12.3
-    assert reactions[0].name == "my first order loss"
-
-
-def validate_photolysis(reactions):
-    assert reactions[0].type == ReactionType.Photolysis
-    assert reactions[0].gas_phase == "gas"
-    assert extract_components(reactions[0].reactants) == [
-        {"species name": "B", "coefficient": 1}
-    ]
-    assert extract_components(reactions[0].products) == [
-        {"species name": "C", "coefficient": 1}
-    ]
-    assert reactions[0].scaling_factor == 12.3
-    assert reactions[0].name == "photo B"
-
-
-def validate_surface(reactions):
-    assert reactions[0].type == ReactionType.Surface
-    assert reactions[0].gas_phase == "gas"
-    assert extract_components([reactions[0].gas_phase_species]) == [
-        {"species name": "A", "coefficient": 1}
-    ]
-    assert reactions[0].reaction_probability == 2.0e-2
-    assert extract_components(reactions[0].gas_phase_products) == [
-        {"species name": "B", "coefficient": 1},
-        {"species name": "C", "coefficient": 1},
-    ]
-    assert reactions[0].aerosol_phase == "surface reacting phase"
-    assert reactions[0].name == "my surface"
-
-
-def validate_troe(reactions):
-    assert reactions[0].type == ReactionType.Troe
-    assert reactions[0].gas_phase == "gas"
-    assert extract_components(reactions[0].reactants) == [
-        {"species name": "B", "coefficient": 1},
-        {"species name": "M", "coefficient": 1},
-    ]
-    assert extract_components(reactions[0].products) == [
-        {"species name": "C", "coefficient": 1}
-    ]
-    assert reactions[0].k0_A == 1.2e-12
-    assert reactions[0].k0_B == 167
-    assert reactions[0].k0_C == 3
-    assert reactions[0].kinf_A == 136
-    assert reactions[0].kinf_B == 5
-    assert reactions[0].kinf_C == 24
-    assert reactions[0].Fc == 0.9
-    assert reactions[0].N == 0.8
-    assert reactions[0].name == "my troe"
-
-
-def validate_branched_no_ro2(reactions):
-    assert reactions[0].type == ReactionType.Branched
-    assert reactions[0].gas_phase == "gas"
-    assert extract_components(reactions[0].reactants) == [
-        {"species name": "A", "coefficient": 1}
-    ]
-    assert extract_components(reactions[0].alkoxy_products) == [
-        {"species name": "B", "coefficient": 1}
-    ]
-    assert extract_components(reactions[0].nitrate_products) == [
-        {"species name": "C", "coefficient": 1}
-    ]
-    assert reactions[0].X == 1.2e-4
-    assert reactions[0].Y == 167
-    assert reactions[0].a0 == 0.15
-    assert reactions[0].n == 9
-    assert reactions[0].name == "my branched"
-
-
-def validate_tunneling(reactions):
-    assert reactions[0].type == ReactionType.Tunneling
-    assert reactions[0].gas_phase == "gas"
-    assert extract_components(reactions[0].reactants) == [
-        {"species name": "B", "coefficient": 1}
-    ]
-    assert extract_components(reactions[0].products) == [
-        {"species name": "C", "coefficient": 1}
-    ]
-    assert reactions[0].A == 123.45
-    assert reactions[0].B == 1200.0
-    assert reactions[0].C == 1.0e8
-    assert reactions[0].name == "my tunneling"
-
-
-def validate_wet_deposition(reactions):
-    assert reactions[0].type == ReactionType.WetDeposition
-    assert reactions[0].name == "rxn cloud"
-    assert reactions[0].aerosol_phase == "cloud"
-    assert reactions[0].scaling_factor == 12.3
-
-
-def validate_user_defined(reactions):
