Merge branch 'dokken/v0.5.0' into 'master'

Bump versions

See merge request wp2/mpc!192

.github/workflows/sonarcloud.yml

@@ -14,7 +14,7 @@ jobs:
     container: dolfinx/dev-env
     env:
       SONAR_SCANNER_VERSION:
-        4.6.2.2472 # Find the latest version in at:
+        4.7.0.2747 # Find the latest version in at:
         # https://github.com/SonarSource/sonar-scanner-cli/tags
       SONAR_SERVER_URL: "https://sonarcloud.io"
       BUILD_WRAPPER_OUT_DIR: build_wrapper_output_directory # Directory where build-wrapper output will be placed
@@ -54,16 +54,16 @@ jobs:
           echo "$HOME/.sonar/build-wrapper-linux-x86" >> $GITHUB_PATH
       - name: Install FEniCS Python components
         run: |
-          python3 -m pip install git+https://github.com/FEniCS/ufl.git
-          python3 -m pip install git+https://github.com/FEniCS/basix.git
-          python3 -m pip install git+https://github.com/FEniCS/ffcx.git
+          python3 -m pip install git+https://github.com/FEniCS/ufl.git@2022.2.0
+          python3 -m pip install git+https://github.com/FEniCS/basix.git@v0.5.0
+          python3 -m pip install git+https://github.com/FEniCS/ffcx.git@v0.5.0
 
       - name: Get DOLFINx
         uses: actions/checkout@v2
         with:
           path: ./dolfinx
           repository: FEniCS/dolfinx
-          ref: main
+          ref: v0.5.0
 
       - name: Configure C++ (dolfinx)
         run: |

.github/workflows/test_mpc.yml

@@ -15,7 +15,7 @@ jobs:
   build:
     if: "!(contains(github.event.head_commit.message, '[ci skip]') || contains(github.event.head_commit.message, '[skip ci]'))"
     runs-on: ubuntu-20.04
-    container: dolfinx/dev-env
+    container: dolfinx/dev-env:v0.5.0
 
     strategy:
       matrix:
@@ -32,11 +32,11 @@ jobs:
       OMPI_MCA_mpi_yield_when_idle: 1
       OMPI_MCA_hwloc_base_binding_policy: none
       HDF5_MPI: "ON"
-      HDF5_DIR: "/usr/lib/x86_64-linux-gnu/hdf5/mpich/"
+      HDF5_DIR: "/usr/local/"
       MPC_BUILD_MODE: "Debug"
       MPC_CMAKE_CXX_FLAGS: "-Wall -Werror -g -pedantic -Ofast -march=native"
-      PYTHONPATH: "/usr/local/dolfinx-${PETSC_TYPE}/lib/python3.8/dist-packages:/usr/local/lib"
-      LD_LIBRARY_PATH: "/usr/local/petsc/${PETSC_ARCH}/lib/:/usr/lib/x86_64-linux-gnu/hdf5/mpich/"
+      PYTHONPATH: "/usr/local/dolfinx-${PETSC_TYPE}/lib/python3.10/dist-packages:/usr/local/lib"
+      LD_LIBRARY_PATH: "/usr/local/petsc/${PETSC_ARCH}/lib/:/usr/local"
 
     steps:
       - uses: actions/checkout@v2
@@ -59,23 +59,23 @@ jobs:
         with:
           path: ./basix
           repository: FEniCS/basix
-          ref: main
+          ref: v0.5.0
 
       - name: Install UFL, Basix, FFCx
         run: |
           cmake -G Ninja -B build-basix -DCMAKE_BUILD_TYPE="Release" -S ./basix/cpp/
           cmake --build build-basix --parallel 3
           cmake --install build-basix
           BUILD_TYPE="Release" pip3 install ./basix/python
-          python3 -m pip install git+https://github.com/FEniCS/ufl.git
-          python3 -m pip install git+https://github.com/FEniCS/ffcx.git
+          python3 -m pip install git+https://github.com/FEniCS/ufl.git@2022.2.0
+          python3 -m pip install git+https://github.com/FEniCS/ffcx.git@v0.5.0
 
       - name: Get DOLFINx
         uses: actions/checkout@v2
         with:
           path: ./dolfinx
           repository: FEniCS/dolfinx
-          ref: main
+          ref: v0.5.0
 
