Merge remote-tracking branch 'origin/master' into JDBetteridge/faster…

…_tests

.gitattributes

@@ -1 +1,9 @@
+# Set default behaviour, in case users don't have core.autocrlf set.
+* text=auto
+
+# Whitespace
+* whitespace=tab-in-indent,space-before-tab,trailing-space,tabwidth=2
+*.{py,pyx,pxd,pxi} whitespace=tab-in-indent,space-before-tab,trailing-space,tabwidth=4
+Makefile whitespace=space-before-tab,trailing-space,tabwidth=2
+pyop2/_version.py export-subst
 firedrake/_version.py export-subst

.github/workflows/build-mac.yml

@@ -0,0 +1,61 @@
+name: Install and test Firedrake (macOS)
+
+on:
+  push:
+    branches:
+      - master
+  pull_request:
+    # By default this workflow is run on the "opened", "synchronize" and
+    # "reopened" events. We add "labelled" so it will run if the PR is given a label.
+    types: [opened, synchronize, reopened, labeled]
+
+concurrency:
+  # Cancels jobs running if new commits are pushed
+  group: >
+    ${{ github.workflow }}-
+    ${{ github.event.pull_request.number || github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  build:
+    name: Build Firedrake (macOS)
+    runs-on: [self-hosted, macOS]
+    # Only run this action if we are pushing to master or the PR is labelled "macOS"
+    if: ${{ (github.ref == 'refs/heads/master') || contains(github.event.pull_request.labels.*.name, 'macOS') }}
+    env:
+      FIREDRAKE_CI_TESTS: 1  # needed to symlink the checked out branch into the venv
+      OMP_NUM_THREADS: 1
+      OPENBLAS_NUM_THREADS: 1
+    steps:
+      - name: Add homebrew to PATH
+        # https://docs.github.com/en/actions/writing-workflows/choosing-what-your-workflow-does/workflow-commands-for-github-actions#adding-a-system-path
+        run: echo "/opt/homebrew/bin" >> "$GITHUB_PATH"
+      - uses: actions/checkout@v4
+      - name: Pre-run cleanup
+        if: ${{ always() }}
+        run: |
+          cd ..
+          rm -rf firedrake_venv
+      - name: Install Python
+        run: brew install python python-setuptools
+      - name: Build Firedrake
+        run: |
+          cd ..
+          "$(brew --prefix)/bin/python3" \
+            firedrake/scripts/firedrake-install \
+            --venv-name firedrake_venv \
+            --disable-ssh \
+            || (cat firedrake-install.log && /bin/false)
+      - name: Run smoke tests
+        run: |
+          . ../firedrake_venv/bin/activate
+          python -m pytest -v tests/firedrake/regression/ -k "poisson_strong or stokes_mini or dg_advection"
+          # also test for 'problem libraries' (spatialindex and libsupermesh)
+          python -m pytest -v tests/firedrake/regression/test_locate_cell.py
+          python -m pytest -v tests/firedrake/supermesh/test_assemble_mixed_mass_matrix.py
+        timeout-minutes: 30
+      - name: Post-run cleanup
+        if: ${{ always() }}
+        run: |
+          cd ..
+          rm -rf firedrake_venv

.github/workflows/build.yml

@@ -66,6 +66,7 @@ jobs:
             --mpicxx="$MPICH_DIR"/mpicxx \
             --mpif90="$MPICH_DIR"/mpif90 \
             --mpiexec="$MPICH_DIR"/mpiexec \
+            --mpihome="$MPICH_DIR"/.. \
             --venv-name firedrake_venv \
             --no-package-manager \
             --disable-ssh \
@@ -97,7 +98,7 @@ jobs:
           . ../firedrake_venv/bin/activate
           echo OMP_NUM_THREADS is "$OMP_NUM_THREADS"
           echo OPENBLAS_NUM_THREADS is "$OPENBLAS_NUM_THREADS"
-          python -m pytest -v tests/test_0init.py
+          python -m pytest -v tests/firedrake/test_0init.py
           python -m pytest \
             --durations=200 \
             --timeout=1800 \
@@ -106,7 +107,7 @@ jobs:
             -m "not parallel" \
             -n 12 --dist worksteal \
             --junit-xml=firedrake1.xml \
-            -sv tests
+            -sv tests/firedrake
         timeout-minutes: 60
       - name: Test Firedrake 2 ranks
         run: |
@@ -122,7 +123,7 @@ jobs:
             -o faulthandler_timeout=1860 \
             --junit-xml=firedrake2_\$MPISPAWN_TASK_ID1.xml \
             -m "parallel[\$MPISPAWN_WORLD_SIZE] and not broken" \
-            -v tests
+            -v tests/firedrake
         timeout-minutes: 30
       - name: Test Firedrake 3 ranks
         run: |
@@ -138,7 +139,7 @@ jobs:
             -o faulthandler_timeout=1860 \
             --junit-xml=firedrake3_\$MPISPAWN_TASK_ID1.xml \
             -m "parallel[\$MPISPAWN_WORLD_SIZE] and not broken" \
-            -v tests
+            -v tests/firedrake
         timeout-minutes: 60
       - name: Test Firedrake 4 ranks
         run: |
@@ -154,7 +155,7 @@ jobs:
             -o faulthandler_timeout=1860 \
             --junit-xml=firedrake4_\$MPISPAWN_TASK_ID1.xml \
             -m "parallel[\$MPISPAWN_WORLD_SIZE] and not broken" \
-            -v tests
+            -v tests/firedrake
         timeout-minutes: 30
       - name: Test Firedrake 6 ranks
         run: |
@@ -167,7 +168,7 @@ jobs:
             -o faulthandler_timeout=1860 \
             --junit-xml=firedrake6.xml \
             -m "parallel[6] and not broken" \
-            -sv tests
+            -sv tests/firedrake
         timeout-minutes: 30
       - name: Test Firedrake 7 ranks
         run: |
@@ -180,7 +181,7 @@ jobs:
             -o faulthandler_timeout=1860 \
             --junit-xml=firedrake7.xml \
             -m "parallel[7] and not broken" \
-            -sv tests
+            -sv tests/firedrake
         timeout-minutes: 30
       - name: Test Firedrake 8 ranks
         run: |
@@ -193,7 +194,7 @@ jobs:
             -o faulthandler_timeout=1860 \
             --junit-xml=firedrake8.xml \
             -m "parallel[8] and not broken" \
-            -sv tests
+            -sv tests/firedrake
         timeout-minutes: 30
       - name: Publish Test Report
         uses: mikepenz/[email protected]

.github/workflows/docker_reuse.yml

@@ -31,15 +31,15 @@ jobs:
       - name: Check out the repo
         uses: actions/checkout@v4
       - name: Log in to Docker Hub
-        uses: docker/login-action@v2
+        uses: docker/login-action@v3
         with:
           username: ${{ secrets.DOCKERHUB_USER }}
           password: ${{ secrets.DOCKERHUB_TOKEN }}
       - name: Set up Docker Buildx
         id: buildx
-        uses: docker/setup-buildx-action@v2
+        uses: docker/setup-buildx-action@v3
       - name: Build and push ${{ inputs.target }}
-        uses: docker/build-push-action@v4
+        uses: docker/build-push-action@v6
         with:
           push: true
           no-cache: true

.github/workflows/lint.yml

@@ -14,7 +14,7 @@ jobs:
     steps:
       - uses: actions/checkout@v4
       - name: Setup python
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: 3.8
       - name: Setup flake8 annotations

