Add some docs¨

src/circulation/base.py

@@ -77,6 +77,32 @@ def deep_update(d, u):
 
 
 class CirculationModel(ABC):
+    """Base class for circulation models
+
+    Parameters
+    ----------
+    parameters : dict[str, Any] | None, optional
+        Parameters used in the model, by default None which uses the default parameters
+    add_units : bool, optional
+        Add units to the parameters, by default False. Note that adding units
+        will drastically slow down the simulation, so it is recommended to
+        use this only for testing purposes.
+    callback : base.CallBack | None, optional
+        Optional callback function which is called at every time step, by default None.
+        The callback function take three arguments: the model, the current time,
+        and a boolean flag `save` which indicates if the current state should be saved.
+    verbose : bool, optional
+        Print additional information, by default False
+    comm : mpi4py.MPI_InterComm optional
+        MPI communicator, by default None
+    callback_save_state : base.CallBack | None, optional
+        Optional callback function called every time the state should be saved, by default None.
+        The function should take three arguments: the model, the current time, and a boolean
+        flag `save` which indicates if the current state should be saved.
+    initial_state : dict[str, float] | None, optional
+        Initial state of the model, by default None which uses the default initial state
+    """
+
     def __init__(
         self,
         parameters: dict[str, Any] | None = None,

src/circulation/bestel.py

@@ -37,12 +37,12 @@ class BestelActivation:
     Notes
     -----
     The active stress is taken from Bestel et al. [3]_, characterized through
-    a time-dependent stress function \tau solution to the evolution equation
+    a time-dependent stress function :math:`\tau` solution to the evolution equation
 
     .. math::
         \dot{\tau}(t) = -|a(t)|\tau(t) + \sigma_0|a(t)|_+
 
-    being a(\cdot) the activation function and \sigma_0 contractility,
+    with :math:`a(\cdot)` being the activation function and \sigma_0 contractility,
     where each remaining term is described below:
 
     .. math::
@@ -145,7 +145,7 @@ class BestelPressure:
         \dot{p}(t) = -|b(t)|p(t) + \sigma_{\mathrm{mid}}|b(t)|_+
         + \sigma_{\mathrm{pre}}|g_{\mathrm{pre}}(t)|
 
-    being b(\cdot) the activation function described below:
+    with :math:`b(\cdot)` being the activation function described below:
 
     .. math::
         b(t) =& a_{\mathrm{pre}}(t) + \alpha_{\mathrm{pre}}g_{\mathrm{pre}}(t)

src/circulation/regazzoni2020.py

@@ -20,6 +20,35 @@ class Regazzoni2020(base.CirculationModel):
         closed-loop blood circulation. Part I: model derivation", arXiv (2020)
         https://arxiv.org/abs/2011.15040
 
+    Parameters
+    ----------
+    parameters : dict[str, Any] | None, optional
+        Parameters used in the model, by default None which uses the default parameters
+    p_LV_func : Callable[[float, float], float] | None, optional
+        Optional function to calculate the pressure in the LV, by default None.
+        The function should take the volume in the LV as the first argument and
+        the time as the second argument, and return the pressure in the LV
+    p_BiV_func : Callable[[float, float, float], float] | None, optional
+        Optional function to calculate the pressure in the LV and RV, by default None.
+        The function should take the volume in the LV as the first argument, the volume
+        in the RV as the second argument, and the time as the third argument, and return
+        a tuple (plv, prv) with the pressures in the LV and RV.
+    add_units : bool, optional
+        Add units to the parameters, by default False. Note that adding units
+        will drastically slow down the simulation, so it is recommended to
+        use this only for testing purposes.
+    callback : base.CallBack | None, optional
+        Optional callback function, by default None. The callback function takes
+        three arguments: the model, the current time, and a boolean flag `save`
+        which indicates if the current state should be saved.
+    verbose : bool, optional
+        Print additional information, by default False
+    comm : mpi4py.MPI_InterComm optional
+        MPI communicator, by default None
+    outdir : Path, optional
+        Output directory, by default Path("results-regazzoni")
+    initial_state : dict[str, float] | None, optional
+        Initial state of the model, by default None which uses the default initial state
     """
 
     def __init__(