Improvements for v0.7.0 release (#77)

* Fixes for vector elements * Single real precsision tested with all tests and demos. Supported almost everywhere * Add stokes demo to docs. * Rewrite usage of comms * Fix BP4 engine choice for VTX * Try fixing coverage issues of relative imports
jorgensd · Oct 28, 2023 · 33ff717 · 33ff717
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diff --git a/.github/actions/install-dolfinx/action.yaml b/.github/actions/install-dolfinx/action.yaml
@@ -25,22 +25,22 @@ inputs:
   petsc_arch:  # id of input
     description: 'PETSc Arch'
     required: false
-    default: 'linux-gnu-real-32'
+    default: 'linux-gnu-real64-32'
 
 runs:
   using: composite
 
 
   steps:
     - name: Get Basix
-      uses: actions/checkout@v3
+      uses: actions/checkout@v4
       with:
         path: ./basix
         repository: FEniCS/basix
         ref: ${{ inputs.basix }}
 
     - name: Get DOLFINx
-      uses: actions/checkout@v3
+      uses: actions/checkout@v4
       with:
         path: ./dolfinx
         repository: FEniCS/dolfinx

diff --git a/.github/workflows/build_docs.yml b/.github/workflows/build_docs.yml
@@ -10,11 +10,11 @@ on:
 jobs:
   build:
     runs-on: ubuntu-22.04
-    container: ghcr.io/fenics/dolfinx/dev-env:nightly
+    container: ghcr.io/fenics/dolfinx/dev-env:v0.7.0-mpich
     env:
       # Directory that will be published on github pages
-      PUBLISH_DIR: ./docs/_build/html
-      PETSC_ARCH: "linux-gnu-real-32"
+      PUBLISH_DIR: ./_build/html
+      PETSC_ARCH: "linux-gnu-real64-32"
 
     steps:
     - uses: actions/checkout@v4
@@ -32,7 +32,7 @@ jobs:
       run: python3 -m pip -v install python/[docs]
 
     - name: Build docs
-      run: jupyter book build docs
+      run: jupyter book build .
 
     - name: Upload documentation as artifact
       uses: actions/upload-artifact@v3

diff --git a/.github/workflows/deploy-pages.yml b/.github/workflows/deploy-pages.yml
@@ -46,16 +46,16 @@ jobs:
           path: "./public/code-coverage-report"
 
       - name: Upload artifact
-        uses: actions/upload-pages-artifact@v1
+        uses: actions/upload-pages-artifact@v2
         with:
           path: "./public"
 
       - name: Checkout
         uses: actions/checkout@v4
 
       - name: Setup Pages
-        uses: actions/configure-pages@v2
+        uses: actions/configure-pages@v3
 
       - name: Deploy to GitHub Pages
         id: deployment
-        uses: actions/deploy-pages@v1
+        uses: actions/deploy-pages@v2
diff --git a/.github/workflows/docker.yml b/.github/workflows/docker.yml
@@ -23,26 +23,26 @@ jobs:
         uses: actions/checkout@v4
 
       - name: Set up QEMU
-        uses: docker/setup-qemu-action@v2
+        uses: docker/setup-qemu-action@v3
 
       - name: Set up Docker Buildx
-        uses: docker/setup-buildx-action@v2
+        uses: docker/setup-buildx-action@v3
 
       - name: Log in to the Container registry
-        uses: docker/login-action@v2
+        uses: docker/login-action@v3
         with:
           registry: ${{ env.REGISTRY }}
           username: ${{ github.actor }}
           password: ${{ secrets.GITHUB_TOKEN }}
 
       - name: Extract metadata (tags, labels) for Docker
         id: meta
-        uses: docker/metadata-action@v4
+        uses: docker/metadata-action@v5
         with:
           images: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}
 
       - name: Build and push Docker image
-        uses: docker/build-push-action@v3
+        uses: docker/build-push-action@v5
         with:
           context: .
           push: true

diff --git a/.github/workflows/sonarcloud.yml b/.github/workflows/sonarcloud.yml
@@ -7,7 +7,6 @@ on:
     branches:
       - main
 