-    assert reactions[0].type == ReactionType.UserDefined
-    assert reactions[0].gas_phase == "gas"
-    assert extract_components(reactions[0].reactants) == [
-        {"species name": "A", "coefficient": 1},
-        {"species name": "B", "coefficient": 1},
-    ]
-    assert extract_components(reactions[0].products) == [
-        {"species name": "C", "coefficient": 1.3}
-    ]
-    assert reactions[0].scaling_factor == 12.3
-    assert reactions[0].name == "my user defined"
-    assert reactions[0].other_properties == {}
-
-
-def validate_full_v1_mechanism(mechanism):
-    assert mechanism is not None
-    assert mechanism.name == "Full Configuration"
-    assert len(mechanism.species) == 11
-    validate_species(mechanism.species)
-    assert len(mechanism.phases) == 4
-    validate_phases(mechanism.phases)
-    assert len(mechanism.reactions.aqueous_equilibrium) == 1
-    validate_aqueous_equilibrium(mechanism.reactions.aqueous_equilibrium)
-    assert len(mechanism.reactions.arrhenius) == 2
-    validate_arrhenius(mechanism.reactions.arrhenius)
-    assert len(mechanism.reactions.branched) == 1
-    validate_branched_no_ro2(mechanism.reactions.branched)
-    assert len(mechanism.reactions.condensed_phase_arrhenius) == 2
-    validate_condensed_phase_arrhenius(mechanism.reactions.condensed_phase_arrhenius)
-    assert len(mechanism.reactions.condensed_phase_photolysis) == 1
-    validate_condensed_phase_photolysis(
-        mechanism.reactions.condensed_phase_photolysis
-    )
-    assert len(mechanism.reactions.emission) == 1
-    validate_emission(mechanism.reactions.emission)
-    assert len(mechanism.reactions.first_order_loss) == 1
-    validate_first_order_loss(mechanism.reactions.first_order_loss)
-    assert len(mechanism.reactions.henrys_law) == 1
-    validate_henrys_law(mechanism.reactions.henrys_law)
-    assert len(mechanism.reactions.photolysis) == 1
-    validate_photolysis(mechanism.reactions.photolysis)
-    assert len(mechanism.reactions.simpol_phase_transfer) == 1
-    validate_simpol_phase_transfer(mechanism.reactions.simpol_phase_transfer)
-    assert len(mechanism.reactions.surface) == 1
-    validate_surface(mechanism.reactions.surface)
-    assert len(mechanism.reactions.troe) == 1
-    validate_troe(mechanism.reactions.troe)
-    assert len(mechanism.reactions.tunneling) == 1
-    validate_tunneling(mechanism.reactions.tunneling)
-    assert len(mechanism.reactions.wet_deposition) == 1
-    validate_wet_deposition(mechanism.reactions.wet_deposition)
-    assert len(mechanism.reactions.user_defined) == 1
-    validate_user_defined(mechanism.reactions.user_defined)
-    assert mechanism.version.major == 1
-    assert mechanism.version.minor == 0
-    assert mechanism.version.patch == 0
-    assert len(mechanism.reactions) == 17
-    for reaction in mechanism.reactions:
-        assert reaction is not None
-        assert isinstance(reaction.type, _ReactionType)
+from test_util_full_mechanism import get_fully_defined_mechanism, validate_full_v1_mechanism
 
 
 def test_parsed_full_v1_configuration():
@@ -415,251 +22,8 @@ def test_parser_reports_bad_files():
 
 
 def test_hard_coded_full_v1_configuration():
-
-    # Chemical species
-    A = Species(name="A", other_properties={"__absolute tolerance": "1.0e-30"})
-    B = Species(name="B", tracer_type="AEROSOL")
-    C = Species(name="C", tracer_type="THIRD_BODY")
-    M = Species(name="M")