       - name: Configure C++ (dolfinx)
         run: |

.gitlab-ci.yml

@@ -1,42 +1,3 @@
-# quick-tests:
-#   stage: test
-#   tags:
-#     - docker
-#   except:
-#     - master
-#     - schedules
-#   image:
-#     name: dolfinx/dolfinx
-#     entrypoint: [""]
-#   parallel:
-#     matrix:
-#       - PETSC_TYPE: ["real", "complex"]
-
-#   variables:
-#     PETSC_ARCH: "linux-gnu-${PETSC_TYPE}-32"
-#     DOLFINX_DIR: "dolfinx-${PETSC_TYPE}"
-#     PYTHONPATH: "/usr/local/dolfinx-${PETSC_TYPE}/lib/python3.10/dist-packages:/usr/local/lib/"
-#     LD_LIBRARY_PATH: "/usr/local/petsc/${PETSC_ARCH}/lib/:/usr/local/lib/"
-#     MPC_CMAKE_CXX_FLAGS: "-Wall -Werror -g -pedantic -Ofast -march=native"
-#     MPC_CMAKE_BUILD_TYPE: "Release"
-
-#   before_script:
-#     - flake8 .
-#     - pip3 install mypy
-#     - cd python
-#     - python3 -m mypy . --exclude=build
-#     - cd ..
-#     - cmake -G Ninja -DCMAKE_BUILD_TYPE=${MPC_CMAKE_BUILD_TYPE} -DCMAKE_CXX_FLAGS="${MPC_CMAKE_CXX_FLAGS}"  -B build-dir -S ./cpp
-#     - cmake --build build-dir --parallel 3
-#     - cmake --install build-dir
-#     - BUILD_TYPE=$MPC_CMAKE_BUILD_TYPE CXX_FLAGS="${MPC_CMAKE_CXX_FLAGS}" pip3 install ./python
-
-#   script:
-#     - python3 -m pytest python/tests -v
-#     - mpirun -n 2 python3 -m pytest python/tests
-#     - mpirun -n 3 python3 -m pytest python/tests
-#     - mpirun -n 4 python3 -m pytest python/tests
-
 run-demos:
   stage: test
   only:
@@ -46,25 +7,25 @@ run-demos:
   tags:
     - docker
   image:
-    name: dolfinx/dev-env
+    name: dolfinx/dev-env:v0.5.0
     entrypoint: [""]
   parallel:
     matrix:
       - PETSC_TYPE: ["real", "complex"]
   variables:
     PETSC_ARCH: "linux-gnu-${PETSC_TYPE}-32"
     DOLFINX_DIR: "dolfinx-${PETSC_TYPE}"
-    BASIX_BRANCH: "main"
-    FFCX_BRANCH: "main"
-    UFL_BRANCH: "main"
-    DOLFINX_BRANCH: "main"
+    BASIX_BRANCH: "v0.5.0"
+    FFCX_BRANCH: "v0.5.0"
+    UFL_BRANCH: "2022.2.0"
+    DOLFINX_BRANCH: "v0.5.0"
     PYTHONPATH: "/usr/local/dolfinx-${PETSC_TYPE}/lib/python3.10/dist-packages:/usr/local/lib/"
     LD_LIBRARY_PATH: "/usr/local/petsc/${PETSC_ARCH}/lib/:/usr/local/lib/"
     MPC_CMAKE_CXX_FLAGS: "-Wall -Werror -g -pedantic -Ofast -march=native"
     MPC_BUILD_MODE: "Debug"
     CC: "mpicc"
     HDF5_MPI: "ON"
-    HDF5_DIR: "/usr/lib/x86_64-linux-gnu/hdf5/mpich/"
+    HDF5_DIR: "/usr/local"
 
   before_script:
     - flake8 python/
@@ -73,24 +34,18 @@ run-demos:
     - python3 -m mypy . --exclude=build
     - cd ..
     - pip3 install --no-cache-dir --no-binary=h5py h5py
-    - git clone https://github.com/FEniCS/basix.git
-    - cd basix
-    - git checkout ${BASIX_BRANCH}
-    - cd ..
+    - git clone -b ${BASIX_BRANCH} --single-branch --depth 1 https://github.com/FEniCS/basix.git
     - cmake -G Ninja -B build-basix -DCMAKE_BUILD_TYPE="Release" -S ./basix/cpp/
     - cmake --build build-basix --parallel 3
     - cmake --install build-basix
     - BUILD_TYPE="Release" pip3 install ./basix/python
     - python3 -m pip install git+https://github.com/FEniCS/ufl.git@${UFL_BRANCH}
     - python3 -m pip install git+https://github.com/FEniCS/ffcx.git@${FFCX_BRANCH}
-    - git clone https://github.com/fenics/dolfinx.git
-    - cd dolfinx
-    - git checkout ${DOLFINX_BRANCH}
-    - cmake -G Ninja -DCMAKE_BUILD_TYPE="Release" -B build-dolfinx -S ./cpp/
+    - git clone -b ${DOLFINX_BRANCH} --single-branch --depth 1 https://github.com/FEniCS/dolfinx.git && \
+    - cmake -G Ninja -DCMAKE_BUILD_TYPE="Release" -B build-dolfinx -S ./dolfinx/cpp/
     - cmake --build build-dolfinx
     - cmake --install build-dolfinx
-    - BUILD_TYPE="Release" python3 -m pip -v install ./python/
-    - cd ..
+    - BUILD_TYPE="Release" python3 -m pip -v install ./dolfinx/python/
     - cmake -G Ninja -B build-dir -DCMAKE_BUILD_TYPE=${MPC_BUILD_MODE} -DCMAKE_CXX_FLAGS="${MPC_CMAKE_CXX_FLAGS}" -S cpp/
     - cmake --build build-dir --parallel 3
     - cmake --install build-dir

Changelog.md

@@ -1,6 +1,9 @@
 # Changelog
 
 ## main
+- No changes
+
+## v0.5.0 (12.08.2022)
  - Minimal C++ standard is now [C++20](https://en.cppreference.com/w/cpp/20)
  - Deprecating GMSH IO functions from `dolfinx_mpc.utils`, see: [DOLFINx PR: 2261](https://github.com/FEniCS/dolfinx/pull/2261) for details.
  - Various API changes in DOLFINx relating to `dolfinx.common.IndexMap`.

Dockerfile

@@ -1,14 +1,13 @@
-FROM dolfinx/dolfinx:v0.4.1 as dolfinx-mpc
+FROM dolfinx/dolfinx:v0.5.0 as dolfinx-mpc
 WORKDIR /tmp
 # Set env variables
 ENV HDF5_MPI="ON" \
     CC=mpicc \
-    HDF5_DIR="/usr/lib/x86_64-linux-gnu/hdf5/mpich/"
+    HDF5_DIR="/usr/local"
 
 # Install dolfinx_mpc
-RUN  git clone https://github.com/jorgensd/dolfinx_mpc.git  && \
+RUN git clone -b v0.5.0 --single-branch --depth 1 https://github.com/jorgensd/dolfinx_mpc.git && \
     cd dolfinx_mpc && \
-    git checkout a6fa82ac0160ac1a5d91682c4c05dd63a5489f2c && \
     cmake -G Ninja -DCMAKE_BUILD_TYPE=Developer -B build-dir cpp/ && \
     ninja install -j4  -C build-dir && \
     pip3 install python/. --upgrade

README.md

@@ -31,10 +31,10 @@ These assemblers are written in C++, but have equivalent Python assemblers in th
 
 # Installation
 
-Version 0.4.1 is available as an docker image at [DockerHub](https://hub.docker.com/r/dokken92/dolfinx_mpc)
+Version 0.5.0 is available as an docker image at [DockerHub](https://hub.docker.com/r/dokken92/dolfinx_mpc)
 and can be ran using
 ```bash
-docker run -ti -v $(pwd):/root/shared -w /root/shared dokken92/dolfinx_mpc:v0.4.1
+docker run -ti -v $(pwd):/root/shared -w /root/shared dokken92/dolfinx_mpc:v0.5.0
 ```
 
 To install the latest version (master branch), you need to install the latest release of [dolfinx](https://github.com/FEniCS/dolfinx).

cpp/CMakeLists.txt

@@ -4,7 +4,7 @@ cmake_minimum_required(VERSION 3.10)
 
 #------------------------------------------------------------------------------
 # Set project name and version number
-project(DOLFINX_MPC VERSION "0.4.1.0")
+project(DOLFINX_MPC VERSION "0.5.0.0")
 
 #------------------------------------------------------------------------------
 # Set CMake options, see `cmake --help-policy CMP000x`
@@ -90,13 +90,13 @@ set_package_properties(UFC PROPERTIES TYPE REQUIRED
   URL "https://github.com/fenics/ffcx")
 
 # Check for required package DOLFINX
-find_package(DOLFINX 0.4.2 REQUIRED)
+find_package(DOLFINX 0.5.0 REQUIRED)
 set_package_properties(DOLFINX PROPERTIES TYPE REQUIRED
     DESCRIPTION "New generation Dynamic Object-oriented Library for - FINite element computation"
     URL "https://github.com/FEniCS/dolfinx"
     PURPOSE "Main dependency of library")
 
-find_package(Basix 0.4.2 REQUIRED)
+find_package(Basix 0.5.0 REQUIRED)
 set_package_properties(basix PROPERTIES TYPE REQUIRED
       DESCRIPTION "FEniCS tabulation library"
       URL "https://github.com/fenics/basix")

cpp/utils.cpp

@@ -692,7 +692,7 @@ xt::xtensor<double, 3> dolfinx_mpc::evaluate_basis_functions(
   }
 
   // Return early if we have no points
-  std::array<std::size_t, 4> basis_shape
+  [[maybe_unused]] std::array<std::size_t, 4> basis_shape
       = element->basix_element().tabulate_shape(0, x.shape(0));
   assert(basis_shape[2] == space_dimension);
   assert(basis_shape[3] == value_size);

python/benchmarks/bench_contact_3D.py

@@ -120,7 +120,7 @@ def over_plane(p0, p1, p2):
     top_cube = over_plane(if_points[:, 0], if_points[:, 1], if_points[:, 2])
     for facet in i_facets:
         i_cells = facet_to_cell.links(facet)
-        assert(len(i_cells == 1))
+        assert len(i_cells == 1)
         i_cell = i_cells[0]
         if top_cube(cell_midpoints[i_cell]):
             top_interface.append(facet)

python/benchmarks/post_proc.py

@@ -48,7 +48,7 @@ def visualize_side_by_side(dofs):
     ax.set_xticks(range(len(dofs)))
     labels = dofs
     ax.set_xticklabels(labels)
-    assert(np.allclose(procs, procs[0]))
+    assert np.allclose(procs, procs[0])
 
     # Shrink current axis by 20%
     box = ax.get_position()

python/demos/create_and_export_mesh.py

@@ -420,7 +420,7 @@ def over_line(p0, p1):
         facet_to_cell = mesh.topology.connectivity(fdim, tdim)
         for facet in i_facets:
             i_cells = facet_to_cell.links(facet)
-            assert(len(i_cells == 1))
+            assert len(i_cells == 1)
             i_cell = i_cells[0]
             if top_cube(cell_midpoints[i_cell]):
                 top_interface.append(facet)
@@ -541,7 +541,7 @@ def over_plane(p0, p1, p2):
         top_cube = over_plane(if_points[:, 0], if_points[:, 1], if_points[:, 2])
         for facet in i_facets:
             i_cells = facet_to_cell.links(facet)
-            assert(len(i_cells == 1))
+            assert len(i_cells) == 1
             i_cell = i_cells[0]
             if top_cube(cell_midpoints[i_cell]):
                 top_interface.append(facet)

python/demos/demo_elasticity_disconnect.py

@@ -29,7 +29,7 @@
 r2, r2_tag = 0.8, 3
 outer_tag = 1
 inner_tag = 2
-assert(r0 < r1 and r1 < r2)
+assert r0 < r1 and r1 < r2
 
 
 gmsh.initialize()

python/demos/demo_periodic3d_topological.py

@@ -122,7 +122,7 @@ def periodic_relation(x):
     old_local = u_out.x.map.size_local * u_out.x.bs
     old_ghosts = u_out.x.map.num_ghosts * u_out.x.bs
     mpc_local = u_h.x.map.size_local * u_h.x.bs
-    assert(old_local == mpc_local)
+    assert old_local == mpc_local
     u_out.x.array[:old_local + old_ghosts] = u_h.x.array[:mpc_local + old_ghosts]
     u_out.name = "u_" + ext
     fname = f"results/demo_periodic3d_{ext}.bp"

python/dolfinx_mpc/assemble_matrix.py

@@ -43,7 +43,7 @@ def assemble_matrix(form: _fem.FormMetaClass,
         The assembled bi-linear form
     """
     if not isinstance(constraint, Sequence):
-        assert(form.function_spaces[0] == form.function_spaces[1])
+        assert form.function_spaces[0] == form.function_spaces[1]
         constraint = (constraint, constraint)
 
