Refactor CI workflows

.github/dependabot.yaml

@@ -1,5 +1,26 @@
 version: 2
 updates:
+- package-ecosystem: "github-actions"
+  directory: "/"
+  target-branch: trunk-patch
+  schedule:
+    interval: "monthly"
+    time: "07:00"
+    timezone: "EST5EDT"
+  pull-request-branch-name:
+    separator: "-"
+  open-pull-requests-limit: 2
+  reviewers:
+  - joaander
+  groups:
+    actions-version:
+      applies-to: version-updates
+      patterns:
+      - '*'
+    actions-security:
+      applies-to: security-updates
+      patterns:
+      - '*'
 - package-ecosystem: "pip"
   directory: "/"
   target-branch: trunk-patch

.github/workflows/build_and_test.yaml

@@ -0,0 +1,242 @@
+name: Build and test
+
+on:
+  workflow_call:
+    inputs:
+      config:
+        type: string
+        required: true
+      image:
+        type: string
+        required: true
+      build_runner:
+        type: string
+        required: true
+        default: ubuntu-latest
+      test_runner:
+        type: string
+        required: true
+        default: ubuntu-latest
+      test_docker_options:
+        type: string
+        required: false
+      validate:
+        type: string
+        required: false
+
+env:
+  # prevent deadlocked MPI tests from causing the job to cancel
+  MPIEXEC_TIMEOUT: 3000
+  # allow mpirun to execute as root in the tests
+  OMPI_ALLOW_RUN_AS_ROOT: 1
+  OMPI_ALLOW_RUN_AS_ROOT_CONFIRM: 1
+  # allow openmpi to oversubscribe cores
+  OMPI_MCA_rmaps_base_oversubscribe: 1
+  # prevent errors from mis-configured openib systems
+  OMPI_MCA_btl: "vader,self"
+  # skip running the CPU tests in GPU builds
+  _HOOMD_SKIP_CPU_TESTS_WHEN_GPUS_PRESENT_: 1
+  # Require GPU tests in GPU builds.
+  _HOOMD_REQUIRE_GPU_TESTS_IN_GPU_BUILDS_: 1
+  # import HOOMD out of the build directory
+  PYTHONPATH: ${{ github.workspace }}/install
+
+jobs:
+  build:
+    runs-on: ${{ fromJson(inputs.build_runner) }}
+    container:
+      image: ${{ inputs.image == '' && null || inputs.image }}
+
+    steps:
+    - name: Set Werror on recent compilers
+      run: |
+        echo "CXXFLAGS=-Werror" >> $GITHUB_ENV
+    - name: Clean workspace
+      run: ( shopt -s dotglob nullglob; rm -rf ./* )
+      shell: bash
+    - name: Checkout
+      uses: actions/checkout@a5ac7e51b41094c92402da3b24376905380afc29 # v4.1.6
+      with:
+        path: code
+        submodules: true
+
+    - name: Configure
+      run: |
+        if [[ ${BUILD_DEBUG} == "true" ]]; then BUILD_TYPE="Debug"; else BUILD_TYPE="Release"; fi
+        echo "BUILD_TYPE=${BUILD_TYPE}"
+        cmake -S code -B build -GNinja \
+                               -DCMAKE_BUILD_TYPE=${BUILD_TYPE} \
+                               -DENABLE_GPU=${ENABLE_GPU:-"OFF"} \
+                               -DENABLE_MPI=${ENABLE_MPI:-"OFF"} \
+                               -DENABLE_TBB=${ENABLE_TBB:-"OFF"} \
+                               -DENABLE_LLVM=${ENABLE_LLVM:-"OFF"} \
+                               -DBUILD_MD=${BUILD_MD:-"ON"} \
+                               -DBUILD_MPCD=${BUILD_MD:-"ON"} \
+                               -DBUILD_METAL=${BUILD_MD:-"ON"} \
+                               -DBUILD_HPMC=${BUILD_HPMC:-"ON"} \
+                               -DCUDA_ARCH_LIST="60;70" \
+                               -DENABLE_DEBUG_JIT=ON \
