Chore: Cleanup prerelease

src/core/bio_process/calcification.py

@@ -1,10 +1,11 @@
 from src.core import RESHAPE
+from src.core.common.constants import Constants
 
 
 class Calcification:
     """Calcification rate."""
 
-    def __init__(self, constants):
+    def __init__(self, constants: Constants = Constants()):
         """Calcification rate."""
         self.ad = 1
         self.constants = constants

src/core/bio_process/flow.py

@@ -2,13 +2,21 @@
 from scipy.optimize import newton
 
 from src.core import RESHAPE
+from src.core.common.constants import Constants
 from src.core.common.space_time import CoralOnly, DataReshape
 
 
 class Flow:
     """Flow micro-environment."""
 
-    def __init__(self, constants, u_current, u_wave, h, peak_period):
+    def __init__(
+        self,
+        u_current,
+        u_wave,
+        h,
+        peak_period,
+        constants: Constants = Constants(),
+    ):
         """
         :param u_current: current flow velocity [m s-1]
         :param u_wave: wave flow velocity [m s-1]

src/core/bio_process/light.py

@@ -1,10 +1,11 @@
-from typing import Union
+from typing import Optional, Union
 
 import numpy as np
 
 from src.core import RESHAPE
 from src.core.common.constants import Constants
-from src.core.common.space_time import CoralOnly, DataReshape
+from src.core.common.space_time import DataReshape
+from src.core.coral.coral_only import CoralOnly
 
 LightVariable = Union[float, list, tuple, np.ndarray]
 
@@ -14,16 +15,15 @@ class Light:
 
     def __init__(
         self,
-        constants: Constants,
         light_in: LightVariable,
         lac: LightVariable,
         depth: LightVariable,
+        constants: Constants = Constants(),
     ):
         """
         Light micro-environment.
 
         Args:
-            constants (Constants): Constants required for this class.
             light_in (LightVariable): Incoming light-intensity at the water-air interface [u mol photons m-2 s-1]
             lac (LightVariable): light-attenuation coefficient [m-1]
             depth (LightVariable): water depth [m]

src/core/bio_process/morphology.py

@@ -1,6 +1,7 @@
 import numpy as np
 
 from src.core import RESHAPE
+from src.core.common.constants import Constants
 from src.core.coral.coral_model import Coral
 
 
@@ -11,7 +12,9 @@ class Morphology:
     __rp_optimal = None
     __rs_optimal = None
 
-    def __init__(self, constants, calc_sum, light_in, dt_year=1):
+    def __init__(
+        self, calc_sum, light_in, dt_year=1, constants: Constants = Constants()
+    ):
         """
         Morphological development.
 

src/core/bio_process/photosynthesis.py

@@ -2,14 +2,15 @@
 import pandas as pd
 
 from src.core import RESHAPE
+from src.core.common.constants import Constants
 from src.core.common.space_time import DataReshape
 from src.core.coral.coral_model import Coral
 
 
 class Photosynthesis:
     """Photosynthesis."""
 
-    def __init__(self, constants, light_in, first_year):
+    def __init__(self, light_in, first_year, constants: Constants = Constants()):
         """
         Photosynthetic efficiency based on photosynthetic dependencies.
 

src/core/bio_process/population_states.py

@@ -1,6 +1,9 @@
+from typing import Optional
+
 import numpy as np
 
 from src.core import RESHAPE
+from src.core.common.constants import Constants
 from src.core.coral.coral_model import Coral
 
 
@@ -9,7 +12,7 @@ class PopulationStates:
 
     # TODO: Check this class; incl. writing tests
 
-    def __init__(self, constants, dt=1):
+    def __init__(self, constants: Constants = Constants(), dt: Optional[float] = 1):
         """Population dynamics.
 
         :param dt: time step [yrs], defaults to one

src/core/bio_process/recruitment.py

@@ -1,8 +1,8 @@
 from src.core import RESHAPE
 from src.core.base_model import ExtraModel
 from src.core.common.constants import Constants
-from src.core.common.space_time import CoralOnly
 from src.core.coral.coral_model import Coral
+from src.core.coral.coral_only import CoralOnly
 
 
 class Recruitment(ExtraModel):

src/core/bio_process/temperature.py

@@ -1,9 +1,10 @@
 from src.core import RESHAPE
+from src.core.common.constants import Constants
 from src.core.coral.coral_model import Coral
 
 
 class Temperature:
-    def __init__(self, constants, temperature):
+    def __init__(self, temperature, constants: Constants = Constants()):
         """
         Thermal micro-environment.
 

