Fix errors and add mypy to CI

.github/workflows/ccpp.yml

@@ -79,6 +79,13 @@ jobs:
           python3 -m isort --check dolfinx
           python3 -m isort --check demo
           python3 -m isort --check test
+      - name: mypy checks (non-blocking)
+        continue-on-error: true
+        run: |
+          cd python/
+          mypy dolfinx
+          mypy demo
+          mypy test
       - name: clang-format C++ checks (non-blocking)
         continue-on-error: true
         run: |

docker/Dockerfile

@@ -176,7 +176,7 @@ RUN if [ "$MPI" = "mpich" ]; then \
 # - Second set of packages are recommended and/or required to build
 #   documentation or run tests.
 RUN pip3 install --no-binary="numpy" --no-cache-dir cffi mpi4py numba numpy==${NUMPY_VERSION} scipy && \
-    pip3 install --no-cache-dir cppimport flake8 isort jupytext matplotlib myst-parser pybind11==${PYBIND11_VERSION} pytest pytest-xdist sphinx sphinx_rtd_theme
+    pip3 install --no-cache-dir cppimport flake8 isort jupytext matplotlib mypy myst-parser pybind11==${PYBIND11_VERSION} pytest pytest-xdist sphinx sphinx_rtd_theme
 
 # Install xtl, xtensor
 RUN git clone -b ${XTL_VERSION} --single-branch --depth 1 https://github.com/xtensor-stack/xtl.git && \

python/demo/demo_gmsh.py

@@ -32,6 +32,7 @@
 from dolfinx.mesh import CellType, create_mesh, meshtags_from_entities
 
 from mpi4py import MPI
+
 # -
 
 # Generate a mesh on each rank with the gmsh API, and create a DOLFINx
@@ -119,7 +120,7 @@
 entities, values = distribute_entity_data(msh, 2, marked_facets, facet_values)
 
 msh.topology.create_connectivity(2, 0)
-mt = meshtags_from_entities(msh, 2, create_adjacencylist(entities), np.int32(values))
+mt = meshtags_from_entities(msh, 2, create_adjacencylist(entities), values)
 mt.name = "ball_d1_surface"
 
 with XDMFFile(MPI.COMM_WORLD, "out_gmsh/mesh.xdmf", "w") as file:
@@ -179,7 +180,7 @@
 
 entities, values = distribute_entity_data(msh, 2, marked_facets, facet_values)
 msh.topology.create_connectivity(2, 0)
-mt = meshtags_from_entities(msh, 2, create_adjacencylist(entities), np.int32(values))
+mt = meshtags_from_entities(msh, 2, create_adjacencylist(entities), values)
 mt.name = "ball_d2_surface"
 with XDMFFile(MPI.COMM_WORLD, "out_gmsh/mesh.xdmf", "a") as file:
     file.write_mesh(msh)
@@ -256,7 +257,7 @@
 
 entities, values = distribute_entity_data(msh, 2, marked_facets, facet_values)
 msh.topology.create_connectivity(2, 0)
-mt = meshtags_from_entities(msh, 2, create_adjacencylist(entities), np.int32(values))
+mt = meshtags_from_entities(msh, 2, create_adjacencylist(entities), values)
 mt.name = "hex_d2_surface"
 
 with XDMFFile(MPI.COMM_WORLD, "out_gmsh/mesh.xdmf", "a") as file:

python/demo/demo_lagrange_variants.py

@@ -18,8 +18,11 @@
 # We begin this demo by importing everything we require.
 
 # +
+import matplotlib.pylab as plt
 import numpy as np
 
+import basix
+import basix.ufl_wrapper
 import ufl
 from dolfinx import fem, mesh
 from ufl import ds, dx, grad, inner
@@ -31,16 +34,12 @@
     print("Demo should only be executed with DOLFINx real mode")
     exit(0)
 
-import matplotlib.pylab as plt
-
 # -
 
 # In addition to the imports seen in other demos, we also import Basix
 # and its UFL wrapper directly. Basix is the element definition and
 # tabulation library that is used by FEniCSx.
 
