musica 0.12.0__cp312-cp312-win32.whl → 0.12.1__cp312-cp312-win32.whl

musica/test/examples/v1/full_configuration/full_configuration.json

@@ -101,22 +101,12 @@
     }
   ],
   "reactions": [
-    {
-      "type": "HL_PHASE_TRANSFER",
-      "gas phase": "gas",
-      "gas-phase species": "H2O2",
-      "aerosol phase": "aqueous aerosol",
-      "aerosol-phase species": "H2O2_aq",
-      "aerosol-phase water": "H2O_aq",
-      "name": "my henry's law",
-      "__irrelevant": "2"
-    },
     {
       "type": "SIMPOL_PHASE_TRANSFER",
       "gas phase": "gas",
       "gas-phase species": "ethanol",
-      "aerosol phase": "aqueous aerosol",
-      "aerosol-phase species": "ethanol_aq",
+      "condensed phase": "aqueous aerosol",
+      "condensed-phase species": "ethanol_aq",
       "B": [
         -1.97E+03,
         2.91E+00,
@@ -128,8 +118,8 @@
     },
     {
       "type": "AQUEOUS_EQUILIBRIUM",
-      "aerosol phase": "aqueous aerosol",
-      "aerosol-phase water": "H2O_aq",
+      "condensed phase": "aqueous aerosol",
+      "condensed-phase water": "H2O_aq",
       "A": 1.14e-2,
       "C": 2300.0,
       "k_reverse": 0.32,
@@ -154,8 +144,7 @@
     },
     {
       "type": "CONDENSED_PHASE_ARRHENIUS",
-      "aerosol phase": "aqueous aerosol",
-      "aerosol-phase water": "H2O_aq",
+      "condensed phase": "aqueous aerosol",
       "A": 123.45,
       "Ea": 123.45,
       "B": 1.3,
@@ -182,8 +171,7 @@
     },
     {
       "type": "CONDENSED_PHASE_ARRHENIUS",
-      "aerosol phase": "aqueous aerosol",
-      "aerosol-phase water": "H2O_aq",
+      "condensed phase": "aqueous aerosol",
       "A": 123.45,
       "C": 123.45,
       "B": 1.3,
@@ -209,8 +197,7 @@
     },
     {
       "type": "CONDENSED_PHASE_PHOTOLYSIS",
-      "aerosol phase": "aqueous aerosol",
-      "aerosol-phase water": "H2O_aq",
+      "condensed phase": "aqueous aerosol",
       "reactants": [
         {
           "species name": "H2O2_aq",
@@ -287,7 +274,7 @@
           "coefficient": 1
         }
       ],
-      "aerosol phase": "surface reacting phase",
+      "condensed phase": "surface reacting phase",
       "name": "my surface",
       "__irrelevant": "2"
     },
@@ -321,6 +308,36 @@
       "name": "my troe",
       "__irrelevant": "2"
     },
+    {
+      "type": "TERNARY_CHEMICAL_ACTIVATION",
+      "gas phase": "gas",
+      "name": "my ternary chemical activation",
+      "reactants": [
+        {
+          "species name": "B",
+          "coefficient": 1
+        },
+        {
+          "species name": "M",
+          "coefficient": 1
+        }
+      ],
+      "products": [
+        {
+          "species name": "C",
+          "coefficient": 1
+        }
+      ],
+      "k0_A": 32.1,
+      "k0_B": -2.3,
+      "k0_C": 102.3,
+      "kinf_A": 63.4,
+      "kinf_B": -1.3,
+      "kinf_C": 908.5,
+      "Fc": 1.3,
+      "N": 32.1,
+      "__irrelevant": "2"
+    },
     {
       "type": "BRANCHED_NO_RO2",
       "gas phase": "gas",
@@ -372,7 +389,7 @@
     },
     {
       "type": "WET_DEPOSITION",
-      "aerosol phase": "cloud",
+      "condensed phase": "cloud",
       "name": "rxn cloud",
       "scaling factor": 12.3,
       "__irrelevant": "2"

