From d3aa85bf4096d01850e213168fad4316e006e746 Mon Sep 17 00:00:00 2001
From: "Joshua A. Anderson" <joaander@umich.edu>
Date: Wed, 5 Jun 2024 12:55:12 -0400
Subject: [PATCH 01/32] Disable existing test workflow.

---
 .github/workflows/test.yml | 16 ++++++++--------
 1 file changed, 8 insertions(+), 8 deletions(-)

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index 4d4ed74f3a..4c7088d037 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -7,14 +7,14 @@ concurrency:
   cancel-in-progress: true
 
 on:
-  pull_request:
-      types: [opened, labeled, reopened, synchronize]
-
-  # Trigger on pushes to the trunk branches. This prevents building commits twice when the pull
-  # request source branch is in the same repository.
-  push:
-    branches:
-    - "trunk-*"
+  # pull_request:
+  #     types: [opened, labeled, reopened, synchronize]
+
+  # # Trigger on pushes to the trunk branches. This prevents building commits twice when the pull
+  # # request source branch is in the same repository.
+  # push:
+  #   branches:
+  #   - "trunk-*"
 
   # Trigger on request.
   workflow_dispatch:

From ee0864f27e6f594f7fb13adb88def3bed1329e3d Mon Sep 17 00:00:00 2001
From: "Joshua A. Anderson" <joaander@umich.edu>
Date: Wed, 5 Jun 2024 12:55:48 -0400
Subject: [PATCH 02/32] 1:1 mapping of jinja workflow to reusable workflows

Release test configurations have not yet been added.
---
 .github/workflows/build_and_test.yaml | 268 ++++++++++++++++++++++++++
 .github/workflows/tests_new.yaml      |  89 +++++++++
 2 files changed, 357 insertions(+)
 create mode 100644 .github/workflows/build_and_test.yaml
 create mode 100644 .github/workflows/tests_new.yaml

diff --git a/.github/workflows/build_and_test.yaml b/.github/workflows/build_and_test.yaml
new file mode 100644
index 0000000000..2793c63d58
--- /dev/null
+++ b/.github/workflows/build_and_test.yaml
@@ -0,0 +1,268 @@
+name: Build and test
+
+on:
+  workflow_call:
+    inputs:
+      config:
+        type: string
+        required: true
+      container_prefix:
+        type: string
+        required: true
+      build_runner:
+        type: string
+        required: true
+        default: "[self-hosted,jetstream2,CPU]"
+      test_runner:
+        type: string
+        required: true
+        default: ubuntu-latest
+      test_docker_options:
+        type: string
+        required: false
+      validate:
+        type: boolean
+        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: ${{ github.workspace }}/install
+
+jobs:
+  build:
+    name: Build [${{ inputs.config }}]
+    runs-on: ${{fromJson(inputs.build_runner) }}
+    container:
+      image: glotzerlab/ci:2024.06.04-${{ inputs.container_prefix }}
+
+    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))
+      working-directory: build
+    - name: Configure plugins
+      run : |
+        mkdir -p build-example-plugins
+        cd build-example-plugins
+        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))
+      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 $HOME/* )
+      shell: bash
+
+
+  pytest:
+    name: Run pytest [${{ inputs.config }}]
+    needs: build
+    runs-on: ${{ fromJson(inputs.test_runner) }}
+    container:
+      image: glotzerlab/ci:2024.06.04-${{ inputs.container_prefix }}
+      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
+
+    - 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
+
+    - name: Clean workspace
+      run: ( shopt -s dotglob nullglob; rm -rf ./* )
+      shell: bash
+    - name: Clean HOME
+      run: ( shopt -s dotglob nullglob; rm -rf $HOME/* )
+      shell: bash
+
+
+  ctest:
+    name: Run ctest [${{ inputs.config }}]
+    needs: build
+    runs-on: ${{ fromJson(inputs.test_runner) }}
+    container:
+      image: glotzerlab/ci:2024.06.04-${{ inputs.container_prefix }}
+      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 $HOME/* )
+      shell: bash
+
+
+  validate:
+    name: Validate [${{ inputs.config }}]
+    needs: build
+    runs-on: ${{ fromJson(inputs.test_runner) }}
+    container:
+      image: glotzerlab/ci:2024.06.04-${{ inputs.container_prefix }}
+      options: ${{ inputs.test_docker_options }} -e CUDA_VISIBLE_DEVICES
+
+    if: ${{ contains(github.event.pull_request.labels.*.name, 'validate') && inputs.validate }}
+    steps:
+    - name: Clean workspace
+      run: ( shopt -s dotglob nullglob; rm -rf ./* )
+      shell: bash
+    - name: Checkout
+      uses: actions/checkout@a5ac7e51b41094c92402da3b24376905380afc29 # v4.1.6
+      with:
+        path: code
+        submodules: true
+
+    - name: Download install
+      uses: actions/download-artifact@65a9edc5881444af0b9093a5e628f2fe47ea3b2e # v4.1.7
+      with:
+        name: install-${{ inputs.config }}-${{ github.sha }}
+    - name: Untar install
+      run: tar --use-compress-program='zstd -10 -T0' -xvf install.tar
+
+    - name: Run pytest (serial)
+      if: ${{ !contains(inputs.config, 'mpi') }}
+      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 (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 -p hoomd.pytest_plugin_validate -m validate --validate || (( cat pytest.out.1 && exit 1 ))
+    - name: Run howto guides (serial)
+      if: ${{ contains(inputs.config, 'llvm') }}  # 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
diff --git a/.github/workflows/tests_new.yaml b/.github/workflows/tests_new.yaml
new file mode 100644
index 0000000000..06e57f34ca
--- /dev/null
+++ b/.github/workflows/tests_new.yaml
@@ -0,0 +1,89 @@
+name: Tests (new)
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+on:
+  pull_request:
+      types: [opened, labeled, reopened, synchronize]
+
+  push:
+    branches:
+    - "trunk-*"
+
+  workflow_dispatch:
+
+jobs:
+  start_action_runners:
+    name: Start action runners
+    runs-on: ubuntu-latest
+    steps:
+    - name: Use jetstream2-admin/start
+      uses: glotzerlab/jetstream2-admin/start@v1.2.5
+      with:
+        OS_APPLICATION_CREDENTIAL_ID: ${{ secrets.OS_APPLICATION_CREDENTIAL_ID }}
+        OS_APPLICATION_CREDENTIAL_SECRET: ${{ secrets.OS_APPLICATION_CREDENTIAL_SECRET }}
+
+  typical:
+    name: Build and test typical configurations
+    uses: ./.github/workflows/build_and_test.yaml
+    with:
+      config: ${{ join(matrix.config, '_') }}
+      container_prefix: ${{ matrix.config[0] }}
+      build_runner: ${{ toJson(matrix.build_runner) }}
+      test_runner: ${{ toJson(matrix.test_runner) }}
+      test_docker_options: ${{ matrix.test_docker_options }}
+      validate: ${{ matrix.validate }}
+
+    strategy:
+      fail-fast: false
+      matrix:
+        include:
+        - config: [clang14_py311, mpi, tbb, llvm]
+          build_runner: [self-hosted,jetstream2,CPU]
+          test_runner: ubuntu-latest
+          validate: true
+
+        - config: [gcc13_py312]
+          build_runner: [self-hosted,jetstream2,CPU]
+          test_runner: ubuntu-latest
+          validate: true
+
+        - config: [cuda120_gcc11_py310, mpi, llvm]
+          build_runner: [self-hosted,jetstream2,CPU]
+          test_runner: [self-hosted,GPU]
+          test_docker_options: '--gpus=all --device /dev/nvidia0 --device /dev/nvidia1 --device /dev/nvidia-uvm --device /dev/nvidia-uvm-tools --device /dev/nvidiactl'
+          validate: true
+          
+        - config: [cuda120_gcc11_py310]
+          build_runner: [self-hosted,jetstream2,CPU]
+          test_runner: [self-hosted,GPU]
+          test_docker_options: '--gpus=all --device /dev/nvidia0 --device /dev/nvidia1 --device /dev/nvidia-uvm --device /dev/nvidia-uvm-tools --device /dev/nvidiactl'
+          validate: true
+          
+        - config: [gcc13_py312, nomd]
+          build_runner: [self-hosted,jetstream2,CPU]
+          test_runner: ubuntu-latest
+          validate: false
+          
+        - config: [gcc13_py312, nohpmc]
+          build_runner: [self-hosted,jetstream2,CPU]
+          test_runner: ubuntu-latest
+          validate: false
+
+        - config: [gcc13_py312, nomd, nohpmc]
+          build_runner: [self-hosted,jetstream2,CPU]
+          test_runner: ubuntu-latest
+          validate: false
+          
+        - config: [cuda120_gcc11_py310 mpi, llvm, debug]
+          build_runner: [self-hosted,jetstream2,CPU]
+          test_runner: [self-hosted,GPU]
+          test_docker_options: '--gpus=all --device /dev/nvidia0 --device /dev/nvidia1 --device /dev/nvidia-uvm --device /dev/nvidia-uvm-tools --device /dev/nvidiactl'
+          validate: false
+          
+        - config: [gcc9_py39]
+          build_runner: [self-hosted,jetstream2,CPU]
+          test_runner: ubuntu-latest
+          validate: false

From e867cd033e6d9266bbcc0935a77862b6f065a4dd Mon Sep 17 00:00:00 2001
From: "Joshua A. Anderson" <joaander@umich.edu>
Date: Wed, 5 Jun 2024 14:07:39 -0400
Subject: [PATCH 03/32] Test on GitHub provided runners for now.

