Updates for development (#11)

* Update to dev. * More fixes for dev. * Fix and switch to ruff. * Ruff format. * More ruff fixes. * Remove C++ - can add back in as it will need to be totally rethought. * Fix. * Remove setup.cfg
FEniCS-Shells · Mar 26, 2024 · 702e0c2 · 702e0c2
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diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
@@ -14,26 +14,18 @@ on:
 jobs:
   build-and-test:
     runs-on: ubuntu-latest
-    container: ghcr.io/fenics/dolfinx/dolfinx:v0.7.2
+    container: ghcr.io/fenics/dolfinx/dolfinx:nightly
     steps:
       - name: Checkout
         uses: actions/checkout@v3
 
-      - name: Flake8 checks
+      - name: ruff checks
         run: |
-          python3 -m flake8 fenicsx_shells
-          cd demo && python3 -m flake8 . && cd ../
-          python3 -m flake8 test
-      - name: isort checks (non-blocking)
-        continue-on-error: true
-        run: |
-          python3 -m isort --check fenicsx_shells
-          python3 -m isort --check demo
-          python3 -m isort --check test
+          ruff check .
+          ruff format --check .
       
       - name: Install FEniCSx-Shells
         run: |
-          pip install scikit-build-core[pyproject] # TO REMOVE ONCE 0.8.0 RELEASED
           python3 -m pip install --no-build-isolation --check-build-dependencies .
 
       - name: Build documentation

diff --git a/CMakeLists.txt b/CMakeLists.txt
diff --git a/demo/conftest.py b/demo/conftest.py
@@ -2,10 +2,13 @@
 
 
 def pytest_addoption(parser):
-    parser.addoption("--mpiexec", action="store", default="mpirun",
-                     help="Name of program to run MPI, e.g. mpiexex")
-    parser.addoption("--num-proc", action="store", default=1,
-                     help="Number of MPI processes to use")
+    parser.addoption(
+        "--mpiexec",
+        action="store",
+        default="mpirun",
+        help="Name of program to run MPI, e.g. mpiexex",
+    )
+    parser.addoption("--num-proc", action="store", default=1, help="Number of MPI processes to use")
 
 
 @pytest.fixture

diff --git a/demo/demo_kirchhoff-love-clamped.py b/demo/demo_kirchhoff-love-clamped.py
@@ -35,17 +35,17 @@
 # We begin by importing the necessary functionality from DOLFINx, UFL and
 # PETSc.
 
+from mpi4py import MPI
+
 import numpy as np
 
 import dolfinx
 import ufl
-from dolfinx.fem import FunctionSpace, dirichletbc
+from basix.ufl import element, mixed_element
+from dolfinx.fem import dirichletbc, functionspace
 from dolfinx.fem.petsc import LinearProblem
 from dolfinx.mesh import CellType, create_unit_square
-from ufl import (FacetNormal, FiniteElement, Identity, Measure, MixedElement,
-                 grad, inner, sym, tr)
-
-from mpi4py import MPI
+from ufl import FacetNormal, Identity, Measure, grad, inner, sym, tr
 
 # We then create a two-dimensional mesh of the mid-plane of the plate $\Omega =
 # [0, 1] \times [0, 1]$.
@@ -65,9 +65,10 @@
 
 # +
 k = 2
-U_el = MixedElement([FiniteElement("Lagrange", ufl.triangle, k + 1),
-                     FiniteElement("HHJ", ufl.triangle, k)])
-U = FunctionSpace(mesh, U_el)
+U_el = mixed_element(
+    [element("Lagrange", mesh.basix_cell(), k + 1), element("HHJ", mesh.basix_cell(), k)]
+)
+U = functionspace(mesh, U_el)
 
 w, M = ufl.TrialFunctions(U)
 w_t, M_t = ufl.TestFunctions(U)
@@ -148,7 +149,7 @@ def k_theta(theta):
 
 def k_M(M):
     """Bending strain tensor in terms of bending moments"""
-    return (12.0/(E*t**3))*((1.0 + nu)*M - nu*Identity(2)*tr(M))
+    return (12.0 / (E * t**3)) * ((1.0 + nu) * M - nu * Identity(2) * tr(M))
 
 
 def nn(M):
@@ -163,14 +164,16 @@ def inner_divdiv(M, theta):
     """Discrete div-div inner product"""
     n = FacetNormal(M.ufl_domain())
     M_nn = nn(M)
-    result = -inner(M, k_theta(theta))*dx + inner(M_nn("+"),
-                                                  ufl.jump(theta, n))*dS + inner(M_nn, ufl.dot(theta, n))*ds
+    result = (
+        -inner(M, k_theta(theta)) * dx
+        + inner(M_nn("+"), ufl.jump(theta, n)) * dS
+        + inner(M_nn, ufl.dot(theta, n)) * ds
+    )
     return result
 
 
-a = inner(k_M(M), M_t)*dx + inner_divdiv(M_t, theta(w)) + \
-    inner_divdiv(M, theta(w_t))
-L = -inner(t**3, w_t)*dx
+a = inner(k_M(M), M_t) * dx + inner_divdiv(M_t, theta(w)) + inner_divdiv(M, theta(w_t))
+L = -inner(t**3, w_t) * dx
 
 
 def all_boundary(x):
@@ -187,15 +190,14 @@ def all_boundary(x):
 # TODO: Add table like TDNNS example.
 