musica/test/examples/v1/full_configuration/full_configuration.yaml

@@ -65,19 +65,11 @@ phases:
   - B
   - C
 reactions:
-- type: HL_PHASE_TRANSFER
-  gas phase: gas
-  gas-phase species: H2O2
-  aerosol phase: aqueous aerosol
-  aerosol-phase species: H2O2_aq
-  aerosol-phase water: H2O_aq
-  name: my henry's law
-  __irrelevant: "2"
 - type: SIMPOL_PHASE_TRANSFER
   gas phase: gas
   gas-phase species: ethanol
-  aerosol phase: aqueous aerosol
-  aerosol-phase species: ethanol_aq
+  condensed phase: aqueous aerosol
+  condensed-phase species: ethanol_aq
   B:
   - -1970
   - 2.91
@@ -86,8 +78,8 @@ reactions:
   name: my simpol
   __irrelevant: "2"
 - type: AQUEOUS_EQUILIBRIUM
-  aerosol phase: aqueous aerosol
-  aerosol-phase water: H2O_aq
+  condensed phase: aqueous aerosol
+  condensed-phase water: H2O_aq
   A: 0.0114
   C: 2300
   k_reverse: 0.32
@@ -102,8 +94,7 @@ reactions:
   name: my aqueous eq
   __irrelevant: "2"
 - type: CONDENSED_PHASE_ARRHENIUS
-  aerosol phase: aqueous aerosol
-  aerosol-phase water: H2O_aq
+  condensed phase: aqueous aerosol
   A: 123.45
   Ea: 123.45
   B: 1.3
@@ -120,8 +111,7 @@ reactions:
   name: my condensed arrhenius
   __irrelevant: "2"
 - type: CONDENSED_PHASE_ARRHENIUS
-  aerosol phase: aqueous aerosol
-  aerosol-phase water: H2O_aq
+  condensed phase: aqueous aerosol
   A: 123.45
   C: 123.45
   B: 1.3
@@ -137,8 +127,7 @@ reactions:
     coefficient: 1
   name: my other condensed arrhenius
 - type: CONDENSED_PHASE_PHOTOLYSIS
-  aerosol phase: aqueous aerosol
-  aerosol-phase water: H2O_aq
+  condensed phase: aqueous aerosol
   reactants:
   - species name: H2O2_aq
     coefficient: 1
@@ -184,7 +173,7 @@ reactions:
     coefficient: 1
   - species name: C
     coefficient: 1
-  aerosol phase: surface reacting phase
+  condensed phase: surface reacting phase
   name: my surface
   __irrelevant: "2"
 - type: TROE
@@ -207,6 +196,26 @@ reactions:
   N: 0.8
   name: my troe
   __irrelevant: "2"
+- type: TERNARY_CHEMICAL_ACTIVATION
+  gas phase: gas
+  name: my ternary chemical activation
+  reactants:
+  - species name: B
+    coefficient: 1
+  - species name: M
+    coefficient: 1
+  products:
+  - species name: C
+    coefficient: 1
+  k0_A: 32.1
+  k0_B: -2.3
+  k0_C: 102.3
+  kinf_A: 63.4
+  kinf_B: -1.3
+  kinf_C: 908.5
+  Fc: 1.3
+  "N": 32.1
+  __irrelevant: "2"
 - type: BRANCHED_NO_RO2
   gas phase: gas
   reactants:
@@ -238,7 +247,7 @@ reactions:
     coefficient: 1
   __irrelevant: "2"
 - type: WET_DEPOSITION
-  aerosol phase: cloud
+  condensed phase: cloud
   name: rxn cloud
   scaling factor: 12.3
   __irrelevant: "2"

musica/test/{test_analytical.py → integration/test_analytical.py}

@@ -118,7 +118,6 @@ def TestMultipleGridCell(solver, state, num_grid_cells, time_step, places=5):
         rate_constants["USER.reaction 2"].append(
             0.002 + random.uniform(-0.0001, 0.0001))
 
-
     state.set_conditions(temperatures, pressures)  # Air density should be calculated in the state
     state.set_concentrations(concentrations)
     state.set_user_defined_rate_parameters(rate_constants)