     # Generate matrix with MPC sparsity pattern

python/dolfinx_mpc/multipointconstraint.py

@@ -59,7 +59,7 @@ def add_constraint(self, V: _fem.FunctionSpace, slaves: npt.NDArray[numpy.int32]
                 masters_of_owned_slave[i] = masters[offsets[i]:offsets[i+1]]
 
         """
-        assert(V == self.V)
+        assert V == self.V
         self._already_finalized()
 
         if len(slaves) > 0:

python/dolfinx_mpc/numba/assemble_matrix.py

@@ -182,7 +182,7 @@ def add_diagonal(A: int, dofs: npt.NDArray[numpy.int32], diagval: _PETSc.ScalarT
     for dof in dofs:
         dof_list[0] = dof
         ierr_loc = set_values_local(A, 1, ffi_fb(dof_list), 1, ffi_fb(dof_list), ffi_fb(dof_value), mode)
-        assert(ierr_loc == 0)
+        assert ierr_loc == 0
     sink(dof_list, dof_value)
 
 
@@ -266,7 +266,7 @@ def assemble_slave_cells(A: int,
         # Insert local contribution
         ierr_loc = set_values_local(A, block_size * num_dofs_per_element, ffi_fb(local_dofs),
                                     block_size * num_dofs_per_element, ffi_fb(local_dofs), ffi_fb(A_contribution), mode)
-        assert(ierr_loc == 0)
+        assert ierr_loc == 0
 
     sink(A_contribution, local_dofs)
 
@@ -342,14 +342,14 @@ def modify_mpc_cell(A: int, num_dofs: int, block_size: int,
                 mpc_dofs[j * block_size + k] = local_blocks[j] * block_size + k
         mpc_dofs[local_index] = master
         ierr_row = set_values_local(A, block_size * num_dofs, ffi_fb(mpc_dofs), 1, ffi_fb(m0), ffi_fb(Arow), mode)
-        assert(ierr_row == 0)
+        assert ierr_row == 0
 
         # Add slave row to master row
         ierr_col = set_values_local(A, 1, ffi_fb(m0), block_size * num_dofs, ffi_fb(mpc_dofs), ffi_fb(Acol), mode)
-        assert(ierr_col == 0)
+        assert ierr_col == 0
 
         ierr_master = set_values_local(A, 1, ffi_fb(m0), 1, ffi_fb(m0), ffi_fb(Am0m1), mode)
-        assert(ierr_master == 0)
+        assert ierr_master == 0
 
         # Add contributions for other masters relating to slaves on the given cell
         for j in range(num_flattened_masters):
@@ -361,7 +361,7 @@ def modify_mpc_cell(A: int, num_dofs: int, block_size: int,
             m1[0] = other_master
             Am0m1[0, 0] = coeff * other_coeff * Ae_original[local_index, other_local_index]
             ierr_other_masters = set_values_local(A, 1, ffi_fb(m0), 1, ffi_fb(m1), ffi_fb(Am0m1), mode)
-            assert(ierr_other_masters == 0)
+            assert ierr_other_masters == 0
 
     sink(Arow, Acol, Am0m1, m0, m1, mpc_dofs)
 
@@ -450,6 +450,6 @@ def assemble_exterior_slave_facets(A: int, kernel: cffi.FFI,
         ierr_loc = set_values_local(A, block_size * num_dofs_per_element, ffi.from_buffer(local_dofs),
                                     block_size * num_dofs_per_element, ffi.from_buffer(local_dofs),
                                     ffi.from_buffer(A_contribution), mode)
-        assert(ierr_loc == 0)
+        assert ierr_loc == 0
 
     sink(A_contribution, local_dofs)