Merge branch 'jhale/try-cffi-backport' of github.com:FEniCS/dolfinx i…

…nto jhale/try-cffi-backport
FEniCS · Oct 18, 2024 · 4f0f202 · 4f0f202
2 parents 8a55d2b + 4dbf26b
commit 4f0f202
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diff --git a/.github/dependabot.yml b/.github/dependabot.yml
@@ -9,3 +9,7 @@ updates:
     directory: "/" # Location of package manifests
     schedule:
       interval: "weekly"
+  - package-ecosystem: "pip" # See documentation for possible values
+    directory: "python/"
+    schedule:
+      interval: "weekly"
diff --git a/.github/workflows/conda.yml b/.github/workflows/conda.yml
@@ -2,8 +2,8 @@ name: Conda install
 
 on:
   # Uncomment the below 'push' to trigger on push
-  # push:
-  #   branches:
+  #push:
+  #  branches:
   #     - "**"
   schedule:
     # '*' is a special character in YAML, so string must be quoted
@@ -15,52 +15,52 @@ jobs:
     name: Install and test
     strategy:
       matrix:
-        os: [ubuntu-latest, macos-13, macos-14]
+        os: [ubuntu-latest, macos-13, macos-14, windows-2022]
+        python-version: ["3.9", "3.10", "3.11", "3.12"]
+        petsc-scalar-type: ["real"]
+        include:
+          - os: ubuntu-latest
+            python-version: "3.12"
+            petsc-scalar-type: "complex"
     runs-on: ${{ matrix.os }}
     timeout-minutes: 30
+    # This is necessary to ensure conda environment is activated in every step.
+    defaults:
+      run:
+        shell: bash -el {0}
 