-
 jobs:
   build:
     name: Build
@@ -16,15 +15,15 @@ jobs:
     # avoid running on pull requests from forks
     # which don't have access to secrets
     if: (github.event_name != 'pull_request' || github.event.pull_request.head.repo.full_name == github.repository)
-    container: ghcr.io/fenics/test-env:nightly-mpich
+    container: ghcr.io/fenics/dolfinx/dev-env:v0.7.0
 
     env:
-      SONAR_SCANNER_VERSION:
-        4.8.0.2856 # Find the latest version in at:
-        # https://github.com/SonarSource/sonar-scanner-cli/tags
+      SONAR_SCANNER_VERSION: 5.0.1.3006 # 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
-      PETSC_ARCH: linux-gnu-real-32
+      PETSC_ARCH: linux-gnu-real64-32
+
+      PETSC_DIR: /usr/local/petsc
     steps:
       - uses: actions/checkout@v4
         with:
@@ -35,12 +34,12 @@ jobs:
           apt-get -y update
           apt-get install unzip
 
-      - name: Set up JDK 11
+      - name: Set up JDK 17
         uses: actions/setup-java@v3
         with:
-          distribution: 'zulu'
-          java-version: 11
-
+          distribution: "zulu"
+          java-version: 17
+  
       - name: Cache SonarCloud packages
         uses: actions/cache@v3
         with:
@@ -67,7 +66,9 @@ jobs:
 
       - name: Install DOLFINx
         uses: ./.github/actions/install-dolfinx
-
+        with:
+          petsc_arch: ${PETSC_ARCH}
+
       - name: Run build-wrapper
         run: |
           cmake -S ./cpp -B build-mpc
@@ -87,4 +88,4 @@ jobs:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
           SONAR_TOKEN: ${{ secrets.SONAR_TOKEN }}
         run: |
-          sonar-scanner --define sonar.host.url="${{ env.SONAR_SERVER_URL }}" --define sonar.cfamily.build-wrapper-output="${{ env.BUILD_WRAPPER_OUT_DIR }}"
+          sonar-scanner --define sonar.host.url="${{ env.SONAR_SERVER_URL }}" --define sonar.cfamily.build-wrapper-output="${{ env.BUILD_WRAPPER_OUT_DIR }}"
diff --git a/.github/workflows/test_mpc.yml b/.github/workflows/test_mpc.yml
@@ -14,12 +14,18 @@ on:
 jobs:
   build:
     runs-on: ubuntu-latest
-    container: ghcr.io/fenics/test-env:nightly-mpich
+    container: ghcr.io/fenics/dolfinx/dev-env:v0.7.0
 
     strategy:
       matrix:
         build_mode: [Release, Debug]
-        petsc_arch: [real, complex]
+        petsc_arch:
+          [
+            linux-gnu-complex128-32,
+            linux-gnu-complex64-32,
+            linux-gnu-real64-32,
+            linux-gnu-real32-32,
+          ]
         # Due to: https://gitlab.com/petsc/petsc/-/issues/1288
         CXX: [c++]
         #, clang++]
@@ -31,13 +37,13 @@ jobs:
         #   - CC: clang
         #     CXX: c++
     env:
-      DOLFINX_BRANCH: "main"
-      BASIX_BRANCH: "main"
-      UFL_BRANCH: "main"
-      FFCX_BRANCH: "main"
+      DOLFINX_BRANCH: "v0.7.1"
+      BASIX_BRANCH: "v0.7.0"
+      UFL_BRANCH: "2023.2.0"
+      FFCX_BRANCH: "v0.7.0"
       CC: ${{ matrix.CC }}
       CXX: ${{ matrix.CXX }}
-      PETSC_ARCH: "linux-gnu-${{ matrix.petsc_arch }}-32"
+      PETSC_ARCH: "${{ matrix.petsc_arch }}"
       OMPI_ALLOW_RUN_AS_ROOT: 1
       OMPI_ALLOW_RUN_AS_ROOT_CONFIRM: 1
       OMPI_MCA_rmaps_base_oversubscribe: 1
@@ -73,10 +79,9 @@ jobs:
           cd python
           python3 -m mypy . --exclude=build
 
-      - name: Install h5py (https://github.com/h5py/h5py/issues/2222)
+      - name: Install h5py
         run: |
-          python3 -m pip install mpi4py cython numpy
-          python3 -m pip install --no-cache-dir --no-binary=h5py h5py  --no-build-isolation
+          python3 -m pip install --no-cache-dir --no-binary=h5py h5py
 
       - name: Install DOLFINx
         uses: ./.github/actions/install-dolfinx
@@ -94,10 +99,11 @@ jobs:
           cmake --install build-dir
 
