DO NOT SQUASH Add PyOP2 to Firedrake repository

.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.yml

@@ -59,7 +59,7 @@ jobs:
           cd ..
           # Linting should ignore unquoted shell variable $COMPLEX
           # shellcheck disable=SC2086
-          ./firedrake/scripts/firedrake-install \
+          ./firedrake/firedrake/scripts/firedrake-install \
             $COMPLEX \
             --honour-petsc-dir \
             --mpicc="$MPICH_DIR"/mpicc \
@@ -96,15 +96,15 @@ 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 \
             --timeout-method=thread \
             -o faulthandler_timeout=1860 \
             -n 12 --dist worksteal \
             --junit-xml=firedrake.xml \
-            -sv tests
+            -sv tests/firedrake
         timeout-minutes: 120
       - name: Publish Test Report
         uses: mikepenz/[email protected]

.github/workflows/pip.yml

@@ -0,0 +1,129 @@
+name: Pip install Firedrake
+
+on:
+  # Push to master or PR
+  push:
+    branches:
+      - master
+  pull_request:
+
+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"
+    runs-on: ubuntu-latest
+    container:
+      image: firedrakeproject/firedrake-env:latest
+      options: --user root
+    defaults:
+      run:
+        shell: bash
+        working-directory: /home/firedrake
+    strategy:
+      # Don't immediately kill real if complex fails and vice versa.
+      fail-fast: false
+      matrix:
+        include:
+          - scalar-type: real
+            petsc_arch: default
+          - scalar-type: complex
+            petsc_arch: complex
+    env:
+      # PETSC_DIR, HDF5_DIR and MPICH_DIR are set inside the docker image
+      FIREDRAKE_CI_TESTS: 1
+      PYOP2_CI_TESTS: 1
+      PETSC_ARCH: ${{ matrix.petsc_arch }}
+      OMP_NUM_THREADS: 1
+      OPENBLAS_NUM_THREADS: 1
+      RDMAV_FORK_SAFE: 1
+    steps:
+      - name: Cleanup
+        if: ${{ always() }}
+        run: rm -rf pip_venv
+
+      - name: Create a venv
+        run: |
+          python3 -m venv pip_venv
+          ln -s /__w/firedrake/firedrake/src pip_venv/
+
+      - uses: actions/checkout@v4
+        with:
+          path: src/firedrake
+
+      - name: Install libsupermesh
+        run: |
+          source pip_venv/bin/activate
+          python -m pip install 'rtree>=1.2'
+          cd pip_venv/src
+          git clone https://github.com/firedrakeproject/libsupermesh.git
+          mkdir -p libsupermesh/build
+          cd libsupermesh/build
+          cmake .. \
+            -DBUILD_SHARED_LIBS=ON \
+            -DCMAKE_INSTALL_PREFIX="$VIRTUAL_ENV" \
+            -DMPI_C_COMPILER="$MPICH_DIR/mpicc" \
+            -DMPI_CXX_COMPILER="$MPICH_DIR/mpicxx" \
+            -DMPI_Fortran_COMPILER="$MPICH_DIR/mpif90" \
+            -DCMAKE_Fortran_COMPILER="$MPICH_DIR/mpif90" \
+            -DMPIEXEC_EXECUTABLE="$MPICH_DIR/mpiexec"
+          make
+          make install
+
+      - name: Pip install
+        run: |
+          source pip_venv/bin/activate
+          cd pip_venv/src
+          export CC="$MPICH_DIR/mpicc"
+          export CXX="$MPICH_DIR/mpicxx"
+          export MPICC="$MPICH_DIR/mpicc"
+          export MPI_HOME="$PETSC_DIR/packages"
+          pip install \
+            --log=firedrake-install.log \
+            --no-binary mpi4py,h5py \
+            -v -e './firedrake[test]'
+
+      - name: Add mpiexec to the venv and install timeout
+        run: |
+          source pip_venv/bin/activate
+          cat << EOF > "$VIRTUAL_ENV/bin/mpiexec"
+          #!/bin/bash
+          "$MPICH_DIR"/mpiexec "\$@"
+          EOF
+          chmod +x "$VIRTUAL_ENV"/bin/mpiexec
+          pip install -U pytest-timeout
+
+      - name: Run Firedrake smoke tests
+        run: |
+          source pip_venv/bin/activate
+          cd pip_venv/src/firedrake
+          pytest -v tests/firedrake/test_0init.py
+          pytest \
+            --durations=200 \
+            --timeout=1800 \
+            --timeout-method=thread \
+            -o faulthandler_timeout=1860 \
+            -n 12 --dist worksteal \
+            --junit-xml=firedrake.xml \
+            -sv tests/firedrake/regression -k "poisson_strong or stokes_mini or dg_advection"
+        timeout-minutes: 120
+
+      - name: Publish Test Report
+        uses: mikepenz/[email protected]
+        if: ${{ always() && ( github.ref != 'refs/heads/master') }}
+        with:
+          report_paths: '/home/firedrake/pip_venv/src/firedrake/firedrake.xml'
+          comment: true
+          check_name: "Firedrake ${{ matrix.scalar-type }}"
+          updateComment: true
+          flaky_summary: true
+
+      - name: Cleanup
+        # Belt and braces: clean up before and after the run.
+        if: ${{ always() }}
+        run: rm -rf pip_venv