+                               -DCMAKE_INSTALL_PREFIX=${GITHUB_WORKSPACE}/install \
+                               -DPLUGINS=""
+      env:
+        ENABLE_GPU: ${{ contains(inputs.config, 'cuda') }}
+        ENABLE_MPI: ${{ contains(inputs.config, 'mpi') }}
+        ENABLE_TBB: ${{ contains(inputs.config, 'tbb') }}
+        ENABLE_LLVM: ${{ contains(inputs.config, 'llvm') }}
+        BUILD_MD: ${{ !contains(inputs.config, 'nomd') }}
+        BUILD_HPMC: ${{ !contains(inputs.config, 'nohpmc') }}
+        BUILD_DEBUG: ${{ contains(inputs.config, 'debug') }}
+      shell: bash
+
+    - name: Build
+      run: ninja install -j $(($(getconf _NPROCESSORS_ONLN) + 2)) -k 0
+      working-directory: build
+
+    - name: Configure plugins
+      run : |
+        if [[ ${BUILD_DEBUG} == "true" ]]; then BUILD_TYPE="Debug"; else BUILD_TYPE="Release"; fi
+        echo "BUILD_TYPE=${BUILD_TYPE}"
+        CMAKE_PREFIX_PATH=${GITHUB_WORKSPACE}/install cmake -S code/example_plugins -B build-example-plugins -GNinja -DCMAKE_BUILD_TYPE=${BUILD_TYPE}
+      env:
+        BUILD_DEBUG: ${{ contains(inputs.config, 'debug') }}
+      shell: bash
+
+    - name: Build plugins
+      run: ninja install -j $(($(getconf _NPROCESSORS_ONLN) + 2)) -k 0
+      working-directory: build-example-plugins
+
+    - name: Remove object files
+      run: find build -type f -name '*.o' -delete
+
+    - name: 'Tar build'
+      run: tar --use-compress-program='zstd -10 -T0' -cvf build.tar build
+
+    - name: 'Tar install'
+      run: tar --use-compress-program='zstd -10 -T0' -cvf install.tar install
+
+    - name: 'Upload build'
+      uses: actions/upload-artifact@65462800fd760344b1a7b4382951275a0abb4808 # v4.3.3
+      with:
+        name: build-${{ inputs.config }}-${{ github.sha }}
+        path: build.tar
+        retention-days: 7
+    - name: 'Upload install'
+      uses: actions/upload-artifact@65462800fd760344b1a7b4382951275a0abb4808 # v4.3.3
+      with:
+        name: install-${{ inputs.config }}-${{ github.sha }}
+        path: install.tar
+        retention-days: 7
+
+    - name: Clean workspace
+      run: ( shopt -s dotglob nullglob; rm -rf ./* )
+      shell: bash
+    - name: Clean HOME
+      run: ( shopt -s dotglob nullglob; rm -rf $HOME/* )
+      shell: bash
+
+
+  pytest:
+    needs: build
+    runs-on: ${{ fromJson(inputs.test_runner) }}
+    container:
+      image: ${{ inputs.image == '' && null || inputs.image }}
+      options: ${{ inputs.test_docker_options }} -e CUDA_VISIBLE_DEVICES
+
+    steps:
+    - name: Clean workspace
+      run: ( shopt -s dotglob nullglob; rm -rf ./* )
+      shell: bash
+    - name: Checkout
+      uses: actions/checkout@a5ac7e51b41094c92402da3b24376905380afc29 # v4.1.6
+      with:
+        path: code
+        submodules: true
+
+    - name: Download install
+      uses: actions/download-artifact@65a9edc5881444af0b9093a5e628f2fe47ea3b2e # v4.1.7
+      with:
+        name: install-${{ inputs.config }}-${{ github.sha }}
+    - name: Untar install
+      run: tar --use-compress-program='zstd -10 -T0' -xvf install.tar
+
+    ### Unit tests
+    - name: Run pytest (serial)
+      run: python3 -m pytest --pyargs hoomd -x -v -ra --durations=0 --durations-min=0.1
+
+    - name: Run pytest (mpi)
+      if: ${{ contains(inputs.config, 'mpi') }}