     steps:
-      - name: Install conda (macOS)
-        if: runner.os == 'macOS'
+      - uses: conda-incubator/setup-miniconda@v3
+        with:
+          auto-update-conda: true
+          python-version: ${{ matrix.python-version }}
+
+      # TODO: These could probably be merged into one cross-platform step.
+      - name: Install DOLFINx with MPICH (Unix-like)
+        if: ${{ runner.os == 'macOS' || runner.os == 'Linux' }}
         run: |
-          brew install anaconda
-          echo "/opt/homebrew/anaconda3/bin:/usr/local/anaconda3/bin" >> $GITHUB_PATH
-      - name: Update conda
+          conda install -c conda-forge fenics-dolfinx mpich petsc=*=${{ matrix.petsc-scalar-type }}*
+      - name: Install DOLFINx (Windows)
+        if: ${{ runner.os == 'Windows' }}
         run: |
-          conda update conda
-
-      - name: Install DOLFINx (py3-10)
-        run: |
-          conda create -n env3-10 -c conda-forge python=3.10 fenics-dolfinx mpich
-          conda env export -n env3-10
-      - name: Test (py3-10)
-        run: |
-          conda run -n env3-10 python -c "from mpi4py import MPI; import dolfinx; dolfinx.mesh.create_rectangle(comm=MPI.COMM_WORLD, points=((0, 0), (2, 1)), n=(32, 16))"
-          conda run -n env3-10 mpirun -np 2 python -c "from mpi4py import MPI; import dolfinx; dolfinx.mesh.create_rectangle(comm=MPI.COMM_WORLD, points=((0, 0), (2, 1)), n=(32, 16))"
-
-      - name: Install DOLFINx (py3-11)
-        run: |
-          conda create -n env3-11 -c conda-forge python=3.11 fenics-dolfinx mpich
-          conda env export -n env3-11
-      - name: Test (py3-11)
-        run: |
-          conda run -n env3-11 python -c "from mpi4py import MPI; import dolfinx; dolfinx.mesh.create_rectangle(comm=MPI.COMM_WORLD, points=((0, 0), (2, 1)), n=(32, 16))"
-          conda run -n env3-11 mpirun -np 2 python -c "from mpi4py import MPI; import dolfinx; dolfinx.mesh.create_rectangle(comm=MPI.COMM_WORLD, points=((0, 0), (2, 1)), n=(32, 16))"
-
-      - name: Install DOLFINx (py3-12)
-        run: |
-          conda create -n env3-12 -c conda-forge python=3.12 fenics-dolfinx mpich
-          conda env export -n env3-12
-      - name: Test (py3-12)
-        run: |
-          conda run -n env3-12 python -c "from mpi4py import MPI; import dolfinx; dolfinx.mesh.create_rectangle(comm=MPI.COMM_WORLD, points=((0, 0), (2, 1)), n=(32, 16))"
-          conda run -n env3-12 mpirun -np 2 python -c "from mpi4py import MPI; import dolfinx; dolfinx.mesh.create_rectangle(comm=MPI.COMM_WORLD, points=((0, 0), (2, 1)), n=(32, 16))"
-
-      - name: Install DOLFINx (py3-12, petsc-complex)
+          conda install -c conda-forge fenics-dolfinx
+      
+      - name: Test (Unix-like)
+        if: ${{ runner.os == 'macOS' || runner.os == 'Linux' }}
         run: |
-          conda create -n env3-12-complex -c conda-forge python=3.12 fenics-dolfinx petsc=*=complex* mpich
-          conda env export -n env3-12-complex
-      - name: Test (py3-12-complex)
+          conda info
+          conda list
+          mpiexec --version
+          mpiexec -v -np 1 python -c "from mpi4py import MPI; import dolfinx; dolfinx.mesh.create_rectangle(comm=MPI.COMM_WORLD, points=((0, 0), (2, 1)), n=(32, 16))"
+          mpiexec -v -np 2 python -c "from mpi4py import MPI; import dolfinx; dolfinx.mesh.create_rectangle(comm=MPI.COMM_WORLD, points=((0, 0), (2, 1)), n=(32, 16))"
+ 
+      # NOTE: Late 2024, Intel MPI is only correctly setup using cmd.exe.
+      - name: Test (Windows)
+        if: ${{ runner.os == 'Windows' }}
+        shell: cmd /C CALL {0}
         run: |
-          conda run -n env3-12-complex python -c "from mpi4py import MPI; import dolfinx; dolfinx.mesh.create_rectangle(comm=MPI.COMM_WORLD, points=((0, 0), (2, 1)), n=(32, 16))"
-          conda run -n env3-12-complex mpirun -np 2 python -c "from mpi4py import MPI; import dolfinx; dolfinx.mesh.create_rectangle(comm=MPI.COMM_WORLD, points=((0, 0), (2, 1)), n=(32, 16))"
+          conda info
+          conda list
+          mpiexec --version
+          mpiexec -v -np 1 python -c "from mpi4py import MPI; import dolfinx; dolfinx.mesh.create_rectangle(comm=MPI.COMM_WORLD, points=((0, 0), (2, 1)), n=(32, 16))"
+          mpiexec -v -np 2 python -c "from mpi4py import MPI; import dolfinx; dolfinx.mesh.create_rectangle(comm=MPI.COMM_WORLD, points=((0, 0), (2, 1)), n=(32, 16))"
diff --git a/.github/workflows/spack.yml b/.github/workflows/spack.yml
@@ -20,7 +20,7 @@ on:
         type: string
       dolfinx_version:
         description: "DOLFINx release branch/tag to test"
-        default: "0.8.0"
+        default: "0.9.0"
         type: string
 
 jobs:
@@ -34,7 +34,7 @@ jobs:
       PRTE_MCA_rmaps_default_mapping_policy: :oversubscribe   # Newer OpenMPI
       OMPI_MCA_rmaps_base_oversubscribe: true                 # Older OpenMPI
 
-      DOLFINX_RELEASE_VERSION: "${{ github.event_name != 'workflow_dispatch' && '0.8.0' || github.event.inputs.dolfinx_version }}"
+      DOLFINX_RELEASE_VERSION: "${{ github.event_name != 'workflow_dispatch' && '0.9.0' || github.event.inputs.dolfinx_version }}"
 
     steps:
       - name: Get Spack
@@ -100,7 +100,6 @@ jobs:
           spack env create cpp-release-test
           spack env activate cpp-release-test
           spack add fenics-dolfinx@${DOLFINX_RELEASE_VERSION}+adios2 cmake py-fenics-ffcx
-          spack add py-nanobind@1.9
           spack install
           cd dolfinx-release/cpp/
           cd demo/poisson

diff --git a/README.md b/README.md
@@ -78,23 +78,21 @@ comprehensive instructions.
 