musica/test/integration/test_carma.py

@@ -0,0 +1,227 @@
+import pytest
+import musica
+
+available = musica.backend.carma_available()
+pytestmark = pytest.mark.skipif(
+    not available, reason="CARMA backend is not available")
+
+
+def test_carma_version():
+    version = musica.carma.version
+    assert version is not None
+    assert isinstance(version, str)
+    print(f"CARMA version: {version}")
+
+
+def test_carma_with_all_components():
+    """Test CARMA with multiple groups, elements, solutes, and gases"""
+    params = musica.CARMAParameters()
+    params.nz = 1
+    params.ny = 1
+    params.nx = 1
+    params.nbin = 3
+    params.dtime = 900.0
+    params.deltaz = 500.0
+    params.zmin = 1000.0
+
+    # Set up wavelength bins
+    params.wavelength_bins = [
+        musica.carma.CARMAWavelengthBin(
+            center=550e-9, width=50e-9, do_emission=True),   # 550 nm ± 25 nm
+        musica.carma.CARMAWavelengthBin(
+            center=850e-9, width=100e-9, do_emission=True)  # 850 nm ± 50 nm
+    ]
+
+    # Group 1: Aluminum particles (sphere)
+    aluminum_group = musica.carma.CARMAGroupConfig(
+        name="aluminum",
+        shortname="ALUM",
+        rmin=1e-8,
+        rmrat=2.0,
+        ishape=musica.carma.ParticleShape.SPHERE,
+        eshape=1.0,
+        is_fractal=False,
+        do_vtran=True,
+        do_drydep=True,
+        df=[1.8, 1.8, 1.8]  # fractal dimension per bin
+    )
+    params.groups.append(aluminum_group)
+
+    # Group 2: Sulfate particles (sphere, with swelling)
+    sulfate_group = musica.carma.CARMAGroupConfig(
+        name="sulfate",
+        shortname="SULF",
+        rmin=5e-9,
+        rmrat=2.5,
+        ishape=musica.carma.ParticleShape.SPHERE,
+        eshape=1.0,
+        swelling_approach={
+            "algorithm": musica.carma.ParticleSwellingAlgorithm.FITZGERALD,
+            "composition": musica.carma.ParticleSwellingComposition.AMMONIUM_SULFATE
+        },
+        is_sulfate=True,
+        do_wetdep=True,
+        do_vtran=True,
+        solfac=0.8,
+        df=[2.0, 2.0, 2.0]
+    )
+    params.groups.append(sulfate_group)
+
+    # Group 3: Ice particles (hexagon)
+    ice_group = musica.carma.CARMAGroupConfig(
+        name="ice",
+        shortname="ICE",
+        rmin=2e-8,
+        rmrat=3.0,
+        ishape=musica.carma.ParticleShape.HEXAGON,
+        eshape=2.0,  # aspect ratio
+        is_ice=True,
+        is_cloud=True,
+        do_vtran=True,
+        df=[1.5, 1.5, 1.5]
+    )
+    params.groups.append(ice_group)
+
+    # Element 1: Aluminum core (Group 1)
+    aluminum_element = musica.carma.CARMAElementConfig(
+        igroup=1,
+        name="Aluminum",
+        shortname="AL",
+        rho=2.70,  # g/cm³
+        itype=musica.carma.ParticleType.INVOLATILE,
+        icomposition=musica.carma.ParticleComposition.ALUMINUM,
+        kappa=0.0,
+        is_shell=False  # core
+    )
+    params.elements.append(aluminum_element)
+
+    # Element 2: Sulfate (Group 2)
+    sulfate_element = musica.carma.CARMAElementConfig(
+        igroup=2,
+        isolute=1,  # linked to first solute
+        name="Sulfate",
+        shortname="SO4",
+        rho=1.84,  # g/cm³
+        itype=musica.carma.ParticleType.VOLATILE,
+        icomposition=musica.carma.ParticleComposition.SULFURIC_ACID,
+        kappa=0.61,  # hygroscopicity
+        is_shell=True
+    )
+    params.elements.append(sulfate_element)
+
+    # Element 3: Water on sulfate (Group 2)
+    water_element = musica.carma.CARMAElementConfig(
+        igroup=2,
+        name="Water",