+      run: mpirun -n 2 ${GITHUB_WORKSPACE}/install/hoomd/pytest/pytest-openmpi.sh --pyargs hoomd -x -v -ra --durations=0 --durations-min=0.1 || (( cat pytest.out.1 && exit 1 ))
+
+    - name: Run pytest (serial without cupy)
+      if: ${{ contains(inputs.config, 'cuda') }}
+      run: python3 -m pytest --pyargs hoomd -x -v -ra --durations=0 --durations-min=0.1 -m cupy_optional
+      env:
+        _HOOMD_DISALLOW_CUPY_: 1
+
+    - name: Run pytest (mpi without cupy)
+      if: ${{ contains(inputs.config, 'cuda') && contains(inputs.config, 'mpi') }}
+      run: mpirun -n 2 ${GITHUB_WORKSPACE}/install/hoomd/pytest/pytest-openmpi.sh --pyargs hoomd -x -v -ra --durations=0 --durations-min=0.1 -m cupy_optional || (( cat pytest.out.1 && exit 1 ))
+      env:
+        _HOOMD_DISALLOW_CUPY_: 1
+
+    ### Validation tests
+    - name: Run pytest -m validate (serial)
+      if: ${{ !contains(inputs.config, 'mpi') && contains(github.event.pull_request.labels.*.name, 'validate') && inputs.validate == 'true' }}
+      run: python3 -m pytest --pyargs hoomd -x -v -ra --durations=0 --durations-min=0.1 -p hoomd.pytest_plugin_validate -m validate --validate
+
+    - name: Run pytest -m validate (mpi)
+      if: ${{ contains(inputs.config, 'mpi') && contains(github.event.pull_request.labels.*.name, 'validate') && inputs.validate == 'true' }}
+      run: mpirun -n 2 ${GITHUB_WORKSPACE}/install/hoomd/pytest/pytest-openmpi.sh --pyargs hoomd -x -v -ra --durations=0 --durations-min=0.1 -p hoomd.pytest_plugin_validate -m validate --validate || (( cat pytest.out.1 && exit 1 ))
+
+    - name: Run howto guides (serial)
+      if: ${{ contains(inputs.config, 'llvm') && contains(github.event.pull_request.labels.*.name, 'validate') && inputs.validate == 'true' }}  # some examples require LLVM
+      run: 'for i in *.py; do echo "Running howto: $i" && python3 $i || exit 1; done'
+      working-directory: code/sphinx-doc/howto
+
+    - name: Clean workspace
+      run: ( shopt -s dotglob nullglob; rm -rf ./* )
+      shell: bash
+    - name: Clean HOME
+      run: ( shopt -s dotglob nullglob; rm -rf $HOME/* )
+      shell: bash
+
+
+  ctest:
+    needs: build
+    runs-on: ${{ fromJson(inputs.test_runner) }}
+    container:
+      image: ${{ inputs.image == '' && null || inputs.image }}
+      options: ${{ inputs.test_docker_options }} -e CUDA_VISIBLE_DEVICES
+
+    steps:
+    - name: Clean workspace
+      run: ( shopt -s dotglob nullglob; rm -rf ./* )
+      shell: bash
+    - name: Checkout
+      uses: actions/checkout@a5ac7e51b41094c92402da3b24376905380afc29 # v4.1.6
+      with:
+        path: code
+        submodules: true
+
+    - name: Download build
+      uses: actions/download-artifact@65a9edc5881444af0b9093a5e628f2fe47ea3b2e # v4.1.7
+      with:
+        name: build-${{ inputs.config }}-${{ github.sha }}
+    - name: Untar build
+      run: tar --use-compress-program='zstd -10 -T0' -xvf build.tar
+
+    - name: Run tests
+      run: >-
+        ctest
+        -T test
+        --output-on-failure
+        --test-output-size-failed 1048576
+        --test-output-size-passed 1048576
+      working-directory: build
+
+    - name: Clean workspace
+      run: ( shopt -s dotglob nullglob; rm -rf ./* )
+      shell: bash
+    - name: Clean HOME
+      run: ( shopt -s dotglob nullglob; rm -rf $HOME/* )
+      shell: bash