.github/workflows/pyop2.yml

@@ -0,0 +1,119 @@
+name: PyOP2
+
+# Trigger the workflow on push or pull request,
+# but only for the master branch
+on:
+  push:
+    branches:
+      - master
+  pull_request:
+    branches:
+      - master
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    strategy:
+      # Don't immediately kill all if one Python version fails
+      fail-fast: false
+      matrix:
+        python-version: ['3.10', '3.11', '3.12', '3.13']
+    env:
+      CC: mpicc
+      PETSC_DIR: ${{ github.workspace }}/petsc
+      PETSC_ARCH: default
+      RDMAV_FORK_SAFE: 1
+      PYOP2_CI_TESTS: 1
+    timeout-minutes: 60
+
+    steps:
+      - name: Install system dependencies
+        shell: bash
+        run: |
+          sudo apt update
+          sudo apt install build-essential mpich libmpich-dev \
+            libblas-dev liblapack-dev gfortran libhwloc-dev libfabric-dev
+
+      - name: Set correct Python version
+        uses: actions/setup-python@v5
+        id: setup-python
+        with:
+          python-version: ${{ matrix.python-version }}
+          # By default setup-python pollutes the environment in such a way that virtual
+          # environments cannot be used. This prevents us from building libsupermesh because
+          # it relies on having rtree installed into a venv.
+          # https://github.com/actions/setup-python/issues/851
+          # https://github.com/actions/setup-python/blob/main/docs/advanced-usage.md#using-update-environment-flag
+          update-environment: false
+
+      - name: Create virtual environment
+        shell: bash
+        run: |
+          ${{ steps.setup-python.outputs.python-path }} -m venv venv
+
+      - name: Clone PETSc
+        uses: actions/checkout@v4
+        with:
+          repository: firedrakeproject/petsc
+          path: ${{ env.PETSC_DIR }}
+
+      - name: Build and install PETSc
+        shell: bash
+        working-directory: ${{ env.PETSC_DIR }}
+        run: |
+          ./configure \
+            --download-hdf5 \
+            --with-debugging=1 \
+            --with-shared-libraries=1 \
+            --with-c2html=0 \
+            --with-fortran-bindings=0
+          make
+
+      - name: Install libsupermesh
+        shell: bash
+        run: |
+          source venv/bin/activate
+          python -m pip install 'rtree>=1.2'
+          git clone https://github.com/firedrakeproject/libsupermesh.git
+          mkdir -p libsupermesh/build
+          cd libsupermesh/build
+          cmake .. \
+            -DBUILD_SHARED_LIBS=ON \
+            -DCMAKE_INSTALL_PREFIX="$VIRTUAL_ENV" \
+            -DMPI_C_COMPILER=mpicc \
+            -DMPI_CXX_COMPILER=mpicxx \
+            -DMPI_Fortran_COMPILER=mpif90 \
+            -DCMAKE_Fortran_COMPILER=mpif90 \
+            -DMPIEXEC_EXECUTABLE=mpiexec
+          make
+          make install
+
+      - name: Checkout PyOP2
+        uses: actions/checkout@v4
+        with:
+          path: PyOP2
+
+      - name: Install PyOP2 dependencies
+        shell: bash
+        working-directory: PyOP2
+        run: |
+          source ../venv/bin/activate
+          python -m pip install -U pip
+          python -m pip install -U pytest-timeout
+
+      - name: Install PyOP2
+        shell: bash
+        working-directory: PyOP2
+        run: |
+          source ../venv/bin/activate
+          python -m pip install -v ".[test]"
+
+      - name: Run tests
+        shell: bash
+        working-directory: PyOP2
+        run: |
+          source ../venv/bin/activate
+          # Running parallel test cases separately works around a bug in pytest-mpi
+          pytest -k "not parallel" --tb=native --timeout=480 --timeout-method=thread -o faulthandler_timeout=540 -v tests/pyop2
+          mpiexec -n 3 pytest -k "parallel[3]" --tb=native --timeout=480 --timeout-method=thread -o faulthandler_timeout=540 -v tests/pyop2
+        timeout-minutes: 10

