Merge pull request #543 from RemDelaporteMathurin/formatting

Formatting

festim/boundary_conditions/boundary_condition.py

@@ -9,7 +9,6 @@ class BoundaryCondition:
     """
 
     def __init__(self, surfaces, field) -> None:
-
         if not isinstance(surfaces, list):
             surfaces = [surfaces]
         self.surfaces = surfaces

festim/boundary_conditions/dirichlets/custom_dc.py

@@ -27,7 +27,6 @@ def fun(T, solute, param1):
     """
 
     def __init__(self, surfaces, function, field=0, **prms) -> None:
-
         super().__init__(surfaces, field=field, value=None)
         self.function = function
         self.prms = prms

festim/boundary_conditions/dirichlets/dirichlet_bc.py

@@ -138,7 +138,6 @@ class BoundaryConditionExpression(f.UserExpression):
     """
 
     def __init__(self, T, eval_function, **kwargs):
-
         super().__init__()
 
         self._T = T

festim/concentration/traps/extrinsic_trap.py

@@ -80,7 +80,6 @@ def __init__(
         id=None,
         **kwargs,
     ):
-
         super().__init__(
             k_0,
             E_k,

festim/concentration/traps/trap.py

@@ -39,7 +39,6 @@ class Trap(Concentration):
     """
 
     def __init__(self, k_0, E_k, p_0, E_p, materials, density, id=None):
-
         super().__init__()
         self.id = id
         self.k_0 = k_0

festim/exports/derived_quantities/derived_quantities.py

@@ -30,7 +30,6 @@ def __init__(
         nb_iterations_between_compute: int = 1,
         nb_iterations_between_exports: int = None,
     ) -> None:
-
         self.filename = filename
         self.nb_iterations_between_compute = nb_iterations_between_compute
         self.nb_iterations_between_exports = nb_iterations_between_exports
@@ -82,7 +81,6 @@ def assign_properties_to_quantities(self, materials):
             quantity.H = materials.H
 
     def compute(self, t):
-
         # TODO need to support for soret flag in surface flux
         row = [t]
         for quantity in self.derived_quantities:
@@ -182,7 +180,6 @@ def filter(
 
         # iterate through derived_quantities
         for quantity in self.derived_quantities:
-
             # initialise flags to False
             match_surface, match_volume, match_field, match_instance = (
                 False,

festim/exports/derived_quantities/derived_quantity.py

@@ -8,7 +8,6 @@ class DerivedQuantity(Export):
     """
 
     def __init__(self, field) -> None:
-
         super().__init__(field=field)
         self.dx = None
         self.ds = None

festim/exports/derived_quantities/maximum_surface.py

@@ -12,7 +12,6 @@ class MaximumSurface(DerivedQuantity):
     """
 
     def __init__(self, field, surface) -> None:
-
         super().__init__(field)
         self.surface = surface
         self.title = "Maximum {} surface {}".format(self.field, self.surface)

festim/exports/derived_quantities/minimum_surface.py

@@ -12,7 +12,6 @@ class MinimumSurface(DerivedQuantity):
     """
 
     def __init__(self, field, surface) -> None:
-
         super().__init__(field)
         self.surface = surface
         self.title = "Minimum {} surface {}".format(self.field, self.surface)

festim/exports/exports.py

@@ -13,7 +13,6 @@ def __init__(self, exports=[]) -> None:
     def write(self, label_to_function, dt):
         for export in self.exports:
             if isinstance(export, festim.DerivedQuantities):
-
                 # compute derived quantities
                 if export.is_compute(self.nb_iterations):
                     # check if function has to be projected

festim/exports/trap_density_xdmf.py

@@ -10,7 +10,6 @@ class TrapDensityXDMF(XDMFExport):
     """
 
     def __init__(self, trap, **kwargs) -> None:
-
         super().__init__(
             field="1", **kwargs
         )  # field is "1" just to make the code not crash

festim/exports/txt_export.py

@@ -20,7 +20,6 @@ class TXTExport(festim.Export):
     """
 
     def __init__(self, field, times, label, folder) -> None:
-
         super().__init__(field=field)
         self.times = sorted(times)
         self.label = label
@@ -40,7 +39,6 @@ def when_is_next_time(self, current_time):
         return None
 
     def write(self, current_time, dt):
-
         # create a DG1 functionspace
         V_DG1 = f.FunctionSpace(self.function.function_space().mesh(), "DG", 1)
 

festim/exports/xdmf_export.py

@@ -32,7 +32,6 @@ class XDMFExport(Export):
     def __init__(
         self, field, label=None, filename=None, mode=1, checkpoint=True, folder=None
     ) -> None:
-
         super().__init__(field=field)
         self.label = label
         self.folder = folder
@@ -123,7 +122,6 @@ def write(self, t):
         self.function.rename(self.label, "label")
 
         if self.checkpoint:
-
             # warn users if checkpoint is True and 1D
             dimension = self.function.function_space().mesh().topology().dim()
             if dimension == 1:

festim/generic_simulation.py

@@ -85,7 +85,6 @@ def __init__(
         exports=None,
         log_level=40,
     ):
-
         self.log_level = log_level
 