---
 .github/workflows/build_and_test.yaml | 10 +++++++---
 .github/workflows/tests_new.yaml      | 12 ++++++------
 2 files changed, 13 insertions(+), 9 deletions(-)

diff --git a/.github/workflows/build_and_test.yaml b/.github/workflows/build_and_test.yaml
index 2793c63d58..758175f7cc 100644
--- a/.github/workflows/build_and_test.yaml
+++ b/.github/workflows/build_and_test.yaml
@@ -23,7 +23,7 @@ on:
       validate:
         type: boolean
         required: false
-      
+
 env:
   # prevent deadlocked MPI tests from causing the job to cancel
   MPIEXEC_TIMEOUT: 3000
@@ -88,29 +88,33 @@ jobs:
         BUILD_HPMC: ${{ !contains(inputs.config, 'nohpmc') }}
         BUILD_DEBUG: ${{ contains(inputs.config, 'debug') }}
       shell: bash
+
     - name: Build
       run: ninja install -j $(($(getconf _NPROCESSORS_ONLN) + 2))
       working-directory: build
+
     - name: Configure plugins
       run : |
-        mkdir -p build-example-plugins
-        cd build-example-plugins
         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))
       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:
diff --git a/.github/workflows/tests_new.yaml b/.github/workflows/tests_new.yaml
index 06e57f34ca..453db46b54 100644
--- a/.github/workflows/tests_new.yaml
+++ b/.github/workflows/tests_new.yaml
@@ -55,18 +55,18 @@ jobs:
           test_runner: [self-hosted,GPU]
           test_docker_options: '--gpus=all --device /dev/nvidia0 --device /dev/nvidia1 --device /dev/nvidia-uvm --device /dev/nvidia-uvm-tools --device /dev/nvidiactl'
           validate: true
-          
+
         - config: [cuda120_gcc11_py310]
           build_runner: [self-hosted,jetstream2,CPU]
           test_runner: [self-hosted,GPU]
           test_docker_options: '--gpus=all --device /dev/nvidia0 --device /dev/nvidia1 --device /dev/nvidia-uvm --device /dev/nvidia-uvm-tools --device /dev/nvidiactl'
           validate: true
-          
+
         - config: [gcc13_py312, nomd]
           build_runner: [self-hosted,jetstream2,CPU]
           test_runner: ubuntu-latest
           validate: false
-          
+
         - config: [gcc13_py312, nohpmc]
           build_runner: [self-hosted,jetstream2,CPU]
           test_runner: ubuntu-latest
@@ -76,13 +76,13 @@ jobs:
           build_runner: [self-hosted,jetstream2,CPU]
           test_runner: ubuntu-latest
           validate: false
-          
-        - config: [cuda120_gcc11_py310 mpi, llvm, debug]
+
+        - config: [cuda120_gcc11_py310, mpi, llvm, debug]
           build_runner: [self-hosted,jetstream2,CPU]
           test_runner: [self-hosted,GPU]
           test_docker_options: '--gpus=all --device /dev/nvidia0 --device /dev/nvidia1 --device /dev/nvidia-uvm --device /dev/nvidia-uvm-tools --device /dev/nvidiactl'
           validate: false
-          
+
         - config: [gcc9_py39]
           build_runner: [self-hosted,jetstream2,CPU]
           test_runner: ubuntu-latest

From ce06d81ac72299f56b6daba12c917768c448a6b5 Mon Sep 17 00:00:00 2001
From: "Joshua A. Anderson" <joaander@umich.edu>
Date: Wed, 5 Jun 2024 15:09:51 -0400
Subject: [PATCH 04/32] Attempt to improve job names.

---
 .github/workflows/build_and_test.yaml | 18 +++++++-----------
 .github/workflows/tests_new.yaml      |  2 +-
 2 files changed, 8 insertions(+), 12 deletions(-)

diff --git a/.github/workflows/build_and_test.yaml b/.github/workflows/build_and_test.yaml
index 758175f7cc..9cae65f24f 100644
--- a/.github/workflows/build_and_test.yaml
+++ b/.github/workflows/build_and_test.yaml
@@ -23,7 +23,7 @@ on:
       validate:
         type: boolean
         required: false
-
+      
 env:
   # prevent deadlocked MPI tests from causing the job to cancel
   MPIEXEC_TIMEOUT: 3000
@@ -43,7 +43,6 @@ env:
 
 jobs:
   build:
-    name: Build [${{ inputs.config }}]
     runs-on: ${{fromJson(inputs.build_runner) }}
     container:
       image: glotzerlab/ci:2024.06.04-${{ inputs.container_prefix }}
@@ -88,11 +87,11 @@ jobs:
         BUILD_HPMC: ${{ !contains(inputs.config, 'nohpmc') }}
         BUILD_DEBUG: ${{ contains(inputs.config, 'debug') }}
       shell: bash
-
+      
     - name: Build
       run: ninja install -j $(($(getconf _NPROCESSORS_ONLN) + 2))
       working-directory: build
-
+      
     - name: Configure plugins
       run : |
         if [[ ${BUILD_DEBUG} == "true" ]]; then BUILD_TYPE="Debug"; else BUILD_TYPE="Release"; fi
@@ -101,20 +100,20 @@ jobs:
       env:
         BUILD_DEBUG: ${{ contains(inputs.config, 'debug') }}
       shell: bash
-
+      
     - name: Build plugins
       run: ninja install -j $(($(getconf _NPROCESSORS_ONLN) + 2))
       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:
@@ -137,7 +136,6 @@ jobs:
 
 
   pytest:
-    name: Run pytest [${{ inputs.config }}]
     needs: build
     runs-on: ${{ fromJson(inputs.test_runner) }}
     container:
@@ -186,7 +184,6 @@ jobs:
 
 
   ctest:
-    name: Run ctest [${{ inputs.config }}]
     needs: build
     runs-on: ${{ fromJson(inputs.test_runner) }}
     container:
@@ -228,7 +225,6 @@ jobs:
 
 
   validate:
-    name: Validate [${{ inputs.config }}]
     needs: build
     runs-on: ${{ fromJson(inputs.test_runner) }}
     container:
diff --git a/.github/workflows/tests_new.yaml b/.github/workflows/tests_new.yaml
index 453db46b54..546c150baf 100644
--- a/.github/workflows/tests_new.yaml
+++ b/.github/workflows/tests_new.yaml
@@ -26,7 +26,7 @@ jobs:
         OS_APPLICATION_CREDENTIAL_SECRET: ${{ secrets.OS_APPLICATION_CREDENTIAL_SECRET }}
 
   typical:
-    name: Build and test typical configurations
+    name: "${{ join(matrix.config, '_') }}"
     uses: ./.github/workflows/build_and_test.yaml
     with:
       config: ${{ join(matrix.config, '_') }}

From 8cf8cb6606b84f5378972286fc382c29e9d41ab2 Mon Sep 17 00:00:00 2001
From: "Joshua A. Anderson" <joaander@umich.edu>
Date: Wed, 5 Jun 2024 15:26:04 -0400
Subject: [PATCH 05/32] Remove duplicate and add release tests.

---
 .github/workflows/build_and_test.yaml |  6 +--
 .github/workflows/test.yml            |  2 +-
 .github/workflows/tests_new.yaml      | 70 +++++++++++++++++----------
 3 files changed, 46 insertions(+), 32 deletions(-)

diff --git a/.github/workflows/build_and_test.yaml b/.github/workflows/build_and_test.yaml
index 9cae65f24f..da2b8cfa4b 100644
--- a/.github/workflows/build_and_test.yaml
+++ b/.github/workflows/build_and_test.yaml
@@ -9,10 +9,6 @@ on:
       container_prefix:
         type: string
         required: true
-      build_runner:
-        type: string
-        required: true
-        default: "[self-hosted,jetstream2,CPU]"
       test_runner:
         type: string
         required: true
@@ -43,7 +39,7 @@ env:
 
 jobs:
   build:
-    runs-on: ${{fromJson(inputs.build_runner) }}
+    runs-on: [self-hosted,jetstream2,CPU]
     container:
       image: glotzerlab/ci:2024.06.04-${{ inputs.container_prefix }}
 
diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index 4c7088d037..0defdbd3ab 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -1,4 +1,4 @@
-name: Test
+name: Test (old)
 # Edit the `test.yml` in `.github/workflows/templates` and run `make_workflows.py` to update the
 # workflow.
 
diff --git a/.github/workflows/tests_new.yaml b/.github/workflows/tests_new.yaml
index 546c150baf..a006523261 100644
--- a/.github/workflows/tests_new.yaml
+++ b/.github/workflows/tests_new.yaml
@@ -1,4 +1,4 @@
-name: Tests (new)
+name: Test
 
 concurrency:
   group: ${{ github.workflow }}-${{ github.ref }}
@@ -31,59 +31,77 @@ jobs:
     with:
       config: ${{ join(matrix.config, '_') }}
       container_prefix: ${{ matrix.config[0] }}
-      build_runner: ${{ toJson(matrix.build_runner) }}
-      test_runner: ${{ toJson(matrix.test_runner) }}
+      # Default to ubuntu-latest when unset
+      test_runner: ${{ matrix.test_runner == '' && 'ubuntu-latest' || toJson(matrix.test_runner) }}
       test_docker_options: ${{ matrix.test_docker_options }}
-      validate: ${{ matrix.validate }}
+      # Default to false when unset
+      validate: ${{ matrix.validate == '' && false || matrix.validate }}
 
     strategy:
       fail-fast: false
       matrix:
         include:
         - config: [clang14_py311, mpi, tbb, llvm]
-          build_runner: [self-hosted,jetstream2,CPU]
-          test_runner: ubuntu-latest
           validate: true
 
         - config: [gcc13_py312]
-          build_runner: [self-hosted,jetstream2,CPU]
-          test_runner: ubuntu-latest
           validate: true
 