-import basix
-import basix.ufl_wrapper
 
 # ## Equispaced points vs GLL points
 # The basis function of Lagrange elements are defined by placing points
@@ -184,10 +183,9 @@ def saw_tooth(x):
             for i in range(51):
                 pts.append([cell / 10 + i / 50 / 10, 0, 0])
                 cells.append(cell)
-        pts = np.array(pts)
         values = uh.eval(pts, cells)
-        plt.plot(pts[:, 0], [saw_tooth(i[0]) for i in pts], "k--")
-        plt.plot(pts[:, 0], values, "r-")
+        plt.plot(pts, [saw_tooth(i[0]) for i in pts], "k--")
+        plt.plot(pts, values, "r-")
 
         plt.legend(["function", "approximation"])
         plt.ylim([-0.1, 0.4])

python/demo/demo_pyvista.py

@@ -109,7 +109,7 @@ def in_circle(x):
     midpoints = compute_midpoints(msh, msh.topology.dim, list(np.arange(num_cells, dtype=np.int32)))
     cell_tags = meshtags(msh, msh.topology.dim, np.arange(num_cells), in_circle(midpoints))
 
-    cells, types, x = plot.create_vtk_mesh(msh, msh.topology.dim)
+    cells, types, x = plot.create_vtk_mesh(msh)
     grid = pyvista.UnstructuredGrid(cells, types, x)
 
     # As the mesh tags contain a value for every cell in the
@@ -129,7 +129,7 @@ def in_circle(x):
     # only consisting of those entities that has value one in the
     # mesh tags
     cells, types, x = plot.create_vtk_mesh(
-        msh, msh.topology.dim, cell_tags.indices[cell_tags.values == 1])
+        msh, entities=cell_tags.indices[cell_tags.values == 1])
 
     # We add this grid to the second plotter
     sub_grid = pyvista.UnstructuredGrid(cells, types, x)
@@ -191,7 +191,7 @@ def in_circle(x):
     # that as we have done previously
     num_cells = msh.topology.index_map(msh.topology.dim).size_local
     cell_entities = np.arange(num_cells, dtype=np.int32)
-    cells, types, x = plot.create_vtk_mesh(msh, msh.topology.dim, cell_entities)
+    cells, types, x = plot.create_vtk_mesh(msh, entities=cell_entities)
     org_grid = pyvista.UnstructuredGrid(cells, types, x)
 
     # We visualize the data
@@ -225,7 +225,7 @@ def plot_nedelec():
                      position="upper_edge", font_size=14, color="black")
 
     # Next, we create a pyvista.UnstructuredGrid based on the mesh
-    pyvista_cells, cell_types, x = plot.create_vtk_mesh(msh, msh.topology.dim)
+    pyvista_cells, cell_types, x = plot.create_vtk_mesh(msh)
     grid = pyvista.UnstructuredGrid(pyvista_cells, cell_types, x)
 
     # Add this grid (as a wireframe) to the plotter

python/demo/demo_tnt-elements.py

@@ -27,6 +27,7 @@
                  grad, inner, sin)
 
 from mpi4py import MPI
+
 # -
 
 # ## Defining a degree 1 TNT element
@@ -68,8 +69,8 @@
 # +
 geometry = basix.geometry(basix.CellType.quadrilateral)
 topology = basix.topology(basix.CellType.quadrilateral)
-x = [[], [], [], []]
-M = [[], [], [], []]
+x = [[], [], [], []]  # type: ignore [var-annotated]
+M = [[], [], [], []]  # type: ignore [var-annotated]
 
 for v in topology[0]:
     x[0].append(np.array(geometry[v]))

python/dolfinx/__init__.py

@@ -12,15 +12,11 @@
 
 stored_dlopen_flags = sys.getdlopenflags()
 
-# Developer note: below is related to OpenMPI
-# Fix dlopen flags (may need reorganising)
+# Developer note: below is related to OpenMPI 
+# Fix dlopen flags
 if "linux" in sys.platform:
-    # FIXME: What with other platforms?
-    try:
-        from ctypes import RTLD_GLOBAL, RTLD_NOW
-    except ImportError:
-        RTLD_NOW = 2
-        RTLD_GLOBAL = 256
+    RTLD_NOW = 2
+    RTLD_GLOBAL = 256
     sys.setdlopenflags(RTLD_NOW | RTLD_GLOBAL)
 del sys
 

python/dolfinx/fem/__init__.py

@@ -14,7 +14,6 @@
 from dolfinx.fem.bcs import (DirichletBCMetaClass, bcs_by_block, dirichletbc,
                              locate_dofs_geometrical, locate_dofs_topological)
 from dolfinx.fem.dofmap import DofMap
-from dolfinx.fem.formmanipulations import adjoint
 from dolfinx.fem.forms import FormMetaClass, extract_function_spaces, form
 from dolfinx.fem.function import (Constant, Expression, Function,
                                   FunctionSpace, TensorFunctionSpace,

python/dolfinx/fem/assemble.py

@@ -1,4 +1,4 @@
-# Copyright (C) 2018-2022 Garth N. Wells
+# Copyright (C) 2018-2022 Garth N. Wells, Jack S. Hale
 #
 # This file is part of DOLFINx (https://www.fenicsproject.org)
 #
@@ -8,13 +8,8 @@
 from __future__ import annotations
 
 import collections
-import typing
-
-if typing.TYPE_CHECKING:
-    from dolfinx.fem.forms import FormMetaClass
-    from dolfinx.fem.bcs import DirichletBCMetaClass
-
 import functools
+import typing
 
 import numpy as np
 
@@ -23,6 +18,8 @@
 from dolfinx import la
 from dolfinx.cpp.fem import pack_coefficients as _pack_coefficients
 from dolfinx.cpp.fem import pack_constants as _pack_constants
+from dolfinx.fem.bcs import DirichletBCMetaClass
+from dolfinx.fem.forms import FormMetaClass, form_types
 
 
 def pack_constants(form: typing.Union[FormMetaClass,
@@ -133,11 +130,17 @@ def assemble_scalar(M: FormMetaClass, constants=None, coeffs=None):
 # -- Vector assembly ---------------------------------------------------------
 
 @functools.singledispatch
-def assemble_vector(L: FormMetaClass, constants=None, coeffs=None) -> la.VectorMetaClass:
+def assemble_vector(L: typing.Any,
+                    constants=None, coeffs=None):
+    return _assemble_vector_form(L, constants, coeffs)
+
+
+@assemble_vector.register(FormMetaClass)
+def _assemble_vector_form(L: form_types, constants=None, coeffs=None) -> la.VectorMetaClass:
     """Assemble linear form into a new Vector.
 
     Args:
-        L: The linear form assemble.
+        L: The linear form to assemble.
         constants: Constants that appear in the form. If not provided,
             any required constants will be computed.
         coeffs: Coefficients that appear in the form. If not provided,
@@ -162,12 +165,12 @@ def assemble_vector(L: FormMetaClass, constants=None, coeffs=None) -> la.VectorM
     b.array[:] = 0
     constants = constants or _pack_constants(L)
     coeffs = coeffs or _pack_coefficients(L)
-    _cpp.fem.assemble_vector(b.array, L, constants, coeffs)
+    _assemble_vector_array(b.array, L, constants, coeffs)
     return b
 
 
 @assemble_vector.register(np.ndarray)
-def _(b: np.ndarray, L: FormMetaClass, constants=None, coeffs=None):
+def _assemble_vector_array(b: np.ndarray, L: FormMetaClass, constants=None, coeffs=None):
     """Assemble linear form into a new Vector.
 