.github/workflows/pip-mac.yml

@@ -0,0 +1,111 @@
+name: Pip install Firedrake (macOS)
+
+on:
+  push:
+    branches:
+      - master
+  pull_request:
+    # By default this workflow is run on the "opened", "synchronize" and
+    # "reopened" events. We add "labelled" so it will run if the PR is given a label.
+    types: [opened, synchronize, reopened, labeled]
+
+concurrency:
+  # Cancels jobs running if new commits are pushed
+  group: >
+    ${{ github.workflow }}-
+    ${{ github.event.pull_request.number || github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  build:
+    name: "Build Firedrake using pip (macOS)"
+    runs-on: [self-hosted, macOS]
+    # Only run this action if we are pushing to master or the PR is labelled "macOS"
+    if: ${{ (github.ref == 'refs/heads/master') || contains(github.event.pull_request.labels.*.name, 'macOS') }}
+    env:
+      OMP_NUM_THREADS: 1
+      OPENBLAS_NUM_THREADS: 1
+    steps:
+      - name: Add homebrew to PATH
+        # https://docs.github.com/en/actions/writing-workflows/choosing-what-your-workflow-does/workflow-commands-for-github-actions#adding-a-system-path
+        run: echo "/opt/homebrew/bin" >> "$GITHUB_PATH"
+
+      - name: Install homebrew packages
+        run: brew install gcc autoconf pkg-config make automake cmake ninja libtool boost openblas python python-setuptools mpich
+
+      - name: Cleanup (pre)
+        if: ${{ always() }}
+        run: |
+          rm -rf pip_venv
+          "$(brew --prefix)/bin/python3" -m pip cache purge
+
+      - name: Create a virtual environment
+        run: |
+          "$(brew --prefix)/bin/python3" -m venv pip_venv
+          mkdir pip_venv/src
+
+      - name: Install PETSc
+        run: |
+          cd pip_venv/src
+          git clone https://github.com/firedrakeproject/petsc.git
+          cd petsc
+          ./configure PETSC_DIR="$PWD" PETSC_ARCH=default \
+            --with-shared-libraries=1 \
+            --with-mpi-dir=/opt/homebrew \
+            --with-zlib \
+            --download-bison \
+            --download-hdf5 \
+            --download-hwloc \
+            --download-hypre \
+            --download-metis \
+            --download-mumps \
+            --download-netcdf \
+            --download-pastix \
+            --download-pnetcdf \
+            --download-ptscotch \
+            --download-scalapack \
+            --download-suitesparse \
+            --download-superlu_dist
+          make
+
+      - uses: actions/checkout@v4
+        with:
+          path: pip_venv/src/firedrake
+
+      - name: Pip install
+        run: |
+          export PETSC_DIR="$PWD/pip_venv/src/petsc"
+          export PETSC_ARCH=default
+          export HDF5_DIR="$PETSC_DIR/$PETSC_ARCH"
+          export HDF5_MPI=ON
+          export CC=/opt/homebrew/bin/mpicc
+          export CXX=/opt/homebrew/bin/mpicxx
+          export MPICC="$CC"
+          source pip_venv/bin/activate
+          cd pip_venv/src
+          python -m pip install \
+            --log=firedrake-install.log \
+            --no-binary h5py \
+            -v -e './firedrake[test]'
+
+      - name: Install CI-specific test dependencies
+        run: |
+          source pip_venv/bin/activate
+          python -m pip install -U pytest-timeout
+
+      - name: Run Firedrake smoke tests
+        run: |
+          source pip_venv/bin/activate
+          cd pip_venv/src/firedrake
+          python -m pytest --timeout=1800 -v tests/firedrake/regression \
+            -k "poisson_strong or stokes_mini or dg_advection"
+          # also test for 'problem libraries' (spatialindex and libsupermesh)
+          python -m pytest -v tests/firedrake/regression/test_locate_cell.py
+          python -m pytest -v tests/firedrake/supermesh/test_assemble_mixed_mass_matrix.py
+        timeout-minutes: 30
+
+      - name: Cleanup (post)
+        if: ${{ always() }}
+        run: |
+          rm -rf pip_venv
+          "$(brew --prefix)/bin/python3" -m pip cache purge