Typing cleanup + docker cleanup and numpy upgrade (#129)

* Typing cleanup + docker cleanup and numpy upgrade

* Ignore complaint

.github/workflows/build_docs.yml

@@ -35,7 +35,7 @@ jobs:
           cmake --install build-dir
 
       - name: Install DOLFINx-MPC (Python)
-        run: python3 -m pip -v install --break-system-packages --config-settings=cmake.build-type="Release" --no-build-isolation  ./python/[docs]
+        run: python3 -m pip -v install --config-settings=cmake.build-type="Release" --no-build-isolation  ./python/[docs]
 
       - name: Build docs
         run: jupyter book build .

.github/workflows/test_mpc.yml

@@ -69,23 +69,23 @@ jobs:
           apt-get install -y clang
 
       - name: upgrade pip
-        run: python3 -m pip install --break-system-packages --upgrade setuptools pip
+        run: python3 -m pip install  --upgrade setuptools pip
 
       - name: Check formatting
         run: |
-          python3 -m pip install --break-system-packages ruff
+          python3 -m pip install  ruff
           ruff check
           ruff format
 
       - name: Check typing
         run: |
-          python3 -m pip install --break-system-packages mypy
+          python3 -m pip install  mypy
           cd python
           python3 -m mypy . --exclude=build
 
       - name: Install h5py
         run: |
-          python3 -m pip install --no-build-isolation --break-system-packages --no-cache-dir --no-binary=h5py h5py
+          python3 -m pip install --no-build-isolation  --no-cache-dir --no-binary=h5py h5py
 
       - name: Install DOLFINx
         uses: jorgensd/actions/[email protected]
@@ -103,7 +103,7 @@ jobs:
           cmake --install build-dir
 
       - name: Install DOLFINx-MPC (Python)
-        run: python3 -m pip -v install --break-system-packages --config-settings=cmake.build-type=${MPC_BUILD_MODE} --no-build-isolation  -e python/[test]
+        run: python3 -m pip -v install  --config-settings=cmake.build-type=${MPC_BUILD_MODE} --no-build-isolation  -e python/[test]
 
       - name: Run tests (serial)
         run: coverage run --rcfile=.coveragerc -m mpi4py -m pytest python/tests/ -vs

docker/Dockerfile

@@ -9,21 +9,21 @@ ARG PYTHON_VERSION=3.12
 ENV HDF5_MPI="ON" \
     HDF5_DIR="/usr/local"
 
-RUN python3 -m pip install --break-system-packages -U pip setuptools
+RUN python3 -m pip install  -U pip setuptools
 
 # Install h5py https://github.com/h5py/h5py/issues/2222
-RUN python3 -m pip install --break-system-packages --no-cache-dir --no-binary=h5py git+https://github.com/h5py/h5py.git
-RUN python3 -m pip install --break-system-packages meshio 
+RUN python3 -m pip install --no-cache-dir --no-binary=h5py git+https://github.com/h5py/h5py.git
+RUN python3 -m pip install  meshio 
 
 # Copy DOLFINX_MPC source dir
 COPY . dolfinx_mpc
 
 # Install real mode
 RUN . /usr/local/bin/dolfinx-real-mode && \
     . /usr/local/dolfinx-real/lib/dolfinx/dolfinx.conf && \
-    cmake -G Ninja -DCMAKE_INSTALL_PREFIX=/usr/local/dolfinx-real  -DCMAKE_BUILD_TYPE=Developer -B build-dir-real dolfinx_mpc/cpp/ && \
-    ninja install -j4  -C build-dir-real && \
-    python3 -m pip install -v --break-system-packages --no-build-isolation --check-build-dependencies \
+    cmake -G Ninja -DCMAKE_INSTALL_PREFIX=/usr/local/dolfinx-real -DCMAKE_BUILD_TYPE=Developer -B build-dir-real dolfinx_mpc/cpp/ && \
+    ninja install -j4 -C build-dir-real && \
+    python3 -m pip install -v --no-build-isolation --check-build-dependencies \
     --target /usr/local/dolfinx-real/lib/python${PYTHON_VERSION}/dist-packages --no-dependencies --no-cache-dir ./dolfinx_mpc/python
 
 # Clean repo to remove build dir from pip
@@ -32,9 +32,9 @@ RUN rm -rf dolfinx_mpc/python/build
 # Install complex mode
 RUN . /usr/local/bin/dolfinx-complex-mode && \
     . /usr/local/dolfinx-complex/lib/dolfinx/dolfinx.conf && \
-    cmake -G Ninja  -DCMAKE_INSTALL_PREFIX=/usr/local/dolfinx-complex -DCMAKE_BUILD_TYPE=Developer -B build-dir-complex dolfinx_mpc/cpp/ && \
-    ninja install -j4  -C build-dir-complex && \
-    python3 -m pip install --break-system-packages -v --no-build-isolation --check-build-dependencies \
+    cmake -G Ninja -DCMAKE_INSTALL_PREFIX=/usr/local/dolfinx-complex -DCMAKE_BUILD_TYPE=Developer -B build-dir-complex dolfinx_mpc/cpp/ && \
+    ninja install -j4 -C build-dir-complex && \
+    python3 -m pip install -v --no-build-isolation --check-build-dependencies \
     --target /usr/local/dolfinx-complex/lib/python${PYTHON_VERSION}/dist-packages --no-dependencies --no-cache-dir ./dolfinx_mpc/python
 