     Args:
@@ -201,67 +204,74 @@ def _(b: np.ndarray, L: FormMetaClass, constants=None, coeffs=None):
 
 
 @functools.singledispatch
-def assemble_matrix(a: FormMetaClass, bcs: typing.List[DirichletBCMetaClass] = None,
-                    diagonal: float = 1.0,
-                    constants=None, coeffs=None) -> la.MatrixCSRMetaClass:
+def assemble_matrix(a: typing.Any,
+                    bcs: 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,
+                         diagonal: float = 1.0, constants=None, coeffs=None) -> la.MatrixCSRMetaClass:
     """Assemble bilinear form into a matrix.
 
-    Args:
+        Args:
         a: The bilinear form assemble.
         bcs: Boundary conditions that affect the assembled matrix.
             Degrees-of-freedom constrained by a boundary condition will
-            have their rows/columns zeroed and the value ``diagonal``
-            set on on the matrix diagonal.
+            have their rows/columns zeroed and the value ``diagonal`` set
+            on on the matrix diagonal.
         constants: Constants that appear in the form. If not provided,
             any required constants will be computed.
         coeffs: Coefficients that appear in the form. If not provided,
             any required coefficients will be computed.
 
-    Returns:
-        Matrix representation of the bilinear form ``a``.
-
     Note:
         The returned matrix is not finalised, i.e. ghost values are not
         accumulated.
 
     """
     bcs = [] if bcs is None else bcs
-    A = create_matrix(a)
-    assemble_matrix(A, a, bcs, diagonal, constants, coeffs)
+    constants = _pack_constants(a) if constants is None else constants
+    coeffs = _pack_coefficients(a) if coeffs is None else coeffs
+    _cpp.fem.assemble_matrix(A, a, constants, coeffs, bcs)
+
+    # If matrix is a 'diagonal'block, set diagonal entry for constrained
+    # dofs
+    if a.function_spaces[0] is a.function_spaces[1]:
+        _cpp.fem.insert_diagonal(A, a.function_spaces[0], bcs, diagonal)
     return A
 
 
-@assemble_matrix.register(la.MatrixCSRMetaClass)
-def _(A: la.MatrixCSRMetaClass, a: FormMetaClass,
-      bcs: typing.List[DirichletBCMetaClass] = None,
-      diagonal: float = 1.0, constants=None, coeffs=None) -> la.MatrixCSRMetaClass:
+@assemble_matrix.register(FormMetaClass)
+def _assemble_matrix_form(a: form_types, bcs: typing.List[DirichletBCMetaClass] = None,
+                          diagonal: float = 1.0,
+                          constants=None, coeffs=None) -> la.MatrixCSRMetaClass:
     """Assemble bilinear form into a matrix.
 
-        Args:
+    Args:
         a: The bilinear form assemble.
         bcs: Boundary conditions that affect the assembled matrix.
             Degrees-of-freedom constrained by a boundary condition will
-            have their rows/columns zeroed and the value ``diagonal`` set
-            on on the matrix diagonal.
+            have their rows/columns zeroed and the value ``diagonal``
+            set on on the matrix diagonal.
         constants: Constants that appear in the form. If not provided,
             any required constants will be computed.
         coeffs: Coefficients that appear in the form. If not provided,
             any required coefficients will be computed.
 
+    Returns:
+        Matrix representation of the bilinear form ``a``.
+
     Note:
         The returned matrix is not finalised, i.e. ghost values are not
         accumulated.
 
     """
     bcs = [] if bcs is None else bcs
-    constants = _pack_constants(a) if constants is None else constants
-    coeffs = _pack_coefficients(a) if coeffs is None else coeffs
-    _cpp.fem.assemble_matrix(A, a, constants, coeffs, bcs)
-
-    # If matrix is a 'diagonal'block, set diagonal entry for constrained
-    # dofs
-    if a.function_spaces[0] is a.function_spaces[1]:
-        _cpp.fem.insert_diagonal(A, a.function_spaces[0], bcs, diagonal)
+    A: la.MatrixCSRMetaClass = create_matrix(a)
+    _assemble_matrix_csr(A, a, bcs, diagonal, constants, coeffs)
     return A