Fix mypy checks (typing.Optional) (#2444)

* typing.Optional

* flake

python/dolfinx/common.py

@@ -6,6 +6,7 @@
 """General tools for timing and configuration"""
 
 import functools
+import typing
 
 from dolfinx import cpp as _cpp
 from dolfinx.cpp.common import (IndexMap, git_commit_hash, has_adios2,  # noqa
@@ -63,7 +64,7 @@ class Timer:
         list_timings(comm, [TimingType.wall, TimingType.user])
     """
 
-    def __init__(self, name: str = None):
+    def __init__(self, name: typing.Optional[str] = None):
         if name is None:
             self._cpp_object = _cpp.common.Timer()
         else:

python/dolfinx/fem/assemble.py

@@ -205,14 +205,14 @@ def _assemble_vector_array(b: np.ndarray, L: FormMetaClass, constants=None, coef
 
 @functools.singledispatch
 def assemble_matrix(a: typing.Any,
-                    bcs: typing.List[DirichletBCMetaClass] = None,
+                    bcs: typing.Optional[typing.List[DirichletBCMetaClass]] = None,
                     diagonal: float = 1.0, constants=None, coeffs=None):
     return _assemble_matrix_form(a, bcs, diagonal, constants, coeffs)
 
 
 @assemble_matrix.register
 def _assemble_matrix_csr(A: la.MatrixCSRMetaClass, a: form_types,
-                         bcs: typing.List[DirichletBCMetaClass] = None,
+                         bcs: typing.Optional[typing.List[DirichletBCMetaClass]] = None,
                          diagonal: float = 1.0, constants=None, coeffs=None) -> la.MatrixCSRMetaClass:
     """Assemble bilinear form into a matrix.
 
@@ -245,7 +245,7 @@ def _assemble_matrix_csr(A: la.MatrixCSRMetaClass, a: form_types,
 
 
 @assemble_matrix.register(FormMetaClass)
-def _assemble_matrix_form(a: form_types, bcs: typing.List[DirichletBCMetaClass] = None,
+def _assemble_matrix_form(a: form_types, bcs: typing.Optional[typing.List[DirichletBCMetaClass]] = None,
                           diagonal: float = 1.0,
                           constants=None, coeffs=None) -> la.MatrixCSRMetaClass:
     """Assemble bilinear form into a matrix.

python/dolfinx/fem/bcs.py

@@ -91,7 +91,7 @@ def locate_dofs_topological(V: typing.Union[dolfinx.fem.FunctionSpace, typing.It
 
 class DirichletBCMetaClass:
     def __init__(self, value: typing.Union[Function, Constant, numpy.ndarray],
-                 dofs: numpy.typing.ArrayLike, V: dolfinx.fem.FunctionSpace = None):
+                 dofs: numpy.typing.ArrayLike, V: typing.Optional[dolfinx.fem.FunctionSpace] = None):
         """Representation of Dirichlet boundary condition which is imposed on
         a linear system.
 
@@ -140,7 +140,8 @@ def function_space(self) -> dolfinx.fem.FunctionSpace:
 
 
 def dirichletbc(value: typing.Union[Function, Constant, np.ndarray],
-                dofs: numpy.typing.NDArray[np.int32], V: dolfinx.fem.FunctionSpace = None) -> DirichletBCMetaClass:
+                dofs: numpy.typing.NDArray[np.int32],
+                V: typing.Optional[dolfinx.fem.FunctionSpace] = None) -> DirichletBCMetaClass:
     """Create a representation of Dirichlet boundary condition which
     is imposed on a linear system.
 

python/dolfinx/fem/petsc.py

@@ -536,7 +536,7 @@ class LinearProblem:
     """
 
     def __init__(self, a: ufl.Form, L: ufl.Form, bcs: typing.List[DirichletBCMetaClass] = [],
-                 u: _Function = None, petsc_options={}, form_compiler_options={}, jit_options={}):
+                 u: typing.Optional[_Function] = None, petsc_options={}, form_compiler_options={}, jit_options={}):
         """Initialize solver for a linear variational problem.
 
         Args:

python/dolfinx/io/gmshio.py

@@ -65,7 +65,7 @@ def cell_perm_array(cell_type: CellType, num_nodes: int) -> typing.List[int]:
 if _has_gmsh:
     __all__ += ["extract_topology_and_markers", "extract_geometry", "model_to_mesh", "read_from_msh"]
 
-    def extract_topology_and_markers(model: gmsh.model, name: str = None):
+    def extract_topology_and_markers(model: gmsh.model, name: typing.Optional[str] = None):
         """Extract all entities tagged with a physical marker in the gmsh
         model, and collect the data per cell type.
 
@@ -132,7 +132,7 @@ def extract_topology_and_markers(model: gmsh.model, name: str = None):
 
         return topologies
 
-    def extract_geometry(model: gmsh.model, name: str = None) -> npt.NDArray[np.float64]:
+    def extract_geometry(model: gmsh.model, name: typing.Optional[str] = None) -> npt.NDArray[np.float64]:
         """Extract the mesh geometry from a gmsh model as an array of shape
         (num_nodes, 3), where the i-th row corresponds to the i-th node in the
         mesh.

python/dolfinx/mesh.py

@@ -125,7 +125,7 @@ def locate_entities_boundary(mesh: Mesh, dim: int, marker: typing.Callable) -> n
 }
 
 
-def refine(mesh: Mesh, edges: np.ndarray = None, redistribute: bool = True) -> Mesh:
+def refine(mesh: Mesh, edges: typing.Optional[np.ndarray] = None, redistribute: bool = True) -> Mesh:
     """Refine a mesh
 
     Args: