Ruff fixes

docs/source/conf.py

@@ -37,7 +37,6 @@
 # Add the directory containing your Python script to the Python path
 sys.path.insert(0, os.path.abspath("."))
 
-import map
 
 m = map.generate_map()
 current_dir = os.path.dirname(__file__)

examples/advection_diffusion_multi_material.py

@@ -27,7 +27,6 @@ def half(x):
     )
 
     # Split domain in half and set an interface tag of 5
-    gdim = mesh.geometry.dim
     tdim = mesh.topology.dim
     fdim = tdim - 1
     top_facets = dolfinx.mesh.locate_entities_boundary(mesh, fdim, top_boundary)
@@ -80,10 +79,10 @@ def velocity_func(x):
         values[1] = 0  # Second component remains zero
         return values
 
-    mesh2, mt2, ct2 = generate_mesh(n=10)
-    submesh, cell_map, v_map = dolfinx.mesh.create_submesh(mesh2, ct2.dim, ct2.find(4))[
-        0:3
-    ]
+    mesh2, _mt2, ct2 = generate_mesh(n=10)
+    submesh, _cell_map, _v_map = dolfinx.mesh.create_submesh(
+        mesh2, ct2.dim, ct2.find(4)
+    )[0:3]
     v_cg = basix.ufl.element(
         "Lagrange", submesh.topology.cell_name(), 2, shape=(submesh.geometry.dim,)
     )

examples/convergence_rates.py

@@ -112,7 +112,9 @@ def mms_source(x, t):
     my_problem.settings = F.Settings(
         atol=1e-8,
         rtol=1e-10,
-        final_time=1,  # final time shouldn't be too long so that a potential error at the initial timestep is not negligible
+        # final time shouldn't be too long so that a potential error at the
+        # initial timestep is not negligible
+        final_time=1,
     )
 
     # Forward euler isn't great so dt should be small
@@ -127,7 +129,8 @@ def mms_source(x, t):
     my_problem.run()
 
     computed_solution = my_problem.u
-    # we use the exact final time of the simulation which may differ from the one specified in the settings
+    # we use the exact final time of the simulation which may differ from
+    # the one specified in the settings
     final_time_sim = my_problem.t.value
 
     def exact_solution_end(x):

examples/multi_material_1d.py

@@ -43,7 +43,8 @@
 left_surface = F.SurfaceSubdomain1D(id=1, x=vertices[0])
 right_surface = F.SurfaceSubdomain1D(id=2, x=vertices[-1])
 
-# the ids here are arbitrary in 1D, you can put anything as long as it's not the same as the surfaces
+# the ids here are arbitrary in 1D, you can put anything as long as it's
+# not the same as the surfaces
 my_model.interfaces = [
     F.Interface(6, (left_domain, middle_domain)),
     F.Interface(7, (middle_domain, right_domain)),

examples/multi_material_2d.py

@@ -24,7 +24,6 @@ def half(x):
     )
 
     # Split domain in half and set an interface tag of 5
-    gdim = mesh.geometry.dim
     tdim = mesh.topology.dim
     fdim = tdim - 1
     top_facets = dolfinx.mesh.locate_entities_boundary(mesh, fdim, top_boundary)
@@ -125,11 +124,17 @@ def half(x):
     from dolfinx.mesh import EntityMap  # noqa: F401
 
     legacy_entity_map = False
-    entity_map_wrapper = lambda e_map: list(e_map.values())
+
+    def entity_map_wrapper(e_map):
+        return list(e_map.values())
+
     entity_maps = [sd.cell_map for sd in my_model.volume_subdomains]
 except ImportError:
     legacy_entity_map = True
-    entity_map_wrapper = lambda e_map: e_map
+
+    def entity_map_wrapper(e_map):
+        return e_map
+
     entity_maps = {
         sd.submesh: sd.parent_to_submesh for sd in my_model.volume_subdomains
     }

examples/multi_material_2d_bis.py

@@ -24,7 +24,6 @@ def half(x):
     )
 
     # Split domain in half and set an interface tag of 5
-    gdim = mesh.geometry.dim
     tdim = mesh.topology.dim
     fdim = tdim - 1
     top_facets = dolfinx.mesh.locate_entities_boundary(mesh, fdim, top_boundary)
@@ -168,10 +167,14 @@ def half(x):
     from dolfinx.mesh import EntityMap  # noqa: F401
 
     legacy_entity_map = False
-    entity_map_wrapper = lambda e_map: list(e_map.values())
+
+    def entity_map_wrapper(e_map):
+        return list(e_map.values())
 except ImportError:
     legacy_entity_map = True
-    entity_map_wrapper = lambda e_map: e_map
+
+    def entity_map_wrapper(e_map):
+        return e_map
 
 
 form = dolfinx.fem.form(

examples/multi_material_transient.py

@@ -36,8 +36,8 @@
 left_surface = F.SurfaceSubdomain1D(id=1, x=vertices[0])
 right_surface = F.SurfaceSubdomain1D(id=2, x=vertices[-1])
 
