Merge branch 'main' into 169-air-density

.github/workflows/CI_Tests.yml

@@ -22,11 +22,16 @@ jobs:
         cache: 'pip' 
 
     - name: Install dependencies
-      run: python -m pip install --upgrade pip
+      run: |
+        python -m pip install --upgrade pip
+        pip install -r requirements.txt
 
     - name: Install this package
       run: pip install -e .
 
+    - name: Run pytest
+      run: cd tests && pytest
+
     - name: Run the smoke tests
       run: |
         music_box configFile=tests/configs/analytical_config/my_config.json outputDir=tests/configs/analytical_config

.github/workflows/pep8_autoformat.yml

@@ -0,0 +1,45 @@
+name: Pep8
+
+on:
+  push:
+    branches:
+      - main
+
+jobs:
+  autopep8:
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: autopep8
+        uses: peter-evans/autopep8@v2
+        with:
+          args: --recursive --in-place --aggressive --aggressive .
+
+      - name: Check for changes
+        id: check-changes
+        run: git diff --exit-code
+        continue-on-error: true
+
+      - name: Commit and push changes
+        # a failue of this step means changes were detected
+        if: steps.check-changes.outcome != 'success'
+        run: |
+          git config --global user.name "GitHub Actions"
+          git config --global user.email "[email protected]"
+          git commit -am "Auto-format code using Clang-Format" || echo "No changes to commit"
+
+      - name: Push changes to main-autopep8 branch
+        if: steps.check-changes.outcome != 'success'
+        run: git push origin HEAD:main-autopep8
+
+      - name: Create Pull Request
+        if: steps.check-changes.outcome != 'success'
+        uses: peter-evans/create-pull-request@v6
+        with:
+          token: ${{ secrets.GITHUB_TOKEN }}
+          commit-message: "Auto-format code using autopep8"
+          title: "Auto-format code by autopep8"
+          body: "This is an auto-generated PR with fixes by autopep8."
+          branch: main-autopep8

.github/workflows/publish-package.yml

@@ -1,35 +1,49 @@
-name: Publish a pypi package
+name: Publish Python Package
 
 on:
+  workflow_dispatch:
   release:
-    types: [created]
+    types:
+      - published
 
 jobs:
-  publish_to_pypi:
+  build_sdist:
+    name: Build
     runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v4
+
+    - name: Build SDist and Wheel
+      run: pipx run build --sdist --wheel
+
+    - name: Check metadata
+      run: pipx run twine check dist/*
+
+    - uses: actions/upload-artifact@v4
+      with:
+        name: cibw-sdist
+        path: dist/*
+
+  upload_all:
+    name: Upload release
+    needs: [build_sdist]
+    runs-on: ubuntu-latest
+    environment:
+      name: pypi
+      url: https://pypi.org/p/acom_music_box
     permissions:
-      contents: read
-      packages: write
+      id-token: write
 
     steps:
-      - name: Checkout repository
-        uses: actions/checkout@v4
-
-      - name: Set up Python
-        uses: actions/setup-python@v2
-        with:
-          python-version: '3.9'
-
-      - name: Install dependencies
-        run: |
-          python -m pip install --upgrade pip
-          pip install -r requirements.txt
-
-      - name: Build and publish package
-        env:
-          TWINE_USERNAME: __token__
-          TWINE_PASSWORD: ${{ secrets.PYPI_TOKEN }}
-        run: |
-          pipx run build
-          pipx run twine check dist/*
-          python -m twine upload --repository pypi dist/*
+    - uses: actions/setup-python@v5
+      with:
+        python-version: "3.x"
+
+    - uses: actions/download-artifact@v4
+      with:
+        pattern: cibw-*
+        path: dist
+        merge-multiple: true
+
+    - name: Publish package distributions to PyPI
+      uses: pypa/gh-action-pypi-publish@release/v1

src/acom_music_box/__init__.py

@@ -4,7 +4,7 @@
 This package contains modules for handling various aspects of a music box, 
 including species, products, reactants, reactions, and more.
 """
-__version__ = "2.1.1"
+__version__ = "2.1.5"
 
 from .utils import convert_time, convert_pressure, convert_temperature, convert_concentration
 from .music_box_species import Species

src/acom_music_box/music_box.py

@@ -406,7 +406,7 @@ def generateReactionConfig(self):
 
         return json.dumps(reactionsJson, indent=4)
 
-    def create_solver(self, path_to_config):
+    def create_solver(self, path_to_config, solver_type = musica.micmsolver.rosenbrock, number_of_grid_cells = 1):
         """
         Creates a micm solver object using the CAMP configuration files.
 