-    H2O2 = Species(
-        name="H2O2",
-        HLC_298K_mol_m3_Pa=1.011596348,
-        HLC_exponential_factor_K=6340,
-        diffusion_coefficient_m2_s=1.46e-05,
-        N_star=1.74,
-        molecular_weight_kg_mol=0.0340147,
-        density_kg_m3=1000.0,
-        other_properties={"__absolute tolerance": "1.0e-10"},
-    )
-    ethanol = Species(
-        name="ethanol",
-        diffusion_coefficient_m2_s=0.95e-05,
-        N_star=2.55,
-        molecular_weight_kg_mol=0.04607,
-        other_properties={"__absolute tolerance": "1.0e-20"},
-    )
-    ethanol_aq = Species(
-        name="ethanol_aq",
-        molecular_weight_kg_mol=0.04607,
-        density_kg_m3=1000.0,
-        other_properties={"__absolute tolerance": "1.0e-20"},
-    )
-    H2O2_aq = Species(
-        name="H2O2_aq",
-        molecular_weight_kg_mol=0.0340147,
-        density_kg_m3=1000.0,
-        other_properties={"__absolute tolerance": "1.0e-10"},
-    )
-    H2O_aq = Species(
-        name="H2O_aq",
-        density_kg_m3=1000.0,
-        molecular_weight_kg_mol=0.01801,
-    )
-    aerosol_stuff = Species(
-        name="aerosol stuff",
-        molecular_weight_kg_mol=0.5,
-        density_kg_m3=1000.0,
-        other_properties={"__absolute tolerance": "1.0e-20"},
-    )
-    more_aerosol_stuff = Species(
-        name="more aerosol stuff",
-        molecular_weight_kg_mol=0.2,
-        density_kg_m3=1000.0,
-        other_properties={"__absolute tolerance": "1.0e-20"},
-    )
-
-    # Chemical phases
-    gas = Phase(name="gas", species=[A, B, C, ethanol])
-    aqueous_aerosol = Phase(
-        name="aqueous aerosol",
-        species=[H2O2_aq, H2O_aq, ethanol_aq, A, B, C]
-    )
-    surface_reacting_phase = Phase(
-        name="surface reacting phase",
-        species=[aerosol_stuff, more_aerosol_stuff]
-    )
-    cloud = Phase(name="cloud", species=[B, C])
-
-    # Reactions
-    my_arrhenius = Arrhenius(
-        name="my arrhenius",
-        A=32.1, B=-2.3, C=102.3, D=63.4, E=-1.3,
-        gas_phase=gas,
-        reactants=[B],
-        products=[C]
-    )
-
-    my_other_arrhenius = Arrhenius(
-        name="my other arrhenius",
-        A=29.3, B=-1.5, Ea=101.2, D=82.6, E=-0.98,
-        gas_phase=gas,
-        reactants=[A],
-        products=[(1.2, B)]
-    )
-
-    my_condensed_arrhenius = CondensedPhaseArrhenius(
-        name="my condensed arrhenius",
-        aerosol_phase=aqueous_aerosol,
-        aerosol_phase_water=H2O_aq,
-        A=123.45,
-        B=1.3,
-        Ea=123.45,
-        D=300.0,
-        E=0.6e-5,
-        reactants=[H2O2_aq, H2O_aq],
-        products=[ethanol_aq]
-    )
-
-    my_other_condensed_arrhenius = CondensedPhaseArrhenius(
-        name="my other condensed arrhenius",
-        aerosol_phase=aqueous_aerosol,
-        aerosol_phase_water=H2O_aq,
-        A=123.45,
-        B=1.3,
-        C=123.45,
-        D=300.0,
-        E=0.6e-5,
-        reactants=[H2O2_aq, H2O_aq],
-        products=[ethanol_aq]
-    )
-
-    my_troe = Troe(
-        name="my troe",
-        gas_phase=gas,
-        k0_A=1.2e-12,
-        k0_B=167,
-        k0_C=3,
-        kinf_A=136,
-        kinf_B=5,
-        kinf_C=24,
-        Fc=0.9,
-        N=0.8,
-        reactants=[B, M],
-        products=[C]
-    )
-
-    my_branched = Branched(
-        name="my branched",
-        gas_phase=gas,
-        reactants=[A],
-        alkoxy_products=[B],