+        shortname="H2O",
+        rho=1.0,  # g/cm³
+        itype=musica.carma.ParticleType.CORE_MASS,
+        icomposition=musica.carma.ParticleComposition.WATER,
+        kappa=0.0,
+        is_shell=True
+    )
+    params.elements.append(water_element)
+
+    # Element 4: Ice (Group 3)
+    ice_element = musica.carma.CARMAElementConfig(
+        igroup=3,
+        name="Ice",
+        shortname="ICE",
+        rho=0.92,  # g/cm³
+        itype=musica.carma.ParticleType.INVOLATILE,
+        icomposition=musica.carma.ParticleComposition.ICE,
+        kappa=0.0,
+        is_shell=False
+    )
+    params.elements.append(ice_element)
+
+    # Solute: Sulfate
+    sulfate_solute = musica.carma.CARMASoluteConfig(
+        name="Sulfate",
+        shortname="SO4",
+        ions=2,
+        wtmol=0.1324,  # kg mol-1
+        rho=1840.0  # kg m-3
+    )
+    params.solutes.append(sulfate_solute)
+
+    # Gas: Water vapor
+    water_gas = musica.carma.CARMAGasConfig(
+        name="Water Vapor",
+        shortname="H2O",
+        wtmol=0.01801528,  # kg mol-1
+        ivaprtn=musica.carma.VaporizationAlgorithm.H2O_MURPHY_2005,
+        icomposition=musica.carma.GasComposition.H2O,
+        dgc_threshold=1.0e-6,
+        ds_threshold=1.0e-4
+    )
+    params.gases.append(water_gas)
+
+    # Gas: Sulfuric acid
+    h2so4_gas = musica.carma.CARMAGasConfig(
+        name="Sulfuric Acid",
+        shortname="H2SO4",
+        wtmol=0.098079,  # kg mol-1
+        ivaprtn=musica.carma.VaporizationAlgorithm.H2O_BUCK_1981,
+        icomposition=musica.carma.GasComposition.H2SO4,
+        dgc_threshold=0.05,
+        ds_threshold=0.1
+    )
+    params.gases.append(h2so4_gas)
+
+    # Gas: Sulfur dioxide
+    so2_gas = musica.carma.CARMAGasConfig(
+        name="Sulfur Dioxide",
+        shortname="SO2",
+        wtmol=0.064066,  # kg mol-1
+        ivaprtn=musica.carma.VaporizationAlgorithm.H2O_BUCK_1981,
+        icomposition=musica.carma.GasComposition.SO2,
+        dgc_threshold=0.05,
+        ds_threshold=0.1
+    )
+    params.gases.append(so2_gas)
+
+    # Create CARMA instance and run
+    carma = musica.CARMA(params)
+
+    assert carma is not None
+    assert isinstance(carma, musica.CARMA)
+
+    state = carma.create_state(
+        vertical_center=[16500.0],
+        vertical_levels=[16500.0, 17000.0],
+        pressure=[90000.0],
+        pressure_levels=[101325.0, 90050.0],
+        temperature=[280.0],
+        time=0.0,
+        time_step=900.0,  # 15 minutes
+        longitude=0.0,
+        latitude=0.0,
+        coordinates=musica.carma.CarmaCoordinates.CARTESIAN
+    )
+
+    assert state is not None
+    assert isinstance(state, musica.CARMAState)
+
+    state.set_bin(1, 1, 1.0)
+    state.set_detrain(1, 1, 1.0)
+    state.set_gas(1, 1.4e-3)
+    state.set_temperature(300.0)
+    state.set_air_density(1.2)
+    state.step(land=musica.carma.CARMASurfaceProperties(surface_friction_velocity=0.42, area_fraction=0.3),
+               ocean=musica.carma.CARMASurfaceProperties(
+                   aerodynamic_resistance=0.1),
+               ice=musica.carma.CARMASurfaceProperties(area_fraction=0.2))
+    print(state.get_step_statistics())
+    print(state.get_bins())
+    print(state.get_detrained_masses())
+    print(state.get_environmental_values())
+    print(state.get_gases())
+    print(carma.get_group_properties())
+    print(carma.get_element_properties())
+    print(carma.get_gas_properties())
+    print(carma.get_solute_properties())
+
+
+if __name__ == '__main__':
+    pytest.main([__file__])