         - config: [cuda120_gcc11_py310, mpi, llvm]
-          build_runner: [self-hosted,jetstream2,CPU]
           test_runner: [self-hosted,GPU]
           test_docker_options: '--gpus=all --device /dev/nvidia0 --device /dev/nvidia1 --device /dev/nvidia-uvm --device /dev/nvidia-uvm-tools --device /dev/nvidiactl'
           validate: true
 
         - config: [cuda120_gcc11_py310]
-          build_runner: [self-hosted,jetstream2,CPU]
           test_runner: [self-hosted,GPU]
           test_docker_options: '--gpus=all --device /dev/nvidia0 --device /dev/nvidia1 --device /dev/nvidia-uvm --device /dev/nvidia-uvm-tools --device /dev/nvidiactl'
           validate: true
 
         - config: [gcc13_py312, nomd]
-          build_runner: [self-hosted,jetstream2,CPU]
-          test_runner: ubuntu-latest
-          validate: false
-
+        
         - config: [gcc13_py312, nohpmc]
-          build_runner: [self-hosted,jetstream2,CPU]
-          test_runner: ubuntu-latest
-          validate: false
-
+        
         - config: [gcc13_py312, nomd, nohpmc]
-          build_runner: [self-hosted,jetstream2,CPU]
-          test_runner: ubuntu-latest
-          validate: false
-
+        
         - config: [cuda120_gcc11_py310, mpi, llvm, debug]
-          build_runner: [self-hosted,jetstream2,CPU]
           test_runner: [self-hosted,GPU]
           test_docker_options: '--gpus=all --device /dev/nvidia0 --device /dev/nvidia1 --device /dev/nvidia-uvm --device /dev/nvidia-uvm-tools --device /dev/nvidiactl'
           validate: false
 
         - config: [gcc9_py39]
-          build_runner: [self-hosted,jetstream2,CPU]
-          test_runner: ubuntu-latest
-          validate: false
+
+  release:
+    if: ${{ contains(github.event.pull_request.labels.*.name, 'release') }}
+    name: "${{ join(matrix.config, '_') }}"
+    uses: ./.github/workflows/build_and_test.yaml
+    with:
+      config: ${{ join(matrix.config, '_') }}
+      container_prefix: ${{ matrix.config[0] }}
+      # Default to ubuntu-latest when unset
+      test_runner: ${{ matrix.test_runner == '' && 'ubuntu-latest' || toJson(matrix.test_runner) }}
+      test_docker_options: ${{ matrix.test_docker_options }}
+      # Default to false when unset
+      validate: ${{ matrix.validate == '' && false || matrix.validate }}
+
+    strategy:
+      fail-fast: false
+      matrix:
+        include:
+        - config: [clang18_py312, mpi]
+        - config: [clang17_py312, mpi]
+        - config: [clang16_py312, mpi, llvm]
+        - config: [clang15_py312, mpi, llvm]
+        - config: [clang13_py310, llvm]
+        - config: [clang12_py310, llvm]
+        - config: [clang11_py310, llvm]
+        - config: [gcc14_py312]
+        - config: [gcc12_py311]
+        - config: [gcc11_py310]
+        - config: [gcc10_py310]
+        - config: [cuda118_gcc11_py310, mpi, llvm]
+          test_runner: [self-hosted,GPU]
+          test_docker_options: '--gpus=all --device /dev/nvidia0 --device /dev/nvidia1 --device /dev/nvidia-uvm --device /dev/nvidia-uvm-tools --device /dev/nvidiactl'
+
+        - config: [cuda117_gcc11_py310, mpi, llvm]
+          test_runner: [self-hosted,GPU]
+          test_docker_options: '--gpus=all --device /dev/nvidia0 --device /dev/nvidia1 --device /dev/nvidia-uvm --device /dev/nvidia-uvm-tools --device /dev/nvidiactl'

From 8f9d932b1d3a318f6d8d44d2d57bc5938ce6512e Mon Sep 17 00:00:00 2001
From: "Joshua A. Anderson" <joaander@umich.edu>
Date: Wed, 5 Jun 2024 15:28:16 -0400
Subject: [PATCH 06/32] Add final test gate.

---
 .github/workflows/tests_new.yaml | 11 +++++++++++
 1 file changed, 11 insertions(+)

diff --git a/.github/workflows/tests_new.yaml b/.github/workflows/tests_new.yaml
index a006523261..91ab07edcc 100644
--- a/.github/workflows/tests_new.yaml
+++ b/.github/workflows/tests_new.yaml
@@ -105,3 +105,14 @@ jobs:
         - config: [cuda117_gcc11_py310, mpi, llvm]
           test_runner: [self-hosted,GPU]
           test_docker_options: '--gpus=all --device /dev/nvidia0 --device /dev/nvidia1 --device /dev/nvidia-uvm --device /dev/nvidia-uvm-tools --device /dev/nvidiactl'
+
+  tests_complete:
+    name: Unit test
+    if: always()
+    needs: [typical]
+    runs-on: ubuntu-latest
+
+    steps:
+    - run: jq --exit-status 'all(.result == "success")' <<< '${{ toJson(needs) }}'
+    - name: Done
+      run: exit 0

From 1d99df1b6b8b43d52a3d9466a983e68537266bd3 Mon Sep 17 00:00:00 2001
From: "Joshua A. Anderson" <joaander@umich.edu>
Date: Wed, 5 Jun 2024 15:32:56 -0400
Subject: [PATCH 07/32] Attempt to restore missing jobs.

---
 .github/workflows/build_and_test.yaml |  4 ++--
 .github/workflows/tests_new.yaml      | 13 ++++++-------
 2 files changed, 8 insertions(+), 9 deletions(-)

diff --git a/.github/workflows/build_and_test.yaml b/.github/workflows/build_and_test.yaml
index da2b8cfa4b..90bab289f1 100644
--- a/.github/workflows/build_and_test.yaml
+++ b/.github/workflows/build_and_test.yaml
@@ -17,7 +17,7 @@ on:
         type: string
         required: false
       validate:
-        type: boolean
+        type: string
         required: false
       
 env:
@@ -227,7 +227,7 @@ jobs:
       image: glotzerlab/ci:2024.06.04-${{ inputs.container_prefix }}
       options: ${{ inputs.test_docker_options }} -e CUDA_VISIBLE_DEVICES
 
-    if: ${{ contains(github.event.pull_request.labels.*.name, 'validate') && inputs.validate }}
+    if: ${{ contains(github.event.pull_request.labels.*.name, 'validate') && inputs.validate == 'true' }}
     steps:
     - name: Clean workspace
       run: ( shopt -s dotglob nullglob; rm -rf ./* )
diff --git a/.github/workflows/tests_new.yaml b/.github/workflows/tests_new.yaml
index 91ab07edcc..4b300c2580 100644
--- a/.github/workflows/tests_new.yaml
+++ b/.github/workflows/tests_new.yaml
@@ -35,27 +35,27 @@ jobs:
       test_runner: ${{ matrix.test_runner == '' && 'ubuntu-latest' || toJson(matrix.test_runner) }}
       test_docker_options: ${{ matrix.test_docker_options }}
       # Default to false when unset
-      validate: ${{ matrix.validate == '' && false || matrix.validate }}
+      validate: ${{ matrix.validate == '' && 'false' || matrix.validate }}
 
     strategy:
       fail-fast: false
       matrix:
         include:
         - config: [clang14_py311, mpi, tbb, llvm]
-          validate: true
+          validate: 'true'
 
         - config: [gcc13_py312]
-          validate: true
+          validate: 'true'
 
         - config: [cuda120_gcc11_py310, mpi, llvm]
           test_runner: [self-hosted,GPU]
           test_docker_options: '--gpus=all --device /dev/nvidia0 --device /dev/nvidia1 --device /dev/nvidia-uvm --device /dev/nvidia-uvm-tools --device /dev/nvidiactl'
-          validate: true
+          validate: 'true'
 
         - config: [cuda120_gcc11_py310]
           test_runner: [self-hosted,GPU]
           test_docker_options: '--gpus=all --device /dev/nvidia0 --device /dev/nvidia1 --device /dev/nvidia-uvm --device /dev/nvidia-uvm-tools --device /dev/nvidiactl'
-          validate: true
+          validate: 'true'
 
         - config: [gcc13_py312, nomd]
         
@@ -66,7 +66,6 @@ jobs:
         - config: [cuda120_gcc11_py310, mpi, llvm, debug]
           test_runner: [self-hosted,GPU]
           test_docker_options: '--gpus=all --device /dev/nvidia0 --device /dev/nvidia1 --device /dev/nvidia-uvm --device /dev/nvidia-uvm-tools --device /dev/nvidiactl'
-          validate: false
 
         - config: [gcc9_py39]
 
@@ -81,7 +80,7 @@ jobs:
       test_runner: ${{ matrix.test_runner == '' && 'ubuntu-latest' || toJson(matrix.test_runner) }}
       test_docker_options: ${{ matrix.test_docker_options }}
       # Default to false when unset
-      validate: ${{ matrix.validate == '' && false || matrix.validate }}
+      validate: ${{ matrix.validate == '' && 'false' || matrix.validate }}
 
     strategy:
       fail-fast: false

From 357a5e915d68e430f7c5f5a6939560dd2e89af5c Mon Sep 17 00:00:00 2001
From: "Joshua A. Anderson" <joaander@umich.edu>
Date: Wed, 5 Jun 2024 20:00:49 -0400
Subject: [PATCH 08/32] Combine validate and pytest.

