Add enums and remove python implementation of transfer meshtags in factor of the scifem implementation

Author: jorgensd

docs/source/api/index.rst

@@ -31,10 +31,6 @@ API reference
     :members:
     :show-inheritance:
 
-.. automodule:: festim.helpers_discontinuity
-    :members:
-    :show-inheritance:
-
 .. automodule:: festim.helpers
     :members:
     :show-inheritance:

docs/source/map.py

@@ -1,10 +1,8 @@
 import json
-from folium.plugins import MarkerCluster
-import folium
 
-import requests
+import folium
+from folium.plugins import MarkerCluster
 from PIL import Image
-from io import BytesIO
 
 LOGO_HEIGHT = 60
 

docs/source/userguide/subdomains.rst

@@ -107,7 +107,7 @@ Additional parameters are required for specific simulations. When considering ch
 * :code:`name`: Name for the material.
 * :code:`S_0`: The solubility pre-exponential factor (units depend on the solubility law: Sievert's or Henry's).
 * :code:`E_S`: The solubility activation energy (eV).
-* :code:`solubility_law`: The solubility law, either :code:`"henry"` or :code:`"sievert"`.
+* :code:`solubility_law`: The solubility law, either :code:`"festim.SolubilityLaw.HENRY"` or :code:`festim.SolubilityLaw.SIEVERT`.
 
 For transient heat transfer simulations, thermal conductivity, heat capacity, and density must be defined:
 

examples/advection_diffusion_multi_material.py

@@ -1,9 +1,10 @@
 from mpi4py import MPI
 
+import basix
 import dolfinx
 import dolfinx.fem.petsc
 import numpy as np
-import basix
+
 import festim as F
 
 

examples/surface_reaction_example.py

@@ -1,9 +1,9 @@
-import festim as F
-import numpy as np
-
 import dolfinx.fem as fem
+import numpy as np
 import ufl
 
+import festim as F
+
 
 class FluxFromSurfaceReaction(F.SurfaceFlux):
     def __init__(self, reaction: F.SurfaceReactionBC):

src/festim/__init__.py

@@ -35,7 +35,7 @@
 from .exports.total_surface import TotalSurface
 from .exports.total_volume import TotalVolume
 from .exports.volume_quantity import VolumeQuantity
-from .exports.vtx import VTXSpeciesExport, VTXTemperatureExport, ExportBaseClass
+from .exports.vtx import ExportBaseClass, VTXSpeciesExport, VTXTemperatureExport
 from .exports.xdmf import XDMFExport
 from .heat_transfer_problem import HeatTransferProblem
 from .helpers import (
@@ -49,14 +49,15 @@
     HydrogenTransportProblem,
     HydrogenTransportProblemDiscontinuous,
     HydrogenTransportProblemDiscontinuousChangeVar,
+    InterfaceMethod,
 )
 from .initial_condition import (
-    InitialConditionBase,
     InitialConcentration,
+    InitialConditionBase,
     InitialTemperature,
     read_function_from_file,
 )
-from .material import Material
+from .material import Material, SolubilityLaw
 from .mesh.mesh import Mesh
 from .mesh.mesh_1d import Mesh1D
 from .mesh.mesh_from_xdmf import MeshFromXDMF

src/festim/advection.py

@@ -1,5 +1,4 @@
 from collections.abc import Callable
-from typing import Optional
 
 import basix
 import ufl
@@ -123,7 +122,7 @@ class VelocityField(Value):
     def convert_input_value(
         self,
         function_space: fem.FunctionSpace,
-        t: Optional[fem.Constant] = None,
+        t: fem.Constant | None = None,
     ):
         """Converts a user given value to a relevent fenics object
 

src/festim/boundary_conditions/dirichlet_bc.py

@@ -253,7 +253,7 @@ def create_value(
                         helpers.get_interpolation_points(function_space.element),
                     )
                     self.value_fenics.interpolate(self.bc_expr)
-                except RuntimeError as e:
+                except RuntimeError:
                     # if this fails, it is probably because the temperature is a Function
                     # from the parent mesh and this is used in a mixed domain problem.
                     # In this case, we need to interpolate the temperature on the submesh

src/festim/boundary_conditions/surface_reaction.py

@@ -1,7 +1,8 @@
-from festim.boundary_conditions import ParticleFluxBC
-from festim import k_B
-from dolfinx import fem
 import ufl
+from dolfinx import fem
+
+from festim import k_B
+from festim.boundary_conditions import ParticleFluxBC
 
 
 class SurfaceReactionBCpartial(ParticleFluxBC):

src/festim/exports/maximum_surface.py

@@ -1,4 +1,5 @@
 from mpi4py import MPI
+
 import dolfinx
 import numpy as np