 #### conda
 
-To install the latest release of the Python interface, with pyvista
-support for visualisation, using [conda](https://conda.io):
+To install the latest release of the Python interface, including pyvista for
+visualisation, using [conda](https://conda.io):
 
 ```shell
 conda create -n fenicsx-env
 conda activate fenicsx-env
-conda install -c conda-forge fenics-dolfinx mpich pyvista
+conda install -c conda-forge fenics-dolfinx mpich pyvista # Linux and macOS
+conda install -c conda-forge fenics-dolfinx pyvista pyamg # Windows
 ```
 
-Windows conda packages are currently in beta testing and can be installed using:
-```shell
-conda create -n fenicsx-env
-conda activate fenicsx-env
-conda install -c minrk/label/fenics-windows -c conda-forge fenics-dolfinx=0.9.0.dev
-```
-Because FEniCS uses just-in-time compilation it also necessary to install
-[Microsoft Visual Studio](https://visualstudio.microsoft.com/downloads/).
+*Windows only*: Windows conda packages are currently in beta testing. PETSc and
+petsc4py are not available on Windows; as an alternative we recommend using
+`pyamg` following `python/demo/demo_pyamg.py`. Because FEniCS uses just-in-time
+compilation it necessary to install [Microsoft Visual
+Studio](https://visualstudio.microsoft.com/downloads/).
 
 conda is distributed with [Anaconda](https://www.anaconda.com/) and
 [Miniconda](https://docs.conda.io/en/latest/miniconda.html). The recipe

diff --git a/cpp/cmake/templates/dolfinx.conf.in b/cpp/cmake/templates/dolfinx.conf.in
@@ -1,10 +1,10 @@
 # Helper file for setting non-default DOLFINx environment variables
 
 # Common Unix variables
-export @OS_LIBRARY_PATH_NAME@=@CMAKE_INSTALL_PREFIX@/@CMAKE_INSTALL_LIBDIR@:$@OS_LIBRARY_PATH_NAME@
-export PATH=@CMAKE_INSTALL_PREFIX@/@CMAKE_INSTALL_BINDIR@:$PATH
-export PKG_CONFIG_PATH=@CMAKE_INSTALL_PREFIX@/@CMAKE_INSTALL_LIBDIR@/pkgconfig:$PKG_CONFIG_PATH
-export CMAKE_PREFIX_PATH=@CMAKE_INSTALL_PREFIX@/@CMAKE_INSTALL_LIBDIR@/cmake:$CMAKE_PREFIX_PATH
+export @OS_LIBRARY_PATH_NAME@=@CMAKE_INSTALL_PREFIX@/@CMAKE_INSTALL_LIBDIR@:${@OS_LIBRARY_PATH_NAME@:-}
+export PATH=@CMAKE_INSTALL_PREFIX@/@CMAKE_INSTALL_BINDIR@:${PATH:-}
+export PKG_CONFIG_PATH=@CMAKE_INSTALL_PREFIX@/@CMAKE_INSTALL_LIBDIR@/pkgconfig:${PKG_CONFIG_PATH:-}
+export CMAKE_PREFIX_PATH=@CMAKE_INSTALL_PREFIX@/@CMAKE_INSTALL_LIBDIR@/cmake:${CMAKE_PREFIX_PATH:-}
 
 # Special macOS variables
-export DYLD_FRAMEWORK_PATH=/opt/local/Library/Frameworks:$DYLD_FRAMEWORK_PATH
+export DYLD_FRAMEWORK_PATH=/opt/local/Library/Frameworks:${DYLD_FRAMEWORK_PATH:-}
diff --git a/docker/Dockerfile.test-env b/docker/Dockerfile.test-env
@@ -31,7 +31,7 @@ ARG OPENMPI_PATCH=3
 
 ########################################
 
-FROM ubuntu:24.04 as dev-env
+FROM ubuntu:24.04 AS dev-env
 LABEL maintainer="FEniCS Steering Council <fenics-steering-council@googlegroups.com>"
 LABEL description="FEniCS testing and development environment with PETSc real, complex, 32-bit and 64-bit modes"
 
@@ -143,8 +143,8 @@ RUN if [ "$MPI" = "mpich" ]; then \
     ldconfig && \
     rm -rf /tmp/*
 
-ENV VIRTUAL_ENV /dolfinx-env
-ENV PATH /dolfinx-env/bin:$PATH
+ENV VIRTUAL_ENV=/dolfinx-env
+ENV PATH=/dolfinx-env/bin:$PATH
 RUN python3 -m venv ${VIRTUAL_ENV}
 
 # Install Python packages (via pip)