---
 .github/workflows/build_and_test.yaml | 62 ++++++++-------------------
 .github/workflows/tests_new.yaml      | 15 ++++---
 2 files changed, 26 insertions(+), 51 deletions(-)

diff --git a/.github/workflows/build_and_test.yaml b/.github/workflows/build_and_test.yaml
index 90bab289f1..a3eda9d27d 100644
--- a/.github/workflows/build_and_test.yaml
+++ b/.github/workflows/build_and_test.yaml
@@ -155,22 +155,40 @@ jobs:
     - 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 (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 (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
@@ -218,47 +236,3 @@ jobs:
     - name: Clean HOME
       run: ( shopt -s dotglob nullglob; rm -rf $HOME/* )
       shell: bash
-
-
-  validate:
-    needs: build
-    runs-on: ${{ fromJson(inputs.test_runner) }}
-    container:
-      image: glotzerlab/ci:2024.06.04-${{ inputs.container_prefix }}
-      options: ${{ inputs.test_docker_options }} -e CUDA_VISIBLE_DEVICES
-
-    if: ${{ contains(github.event.pull_request.labels.*.name, 'validate') && inputs.validate == 'true' }}
-    steps:
-    - name: Clean workspace
-      run: ( shopt -s dotglob nullglob; rm -rf ./* )
-      shell: bash
-    - name: Checkout
-      uses: actions/checkout@a5ac7e51b41094c92402da3b24376905380afc29 # v4.1.6
-      with:
-        path: code
-        submodules: true
-
-    - name: Download install
-      uses: actions/download-artifact@65a9edc5881444af0b9093a5e628f2fe47ea3b2e # v4.1.7
-      with:
-        name: install-${{ inputs.config }}-${{ github.sha }}
-    - name: Untar install
-      run: tar --use-compress-program='zstd -10 -T0' -xvf install.tar
-
-    - name: Run pytest (serial)
-      if: ${{ !contains(inputs.config, 'mpi') }}
-      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 (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 -p hoomd.pytest_plugin_validate -m validate --validate || (( cat pytest.out.1 && exit 1 ))
-    - name: Run howto guides (serial)
-      if: ${{ contains(inputs.config, 'llvm') }}  # 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
diff --git a/.github/workflows/tests_new.yaml b/.github/workflows/tests_new.yaml
index 4b300c2580..78c4be65e4 100644
--- a/.github/workflows/tests_new.yaml
+++ b/.github/workflows/tests_new.yaml
@@ -17,16 +17,12 @@ on:
 jobs:
   start_action_runners:
     name: Start action runners
-    runs-on: ubuntu-latest
-    steps:
-    - name: Use jetstream2-admin/start
-      uses: glotzerlab/jetstream2-admin/start@v1.2.5
-      with:
-        OS_APPLICATION_CREDENTIAL_ID: ${{ secrets.OS_APPLICATION_CREDENTIAL_ID }}
-        OS_APPLICATION_CREDENTIAL_SECRET: ${{ secrets.OS_APPLICATION_CREDENTIAL_SECRET }}
+    uses: glotzerlab/jetstream2-admin/.github/workflows/start.yaml@c5d1d59b0b3e069b611f4002bbba4d5ff8e01c60
+    secrets: inherit
 
   typical:
     name: "${{ join(matrix.config, '_') }}"
+    needs: start_action_runners
     uses: ./.github/workflows/build_and_test.yaml
     with:
       config: ${{ join(matrix.config, '_') }}
@@ -72,6 +68,7 @@ jobs:
   release:
     if: ${{ contains(github.event.pull_request.labels.*.name, 'release') }}
     name: "${{ join(matrix.config, '_') }}"
+    needs: start_action_runners
     uses: ./.github/workflows/build_and_test.yaml
     with:
       config: ${{ join(matrix.config, '_') }}
@@ -82,6 +79,10 @@ jobs:
       # Default to false when unset
       validate: ${{ matrix.validate == '' && 'false' || matrix.validate }}
 
+    # TODO: possible to implelemtn fallback to `ubuntu-latest` when actions runners are offline?
+
+    # runs-on: ${{ needs.start_workflow.outputs.exit_code == 3 && 'ubuntu-20.04' || 'ubuntu-24.04' }}
+
     strategy:
       fail-fast: false
       matrix:

From 3893e85d00c3843f7ef3e85c62bd5d9ea06b94d5 Mon Sep 17 00:00:00 2001
From: "Joshua A. Anderson" <joaander@umich.edu>
Date: Thu, 6 Jun 2024 08:07:31 -0400
Subject: [PATCH 09/32] GitHub provided runner fallback.

Use GitHub provided runners when jetstream2 is not available.
---
 .github/workflows/build_and_test.yaml |  6 +++++-
 .github/workflows/tests_new.yaml      | 12 ++++++------
 2 files changed, 11 insertions(+), 7 deletions(-)

diff --git a/.github/workflows/build_and_test.yaml b/.github/workflows/build_and_test.yaml
index a3eda9d27d..9a3e071c6a 100644
--- a/.github/workflows/build_and_test.yaml
+++ b/.github/workflows/build_and_test.yaml
@@ -9,6 +9,10 @@ on:
       container_prefix:
         type: string
         required: true
+      build_runner:
+        type: string
+        required: true
+        default: ubuntu-latest
       test_runner:
         type: string
         required: true
@@ -39,7 +43,7 @@ env:
 
 jobs:
   build:
-    runs-on: [self-hosted,jetstream2,CPU]
+    runs-on: ${{ fromJson(inputs.build_runner) }}
     container:
       image: glotzerlab/ci:2024.06.04-${{ inputs.container_prefix }}
 
diff --git a/.github/workflows/tests_new.yaml b/.github/workflows/tests_new.yaml
index 78c4be65e4..8e145fe300 100644
--- a/.github/workflows/tests_new.yaml
+++ b/.github/workflows/tests_new.yaml
@@ -16,8 +16,8 @@ on:
 
 jobs:
   start_action_runners:
-    name: Start action runners
-    uses: glotzerlab/jetstream2-admin/.github/workflows/start.yaml@c5d1d59b0b3e069b611f4002bbba4d5ff8e01c60
+    name: Start
+    uses: glotzerlab/jetstream2-admin/.github/workflows/start.yaml@a862161adac42e4173f3d142ebd4ddfcde54779b
     secrets: inherit
 
   typical:
@@ -27,6 +27,8 @@ jobs:
     with:
       config: ${{ join(matrix.config, '_') }}
       container_prefix: ${{ matrix.config[0] }}
+      # Use self-hosted runners or fall back to GitHub hosted runners when self-hosted are offline
+      build_runner: ${{ needs.start_action_runners.outputs.active == '0' && 'ubuntu-latest' || '["self-hosted","jetstream2","CPU"]' }}
       # Default to ubuntu-latest when unset
       test_runner: ${{ matrix.test_runner == '' && 'ubuntu-latest' || toJson(matrix.test_runner) }}
       test_docker_options: ${{ matrix.test_docker_options }}
@@ -73,16 +75,14 @@ jobs:
     with:
       config: ${{ join(matrix.config, '_') }}
       container_prefix: ${{ matrix.config[0] }}
+      # Use self-hosted runners or fall back to GitHub hosted runners when self-hosted are offline
+      build_runner: ${{ needs.start_action_runners.outputs.active == '0' && 'ubuntu-latest' || '["self-hosted","jetstream2","CPU"]' }}
       # Default to ubuntu-latest when unset
       test_runner: ${{ matrix.test_runner == '' && 'ubuntu-latest' || toJson(matrix.test_runner) }}
       test_docker_options: ${{ matrix.test_docker_options }}
       # Default to false when unset
       validate: ${{ matrix.validate == '' && 'false' || matrix.validate }}
 
-    # TODO: possible to implelemtn fallback to `ubuntu-latest` when actions runners are offline?
-
-    # runs-on: ${{ needs.start_workflow.outputs.exit_code == 3 && 'ubuntu-20.04' || 'ubuntu-24.04' }}
-
     strategy:
       fail-fast: false
       matrix:

From 49addb054b3b19f5ab293e2481e5dcb1ce80dc90 Mon Sep 17 00:00:00 2001
From: "Joshua A. Anderson" <joaander@umich.edu>
Date: Thu, 6 Jun 2024 13:21:18 -0400
Subject: [PATCH 10/32] Trigger CI.


From 672755901b096512118bb95420d3d0c0832baee7 Mon Sep 17 00:00:00 2001
From: "Joshua A. Anderson" <joaander@umich.edu>
Date: Thu, 6 Jun 2024 13:26:44 -0400
Subject: [PATCH 11/32] Debug testing build_runner.

---
 .github/workflows/build_and_test.yaml | 12 ++++++++++++
 .github/workflows/tests_new.yaml      |  2 +-
 2 files changed, 13 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/build_and_test.yaml b/.github/workflows/build_and_test.yaml
index 9a3e071c6a..34ab0a20f3 100644
--- a/.github/workflows/build_and_test.yaml
+++ b/.github/workflows/build_and_test.yaml
@@ -42,6 +42,18 @@ env:
   PYTHONPATH: ${{ github.workspace }}/install
 
 jobs:
+  debug:
+    runs-on: ubuntu-latest
+    steps:
+      - name: build_runner
+        run: echo ${{ inputs.build_runner }}
+      - name: build_runner_from_json
+        run: echo ${{ fromJson(inputs.build_runner) }}
+      - name: test_runner
+        run: echo ${{ inputs.test_runner }}
+      - name: test_runner_from_json
+        run: echo ${{ fromJson(inputs.test_runner) }}
+
   build:
     runs-on: ${{ fromJson(inputs.build_runner) }}
     container:
diff --git a/.github/workflows/tests_new.yaml b/.github/workflows/tests_new.yaml
index 8e145fe300..58dbf7db2b 100644
--- a/.github/workflows/tests_new.yaml
+++ b/.github/workflows/tests_new.yaml
@@ -28,7 +28,7 @@ jobs:
       config: ${{ join(matrix.config, '_') }}
       container_prefix: ${{ matrix.config[0] }}
       # Use self-hosted runners or fall back to GitHub hosted runners when self-hosted are offline
-      build_runner: ${{ needs.start_action_runners.outputs.active == '0' && 'ubuntu-latest' || '["self-hosted","jetstream2","CPU"]' }}
+      build_runner: ${{ needs.start_action_runners.outputs.active == '0' && toJson('ubuntu-latest') || '["self-hosted","jetstream2","CPU"]' }}
       # Default to ubuntu-latest when unset
       test_runner: ${{ matrix.test_runner == '' && 'ubuntu-latest' || toJson(matrix.test_runner) }}
       test_docker_options: ${{ matrix.test_docker_options }}

From 87bd7223a4b5be818cbe5cd080fd6be69c7db5df Mon Sep 17 00:00:00 2001
From: "Joshua A. Anderson" <joaander@umich.edu>
Date: Thu, 6 Jun 2024 13:37:58 -0400
Subject: [PATCH 12/32] Attempt to fix dynamic runner selection.