         self.settings = settings

festim/initial_condition.py

@@ -21,7 +21,6 @@ class InitialCondition:
     def __init__(
         self, field=0, value=0.0, component=None, label=None, time_step=None
     ) -> None:
-
         # TODO make an inherited class InitialConditionXDMF
         self.field = field
         self.value = value

festim/materials/material.py

@@ -41,7 +41,6 @@ def __init__(
         solubility_law="sievert",
         name=None,
     ) -> None:
-
         self.id = id
         self.name = name
         self.D_0 = D_0

festim/materials/materials.py

@@ -15,7 +15,6 @@ class Materials:
     """
 
     def __init__(self, materials=[]):
-
         self.materials = materials
         self.D = None
         self.S = None

festim/meshing/mesh.py

@@ -23,7 +23,6 @@ class Mesh:
     def __init__(
         self, mesh=None, volume_markers=None, surface_markers=None, type="cartesian"
     ) -> None:
-
         self.mesh = mesh
         self.volume_markers = volume_markers
         self.surface_markers = surface_markers

festim/settings.py

@@ -55,7 +55,6 @@ def __init__(
         update_jacobian=True,
         linear_solver=None,
     ):
-
         # TODO maybe transient and final_time are redundant
         self.transient = transient
         self.final_time = final_time

festim/stepsize.py

@@ -30,7 +30,6 @@ def __init__(
         stepsize_stop_max=None,
         dt_min=None,
     ) -> None:
-
         self.adaptive_stepsize = None
         if stepsize_change_ratio is not None:
             self.adaptive_stepsize = {

test/simulation/test_postprocessing_integration.py

@@ -112,7 +112,6 @@ def test_pure_diffusion(self, my_sim):
             assert data[i][4] == pytest.approx(11)
 
     def test_fluxes(self, my_sim):
-
         my_sim.T = festim.Temperature(100 * festim.x + 200)
         my_sim.T.create_functions(my_sim.mesh)
 

test/system/test_system.py

@@ -600,7 +600,6 @@ def test_run_MMS_steady_state(tmpdir):
     g = sp.diff(v, festim.t) + p * v - k * u * (n_trap - v)
 
     def run(h):
-
         my_materials = festim.Materials(
             [festim.Material(name="mat", id=1, D_0=D_0, E_D=E_D)]
         )

test/unit/test_boundary_conditions.py

@@ -426,6 +426,7 @@ def test_create_expression_dc_custom():
     """Creates a dc_custom bc and checks create_expression returns
     the correct expression
     """
+
     # build
     def func(T, prm1, prm2):
         return 2 * T + prm1 * prm2
@@ -455,6 +456,7 @@ def test_create_form_flux_custom():
     create_form returns
     the correct form
     """
+
     # build
     def func(T, c, prm1, prm2):
         return 2 * T + c + prm1 * prm2
@@ -481,7 +483,6 @@ def func(T, c, prm1, prm2):
     expected_expr = 2 * expr_T + expr_c + expr_prm1 * expr_prm2
     expected_expr = fenics.Expression(sp.printing.ccode(expected_expr), t=0, degree=1)
     for t in range(10):
-
         expected_expr.t = t
         for expr in my_BC.sub_expressions + expressions:
             expr.t = t

test/unit/test_concentration.py

@@ -18,7 +18,6 @@ def test_get_comp_from_expression(self):
                 assert comp(x) == 1 + t - x
 
     def test_get_comp_from_xdmf(self, tmpdir):
-
         # build
         value = 1 + festim.t - festim.x
 

test/unit/test_helpers.py

@@ -41,7 +41,6 @@ def eval(self, x, values):
 
 
 def test_as_constant_or_expression():
-
     # constants
     assert isinstance(as_constant_or_expression(3), Constant)
     assert isinstance(as_constant_or_expression(3.0), Constant)

test/unit/test_meshing.py

@@ -169,7 +169,6 @@ def test_surface_markers(self):
 
 
 def test_create_mesh_xdmf(tmpdir):
-
     # write xdmf file
     mesh = fenics.UnitSquareMesh(10, 10)
     file1 = tmpdir.join("mesh.xdmf")
@@ -202,7 +201,6 @@ def test_create_mesh_xdmf(tmpdir):
 
 
 def test_subdomains_from_xdmf(tmpdir):
-
     # create mesh functions
     mesh = fenics.UnitCubeMesh(6, 6, 6)
     mf_cells = fenics.MeshFunction("size_t", mesh, mesh.topology().dim())

test/unit/test_traps/test_extrinsic_trap.py

@@ -3,7 +3,6 @@
 
 
 class TestExtrinsicTrap:
-
     my_trap = festim.ExtrinsicTrap(
         1,
         1,

test/unit/test_traps/test_trap.py

@@ -361,6 +361,7 @@ def test_user_expression_as_density(self):
         """Test that create_trapping_form creates the correct formulation when
         a fenics.UserExpression is given as density
         """
+
         # build
         class CustomExpression(f.UserExpression):
             def eval(self, value, x):