@@ -417,10 +417,10 @@ def create_solver(self, path_to_config):
             None
         """
         # Create a solver object using the configuration file
-        self.solver = musica.create_solver(path_to_config, musica.micmsolver.rosenbrock, 1)
+        self.solver = musica.create_solver(path_to_config, musica.micmsolver.rosenbrock, number_of_grid_cells)
 
 
-    def solve(self, path_to_output = None):
+    def solve(self, output_path = None):
         """
         Solves the box model simulation and optionally writes the output to a file.
 
@@ -440,9 +440,6 @@ def solve(self, path_to_output = None):
         #sets up initial conditions to be current conditions
         curr_conditions = self.initial_conditions
 
-        #sets up initial concentraion values
-        curr_concentrations = self.initial_conditions.get_concentration_array()
-
         #sets up next condition if evolving conditions is not empty
         next_conditions = None
         next_conditions_time = 0
@@ -541,9 +538,9 @@ def solve(self, path_to_output = None):
             curr_time += self.box_model_options.chem_step_time  
 
         #outputs to file if output is present
-        if(path_to_output != None):
-            logger.info("path_to_output = {}".format(path_to_output))
-            with open(path_to_output, 'w', newline='') as output:
+        if(output_path != None):
+            logger.info("path_to_output = {}".format(output_path))
+            with open(output_path, 'w', newline='') as output:
                 writer = csv.writer(output)
                 writer.writerows(output_array)
 

src/acom_music_box/music_box_conditions.py

@@ -38,6 +38,12 @@ def __init__(self, pressure=None, temperature=None, species_concentrations=None,
         self.temperature = temperature
         self.species_concentrations = species_concentrations if species_concentrations is not None else []
         self.reaction_rates = reaction_rates if reaction_rates is not None else []
+
+    def __repr__(self):
+        return f"Conditions(pressure={self.pressure}, temperature={self.temperature}, species_concentrations={self.species_concentrations}, reaction_rates={self.reaction_rates})"
+
+    def __str__(self):
+        return f"Pressure: {self.pressure}, Temperature: {self.temperature}, Species Concentrations: {self.species_concentrations}, Reaction Rates: {self.reaction_rates}"
 
     @classmethod
     def from_UI_JSON(cls, UI_JSON, species_list, reaction_list):
@@ -129,6 +135,8 @@ def from_config_JSON(cls, path_to_json, config_JSON, species_list, reaction_list
                 species_concentrations.append(SpeciesConcentration(species, concentration))
 
         for species in species_list.species:
+            if species.tracer_type == 'THIRD_BODY':
+                continue
             if not any(conc.species.name == species.name for conc in species_concentrations):
                 species_concentrations.append(SpeciesConcentration(species, 0)) 
 

src/acom_music_box/music_box_reaction.py

@@ -29,6 +29,12 @@ def __init__(self, name=None, reaction_type=None, reactants=None, products=None,
         self.products = products if products is not None else []
         self.scaling_factor = scaling_factor
 
+    def __str__(self):
+        return f"{self.name}: {self.reaction_type}"
+
+    def __repr__(self):
+        return f"{self.name}: {self.reaction_type}"
+
     def add_reactant(self, reactant):
         """
         Add a Reactant instance to the list of reactants.

src/acom_music_box/music_box_reaction_rate.py

@@ -17,3 +17,9 @@ def __init__(self, reaction, rate):
         """
         self.reaction = reaction
         self.rate = rate
+
+    def __str__(self):
+        return f"{self.reaction.name}: {self.rate}"
+
+    def __repr__(self):
+        return f"{self.reaction.name}: {self.rate}"

src/acom_music_box/music_box_species.py

@@ -1,16 +1,15 @@
 class Species:
     """
-    Represents a species with various attributes such as name, absolute tolerance, phase, molecular weight, and density.
+    Represents a species with various attributes such as name, absolute tolerance, phase, molecular weight
 
     Attributes:
         name (str): The name of the species.
         absolute_tolerance (float): The absolute tolerance of the species.
         phase (str): The phase of the species.
         molecular_weight (float): The molecular weight of the species in kg mol^-1.
-        density (float): The density of the species in kg m^-3.
     """
 
-    def __init__(self, name=None, absolute_tolerance=None, phase=None, molecular_weight=None, density=None):
+    def __init__(self, name=None, absolute_tolerance=None, phase=None, molecular_weight=None, tracer_type=None, diffusion_coefficient=None):
         """
         Initializes a new instance of the Species class.
 