---
 .github/workflows/build_and_test.yaml | 8 ++++----
 .github/workflows/tests_new.yaml      | 8 ++++----
 2 files changed, 8 insertions(+), 8 deletions(-)

diff --git a/.github/workflows/build_and_test.yaml b/.github/workflows/build_and_test.yaml
index 34ab0a20f3..b5c2429247 100644
--- a/.github/workflows/build_and_test.yaml
+++ b/.github/workflows/build_and_test.yaml
@@ -46,13 +46,13 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: build_runner
-        run: echo ${{ inputs.build_runner }}
+        run: echo '${{ inputs.build_runner }}'
       - name: build_runner_from_json
-        run: echo ${{ fromJson(inputs.build_runner) }}
+        run: echo '${{ fromJson(inputs.build_runner) }}'
       - name: test_runner
-        run: echo ${{ inputs.test_runner }}
+        run: echo '${{ inputs.test_runner }}'
       - name: test_runner_from_json
-        run: echo ${{ fromJson(inputs.test_runner) }}
+        run: echo '${{ fromJson(inputs.test_runner) }}'
 
   build:
     runs-on: ${{ fromJson(inputs.build_runner) }}
diff --git a/.github/workflows/tests_new.yaml b/.github/workflows/tests_new.yaml
index 58dbf7db2b..a9975a8ea8 100644
--- a/.github/workflows/tests_new.yaml
+++ b/.github/workflows/tests_new.yaml
@@ -17,7 +17,7 @@ on:
 jobs:
   start_action_runners:
     name: Start
-    uses: glotzerlab/jetstream2-admin/.github/workflows/start.yaml@a862161adac42e4173f3d142ebd4ddfcde54779b
+    uses: glotzerlab/jetstream2-admin/.github/workflows/start.yaml@cc78b529b8f408239597619e30c9d47880c3b409
     secrets: inherit
 
   typical:
@@ -30,7 +30,7 @@ jobs:
       # Use self-hosted runners or fall back to GitHub hosted runners when self-hosted are offline
       build_runner: ${{ needs.start_action_runners.outputs.active == '0' && toJson('ubuntu-latest') || '["self-hosted","jetstream2","CPU"]' }}
       # Default to ubuntu-latest when unset
-      test_runner: ${{ matrix.test_runner == '' && 'ubuntu-latest' || toJson(matrix.test_runner) }}
+      test_runner: ${{ matrix.test_runner == '' && toJson('ubuntu-latest') || toJson(matrix.test_runner) }}
       test_docker_options: ${{ matrix.test_docker_options }}
       # Default to false when unset
       validate: ${{ matrix.validate == '' && 'false' || matrix.validate }}
@@ -76,9 +76,9 @@ jobs:
       config: ${{ join(matrix.config, '_') }}
       container_prefix: ${{ matrix.config[0] }}
       # Use self-hosted runners or fall back to GitHub hosted runners when self-hosted are offline
-      build_runner: ${{ needs.start_action_runners.outputs.active == '0' && 'ubuntu-latest' || '["self-hosted","jetstream2","CPU"]' }}
+      build_runner: ${{ needs.start_action_runners.outputs.active == '0' && toJson('ubuntu-latest') || '["self-hosted","jetstream2","CPU"]' }}
       # Default to ubuntu-latest when unset
-      test_runner: ${{ matrix.test_runner == '' && 'ubuntu-latest' || toJson(matrix.test_runner) }}
+      test_runner: ${{ matrix.test_runner == '' && toJson('ubuntu-latest') || toJson(matrix.test_runner) }}
       test_docker_options: ${{ matrix.test_docker_options }}
       # Default to false when unset
       validate: ${{ matrix.validate == '' && 'false' || matrix.validate }}

From 2c47d882e0b9bda44e02f73472de348ee0be1468 Mon Sep 17 00:00:00 2001
From: "Joshua A. Anderson" <joaander@umich.edu>
Date: Thu, 6 Jun 2024 14:13:42 -0400
Subject: [PATCH 13/32] Label validation tests more clearly.

---
 .github/workflows/build_and_test.yaml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/build_and_test.yaml b/.github/workflows/build_and_test.yaml
index b5c2429247..06ad4c3a88 100644
--- a/.github/workflows/build_and_test.yaml
+++ b/.github/workflows/build_and_test.yaml
@@ -192,11 +192,11 @@ jobs:
         _HOOMD_DISALLOW_CUPY_: 1
 
     ### Validation tests
-    - name: Run pytest (serial)
+    - 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 (mpi)
+    - 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 ))
 

From 0ca269cf9971203e487cb804257555bf397494d3 Mon Sep 17 00:00:00 2001
From: "Joshua A. Anderson" <joaander@umich.edu>
Date: Thu, 6 Jun 2024 14:13:49 -0400
Subject: [PATCH 14/32] Use tagged jetstream2-admin

---
 .github/workflows/tests_new.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/tests_new.yaml b/.github/workflows/tests_new.yaml
index a9975a8ea8..c25139e03a 100644
--- a/.github/workflows/tests_new.yaml
+++ b/.github/workflows/tests_new.yaml
@@ -17,7 +17,7 @@ on:
 jobs:
   start_action_runners:
     name: Start
-    uses: glotzerlab/jetstream2-admin/.github/workflows/start.yaml@cc78b529b8f408239597619e30c9d47880c3b409
+    uses: glotzerlab/jetstream2-admin/.github/workflows/start.yaml@c89b62aa89f7886318edb166bc0500cfc658f24f # v1.3.0
     secrets: inherit
 
   typical:

From bf2074e26a949cb3a41b23523249e85975c5701f Mon Sep 17 00:00:00 2001
From: "Joshua A. Anderson" <joaander@umich.edu>
Date: Thu, 6 Jun 2024 14:16:22 -0400
Subject: [PATCH 15/32] Remove the now unused make_workflows and templates.

---
 .github/workflows/make_workflows.py           |  56 --
 .../workflows/templates/configurations.yml    |  39 --
 .github/workflows/templates/release.yml       |  86 ---
 .github/workflows/templates/test.yml          | 306 ---------
 .github/workflows/templates/workflow.yml      |  49 --
 .../workflows/{tests_new.yaml => test.yaml}   |   0
 .github/workflows/test.yml                    | 591 ------------------
 .pre-commit-config.yaml                       |   7 -
 8 files changed, 1134 deletions(-)
 delete mode 100644 .github/workflows/make_workflows.py
 delete mode 100644 .github/workflows/templates/configurations.yml
 delete mode 100644 .github/workflows/templates/release.yml
 delete mode 100644 .github/workflows/templates/test.yml
 delete mode 100644 .github/workflows/templates/workflow.yml
 rename .github/workflows/{tests_new.yaml => test.yaml} (100%)
 delete mode 100644 .github/workflows/test.yml