       - name: Install DOLFINx-MPC (Python)
-        run: CXX_FLAGS="${MPC_CMAKE_CXX_FLAGS}" python3 -m pip -v install python/[test]
+        run: CXX_FLAGS="${MPC_CMAKE_CXX_FLAGS}" python3 -m pip -v install -e python/[test]
+
 
       - name: Run tests (serial)
-        run: coverage run --rcfile=.coveragerc -m mpi4py -m pytest python/tests/
+        run: coverage run --rcfile=.coveragerc -m mpi4py -m pytest python/tests/ -vs
 
       - name: Run tests (2 processes)
         run: mpirun -n 2 coverage run --rcfile=.coveragerc -m mpi4py -m pytest python/tests/ -vs

diff --git a/Changelog.md b/Changelog.md
@@ -1,37 +1,45 @@
 # Changelog
 
-## main
+## v0.7.0
+
 - **API**:
   - Change input of `dolfinx_mpc.MultiPointConstraint.homogenize` and `dolfinx_mpc.backsubstitution` to `dolfinx.fem.Function` instead of `PETSc.Vec`.
-  - Add support for more floating types (`dtype` can now be specified as input for coefficients). In theory this means one could support single precision. Not thoroughly tested.
+  - **New feature**: Add support for more floating types (float32, float64, complex64, complex128). The floating type of a MPC is related to the mesh geometry.
     - This resulted in a minor refactoring of the pybindings, meaning that tte class `dolfinx_mpc.cpp.mpc.MultiPointConstraint` is replaced by `dolfinx_mpc.cpp.mpc.MultiPointConstraint_{dtype}`
+  - Casting scalar-type with `dolfinx.default_scalar_type` instead of `PETSc.ScalarType`
+  - Remove usage of `VectorFunctionSpace`. Use blocked basix element instead.
 - **DOLFINX API-changes**:
   - Use `dolfinx.fem.functionspace(mesh, ("Lagrange", 1, (mesh.geometry.dim, )))` instead of `dolfinx.fem.VectorFunctionSpace(mesh, ("Lagrange", 1))` as the latter is being deprecated.
   - Use `basix.ufl.element` in favor of `ufl.FiniteElement` as the latter is deprecated in DOLFINx.
 
 ## v0.6.1 (30.01.2023)
-  - Fixes for CI
-  - Add auto-publishing CI
-  - Fixes for `h5py` installation
+
+- Fixes for CI
+- Add auto-publishing CI
+- Fixes for `h5py` installation
 
 ## v0.6.0 (27.01.2023)
-  - Remove `dolfinx::common::impl::copy_N` in favor of `std::copy_n` by @jorgensd in #24
-  - Improving and fixing `demo_periodic_gep.py` by @fmonteghetti in #22 and @conpierce8 in #30
-  - Remove xtensor by @jorgensd in #25
-  - Complex valued periodic constraint (scale) by @jorgensd in #34
-  - Implement Hermitian pre-multiplication by @conpierce8 in #38
-  - Fixes for packaging by @mirk in #41, #42, #4
-  - Various updates to dependencies 
+
+- Remove `dolfinx::common::impl::copy_N` in favor of `std::copy_n` by @jorgensd in #24
+- Improving and fixing `demo_periodic_gep.py` by @fmonteghetti in #22 and @conpierce8 in #30
+- Remove xtensor by @jorgensd in #25
+- Complex valued periodic constraint (scale) by @jorgensd in #34
+- Implement Hermitian pre-multiplication by @conpierce8 in #38
+- Fixes for packaging by @mirk in #41, #42, #4
+- Various updates to dependencies
 
 ## 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`.
- - Made code [mypy](https://mypy.readthedocs.io/en/stable/)-compatible (tests added to CI). 
- - Made code [PEP-561](https://peps.python.org/pep-0561/) compatible.
+
+- 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`.
+- Made code [mypy](https://mypy.readthedocs.io/en/stable/)-compatible (tests added to CI).
+- Made code [PEP-561](https://peps.python.org/pep-0561/) compatible.
 
 ## v0.4.0 (30.04.2022)
+
 - **API**:
+
   - **New feature**: Support for nonlinear problems (by @nate-sime) for mpc, see `test_nonlinear_assembly.py` for usage
   - Updated user interface for `dolfinx_mpc.create_slip_constraint`. See documentation for details.
   - **New feature**: Support for periodic constraints on sub-spaces. See `dolfinx_mpc.create_periodic_constraint` for details.
@@ -50,11 +58,13 @@
     - `slave_cells` does now longer exist as it can be gotten implicitly from `cell_to_slaves`.
 