 WORKDIR /root

python/benchmarks/bench_elasticity.py

@@ -216,7 +216,7 @@ def l2b(li):
     h5f.create_dataset("num_dofs", (N,), dtype=np.int32)
     sd = h5f.create_dataset("solve_time", (N, MPI.COMM_WORLD.size), dtype=np.float64)
     solver = "BoomerAMG" if args.boomeramg else "GAMG"
-    sd.attrs["solver"] = np.string_(solver)
+    sd.attrs["solver"] = np.bytes_(solver)
 
     # Loop over refinement levels
     for i in range(N):

python/benchmarks/bench_elasticity_edge.py

@@ -260,9 +260,9 @@ def sigma(v):
     sd = h5f.create_dataset("solve_time", (N, MPI.COMM_WORLD.size), dtype=np.float64)
     solver = "BoomerAMG" if args.boomeramg else "GAMG"
     ct = "Tet" if args.tetra else "Hex"
-    sd.attrs["solver"] = np.string_(solver)
-    sd.attrs["degree"] = np.string_(str(int(args.degree)))
-    sd.attrs["ct"] = np.string_(ct)
+    sd.attrs["solver"] = np.bytes_(solver)
+    sd.attrs["degree"] = np.bytes_(str(int(args.degree)))
+    sd.attrs["ct"] = np.bytes_(ct)
 
     for i in range(N):
         log_info(f"Run {i} in progress")

python/benchmarks/bench_periodic.py

@@ -222,9 +222,9 @@ def periodic_relation(x):
     sd = h5f.create_dataset("solve_time", (N, MPI.COMM_WORLD.size), dtype=np.float64)
     solver = "BoomerAMG" if args.boomeramg else "GAMG"
     ct = "Tet" if args.tetra else "Hex"
-    sd.attrs["solver"] = np.string_(solver)
-    sd.attrs["degree"] = np.string_(str(int(args.degree)))
-    sd.attrs["ct"] = np.string_(ct)
+    sd.attrs["solver"] = np.bytes_(solver)
+    sd.attrs["degree"] = np.bytes_(str(int(args.degree)))
+    sd.attrs["ct"] = np.bytes_(ct)
 
     # Loop over refinements
     for i in range(N):

python/benchmarks/ref_elasticity.py

@@ -237,9 +237,9 @@ def sigma(v):
     sd = h5f.create_dataset("solve_time", (N, MPI.COMM_WORLD.size), dtype=np.float64)
     solver = "BoomerAMG" if args.boomeramg else "GAMG"
     ct = "Tet" if args.tetra else "Hex"
-    sd.attrs["solver"] = np.string_(solver)
-    sd.attrs["degree"] = np.string_(str(int(args.degree)))
-    sd.attrs["ct"] = np.string_(ct)
+    sd.attrs["solver"] = np.bytes_(solver)
+    sd.attrs["degree"] = np.bytes_(str(int(args.degree)))
+    sd.attrs["ct"] = np.bytes_(ct)
 
     # Loop over refinement levels
     for i in range(N):

python/benchmarks/ref_periodic.py

@@ -199,9 +199,9 @@ def dirichletboundary(x):
     sd = h5f.create_dataset("solve_time", (N, MPI.COMM_WORLD.size), dtype=np.float64)
     solver = "BoomerAMG" if args.boomeramg else "GAMG"
     ct = "Tet" if args.tetra else "Hex"
-    sd.attrs["solver"] = np.string_(solver)
-    sd.attrs["degree"] = np.string_(str(int(args.degree)))
-    sd.attrs["ct"] = np.string_(ct)
+    sd.attrs["solver"] = np.bytes_(solver)
+    sd.attrs["degree"] = np.bytes_(str(int(args.degree)))
+    sd.attrs["ct"] = np.bytes_(ct)
     for i in range(N):
         if MPI.COMM_WORLD.rank == 0:
             set_log_level(LogLevel.INFO)

python/demos/demo_elasticity_disconnect_2D.py

@@ -133,12 +133,12 @@ def gather_dof_coordinates(V: FunctionSpace, dofs: np.ndarray):
     coords = x[local_dofs]
     num_nodes = len(coords)
     glob_num_nodes = MPI.COMM_WORLD.allreduce(num_nodes, op=MPI.SUM)
-    recvbuf = None
+    recvbuf = np.empty(0, dtype=V.mesh.geometry.x.dtype)
     if MPI.COMM_WORLD.rank == 0:
         recvbuf = np.zeros(3 * glob_num_nodes, dtype=V.mesh.geometry.x.dtype)
     sendbuf = coords.reshape(-1)
     sendcounts = np.array(MPI.COMM_WORLD.gather(len(sendbuf), 0))
-    MPI.COMM_WORLD.Gatherv(sendbuf, (recvbuf, sendcounts), root=0)
+    MPI.COMM_WORLD.Gatherv(sendbuf, (recvbuf, sendcounts), root=0)  #  type: ignore
     glob_coords = MPI.COMM_WORLD.bcast(recvbuf, root=0).reshape((-1, 3))
     return glob_coords
 

python/dolfinx_mpc/utils/mpc_utils.py

@@ -204,7 +204,7 @@ def rigid_motions_nullspace(V: _fem.FunctionSpace):
         b.scatter_forward()
 
     _la.orthonormalize(nullspace_basis)
-    assert _la.is_orthonormal(nullspace_basis, np.finfo(_x.x.array.dtype).eps)
+    assert _la.is_orthonormal(nullspace_basis, float(np.finfo(_x.x.array.dtype).eps))
     local_size = V.dofmap.index_map.size_local * V.dofmap.index_map_bs
     basis_petsc = [
         PETSc.Vec().createWithArray(x[:local_size], bsize=gdim, comm=V.mesh.comm)  # type: ignore