-        nitrate_products=[C],
-        X=1.2e-4,
-        Y=167,
-        a0=0.15,
-        n=9,
-    )
-
-    my_tunneling = Tunneling(
-        name="my tunneling",
-        gas_phase=gas,
-        reactants=[B],
-        products=[C],
-        A=123.45,
-        B=1200.0,
-        C=1.0e8,
-    )
-
-    my_surface = Surface(
-        name="my surface",
-        gas_phase=gas,
-        gas_phase_species=A,
-        reaction_probability=2.0e-2,
-        gas_phase_products=[B, C],
-        aerosol_phase=surface_reacting_phase,
-    )
-
-    photo_B = Photolysis(
-        name="photo B",
-        gas_phase=gas,
-        reactants=[B],
-        products=[C],
-        scaling_factor=12.3,
-    )
-
-    condensed_photo_B = CondensedPhasePhotolysis(
-        name="condensed photo B",
-        aerosol_phase=aqueous_aerosol,
-        aerosol_phase_water=H2O_aq,
-        reactants=[H2O2_aq],
-        products=[ethanol_aq],
-        scaling_factor=12.3,
-    )
-
-    my_emission = Emission(
-        name="my emission",
-        gas_phase=gas,
-        products=[B],
-        scaling_factor=12.3,
-    )
-
-    my_first_order_loss = FirstOrderLoss(
-        name="my first order loss",
-        gas_phase=gas,
-        reactants=[C],
-        scaling_factor=12.3,
-    )
-
-    my_aqueous_equilibrium = AqueousEquilibrium(
-        name="my aqueous eq",
-        gas_phase=gas,
-        aerosol_phase=aqueous_aerosol,
-        aerosol_phase_water=H2O_aq,
-        A=1.14e-2,
-        C=2300.0,
-        k_reverse=0.32,
-        reactants=[(2, A)],
-        products=[B, C],
-    )
-
-    my_wet_deposition = WetDeposition(
-        name="rxn cloud",
-        aerosol_phase=cloud,
-        scaling_factor=12.3,
-    )
-
-    my_henrys_law = HenrysLaw(
-        name="my henry's law",
-        gas_phase=gas,
-        gas_phase_species=H2O2,
-        aerosol_phase=aqueous_aerosol,
-        aerosol_phase_species=H2O2_aq,
-        aerosol_phase_water=H2O_aq,
-    )
-
-    my_simpol_phase_transfer = SimpolPhaseTransfer(
-        name="my simpol",
-        gas_phase=gas,
-        gas_phase_species=ethanol,
-        aerosol_phase=aqueous_aerosol,
-        aerosol_phase_species=ethanol_aq,
-        B=[-1.97e03, 2.91e00, 1.96e-03, -4.96e-01],
-    )
-
-    user_defined = UserDefined(
-        name="my user defined",
-        gas_phase=gas,
-        reactants=[A, B],
-        products=[(1.3, C)],
-        scaling_factor=12.3,
-    )
-
-    # Mechanism
-    mechanism = Mechanism(
-        name="Full Configuration",
-        species=[A, B, C, M, H2O2, ethanol, ethanol_aq, H2O2_aq, H2O_aq,
-                 aerosol_stuff, more_aerosol_stuff],
-        phases=[gas, aqueous_aerosol, surface_reacting_phase, cloud],
-        reactions=[my_arrhenius, my_other_arrhenius, my_condensed_arrhenius,
-                   my_other_condensed_arrhenius, my_troe, my_branched,
-                   my_tunneling, my_surface, photo_B, condensed_photo_B,
-                   my_emission, my_first_order_loss, my_aqueous_equilibrium,
-                   my_wet_deposition, my_henrys_law, my_simpol_phase_transfer,
-                   user_defined],
-        version=Version(1, 0, 0),
-    )
-
-    validate_full_v1_mechanism(mechanism)
+    MECHANISM_FULLY_DEFINED = get_fully_defined_mechanism()
+    validate_full_v1_mechanism(MECHANISM_FULLY_DEFINED)
 
 
 def test_hard_coded_default_constructed_types():