-# the ids here are arbitrary in 1D, you can put anything as long as it's not the same as the surfaces
-# TODO remove mesh and meshtags from these arguments
+# the ids here are arbitrary in 1D, you can put anything as long as it's not the same
+# as the surfaces
 my_model.interfaces = [
     F.Interface(6, (left_domain, middle_domain)),
     F.Interface(7, (middle_domain, right_domain)),

examples/surface_reaction_example.py

@@ -1,4 +1,5 @@
 import dolfinx.fem as fem
+import matplotlib.pyplot as plt
 import numpy as np
 import ufl
 
@@ -98,7 +99,6 @@ def compute(self, ds):
 my_model.initialise()
 my_model.run()
 
-import matplotlib.pyplot as plt
 
 plt.stackplot(
     H_flux_left.t,

src/festim/__init__.py

@@ -1,3 +1,4 @@
+# ruff: noqa: F401, E402
 from importlib import metadata
 
 try:

src/festim/advection.py

@@ -10,8 +10,7 @@
 
 
 class AdvectionTerm:
-    """
-    Advection term class
+    """Advection term class.
 
     args:
         velocity: the velocity field or function
@@ -22,7 +21,6 @@ class AdvectionTerm:
         velocity: the velocity field or function
         subdomain: the volume subdomain where the velocity is to be applied
         species: the species to which the velocity field is acting on
-
     """
 
     velocity: fem.Function
@@ -94,9 +92,8 @@ def species(self, value):
 
 
 class VelocityField(Value):
-    """
-    A class to handle input values of velocity fields from users and convert them to a
-    relevent fenics object
+    """A class to handle input values of velocity fields from users and convert them to
+    a relevent fenics object.
 
     Args:
         input_value: The value of the user input
@@ -124,7 +121,7 @@ def convert_input_value(
         function_space: fem.FunctionSpace,
         t: fem.Constant | None = None,
     ):
-        """Converts a user given value to a relevent fenics object
+        """Converts a user given value to a relevent fenics object.
 
         Args:
             function_space: the function space of the fenics object
@@ -165,7 +162,7 @@ def convert_input_value(
         nmm_interpolate(self.fenics_object, vel)
 
     def update(self, t: fem.Constant):
-        """Updates the velocity field
+        """Updates the velocity field.
 
         Args:
             t: the time

src/festim/boundary_conditions/dirichlet_bc.py

@@ -14,9 +14,7 @@
 
 
 class DirichletBCBase:
-    """
-    Dirichlet boundary condition class
-    u = value
+    """Dirichlet boundary condition class u = value.
 
     Args:
         subdomain: The surface subdomain where the boundary condition is applied
@@ -28,7 +26,6 @@ class DirichletBCBase:
         value_fenics: The value of the boundary condition in fenics format
         bc_expr: The expression of the boundary condition that is used to
             update the `value_fenics`
-
     """
 
     subdomain: _subdomain.SurfaceSubdomain
@@ -67,14 +64,14 @@ def value_fenics(self, value: None | fem.Function | fem.Constant | np.ndarray):
         if not isinstance(value, (fem.Function, fem.Constant, np.ndarray)):
             # FIXME: Should we allow sending in a callable here?
             raise TypeError(
-                "Value must be a dolfinx.fem.Function, dolfinx.fem.Constant, or a np.ndarray not"
+                "Value must be a dolfinx.fem.Function, dolfinx.fem.Constant, or a np.ndarray not"  # noqa: E501
                 + f"{type(value)}"
             )
         self._value_fenics = value
 
     @property
     def time_dependent(self) -> bool:
-        """Returns true if the value of the boundary condition is time dependent"""
+        """Returns true if the value of the boundary condition is time dependent."""
         if self.value is None:
             return False
         if isinstance(self.value, fem.Constant):
@@ -92,17 +89,20 @@ def define_surface_subdomain_dofs(
     ) -> npt.NDArray[np.int32] | tuple[npt.NDArray[np.int32], npt.NDArray[np.int32]]:
         """Defines the facets and the degrees of freedom of the boundary condition.
 