.github/workflows/zenodo-canary.yml

@@ -25,7 +25,7 @@ jobs:
           pip install requests packaging
       - name: Zenodo API canary
         run: |
-          python scripts/firedrake-install --test-doi-resolution
+          python firedrake/scripts/firedrake-install --test-doi-resolution
       - name: Upload log
         uses: actions/upload-artifact@v4
         if: failure()

.gitignore

@@ -43,3 +43,34 @@ __pycache__/
 /firedrake_configuration/configuration.json
 /firedrake.egg-info
 /docs/source/element_list.csv
+
+
+# Build
+build
+dist
+MANIFEST
+PyOP2.egg-info
+*.py[cdo]
+
+# Extension modules
+sparsity.so
+sparsity.c
+sparsity.cpython*.so
+# Docs
+pyop2.coffee.rst
+pyop2.rst
+pyop2.pdf
+pyop2.aux
+pyop2.log
+
+# Testing
+.pytest-incremental
+.tox
+.vagrant
+
+# Meshes
+*.edge
+*.ele
+*.msh
+*.node
+*.geo

.mailmap

@@ -124,3 +124,22 @@ Joe Wallwork <[email protected]>
 Jingmin Xia <[email protected]>
 Jingmin Xia <[email protected]> <[email protected]>
 
+Gheorghe-Teodor Bercea <[email protected]> <foraker.doc.ic.ac.uk>
+George Boutsioukis <[email protected]>
+David A Ham <[email protected]>
+David A Ham <[email protected]> <[email protected]>
+Miklós Homolya <[email protected]>
+Nicolas Loriant <[email protected]> <[email protected]>
+Nicolas Loriant <[email protected]> <[email protected]>
+Nicolas Loriant <[email protected]> <[email protected]>
+Nicolas Loriant <[email protected]> <[email protected]>
+Nicolas Loriant <[email protected]> <[email protected]>
+Fabio Luporini <[email protected]> <[email protected]>
+Graham Markall <[email protected]> <[email protected]>
+Graham Markall <[email protected]> <[email protected]>
+Andrew McRae <[email protected]> <[email protected]>
+Andrew McRae <[email protected]> <[email protected]>
+Lawrence Mitchell <[email protected]> <[email protected]>
+Lawrence Mitchell <[email protected]> <[email protected]>
+Kaho Sato <[email protected]>
+Reuben W. Nixon-Hill <[email protected]> <[email protected]>

LICENSE

@@ -1,3 +1,4 @@
+Firedrake:
 Firedrake is free software: you can redistribute it and/or modify it under
 the terms of the GNU Lesser General Public License as published by the
 Free Software Foundation, either version 3 of the License, or (at your
@@ -11,3 +12,33 @@ License for more details.
 You should have received a copy of the GNU Lesser General Public
 License along with Firedrake. If not, see <http://www.gnu.org/licenses/>.
 
+PyOP2:
+Copyright (c) 2012, Imperial College London and others. Please see the
+AUTHORS file in the main source directory for a full list of copyright
+holders.  All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+    * Redistributions of source code must retain the above copyright
+      notice, this list of conditions and the following disclaimer.
+    * Redistributions in binary form must reproduce the above copyright
+      notice, this list of conditions and the following disclaimer in the
+      documentation and/or other materials provided with the distribution.
+    * The name of Imperial College London or that of other
+      contributors may not be used to endorse or promote products
+      derived from this software without specific prior written
+      permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTERS
+''AS IS'' AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
+A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
+HOLDERS OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT,
+INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING,
+BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS
+OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR
+TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE
+USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+DAMAGE.

MANIFEST.in

@@ -1,2 +1,5 @@
 include versioneer.py
 include firedrake/_version.py
+recursive-include pyop2 *.c
+include pyop2/_version.py
+