 # +
-boundary_entities = dolfinx.mesh.locate_entities_boundary(
-    mesh, mesh.topology.dim - 1, all_boundary)
+boundary_entities = dolfinx.mesh.locate_entities_boundary(mesh, mesh.topology.dim - 1, all_boundary)
 
 bcs = []
 # Transverse displacement
 boundary_dofs_displacement = dolfinx.fem.locate_dofs_topological(
-    U.sub(0), mesh.topology.dim - 1, boundary_entities)
-bcs.append(dirichletbc(np.array(0.0, dtype=np.float64),
-           boundary_dofs_displacement, U.sub(0)))
+    U.sub(0), mesh.topology.dim - 1, boundary_entities
+)
+bcs.append(dirichletbc(np.array(0.0, dtype=np.float64), boundary_dofs_displacement, U.sub(0)))
 
 
 # -
@@ -204,15 +206,18 @@ def all_boundary(x):
 # centre of the plate.
 
 # +
-problem = LinearProblem(a, L, bcs=bcs, petsc_options={
-                        "ksp_type": "preonly", "pc_type": "lu", "pc_factor_mat_solver_type": "mumps"})
+problem = LinearProblem(
+    a,
+    L,
+    bcs=bcs,
+    petsc_options={"ksp_type": "preonly", "pc_type": "lu", "pc_factor_mat_solver_type": "mumps"},
+)
 u_h = problem.solve()
 
 bb_tree = dolfinx.geometry.bb_tree(mesh, 2)
 point = np.array([[0.5, 0.5, 0.0]], dtype=np.float64)
 cell_candidates = dolfinx.geometry.compute_collisions_points(bb_tree, point)
-cells = dolfinx.geometry.compute_colliding_cells(
-    mesh, cell_candidates, point)
+cells = dolfinx.geometry.compute_colliding_cells(mesh, cell_candidates, point)
 
 w, M = u_h.split()
 

diff --git a/demo/demo_reissner-mindlin-clamped-tdnns.py b/demo/demo_reissner-mindlin-clamped-tdnns.py
@@ -15,8 +15,8 @@
 # conditions using the TDNNS (tangential displacement normal-normal stress)
 # element developed in:
 #
-# Pechstein, A. S., Schöberl, J. The TDNNS method for Reissner–Mindlin plates.
-# Numer. Math. 137, 713–740 (2017).
+# Pechstein, A. S., Schöberl, J. The TDNNS method for Reissner-Mindlin plates.
+# Numer. Math. 137, 713-740 (2017).
 # [doi:10.1007/s00211-017-0883-9](https://doi.org/10.1007/s00211-017-0883-9)
 #
 # The idea behind this element construction is that the rotations, transverse
@@ -37,17 +37,17 @@
 # PETSc.
 
 # +
+from mpi4py import MPI
+
 import numpy as np
 
 import dolfinx
 import ufl
-from dolfinx.fem import Function, FunctionSpace, dirichletbc
+from basix.ufl import element, mixed_element
+from dolfinx.fem import Function, dirichletbc, functionspace
 from dolfinx.fem.petsc import LinearProblem
 from dolfinx.mesh import CellType, create_unit_square
-from ufl import (FacetNormal, FiniteElement, Identity, Measure, MixedElement,
-                 grad, inner, split, sym, tr)
-
-from mpi4py import MPI
+from ufl import FacetNormal, Identity, Measure, grad, inner, split, sym, tr
 
 # -
 
@@ -74,9 +74,11 @@
 
 # +
 k = 3
-U_el = MixedElement([FiniteElement("N2curl", ufl.triangle, k), FiniteElement("Lagrange", ufl.triangle, k + 1),
-                     FiniteElement("HHJ", ufl.triangle, k)])
-U = FunctionSpace(mesh, U_el)
+cell = mesh.basix_cell()
+U_el = mixed_element(
+    [element("N2curl", cell, k), element("Lagrange", cell, k + 1), element("HHJ", cell, k)]
+)
+U = functionspace(mesh, U_el)
 
 u = ufl.TrialFunction(U)
 u_t = ufl.TestFunction(U)
@@ -91,7 +93,7 @@
 # +
 E = 10920.0
 nu = 0.3
-kappa = 5.0/6.0
+kappa = 5.0 / 6.0
 t = 0.001
 # -
 