diff --git a/.github/workflows/make_workflows.py b/.github/workflows/make_workflows.py
deleted file mode 100644
index a23340417a..0000000000
--- a/.github/workflows/make_workflows.py
+++ /dev/null
@@ -1,56 +0,0 @@
-#!/usr/bin/env python3
-# Copyright (c) 2009-2024 The Regents of the University of Michigan.
-# Part of HOOMD-blue, released under the BSD 3-Clause License.
-
-"""Evaluate the workflow jinja templates."""
-
-import jinja2
-import yaml
-import os
-
-if __name__ == '__main__':
-    # change to the directory of the script
-    os.chdir(os.path.dirname(os.path.realpath(__file__)))
-
-    env = jinja2.Environment(loader=jinja2.FileSystemLoader('templates'),
-                             block_start_string='<%',
-                             block_end_string='%>',
-                             variable_start_string='<<',
-                             variable_end_string='>>',
-                             comment_start_string='<#',
-                             comment_end_string='#>',
-                             trim_blocks=True,
-                             lstrip_blocks=True)
-    template = env.get_template('test.yml')
-    with open('templates/configurations.yml', 'r') as f:
-        configurations = yaml.safe_load(f)
-
-    # preprocess configurations and fill out additional fields needed by
-    # `test.yml` to configure the matrix jobs
-    for name, configuration in configurations.items():
-        for entry in configuration:
-            if entry['config'].startswith('[cuda'):
-                entry['build_runner'] = "[self-hosted,jetstream2,CPU]"
-
-                entry['test_runner'] = "[self-hosted,GPU]"
-                # device options needed to access the GPU devices on the runners
-                # because the nvidia container toolkit is built without cgroups
-                # support:
-                # https://aur.archlinux.org/packages/nvidia-container-toolkit
-                entry['test_docker_options'] = \
-                    "--gpus=all --device /dev/nvidia0 " \
-                    "--device /dev/nvidia1 " \
-                    "--device /dev/nvidia-uvm " \
-                    "--device /dev/nvidia-uvm-tools " \
-                    "--device /dev/nvidiactl"
-            else:
-                entry['test_runner'] = "ubuntu-latest"
-                entry['build_runner'] = "[self-hosted,jetstream2,CPU]"
-                entry['test_docker_options'] = ""
-
-    with open('test.yml', 'w') as f:
-        f.write(template.render(configurations))
-
-    template = env.get_template('release.yml')
-    with open('release.yml', 'w') as f:
-        f.write(template.render())
diff --git a/.github/workflows/templates/configurations.yml b/.github/workflows/templates/configurations.yml
deleted file mode 100644
index 8cf0c58a02..0000000000
--- a/.github/workflows/templates/configurations.yml
+++ /dev/null
@@ -1,39 +0,0 @@
-# configurations to build and test on every pull request
-# each entry is a mapping with:
-# - config: a string encoded list containing the docker image name and any number of build options.
-# - The build options are `mpi`, `tbb`, `llvm`, `nomd`, and `nohpmc`.
-unit_test_configurations:
-- config: "[clang14_py311, mpi, tbb, llvm]"
-- config: "[gcc13_py312]"
-- config: "[gcc13_py312, nomd]"
-- config: "[gcc13_py312, nohpmc]"
-- config: "[gcc13_py312, nomd, nohpmc]"
-- config: "[cuda120_gcc11_py310, mpi, llvm, debug]"
-- config: "[cuda120_gcc11_py310, mpi, llvm]"
-- config: "[cuda120_gcc11_py310]"
-- config: "[gcc9_py39]"
-
-# Configurations on which to run longer validation tests. Must be a subset of
-# `unit_test_configurations`
-validate_configurations:
-- config: "[clang14_py311, mpi, tbb, llvm]"
-- config: "[gcc13_py312]"
-- config: "[cuda120_gcc11_py310, mpi, llvm]"
-- config: "[cuda120_gcc11_py310]"
-
-# Configurations to build and test only rarely, such as just before a release.
-# There should be no overlap between this list and `unit_test_configurations`
-release_test_configurations:
-- config: "[clang18_py312, mpi]"
-- config: "[clang17_py312, mpi]"
-- config: "[clang16_py312, mpi, llvm]"
-- config: "[clang15_py312, mpi, llvm]"
-- config: "[clang13_py310, llvm]"
-- config: "[clang12_py310, llvm]"
-- config: "[clang11_py310, llvm]"
-- config: "[gcc14_py312]"
-- config: "[gcc12_py311]"
-- config: "[gcc11_py310]"
-- config: "[gcc10_py310]"
-- config: "[cuda118_gcc11_py310, mpi, llvm]"
-- config: "[cuda117_gcc11_py310, mpi, llvm]"
diff --git a/.github/workflows/templates/release.yml b/.github/workflows/templates/release.yml
deleted file mode 100644
index 21223260fa..0000000000
--- a/.github/workflows/templates/release.yml
+++ /dev/null
@@ -1,86 +0,0 @@
-<% extends "workflow.yml" %>
-<% block name %>
-# Edit `release.yml` in `.github/workflows/templates` and run `make_workflows.py` to update the
-# workflow.
-name: GitHub Release
-<% endblock %>
-<% block on_push_tags %>
-    # Trigger on tags. Tag builds create GitHub releases with the change log and source tarball.
-    tags:
-      - "v*"
-<% endblock %>
-<% block env %>
-env:
-  name: hoomd
-
-defaults:
-  run:
-    shell: bash
-<% endblock %>
-<% block jobs %>
-jobs:
-  release:
-    name: Build release tarball
-    runs-on: ubuntu-latest
-    container:
-      image: << container_prefix >>-ubuntu20.04
-
-    steps:
-      - name: Checkout
-        uses: actions/checkout@v4.1.4
-        with:
-          fetch-depth: 0
-          submodules: true
-          path: code
-
-      - name: Determine last tag via git describe
-        if: ${{ ! startsWith(github.ref, 'refs/tags/v') }}
-        run: echo "tag=$(git describe --abbrev=0)" >> $GITHUB_ENV
-        working-directory: code
-
-      # git describe does not return the current tag in tag pushes on GitHub Actions, use GITHUB_REF instead
-      - name: Determine tag from GITHUB_REF
-        if:  startsWith(github.ref, 'refs/tags/v')
-        run: echo "tag=$(echo ${GITHUB_REF} | sed  -e 's/refs\/tags\///g')" >> $GITHUB_ENV
-
-      - name: Write version change log
-        run: .github/workflows/make-changelog-md.sh  ${tag:1} | tee ${GITHUB_WORKSPACE}/changelog.md
-        working-directory: code
-
-      - name: Copy source
-        run: cp -R code ${name}-${tag:1}
-
-      - name: Remove .git
-        run: rm -rf ${name}-${tag:1}/.git && ls -laR ${name}-${tag:1}
-
-      - name: Tar source
-        run: tar -cvzf ${name}-${tag:1}.tar.gz ${name}-${tag:1}
-
-      - name: Upload release files
-        uses: actions/upload-artifact@v4.3.3
-        with:
-          name: release
-          path: |
-            *.tar.gz
-            changelog.md
-
-  publish:
-    name: Publish [GitHub]
-    needs: [release]
-    runs-on: ubuntu-latest
-
-    steps:
-      - name: Download artifacts
-        uses: actions/download-artifact@v4.1.7
-        with:
-          name: release
-
-      - name: Create release
-        uses: softprops/action-gh-release@v2.0.2
-        if: startsWith(github.ref, 'refs/tags/v')
-        with:
-          files: "*.tar.gz"
-          body_path: changelog.md
-        env:
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-<% endblock %>
diff --git a/.github/workflows/templates/test.yml b/.github/workflows/templates/test.yml
deleted file mode 100644
index bf7f5e6370..0000000000
--- a/.github/workflows/templates/test.yml
+++ /dev/null
@@ -1,306 +0,0 @@
-<% extends "workflow.yml" %>
-<% block name %>
-name: Test
-# Edit the `test.yml` in `.github/workflows/templates` and run `make_workflows.py` to update the
-# workflow.
-<% endblock %>
-<% block on_pull_request %>
-  pull_request:
-      types: [opened, labeled, reopened, synchronize]
-<% endblock %>
-<% block env %>
-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: ${{ github.workspace }}/install
-<% endblock %>
-<% set tar_command="tar --use-compress-program='zstd -10 -T0'" %>
-<% macro job(name, run_tests, configurations, needs='') %>
-    name: << name >> [${{ join(matrix.config, '_') }}]
-    <% if needs != '' %>
-    needs: << needs >>
-    <% endif %>
-    <% if run_tests %>
-    runs-on: ${{ matrix.test_runner }}
-    container:
-      image: << container_prefix >>-${{ matrix.config[0] }}
-      options: ${{ matrix.test_docker_options }} -e CUDA_VISIBLE_DEVICES
-    <% else %>
-    runs-on: ${{ matrix.build_runner }}
-    container:
-      image: << container_prefix >>-${{ matrix.config[0] }}
-    <% endif %>
-    strategy:
-      matrix:
-        include:
-    <% for configuration in configurations %>
-        - {config: << configuration.config >>, build_runner: << configuration.build_runner >>, test_runner: << configuration.test_runner >>, test_docker_options: '<< configuration.test_docker_options >>' }
-    <% endfor %>
-<% endmacro %>
-<% set build_steps %>
-    - name: Configure
-      run: |
-        mkdir -p build
-        cd build
-        if [[ ${BUILD_DEBUG} == "true" ]]; then BUILD_TYPE="Debug"; else BUILD_TYPE="Release"; fi
-        echo "BUILD_TYPE=${BUILD_TYPE}"
-        cmake ../code -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(matrix.config[0], 'cuda') }}
-        ENABLE_MPI: ${{ contains(matrix.config, 'mpi') }}
-        ENABLE_TBB: ${{ contains(matrix.config, 'tbb') }}
-        ENABLE_LLVM: ${{ contains(matrix.config, 'llvm') }}
-        BUILD_MD: ${{ !contains(matrix.config, 'nomd') }}
-        BUILD_HPMC: ${{ !contains(matrix.config, 'nohpmc') }}
-        BUILD_DEBUG: ${{ contains(matrix.config, 'debug') }}