@@ -19,10 +18,24 @@ def __init__(self, name=None, absolute_tolerance=None, phase=None, molecular_wei
             absolute_tolerance (float): The absolute tolerance of the species.
             phase (str): The phase of the species.
             molecular_weight (float): The molecular weight of the species in kg mol^-1.
-            density (float): The density of the species in kg m^-3.
+            tracer_type (str): The type of the tracer. Default is None. Other options are THIRD_BODY or CONSTANT
+            diffusion_coefficient (float): The diffusion coefficient of the species in m^2 s^-1. Default is None.
         """
         self.name = name
         self.absolute_tolerance = absolute_tolerance
         self.phase = phase
         self.molecular_weight = molecular_weight
-        self.density = density 
+        self.tracer_type = tracer_type
+        self.diffusion_coefficient = diffusion_coefficient
+
+    def __repr__(self):
+        return (f"Species(name={self.name!r}, absolute_tolerance={self.absolute_tolerance!r}, "
+                f"phase={self.phase!r}, molecular_weight={self.molecular_weight!r}, "
+                f"tracer_type={self.tracer_type!r}, diffusion_coefficient={self.diffusion_coefficient!r})")
+
+    def __str__(self):
+        return (f"Species: {self.name}, Phase: {self.phase}, "
+                f"Molecular Weight: {self.molecular_weight} kg/mol, "
+                f"Tolerance: {self.absolute_tolerance}, "
+                f"Tracer Type: {self.tracer_type}, "
+                f"Diffusion Coefficient: {self.diffusion_coefficient} m^2/s")

src/acom_music_box/music_box_species_concentration.py

@@ -17,3 +17,10 @@ def __init__(self, species, concentration):
         """
         self.species = species
         self.concentration = concentration
+
+    def __str__(self):
+        return f"{self.species.name}: {self.concentration}"
+
+    def __repr__(self):
+        return f"{self.species.name}: {self.concentration}"
+

src/acom_music_box/music_box_species_list.py

@@ -22,6 +22,7 @@ def __init__(self, species=None, relative_tolerance=1.0e-4):
         """
         self.species = species if species is not None else []
         self.relative_tolerance = relative_tolerance
+        self.tracer_type = None
 
     @classmethod
     def from_UI_JSON(cls, UI_JSON):
@@ -62,7 +63,7 @@ def from_config_JSON(cls, path_to_json, config_JSON):
         species_from_json = []
 
         #gets config file path
-        config_file_path = os.path.dirname(path_to_json) + "/" + config_JSON['model components'][0]['configuration file']
+        config_file_path = os.path.join(os.path.dirname(path_to_json), config_JSON['model components'][0]['configuration file'])
 
         #opnens config path to read species file
         with open(config_file_path, 'r') as json_file:
@@ -74,28 +75,16 @@ def from_config_JSON(cls, path_to_json, config_JSON):
                 with open(species_file_path, 'r') as species_file:
                     species_data = json.load(species_file)
                     #loads species by names from camp files
-                    for properties in species_data['camp-data']:
-                        if properties.get('name') is not None:
-                            name = properties.get('name')
-                            species_from_json.append(Species(name, None, None, None, None))
-
-
-        #chceks if species are in the config file and updates attributes accordingly
-        for chem_spec in config_JSON['chemical species']:
-            for species in species_from_json:
-                if species.name == chem_spec:
-                    # Add attributes to species
-                    if 'absolute tolerance' in chem_spec:
-                        species.absolute_tolerance = chem_spec['absolute tolerance']
-                    if 'molecular weight' in chem_spec:
-                        species.molecular_weight = chem_spec['molecular weight']
-                    if 'density' in chem_spec:
-                        species.density = chem_spec['density']
-                    if 'phase' in chem_spec:
-                        species.phase = chem_spec['phase']
+                    for species in species_data['camp-data']:
+                        if species['type'] == 'CHEM_SPEC':
+                            tolerance = species.get('absolute tolerance', None)
+                            molecular_weight = species.get('molecular weight [kg mol-1]', None)
+                            phase = species.get('phase', None)
+                            diffusion_coefficient = species.get('diffusion coefficient [m2 s-1]', None)
+                            tracer_type = species.get('tracer type', None)
+                            name = species.get('name')
+                            species_from_json.append(Species(name=name, absolute_tolerance=tolerance, molecular_weight=molecular_weight, phase=phase, diffusion_coefficient=diffusion_coefficient, tracer_type=tracer_type))
 
-
-
         return cls(species_from_json)
 
 

tests/configs/chapman_config/camp_data/species.json

@@ -6,7 +6,7 @@
         {
             "name": "M",
             "type": "CHEM_SPEC",
-            "tracer type": "CONSTANT"
+            "tracer type": "THIRD_BODY"
         },
         {
             "name": "Ar",

tests/configs/full_gas_phase_mechanism_config/camp_data/config.json

@@ -1,6 +1 @@
-{
-    "camp-files": [
-        "species.json",
-        "reactions.json"
-    ]
-}
+{"camp-files": ["species.json", "reactions.json"]}