@@ -143,13 +145,13 @@ def k_theta(theta):
 
 def k_M(M):
     """Bending strain tensor in terms of bending moments"""
-    return (12.0/(E*t**3))*((1.0 + nu)*M - nu*Identity(2)*tr(M))
+    return (12.0 / (E * t**3)) * ((1.0 + nu) * M - nu * Identity(2) * tr(M))
 
 
 def nn(M):
     """Normal-normal component of tensor"""
     n = FacetNormal(M.ufl_domain())
-    M_n = M*n
+    M_n = M * n
     M_nn = ufl.dot(M_n, n)
     return M_nn
 
@@ -158,8 +160,11 @@ def inner_divdiv(M, theta):
     """Discrete div-div inner product"""
     n = FacetNormal(M.ufl_domain())
     M_nn = nn(M)
-    result = -inner(M, k_theta(theta))*dx + inner(M_nn("+"),
-                                                  ufl.jump(theta, n))*dS + inner(M_nn, ufl.dot(theta, n))*ds
+    result = (
+        -inner(M, k_theta(theta)) * dx
+        + inner(M_nn("+"), ufl.jump(theta, n)) * dS
+        + inner(M_nn, ufl.dot(theta, n)) * ds
+    )
     return result
 
 
@@ -168,9 +173,13 @@ def gamma(theta, w):
     return grad(w) - theta
 
 
-a = inner(k_M(M), M_t)*dx + inner_divdiv(M_t, theta) + inner_divdiv(M, theta_t) - \
-    ((E*kappa*t)/(2.0*(1.0 + nu)))*inner(gamma(theta, w), gamma(theta_t, w_t))*dx
-L = -inner(1.0*t**3, w_t)*dx
+a = (
+    inner(k_M(M), M_t) * dx
+    + inner_divdiv(M_t, theta)
+    + inner_divdiv(M, theta_t)
+    - ((E * kappa * t) / (2.0 * (1.0 + nu))) * inner(gamma(theta, w), gamma(theta_t, w_t)) * dx
+)
+L = -inner(1.0 * t**3, w_t) * dx
 
 # -
 
@@ -206,19 +215,20 @@ def all_boundary(x):
     return np.full(x.shape[1], True, dtype=bool)
 
 
-boundary_entities = dolfinx.mesh.locate_entities_boundary(
-    mesh, mesh.topology.dim - 1, all_boundary)
+boundary_entities = dolfinx.mesh.locate_entities_boundary(mesh, mesh.topology.dim - 1, all_boundary)
 
 bcs = []
 # Transverse displacement
 boundary_dofs = dolfinx.fem.locate_dofs_topological(
-    U.sub(1), mesh.topology.dim - 1, boundary_entities)
+    U.sub(1), mesh.topology.dim - 1, boundary_entities
+)
 bcs.append(dirichletbc(np.array(0.0, dtype=np.float64), boundary_dofs, U.sub(1)))
 
 # Fix tangential component of rotation
 R = U.sub(0).collapse()[0]
 boundary_dofs = dolfinx.fem.locate_dofs_topological(
-    (U.sub(0), R), mesh.topology.dim - 1, boundary_entities)
+    (U.sub(0), R), mesh.topology.dim - 1, boundary_entities
+)
 
 theta_bc = Function(R)
 bcs.append(dirichletbc(theta_bc, boundary_dofs, U.sub(0)))
@@ -229,15 +239,18 @@ def all_boundary(x):
 # centre of the plate.
 
 # +
-problem = LinearProblem(a, L, bcs=bcs, petsc_options={
-                        "ksp_type": "preonly", "pc_type": "lu", "pc_factor_mat_solver_type": "mumps"})
+problem = LinearProblem(
+    a,
+    L,
+    bcs=bcs,
+    petsc_options={"ksp_type": "preonly", "pc_type": "lu", "pc_factor_mat_solver_type": "mumps"},
+)
 u_h = problem.solve()
 
 bb_tree = dolfinx.geometry.bb_tree(mesh, 2)
 point = np.array([[0.5, 0.5, 0.0]], dtype=np.float64)
 cell_candidates = dolfinx.geometry.compute_collisions_points(bb_tree, point)
-cells = dolfinx.geometry.compute_colliding_cells(
-    mesh, cell_candidates, point)
+cells = dolfinx.geometry.compute_colliding_cells(mesh, cell_candidates, point)
 
 theta, w, M = u_h.split()