-      shell: bash
-    - name: Build
-      run: ninja install -j $(($(getconf _NPROCESSORS_ONLN) + 2))
-      working-directory: build
-    - name: Configure plugins
-      run : |
-        mkdir -p build-example-plugins
-        cd build-example-plugins
-        if [[ ${BUILD_DEBUG} == "true" ]]; then BUILD_TYPE="Debug"; else BUILD_TYPE="Release"; fi
-        echo "BUILD_TYPE=${BUILD_TYPE}"
-        CMAKE_PREFIX_PATH=${GITHUB_WORKSPACE}/install cmake ../code/example_plugins -GNinja -DCMAKE_BUILD_TYPE=${BUILD_TYPE}
-      env:
-        BUILD_DEBUG: ${{ contains(matrix.config, 'debug') }}
-      shell: bash
-    - name: Build plugins
-      run: ninja install -j $(($(getconf _NPROCESSORS_ONLN) + 2))
-      working-directory: build-example-plugins
-<% endset %>
-<% set upload_steps %>
-    - name: Remove object files
-      run: find build -type f -name '*.o' -delete
-    # Tar the build directory to preserve permissions and reduce HTTP requests on upload.
-    - name: 'Tar build'
-      run: << tar_command >> -cvf build.tar build
-    - name: 'Tar install'
-      run: << tar_command >> -cvf install.tar install
-    # Upload the tarballs. Retain the file for a limited time in case developers need to download
-    # and run tests locally for further debugging.
-    - name: 'Upload build'
-      uses: actions/upload-artifact@v4.3.3
-      with:
-        name: build-${{ join(matrix.config, '_') }}-${{ github.sha }}
-        path: build.tar
-        retention-days: 7
-    - name: 'Upload install'
-      uses: actions/upload-artifact@v4.3.3
-      with:
-        name: install-${{ join(matrix.config, '_') }}-${{ github.sha }}
-        path: install.tar
-        retention-days: 7
-<% endset %>
-<% set download_build_steps %>
-    - name: Download build
-      uses: actions/download-artifact@v4.1.7
-      with:
-        name: build-${{ join(matrix.config, '_') }}-${{ github.sha }}
-    - name: Untar build
-      run: << tar_command >> -xvf build.tar
-<% endset %>
-<% set download_install_steps %>
-    - name: Download install
-      uses: actions/download-artifact@v4.1.7
-      with:
-        name: install-${{ join(matrix.config, '_') }}-${{ github.sha }}
-    - name: Untar install
-      run: << tar_command >> -xvf install.tar
-<% endset %>
-<% set pytest_options="--pyargs hoomd -x -v -ra --durations=0 --durations-min=0.1" %>
-<% set pytest_validate_options="-p hoomd.pytest_plugin_validate -m validate --validate" %>
-<% set invoke_pytest_serial="python3 -m pytest" %>
-<% set invoke_pytest_mpi="mpirun -n 2 ${GITHUB_WORKSPACE}/install/hoomd/pytest/pytest-openmpi.sh" %>
-<% set pytest_steps %>
-    - name: Run pytest (serial)
-      run: << invoke_pytest_serial >> << pytest_options >>
-    - name: Run pytest (mpi)
-      if: ${{ contains(matrix.config, 'mpi') }}
-      run: << invoke_pytest_mpi >> << pytest_options >> || (( cat pytest.out.1 && exit 1 ))
-    - name: Run pytest (serial without cupy)
-      if: ${{ contains(matrix.config[0], 'cuda') }}
-      run: << invoke_pytest_serial >> << pytest_options >> -m cupy_optional
-      env:
-        _HOOMD_DISALLOW_CUPY_: 1
-    - name: Run pytest (mpi without cupy)
-      if: ${{ contains(matrix.config[0], 'cuda') && contains(matrix.config, 'mpi') }}
-      run: << invoke_pytest_mpi >> << pytest_options >> -m cupy_optional || (( cat pytest.out.1 && exit 1 ))
-      env:
-        _HOOMD_DISALLOW_CUPY_: 1
-<% endset %>
-<% set ctest_steps %>
-    - name: Run tests
-      run: >-
-        ctest
-        -T test
-        --output-on-failure
-        --test-output-size-failed 1048576
-        --test-output-size-passed 1048576
-      working-directory: build
-<% endset %>
-<% set validate_steps %>
-    - name: Run pytest (serial)
-      if: ${{ !contains(matrix.config, 'mpi') }}
-      run: << invoke_pytest_serial >> << pytest_options >> << pytest_validate_options >>
-    - name: Run pytest (mpi)
-      if: ${{ contains(matrix.config, 'mpi') }}
-      run: << invoke_pytest_mpi >> << pytest_options >> << pytest_validate_options >> || (( cat pytest.out.1 && exit 1 ))
-    - name: Run howto guides (serial)
-      if: ${{ contains(matrix.config, 'llvm') }}  # 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
-<% endset %>
-<% set prepare_steps %>
-    - name: Clean workspace
-      run: ( shopt -s dotglob nullglob; rm -rf ./* )
-      shell: bash
-    - name: Checkout
-      uses: actions/checkout@v4.1.4
-      with:
-        path: code
-        submodules: true
-<% endset %>
-<% set post_cleanup_steps %>
-    - 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
-<% endset %>
-<% block jobs %>
-# Use multiple jobs to reduce the amount of time spent on GPU runners. Use CPU runners for
-# compiling all tests configurations (GPU and CPU), then upload the build directory (sans object
-# files) as an artifact. Test jobs depend on the build job, download the install directory, and run
-# the tests. Upload each build configuration to a separate artifact.
-
-# Github Actions does not support any form of templating at this time, not even YAML anchors.
-# To minimize the number of duplicated lines, encode the job configuration as an array in config:
-# [image, (mpi), (tbb)]
-jobs:
-  start_action_runners:
-    name: Start action runners
-    runs-on: ubuntu-latest
-    steps:
-    - name: Use jetstream2-admin/start
-      uses: glotzerlab/jetstream2-admin/start@v1.2.5
-      with:
-        OS_APPLICATION_CREDENTIAL_ID: ${{ secrets.OS_APPLICATION_CREDENTIAL_ID }}
-        OS_APPLICATION_CREDENTIAL_SECRET: ${{ secrets.OS_APPLICATION_CREDENTIAL_SECRET }}
-
-  build:
-<< job(name='Build', run_tests=False, configurations=unit_test_configurations) >>
-    steps:
-    - name: Set Werror on recent compilers
-      run: |
-        echo "CXXFLAGS=-Werror" >> $GITHUB_ENV
-      if: ${{ !startsWith(matrix.config[0], 'gcc7') }}
-<< prepare_steps >>
-<< build_steps >>
-<< upload_steps >>
-<< post_cleanup_steps >>
-
-  pytest:
-<< job(name='Run pytest', run_tests=True, configurations=unit_test_configurations, needs='build') >>
-    steps:
-<< prepare_steps >>
-<< download_install_steps >>
-<< pytest_steps >>
-<< post_cleanup_steps >>
-
-  ctest:
-<< job(name='Run ctest', run_tests=True, configurations=unit_test_configurations, needs='build') >>
-    steps:
-<< prepare_steps >>
-<< download_build_steps >>
-<< ctest_steps >>
-<< post_cleanup_steps >>
-
-  validate:
-<< job(name='Validate', run_tests=True, configurations=validate_configurations, needs='build') >>
-    if: ${{ contains(github.event.pull_request.labels.*.name, 'validate') }}
-    steps:
-<< prepare_steps >>
-<< download_install_steps >>
-<< validate_steps >>
-<< post_cleanup_steps >>
-
-  build_release:
-<< job(name='Build', run_tests=False, configurations=release_test_configurations) >>
-    if: ${{ contains(github.event.pull_request.labels.*.name, 'release') }}
-    steps:
-<< prepare_steps >>
-<< build_steps >>
-<< upload_steps >>
-<< post_cleanup_steps >>
-
-  pytest_release:
-<< job(name='Run pytest', run_tests=True, configurations=release_test_configurations, needs='build_release') >>
-    if: ${{ contains(github.event.pull_request.labels.*.name, 'release') }}
-    steps:
-<< prepare_steps >>
-<< download_install_steps >>
-<< pytest_steps >>
-<< post_cleanup_steps >>
-
-  ctest_release:
-<< job(name='Run ctest', run_tests=True, configurations=release_test_configurations, needs='build_release') >>
-    if: ${{ contains(github.event.pull_request.labels.*.name, 'release') }}
-    steps:
-<< prepare_steps >>
-<< download_build_steps >>
-<< ctest_steps >>
-<< post_cleanup_steps >>
-
-  # This job is used to provide a single requirement for branch merge conditions. GitHub considers
-  # the check passing even if it is skipped, so this job raises errors when required jobs were not
-  # run.
-  unit_tests_complete:
-    name: Unit test
-    needs: [pytest, ctest, validate]
-    if: ${{ always() && github.event_name == 'pull_request' }}
-    runs-on: ubuntu-latest
-
-    steps:
-      - name: Error if pytest did not succeed
-        if: needs.pytest.result != 'success'
-        run: echo "::error ::pytest tests failed." && exit 1
-      - name: Error if ctest did not succeed
-        if: needs.ctest.result != 'success'
-        run: echo "::error ::ctest tests failed." && exit 1
-      - name: Warn if validate did not run
-        if: needs.validate.result == 'skipped'
-        run: echo "::warning ::Skipped validation tests." && exit 1
-      - name: Error if validate did not succeed
-        if: needs.validate.result != 'success'
-        run: echo "::error ::Validation tests failed." && exit 1
-      - run: echo "Done!"
-<% endblock %>
diff --git a/.github/workflows/templates/workflow.yml b/.github/workflows/templates/workflow.yml
deleted file mode 100644
index f0268bca93..0000000000
--- a/.github/workflows/templates/workflow.yml
+++ /dev/null
@@ -1,49 +0,0 @@
-<% block name %><% endblock %>
-<% set container_prefix="glotzerlab/ci:2024.06.04" %>
-
-<% block concurrency %>
-concurrency:
-  <% block concurrency_group %>
-  group: ${{ github.workflow }}-${{ github.ref }}
-  <% endblock %>
-  <% block concurrency_cancel_in_progress %>
-  cancel-in-progress: true
-  <% endblock %>
-<% endblock %>
-
-<% block on %>
-on:
-  <% block on_pull_request %>
-  # Trigger on pull requests.
-  pull_request:
-  <% endblock %>
-
-  <% block on_push %>