src/core/common/singletons.py

@@ -3,51 +3,27 @@
 throughout the `NBSDynamics` project.
 Although these classes are defined elsewhere, here we implement them as singletons.
 """
-from typing import Optional, Type
-
-from src.core.common.constants import Constants
 from src.core.common.space_time import DataReshape
 
 
-class RESHAPE(DataReshape):
+class Singleton(object):
     """
-    `DataReshape` Singleton.
+    Singleton class representing the design pattern.
+    This class can be used for concepts that are not meant to change state during a simulation
+    such as DataReshape, represented by RESHAPE.
     """
 
-    _instance: Optional[DataReshape] = None
-
-    def __new__(cls: Type[DataReshape], **kwargs) -> DataReshape:
-        """
-        Overriding new method to ensure this class behaves as s singleton.
+    _instance = None
 
-        Args:
-            cls (Type[Constants]): Required instance class.
-
-        Returns:
-            Constants: Singleton for `CommonConstants`
-        """
-        if cls._instance == None:
-            cls._instance = DataReshape(**kwargs).__new__(cls)
+    def __new__(cls, *args, **kwargs):
+        if not isinstance(cls._instance, cls):
+            cls._instance = object.__new__(cls, *args, **kwargs)
         return cls._instance
 
 
-class CommonConstants(Constants):
+class RESHAPE(Singleton, DataReshape):
     """
-    Constants Singleton.
+    `DataReshape` Singleton.
     """
 
-    _instance: Optional[Constants] = None
-
-    def __new__(cls: Type[Constants], **kwargs) -> Constants:
-        """
-        Overriding new method to ensure this class behaves as s singleton.
-
-        Args:
-            cls (Type[Constants]): Required instance class.
-
-        Returns:
-            Constants: Singleton for `CommonConstants`
-        """
-        if cls._instance == None:
-            cls._instance = Constants(**kwargs).__new__(cls)
-        return cls._instance
+    pass

src/core/coral/coral_model.py

@@ -6,7 +6,8 @@
 from src.core import RESHAPE
 from src.core.base_model import ExtraModel
 from src.core.common.constants import Constants
-from src.core.common.space_time import CoralOnly, DataReshape
+from src.core.common.space_time import DataReshape
+from src.core.coral.coral_only import CoralOnly
 
 CoralAttribute = Union[float, list, tuple, np.ndarray]
 

src/core/hydrodynamics/factory.py

@@ -50,3 +50,20 @@ def get_hydrodynamic_model_type(model_name: str) -> HydrodynamicProtocol:
             msg = f"{model_name} not in {[x.__name__ for x in HydrodynamicsFactory.supported_modes]}."
             raise ValueError(msg)
         return hydromodel
+
+    @staticmethod
+    def create(model_name: str, *args, **kwargs) -> HydrodynamicProtocol:
+        """
+        Creates a `HydrodynamicProtocol` based on the model_name type and the dictionary of
+        values (if any) given.
+
+        Args:
+            model_name (str): Model type name.
+
+        Returns:
+            HydrodynamicProtocol: Instance of the requested model.
+        """
+        m_type: HydrodynamicProtocol = HydrodynamicsFactory.get_hydrodynamic_model_type(
+            model_name
+        )
+        return m_type(**kwargs)

src/core/simulation/base_simulation.py

@@ -29,7 +29,8 @@
 
 class BaseSimulation(BaseModel, ABC):
     """
-    Implements the `SimulationProtocol`
+    Implements the `SimulationProtocol`.
+    Facade class that can be implemented through an Adapter pattern.
     CoralModel simulation.
     """
 
@@ -122,14 +123,9 @@ def validate_hydrodynamics_present(
         if field_values is None:
             field_values = dict()
         if isinstance(field_values, dict):
-            model_type = HydrodynamicsFactory.get_hydrodynamic_model_type(
-                field_values.get("mode", values["mode"])
+            return HydrodynamicsFactory.create(
+                field_values.get("mode", values["mode"]), **field_values
             )
-            # Emphasize working dir from explicit definition takes preference over simulation one.
-            field_values["working_dir"] = field_values.get(
-                "working_dir", values["working_dir"]
-            )
-            return model_type(**field_values)
 
