Refactoring

.github/workflows/ci.yml

@@ -27,10 +27,10 @@ jobs:
     - name: Run tests
       shell: bash -l {0}
       run: |
-        python -m pytest test
+        python -m pytest test --cov src/sparging --cov-report xml
 
-    # - name: Upload to codecov
-    #   uses: codecov/codecov-action@v4
-    #   with:
-    #     token: ${{ secrets.CODECOV_TOKEN }}
-    #     files: ./coverage.xml
+    - name: Upload to codecov
+      uses: codecov/codecov-action@v4
+      with:
+        token: ${{ secrets.CODECOV_TOKEN }}
+        files: ./coverage.xml

.gitignore

@@ -56,7 +56,6 @@ cover/
 *.pot
 
 # Django stuff:
-*.log
 local_settings.py
 db.sqlite3
 db.sqlite3-journal
@@ -211,5 +210,6 @@ __marimo__/
 *.csv
 mwe.py
 *.json
+!standard_input.json
 *.ipynb
 *.code-workspace

example2.py

@@ -0,0 +1,77 @@
+from sparging.config import ureg
+from sparging import all_correlations
+from sparging import animation
+from sparging.model import Simulation
+from sparging.inputs import (
+    ColumnGeometry,
+    BreederMaterial,
+    OperatingParameters,
+    SpargingParameters,
+    SimulationInput,
+)
+import logging
+from typing import TYPE_CHECKING
+
+if TYPE_CHECKING:
+    import pint
+
+logger = logging.getLogger(__name__)
+logging.basicConfig(level=logging.WARNING)
+
+
+geom = ColumnGeometry(
+    area=0.2 * ureg.m**2,
+    height=1.0 * ureg.m,
+    nozzle_diameter=0.001 * ureg.m,
+    nb_nozzle=10 * ureg.dimensionless,
+)
+
+flibe = BreederMaterial(
+    name="FLiBe",
+)
+
+operating_params = OperatingParameters(
+    temperature=600 * ureg.celsius,
+    P_top=1 * ureg.atm,
+    flow_g_mol=400 * ureg.sccm,
+    tbr=0.1 * ureg("triton / neutron"),
+    n_gen_rate=1e9 * ureg("neutron / s"),
+)
+
+sparging_params = SpargingParameters(
+    h_l=all_correlations("h_l_briggs"),
+)
+
+
+# class method from_parameters that takes in objects like ColumnGeometry, BreederMaterial, OperatingParameters and returns a SimulationInput object with the appropriate correlations for the given parameters. This method should be able to handle cases where some of the parameters are already provided as correlations and should not overwrite them.
+my_input = SimulationInput.from_parameters(
+    geom, flibe, operating_params, sparging_params
+)
+logger.info(my_input)
+
+
+def profile_source_T(z: pint.Quantity):
+    import numpy as np
+
+    # return np.sin(np.pi / (1 * ureg.m) * z)
+    return 0.5 * (1 + np.cos(0.5 * np.pi / (1 * ureg.m) * z))
+
+
+my_simulation = Simulation(
+    my_input,
+    t_final=3 * ureg.days,
+    signal_irr=lambda t: 1 if t < 12 * ureg.hour else 0,
+    signal_sparging=lambda t: 1,
+    profile_source_T=profile_source_T,
+)
+output = my_simulation.solve()
+
+# # save output to file
+# output.profiles_to_csv(f"output_{tank_height}m.csv")
+
+# # plot results
+# from sparging import plotting
+# plotting.plot_animation(output)
+
+
+animation.create_animation(output, show_activity=True)

pyproject.toml

@@ -50,3 +50,9 @@ addopts = "-v"
 
 [tool.setuptools.package-data]
 sparging = ["*.yaml", "*.yml"]
+
+[tool.coverage.run]
+source = ["src/sparging"]
+omit = [
+    "src/sparging/animation.py"   
+]

src/sparging/__init__.py

@@ -2,11 +2,10 @@
 libra_sparging: A finite element model for sparging processes using FEniCSx/DOLFINX.
 """
 
-from .config import ureg, const_R, const_g, VERBOSE
+from .config import ureg, const_R, const_g
 from .model import SimulationResults
 from .animation import ConcentrationAnimator
-from .helpers import *
-from .correlations import *
+from .correlations import all_correlations, CorrelationGroup, Correlation
 
 __all__ = [
     "SimulationInput",
@@ -15,5 +14,4 @@
     "ureg",
     "const_R",
     "const_g",
-    "VERBOSE",
 ]

src/sparging/config.py

@@ -1,8 +1,6 @@
 from pint import UnitRegistry
 import scipy.constants as const
 
-VERBOSE = False
-
 ureg = UnitRegistry(
     autoconvert_offset_to_baseunit=True
 )  # to deal with offset units (eg: degree celsius)