 - **Performance**:
+
   - Major rewrite of periodic boundary conditions. On average at least a 5 x performance speed-up.
   - The C++ assembler has been fully rewritten.
   - Various improvements to `ContactConstraint`.
 
 - **Bugs**
+
   - Resolved issue where `create_facet_normal_approximation` would give you a 0 normal for a surface dof it was not owned by any of the cells with facets on the surface.
 
 - **DOLFINX API-changes**:
@@ -67,19 +77,22 @@
   - Various internal changes to handle new way of JIT-compliation of `dolfinx::fem::Form_{scalar_type}`
 
 ## 0.3.0 (25.08.2021)
+
 - Minor internal changes
 
 ## 0.2.0 (06.08.2021)
+
 - Add new MPC constraint: Periodic boundary condition constrained geometrically. See `demo_periodic_geometrical.py` for use-case.
-- New: `demo_periodic_gep.py` proposed and initally implemented by [fmonteghetti](https://github.com/fmonteghetti) using SLEPc for eigen-value problems. 
-  This demo illustrates the usage of the new `diagval` keyword argument in the `assemble_matrix` class. 
+- New: `demo_periodic_gep.py` proposed and initally implemented by [fmonteghetti](https://github.com/fmonteghetti) using SLEPc for eigen-value problems.
+  This demo illustrates the usage of the new `diagval` keyword argument in the `assemble_matrix` class.
 
 - **API**:
+
   - Renaming and clean-up of `assemble_matrix` in C++
   - Renaming of Periodic constraint due to additional geometrical constraint, `mpc.create_periodic_constraint` -> `mpc.create_periodic_constraint_geometrical/topological`.
   - Introduce new class `dolfinx_mpc.LinearProblem` mimicking the DOLFINx class (Usage illustrated in `demo_periodic_geometrical.py`)
   - Additional `kwarg` `b: PETSc.Vec` for `assemble_vector` to be able to re-use Vector.
-  - Additional `kwargs`: `form_compiler_parameters` and `jit_parameters` to `assemble_matrix`, `assemble_vector`, to allow usage of fast math etc.  
+  - Additional `kwargs`: `form_compiler_parameters` and `jit_parameters` to `assemble_matrix`, `assemble_vector`, to allow usage of fast math etc.
 
 - **Performance**:
   - Slip condition constructor moved to C++ (Speedup for large problems)
@@ -90,6 +103,6 @@
   - `dolfinx.cpp.la.scatter_forward(x)` is replaced by `x.scatter_forward()`
   - Various interal updates to match DOLFINx API (including dof transformations moved outside of ffcx kernel)
 
-
 ## 0.1.0 (11.05.2021)
+
 - First tagged release of dolfinx_mpc, compatible with [DOLFINx 0.1.0](https://github.com/FEniCS/dolfinx/releases/tag/0.1.0).
diff --git a/docs/_config.yml → _config.yml b/docs/_config.yml → _config.yml
@@ -5,11 +5,10 @@ title: "DOLFINx-MPC: An extension to DOLFINx for multi point constraints"
 author: Jørgen S. Dokken
 copyright: "2022"
 
-# Force re-execution of notebooks on each build.
-# See https://jupyterbook.org/content/execute.html
 execute:
-  execute_notebooks: force
+  execute_notebooks: cache
 
+only_build_toc_files: true
 
 # Information about where the book exists on the web
 repository:
@@ -24,6 +23,7 @@ launch_buttons:
 html:
   use_issues_button: true
   use_repository_button: true
+
 
 parse:
   myst_enable_extensions:
@@ -37,5 +37,10 @@ sphinx:
   - 'sphinx.ext.napoleon'
   - 'sphinx.ext.viewcode'
 
+  config:
 
+     nb_custom_formats:
+        .py:
+            - jupytext.reads
+            - fmt: py
 
diff --git a/_toc.yml b/_toc.yml
@@ -0,0 +1,12 @@
+format: jb-book
+root: index
+
+parts:
+  - caption: "Demos"
+    chapters:
+    - file: "python/demos/demo_stokes.py"
+  - caption: "Python API"
+    chapters:
+    - file: "docs/api"
+    - file: "docs/utils"
+    - file: "docs/numba"