-        Given the input meshtags, find all facets matching the boundary condition subdomain ID,
+        Given the input meshtags, find all facets matching the boundary
+        condition subdomain ID,
         and locate all DOFs associated with the input function space(s).
 
         Note:
-            For sub-spaces, a tuple of sub-spaces are expected as input, and a tuple of arrays
+            For sub-spaces, a tuple of sub-spaces are expected as input, and a
+            tuple of arrays
             associated to each of the function spaces are returned.
 
         Args:
             facet_meshtags: MeshTags describing some facets in the domain
             mesh:
-            function_space: The function space or a tuple of function spaces: (sub, collapsed)
+            function_space: The function space or a tuple of function spaces:
+            (sub, collapsed)
         """
         mesh = (
             function_space[0].mesh
@@ -111,11 +111,11 @@ def define_surface_subdomain_dofs(
         )
         if facet_meshtags.topology != mesh.topology._cpp_object:
             raise ValueError(
-                "Mesh of function-space is not the same as the one used for the meshtags"
+                "Mesh of function-space is not the same as the one used for the meshtags"  # noqa: E501
             )
         if mesh.topology.dim - 1 != facet_meshtags.dim:
             raise ValueError(
-                f"Meshtags of dimension {facet_meshtags.dim}, expected {mesh.topology.dim - 1}"
+                f"Meshtags of dimension {facet_meshtags.dim}, expected {mesh.topology.dim - 1}"  # noqa: E501
             )
         bc_dofs = fem.locate_dofs_topological(
             function_space, facet_meshtags.dim, facet_meshtags.find(self.subdomain.id)
@@ -124,7 +124,7 @@ def define_surface_subdomain_dofs(
         return bc_dofs
 
     def update(self, t: float):
-        """Updates the boundary condition value
+        """Updates the boundary condition value.
 
         Args:
             t: the time
@@ -144,11 +144,13 @@ class FixedConcentrationBC(DirichletBCBase):
     Args:
         subdomain (festim.Subdomain): the surface subdomain where the boundary
             condition is applied
-        value: The value of the boundary condition. It can be a function of space and/or time
+        value: The value of the boundary condition. It can be a function of
+        space and/or time
         species: The name of the species
 
     Attributes:
-        temperature_dependent (bool): True if the value of the bc is temperature dependent
+        temperature_dependent (bool): True if the value of the bc is
+        temperature dependent
 
     Examples:
 
@@ -202,17 +204,18 @@ def create_value(
         K_S: fem.Function = None,
     ):
         """Creates the value of the boundary condition as a fenics object and sets it to
-        self.value_fenics.
-        If the value is a constant, it is converted to a `dolfinx.fem.Constant`.
-        If the value is a function of t, it is converted to  `dolfinx.fem.Constant`.
-        Otherwise, it is converted to a `dolfinx.fem.Function`.Function and the
-        expression of the function is stored in `bc_expr`.
+        self.value_fenics. If the value is a constant, it is converted to a
+        `dolfinx.fem.Constant`. If the value is a function of t, it is converted to
+        `dolfinx.fem.Constant`. Otherwise, it is converted to a
+        `dolfinx.fem.Function`.Function and the expression of the function is stored in
+        `bc_expr`.
 
         Args:
             function_space: the function space
             temperature: The temperature
             t: the time
-            K_S: The solubility of the species. If provided, the value of the boundary condition
+            K_S: The solubility of the species. If provided, the value of the
+            boundary condition
                 is divided by K_S (change of variable method).
         """
         mesh = function_space.mesh
@@ -313,11 +316,10 @@ def create_value(
 class FixedTemperatureBC(DirichletBCBase):
     def create_value(self, function_space: fem.FunctionSpace, t: fem.Constant):
         """Creates the value of the boundary condition as a fenics object and sets it to
-        self.value_fenics.
-        If the value is a constant, it is converted to a `dolfinx.fem.Constant`.
-        If the value is a function of t, it is converted to a `dolfinx.fem.Constant`.
-        Otherwise, it is converted to a` dolfinx.fem.Function` and the
-        expression of the function is stored in `bc_expr`.
+        self.value_fenics. If the value is a constant, it is converted to a
+        `dolfinx.fem.Constant`. If the value is a function of t, it is converted to a
+        `dolfinx.fem.Constant`. Otherwise, it is converted to a` dolfinx.fem.Function`
+        and the expression of the function is stored in `bc_expr`.
 
         Args:
             function_space: the function space