musica/test/integration/test_carma_aluminum.py

@@ -0,0 +1,11 @@
+import pytest
+import musica
+
+available = musica.backend.carma_available()
+pytestmark = pytest.mark.skipif(
+    not available, reason="CARMA backend is not available")
+
+def test_carma_aluminum():
+    from musica.examples import carma_aluminum
+    state = carma_aluminum.run_carma_aluminum_example()
+    assert state is not None, "State should not be None"

musica/test/integration/test_carma_sulfate.py

@@ -0,0 +1,16 @@
+import pytest
+import musica
+
+available = musica.backend.carma_available()
+pytestmark = pytest.mark.skipif(
+    not available, reason="CARMA backend is not available")
+
+def test_carma_sulfate():
+    from musica.examples import carma_sulfate
+    env_state, gas_state, bin_state = carma_sulfate.run_carma_sulfate_example()
+    # Basic assertions to verify the simulation ran successfully
+    assert env_state is not None, "Environmental state should not be None"
+    assert gas_state is not None, "Gas state should not be None"
+    assert bin_state is not None, "Bin state should not be None"
+    # Optionally, check expected dimensions or variables
+    assert hasattr(bin_state, "mass_mixing_ratio"), "Bin state should have mass_mixing_ratio"

musica/test/integration/test_sulfate_box_model.py

@@ -0,0 +1,34 @@
+import pytest
+import musica
+
+available = musica.backend.carma_available()
+pytestmark = pytest.mark.skipif(
+    not available, reason="CARMA backend is not available")
+
+def test_sulfate_box_model():
+    """Test the sulfate box model implementation."""
+    from musica.examples import sulfate_box_model
+    concentrations, times, sulfate_data = sulfate_box_model.run_box_model()
+
+    # Basic assertions to verify the simulation ran successfully
+    assert concentrations is not None, "Concentrations should not be None"
+    assert len(concentrations) > 0, "Should have concentration data"
+    assert times is not None, "Times should not be None"
+    assert len(times) > 0, "Should have time data"
+    assert sulfate_data is not None, "CARMA sulfate data should not be None"
+
+    # Check that we have the expected species
+    expected_species = ["HO2", "H2O2", "SO2", "SO3", "H2SO4", "H2O"]
+    for species in expected_species:
+        assert species in concentrations.columns, f"Missing species: {species}"
+
+    # Check that CARMA data has expected structure
+    assert hasattr(sulfate_data, "mass_mixing_ratio"), "CARMA data should have mass_mixing_ratio"
+    assert "time" in sulfate_data.dims, "CARMA data should have time dimension"
+    assert "bin" in sulfate_data.dims, "CARMA data should have bin dimension"
+
+    print(f"✅ Test passed! Simulated {len(times)} time steps over {times[-1]:.2f} hours")
+    print(f"   Chemical species tracked: {list(concentrations.columns)}")
+    print(f"   CARMA bins: {len(sulfate_data.bin)}")
+    print(f"   Vertical levels: {len(sulfate_data.vertical_center)}")
+

musica/test/integration/test_tuvx.py

@@ -0,0 +1,62 @@
+import pytest
+import musica
+import json
+
+available = musica.backend.tuvx_available()
+pytestmark = pytest.mark.skipif(not available, reason="TUV-x backend is not available")
+
+
+def test_tuvx_version():
+    version = musica.tuvx.version
+    assert version is not None
+    assert isinstance(version, str)
+
+
+def test_full_tuvx(monkeypatch):
+    monkeypatch.chdir("configs/tuvx")
+    file = "tuv_5_4.json"
+    tuvx = musica.TUVX(file)
+    assert tuvx is not None
+
+    heating_rates = tuvx.heating_rate_names
+    photolysis_rates = tuvx.photolysis_rate_names
+    rates = tuvx.run()
+
+    assert len(rates) > 0, "No photolysis rates found"
+    assert len(heating_rates) == 0, "Heating rates should be empty for this config"
+    assert len(photolysis_rates) > 0, "No photolysis rates found"
+
+
+def test_fixed_tuvx(monkeypatch):
+    monkeypatch.chdir("src")
+    file = "test/data/tuvx/fixed/config.json"
+    tuvx = musica.TUVX(file)
+    assert tuvx is not None
+
+    # Access properties multiple times
+    photolysis_names_1 = tuvx.photolysis_rate_names
+    photolysis_names_2 = tuvx.photolysis_rate_names
+    heating_names_1 = tuvx.heating_rate_names
+    heating_names_2 = tuvx.heating_rate_names
+
+    # Verify they return the same object (cached)
+    assert photolysis_names_1 is photolysis_names_2
+    assert heating_names_1 is heating_names_2
+
+    assert len(heating_names_1) > 0, "No heating rates found"
+    assert len(photolysis_names_1) > 0, "No photolysis rates found"
+
+    # these fail to run due to missing solar zenith angle, but that's not required and these should be able to run
+    # rates = tuvx.run()
+    # print(f"Rates: {rates}")
+
+
+def test_tuvx_initialization_errors():
+    """Test error handling during TUVX initialization."""
+    # Test with non-existent file
+    with pytest.raises(FileNotFoundError):
+        musica.TUVX("non_existent_config.json")
+
+
+if __name__ == '__main__':
+    pytest.main([__file__])

