docs(docs/guides/run_simulation.md): Added how-to for simulation runs (…

…#76)

docs/guides/run_simulation.md

@@ -0,0 +1,85 @@
+# How to run a simulation in NBSDynamics
+
+The current package offers the user the possibility to run a simulation with the built-in simulation types, or to create their own simulation with their custom attributes.
+
+## 1. Simulation structure.
+A simulation is based on the [SimulationProtocol](../../reference/simulation/simulation/#simulation-protocol). Thus its required attributes are as follows:
+
+* [Constants](../../reference/common/common/#constants). Definition of constants to be used during the simulation.
+* [Coral](../../reference/coral/coral/#coral-model). Required to represent a morphological model of a coral.
+* [Environment](../../reference/common/common/#environment).
+* [Hydrodynamics](../../reference/hydrodynamics/hydromodels/). Defines the type of simulation that will be run. As per version v0.8.0 the following types are available:
+    * [Reef0D](../../reference/hydrodynamics/hydromodels/#reef0d)
+    * [Reef1D](../../reference/hydrodynamics/hydromodels/#reef1d)
+    * [Transect](../../reference/hydrodynamics/hydromodels/#transect)
+    * [Delft3D](../../reference/hydrodynamics/hydromodels/#delft3d). Simulation through usage of a BMI runner:
+        * [Delft3D - FlowFMModel](../../reference/hydrodynamics/hydromodels/#src.core.hydrodynamics.delft3d.FlowFmModel). Currently under work.
+        * [Delft3D - DimrModel](../../reference/hydrodynamics/hydromodels/#src.core.hydrodynamics.delft3d.DimrModel). Currently under work.
+* [Output](../../reference/output/output/#wrapper). Required to define what output should be stored, how, where and when.
+
+## 2. 'Vanilla' Simulation.
+The user has the possibility to create its custom simulation by calling to the most simple simulation class [`Simulation`](../../reference/simulation/simulation/#src.core.simulation.base_simulation.Simulation). This class allows the user to combine their own set of `Constants`, `Coral`, `Environment`, `Hydrodynamics` and `Output` and then call the predefined `initiate`, `run` or `finalise` methods.
+
+Keep in mind this way of running a simulation implies the user will have to manually configure the Simulation attributes.
+
+## 3. Built-in Simulations.
+A built-in simulation allows the user to only worry about given the required input parameters and then letting the object pre-configure all the data as required for a regular run.
+
+### Available
+As per version NBSDynamics v.0.8.0 the following simulations are fully validated:
+#### Coral Transect Simulation
+A simulation using the [CoralTransectSimulation](../../reference/simulation/simulation/#coral-transect) object. Which will build the simulation around a `Transect` hydrodynamic model. We provide here an example (currently used for testing) of its usage with a Pydantic approach:
+```python
+# 1. Define attributes.
+test_dir = Path("transect_run")
+input_dir = test_dir / "input"
+output_dir = test_dir / "output"
+
+# 2. Prepare model.
+# Define the basic Simulation object, indicating already here the type of hydrodynamics
+run_trans = CoralTransectSimulation(
+    working_dir=test_dir,
+    constants=input_dir / "coral_input.txt",
+    environment=dict(
+        light=input_dir / "TS_PAR.txt",
+        temperature=input_dir / "TS_SST.txt",
+        storm=input_dir / "TS_stormcat2.txt",
+        dates=("2000-01-01", "2100-01-01"),
+    ),
+    hydrodynamics=dict(
+        definition_file=input_dir / "TS_waves.txt",
+        config_file=input_dir / "config.csv",
+    ),
+    output=dict(
+        output_dir=test_dir / "output",
+        map_output=dict(output_params=dict(fme=False)),
+        his_output=dict(output_params=dict(fme=False)),
+    ),
+    coral=dict(
+        dc=0.125,
+        hc=0.125,
+        bc=0.1,
+        tc=0.1,
+        ac=0.2,
+        Csp=0.6,
+    ),
+)
+
+# 3. Run simulation
+run_trans.initiate()
+run_trans.run()
+run_trans.finalise()
+```
+
+### Work in progress
+The following simulations are defined, however their status is not yet final and can therefore not be guaranteed to work.
+
+#### Coral FlowFm Simulation
+Open issue: [#68 Fix Delft3D - FlowFMModel run.](https://github.com/Deltares/NBSDynamics/issues/68)
+
+A simulation using the [CoralFlowFmSimulation](reference/simulation/simulation/#src.core.simulation.coral_delft3d_simulation.CoralFlowFmSimulation) object. Which will build the simulation around a `FlowFMModel` hydrodynamic model.
+
+#### Coral Dimr Simulation
+Open issue: [#69 Fix / Implement Delft3D - DIMR run.](https://github.com/Deltares/NBSDynamics/issues/69)
+
+A simulation using the [CoralDimrSimulation](../../reference/simulation/simulation/#src.core.simulation.coral_delft3d_simulation.CoralDimrSimulation) object. Which will build the simulation around a `DimrModel` hydrodynamic model.

src/core/bio_process/light.py

@@ -27,7 +27,7 @@ def __init__(
             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]
-            datareshape (DataReshape): Core reshape matrix class.
+            constants (Constants): List of constants to be used for this object.
         """
         _reshape = RESHAPE()
         self.I0 = _reshape.variable2matrix(light_in, "time")