         return field_values
 
@@ -283,19 +279,18 @@ def run(self, duration: Optional[int] = None):
                 progress.set_postfix(inner_loop="coral environment")
                 # light micro-environment
                 lme = Light(
-                    constants=self.constants,
                     light_in=time_series_year(self.environment.light, years[i]),
                     lac=time_series_year(self.environment.light_attenuation, years[i]),
                     depth=self.hydrodynamics.water_depth,
                 )
                 lme.rep_light(self.coral)
                 # flow micro-environment
                 fme = Flow(
-                    constants=self.constants,
                     u_current=current_vel,
                     u_wave=wave_vel,
                     h=self.hydrodynamics.water_depth,
                     peak_period=wave_per,
+                    constants=self.constants,
                 )
                 fme.velocities(self.coral, in_canopy=self.constants.fme)
                 fme.thermal_boundary_layer(self.coral)

test/core/bio_process/bio_utils.py

@@ -6,6 +6,11 @@
 from src.core.coral.coral_model import Coral
 
 
+@pytest.fixture(scope="module", autouse=True)
+def default_constants() -> Constants:
+    return Constants()
+
+
 @pytest.fixture(scope="module", autouse=False)
 def matrix_1x1() -> DataReshape:
     RESHAPE().spacetime = (1, 1)
@@ -31,7 +36,6 @@ def valid_coral() -> Coral:
     assert rs.spacetime == (1, 1)
     return Coral(
         **dict(
-            constants=Constants(),
             dc=0.2,
             hc=0.3,
             bc=0.1,
@@ -55,7 +59,6 @@ def coral_2x2() -> Coral:
     assert rs.spacetime == (2, 2)
     return Coral(
         **dict(
-            constants=Constants(),
             dc=0.2,
             hc=0.3,
             bc=0.1,
@@ -69,7 +72,6 @@ def coral_2x2() -> Coral:
 @pytest.fixture(scope="module", autouse=False)
 def no_base_coral_2x2() -> Coral:
     return Coral(
-        constants=Constants(),
         RESHAPE=DataReshape((2, 2)),
         dc=0.4,
         hc=0.3,

test/core/bio_process/test_calcification.py

@@ -4,14 +4,13 @@
 import pytest
 
 from src.core.bio_process.calcification import Calcification
-from src.core.common.constants import Constants
 from src.core.coral.coral_model import Coral
 
 
 class TestCalcification:
     @pytest.fixture(autouse=False)
     def calc_test(self) -> Calcification:
-        return Calcification(Constants())
+        return Calcification()
 
     def test_init_calcification(self, calc_test: Calcification):
         assert calc_test.ad == 1

test/core/bio_process/test_dislodgement.py

@@ -111,7 +111,6 @@ def test_csf1(self, coral_2x2: Coral, reshape_2x2: DataReshape):
     def test_csf2(self):
         dislodgement = Dislodgement()
         coral = Coral(
-            constants=Constants(),
             dc=[0.2, 0],
             hc=[0.3, 0],
             bc=[0.1, 0],

test/core/bio_process/test_flow.py

@@ -9,7 +9,7 @@
 
 class TestFlow:
     def test_init_flow(self, matrix_1x1):
-        flow = Flow(Constants(), 0.1, 0.1, 5, 4)
+        flow = Flow(0.1, 0.1, 5, 4)
         assert flow.uc[0] == 0.1
         assert flow.uw[0] == 0.1
         assert flow.h == 5
@@ -119,7 +119,7 @@ def test_wave_attenuation(self):
 
 class TestFlox2x2:
     def test_initiation(self, matrix_2x2: DataReshape):
-        flow = Flow(Constants(), [0.1, 0.1], [0.1, 0.1], [5, 5], [4, 4])
+        flow = Flow([0.1, 0.1], [0.1, 0.1], [5, 5], [4, 4])
         for i in range(matrix_2x2.space):
             assert float(flow.uc[i]) == 0.1
             assert float(flow.uw[i]) == 0.1

test/core/bio_process/test_light.py

@@ -21,7 +21,7 @@ class TestLight:
     @pytest.fixture(autouse=False)
     def light_test(self, matrix_1x1: DataReshape) -> Light:
         assert matrix_1x1.spacetime == (1, 1)
-        return Light(Constants(), 600, 0.1, 5)
+        return Light(600, 0.1, 5)
 
     def test_initiation(self, light_test: Light):
         assert light_test.I0, pytest.approx(600, tolerance)
@@ -77,7 +77,7 @@ class TestLight2x2:
 
     @pytest.fixture(autouse=False)
     def light_2x2(self) -> Light:
-        return Light(Constants(), [600, 600], [0.1, 0.1], [5, 5])
+        return Light([600, 600], [0.1, 0.1], [5, 5])
 
     def test_initiation(self, light_2x2: Light, matrix_2x2: DataReshape):
         for i in range(matrix_2x2.space):