musica/test/unit/test_parser.py

@@ -0,0 +1,64 @@
+import pytest
+import musica.mechanism_configuration as mc
+from musica.mechanism_configuration import Parser
+from test_util_full_mechanism import get_fully_defined_mechanism, validate_full_v1_mechanism
+
+
+def test_parsed_full_v1_configuration():
+    parser = Parser()
+    extensions = [".yaml", ".json"]
+    for extension in extensions:
+        path = f"musica/test/examples/v1/full_configuration/full_configuration{extension}"
+        mechanism = parser.parse(path)
+        validate_full_v1_mechanism(mechanism)
+
+
+def test_parser_reports_bad_files():
+    parser = Parser()
+    extensions = [".yaml", ".json"]
+    for extension in extensions:
+        path = f"musica/test/examples/_missing_configuration{extension}"
+        with pytest.raises(Exception):
+            parser.parse(path)
+
+
+def test_hard_coded_full_v1_configuration():
+    MECHANISM_FULLY_DEFINED = get_fully_defined_mechanism()
+    validate_full_v1_mechanism(MECHANISM_FULLY_DEFINED)
+
+
+def test_hard_coded_default_constructed_types():
+    arrhenius = mc.Arrhenius()
+    assert arrhenius.type == mc.ReactionType.Arrhenius
+    condensed_phase_arrhenius = mc.CondensedPhaseArrhenius()
+    assert condensed_phase_arrhenius.type == mc.ReactionType.CondensedPhaseArrhenius
+    condensed_phase_photolysis = mc.CondensedPhasePhotolysis()
+    assert condensed_phase_photolysis.type == mc.ReactionType.CondensedPhasePhotolysis
+    emission = mc.Emission()
+    assert emission.type == mc.ReactionType.Emission
+    first_order_loss = mc.FirstOrderLoss()
+    assert first_order_loss.type == mc.ReactionType.FirstOrderLoss
+    henrys_law = mc.HenrysLaw()
+    assert henrys_law.type == mc.ReactionType.HenrysLaw
+    photolysis = mc.Photolysis()
+    assert photolysis.type == mc.ReactionType.Photolysis
+    simpol_phase_transfer = mc.SimpolPhaseTransfer()
+    assert simpol_phase_transfer.type == mc.ReactionType.SimpolPhaseTransfer
+    surface = mc.Surface()
+    assert surface.type == mc.ReactionType.Surface
+    troe = mc.Troe()
+    assert troe.type == mc.ReactionType.Troe
+    ternary_chemical_activation = mc.TernaryChemicalActivation()
+    assert ternary_chemical_activation.type == mc.ReactionType.TernaryChemicalActivation
+    tunneling = mc.Tunneling()
+    assert tunneling.type == mc.ReactionType.Tunneling
+    wet_deposition = mc.WetDeposition()
+    assert wet_deposition.type == mc.ReactionType.WetDeposition
+    branched = mc.Branched()
+    assert branched.type == mc.ReactionType.Branched
+    user_defined = mc.UserDefined()
+    assert user_defined.type == mc.ReactionType.UserDefined
+
+
+if __name__ == "__main__":
+    pytest.main([__file__])

musica/test/{test_serializer.py → unit/test_serializer.py}

@@ -48,7 +48,7 @@ def test_bad_inputs():
 def test_path_creation(tmp_path):
     mechanism = Mechanism(name="Full Configuration")
     path = f"{tmp_path}/non_existant_path/"
-    assert not os.path.exists(path)    
+    assert not os.path.exists(path)
     MechanismSerializer.serialize(mechanism, f"{path}test_mechanism.json")
     assert os.path.exists(path)
 
@@ -57,7 +57,7 @@ def test_overwrite_file(tmp_path):
     mechanism = Mechanism(name="Full Configuration")
     file_path = f'{tmp_path}/test_mechanism.json'
     assert not os.path.exists(file_path)
-    
+
     # write first file
     MechanismSerializer.serialize(mechanism, file_path)
     files = list(tmp_path.iterdir())