-  # Trigger on pushes to the trunk branches. This prevents building commits twice when the pull
-  # request source branch is in the same repository.
-  push:
-    <% block on_push_branches %>
-    branches:
-    - "trunk-*"
-    <% endblock %>
-    <% block on_push_tags %>
-    <% endblock %>
-  <% endblock %>
-
-  <% block on_workflow_dispatch %>
-  # Trigger on request.
-  workflow_dispatch:
-  <% endblock %>
-<% endblock %>
-
-<% block permissions %>
-<% endblock %>
-
-<% block env %>
-<% endblock %>
-
-<% block defaults %>
-<% endblock %>
-
-<% block jobs %>
-<% endblock %>
diff --git a/.github/workflows/tests_new.yaml b/.github/workflows/test.yaml
similarity index 100%
rename from .github/workflows/tests_new.yaml
rename to .github/workflows/test.yaml
diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
deleted file mode 100644
index 0defdbd3ab..0000000000
--- a/.github/workflows/test.yml
+++ /dev/null
@@ -1,591 +0,0 @@
-name: Test (old)
-# Edit the `test.yml` in `.github/workflows/templates` and run `make_workflows.py` to update the
-# workflow.
-
-concurrency:
-  group: ${{ github.workflow }}-${{ github.ref }}
-  cancel-in-progress: true
-
-on:
-  # pull_request:
-  #     types: [opened, labeled, reopened, synchronize]
-
-  # # Trigger on pushes to the trunk branches. This prevents building commits twice when the pull
-  # # request source branch is in the same repository.
-  # push:
-  #   branches:
-  #   - "trunk-*"
-
-  # Trigger on request.
-  workflow_dispatch:
-
-
-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
-
-
-# Use multiple jobs to reduce the amount of time spent on GPU runners. Use CPU runners for
-# compiling all tests configurations (GPU and CPU), then upload the build directory (sans object
-# files) as an artifact. Test jobs depend on the build job, download the install directory, and run
-# the tests. Upload each build configuration to a separate artifact.
-
-# Github Actions does not support any form of templating at this time, not even YAML anchors.
-# To minimize the number of duplicated lines, encode the job configuration as an array in config:
-# [image, (mpi), (tbb)]
-jobs:
-  start_action_runners:
-    name: Start action runners
-    runs-on: ubuntu-latest
-    steps:
-    - name: Use jetstream2-admin/start
-      uses: glotzerlab/jetstream2-admin/start@v1.2.5
-      with:
-        OS_APPLICATION_CREDENTIAL_ID: ${{ secrets.OS_APPLICATION_CREDENTIAL_ID }}
-        OS_APPLICATION_CREDENTIAL_SECRET: ${{ secrets.OS_APPLICATION_CREDENTIAL_SECRET }}
-
-  build:
-    name: Build [${{ join(matrix.config, '_') }}]
-    runs-on: ${{ matrix.build_runner }}
-    container:
-      image: glotzerlab/ci:2024.06.04-${{ matrix.config[0] }}
-    strategy:
-      matrix:
-        include:
-        - {config: [clang14_py311, mpi, tbb, llvm], build_runner: [self-hosted,jetstream2,CPU], test_runner: ubuntu-latest, test_docker_options: '' }
-        - {config: [gcc13_py312], build_runner: [self-hosted,jetstream2,CPU], test_runner: ubuntu-latest, test_docker_options: '' }
-        - {config: [gcc13_py312, nomd], build_runner: [self-hosted,jetstream2,CPU], test_runner: ubuntu-latest, test_docker_options: '' }
-        - {config: [gcc13_py312, nohpmc], build_runner: [self-hosted,jetstream2,CPU], test_runner: ubuntu-latest, test_docker_options: '' }
-        - {config: [gcc13_py312, nomd, nohpmc], build_runner: [self-hosted,jetstream2,CPU], test_runner: ubuntu-latest, test_docker_options: '' }
-        - {config: [cuda120_gcc11_py310, mpi, llvm, debug], build_runner: [self-hosted,jetstream2,CPU], test_runner: [self-hosted,GPU], test_docker_options: '--gpus=all --device /dev/nvidia0 --device /dev/nvidia1 --device /dev/nvidia-uvm --device /dev/nvidia-uvm-tools --device /dev/nvidiactl' }
-        - {config: [cuda120_gcc11_py310, mpi, llvm], build_runner: [self-hosted,jetstream2,CPU], test_runner: [self-hosted,GPU], test_docker_options: '--gpus=all --device /dev/nvidia0 --device /dev/nvidia1 --device /dev/nvidia-uvm --device /dev/nvidia-uvm-tools --device /dev/nvidiactl' }
-        - {config: [cuda120_gcc11_py310], build_runner: [self-hosted,jetstream2,CPU], test_runner: [self-hosted,GPU], test_docker_options: '--gpus=all --device /dev/nvidia0 --device /dev/nvidia1 --device /dev/nvidia-uvm --device /dev/nvidia-uvm-tools --device /dev/nvidiactl' }
-        - {config: [gcc9_py39], build_runner: [self-hosted,jetstream2,CPU], test_runner: ubuntu-latest, test_docker_options: '' }
-
-    steps:
-    - name: Set Werror on recent compilers
-      run: |
-        echo "CXXFLAGS=-Werror" >> $GITHUB_ENV
-      if: ${{ !startsWith(matrix.config[0], 'gcc7') }}
-    - name: Clean workspace
-      run: ( shopt -s dotglob nullglob; rm -rf ./* )
-      shell: bash
-    - name: Checkout
-      uses: actions/checkout@v4.1.4
-      with:
-        path: code
-        submodules: true
-
-    - name: Configure
-      run: |
-        mkdir -p build
-        cd build
-        if [[ ${BUILD_DEBUG} == "true" ]]; then BUILD_TYPE="Debug"; else BUILD_TYPE="Release"; fi
-        echo "BUILD_TYPE=${BUILD_TYPE}"
-        cmake ../code -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(matrix.config[0], 'cuda') }}
-        ENABLE_MPI: ${{ contains(matrix.config, 'mpi') }}
-        ENABLE_TBB: ${{ contains(matrix.config, 'tbb') }}
-        ENABLE_LLVM: ${{ contains(matrix.config, 'llvm') }}
-        BUILD_MD: ${{ !contains(matrix.config, 'nomd') }}
-        BUILD_HPMC: ${{ !contains(matrix.config, 'nohpmc') }}
-        BUILD_DEBUG: ${{ contains(matrix.config, 'debug') }}
-      shell: bash
-    - name: Build
-      run: ninja install -j $(($(getconf _NPROCESSORS_ONLN) + 2))
-      working-directory: build
-    - name: Configure plugins
-      run : |
-        mkdir -p build-example-plugins
-        cd build-example-plugins
-        if [[ ${BUILD_DEBUG} == "true" ]]; then BUILD_TYPE="Debug"; else BUILD_TYPE="Release"; fi
-        echo "BUILD_TYPE=${BUILD_TYPE}"
-        CMAKE_PREFIX_PATH=${GITHUB_WORKSPACE}/install cmake ../code/example_plugins -GNinja -DCMAKE_BUILD_TYPE=${BUILD_TYPE}
-      env:
-        BUILD_DEBUG: ${{ contains(matrix.config, 'debug') }}
-      shell: bash
-    - name: Build plugins
-      run: ninja install -j $(($(getconf _NPROCESSORS_ONLN) + 2))
-      working-directory: build-example-plugins
-
-    - name: Remove object files
-      run: find build -type f -name '*.o' -delete
-    # Tar the build directory to preserve permissions and reduce HTTP requests on upload.
-    - 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
-    # Upload the tarballs. Retain the file for a limited time in case developers need to download
-    # and run tests locally for further debugging.
-    - name: 'Upload build'
-      uses: actions/upload-artifact@v4.3.3
-      with:
-        name: build-${{ join(matrix.config, '_') }}-${{ github.sha }}
-        path: build.tar
-        retention-days: 7
-    - name: 'Upload install'
-      uses: actions/upload-artifact@v4.3.3
-      with:
-        name: install-${{ join(matrix.config, '_') }}-${{ 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 $HOME/* )
-      shell: bash
-
-
-  pytest:
-    name: Run pytest [${{ join(matrix.config, '_') }}]
-    needs: build
-    runs-on: ${{ matrix.test_runner }}
-    container:
-      image: glotzerlab/ci:2024.06.04-${{ matrix.config[0] }}
-      options: ${{ matrix.test_docker_options }} -e CUDA_VISIBLE_DEVICES
-    strategy:
-      matrix:
-        include:
-        - {config: [clang14_py311, mpi, tbb, llvm], build_runner: [self-hosted,jetstream2,CPU], test_runner: ubuntu-latest, test_docker_options: '' }
-        - {config: [gcc13_py312], build_runner: [self-hosted,jetstream2,CPU], test_runner: ubuntu-latest, test_docker_options: '' }
-        - {config: [gcc13_py312, nomd], build_runner: [self-hosted,jetstream2,CPU], test_runner: ubuntu-latest, test_docker_options: '' }
-        - {config: [gcc13_py312, nohpmc], build_runner: [self-hosted,jetstream2,CPU], test_runner: ubuntu-latest, test_docker_options: '' }
-        - {config: [gcc13_py312, nomd, nohpmc], build_runner: [self-hosted,jetstream2,CPU], test_runner: ubuntu-latest, test_docker_options: '' }
-        - {config: [cuda120_gcc11_py310, mpi, llvm, debug], build_runner: [self-hosted,jetstream2,CPU], test_runner: [self-hosted,GPU], test_docker_options: '--gpus=all --device /dev/nvidia0 --device /dev/nvidia1 --device /dev/nvidia-uvm --device /dev/nvidia-uvm-tools --device /dev/nvidiactl' }
-        - {config: [cuda120_gcc11_py310, mpi, llvm], build_runner: [self-hosted,jetstream2,CPU], test_runner: [self-hosted,GPU], test_docker_options: '--gpus=all --device /dev/nvidia0 --device /dev/nvidia1 --device /dev/nvidia-uvm --device /dev/nvidia-uvm-tools --device /dev/nvidiactl' }
-        - {config: [cuda120_gcc11_py310], build_runner: [self-hosted,jetstream2,CPU], test_runner: [self-hosted,GPU], test_docker_options: '--gpus=all --device /dev/nvidia0 --device /dev/nvidia1 --device /dev/nvidia-uvm --device /dev/nvidia-uvm-tools --device /dev/nvidiactl' }
-        - {config: [gcc9_py39], build_runner: [self-hosted,jetstream2,CPU], test_runner: ubuntu-latest, test_docker_options: '' }
-
-    steps:
-    - name: Clean workspace
-      run: ( shopt -s dotglob nullglob; rm -rf ./* )
-      shell: bash
-    - name: Checkout
-      uses: actions/checkout@v4.1.4
-      with:
-        path: code
-        submodules: true
-
-    - name: Download install
-      uses: actions/download-artifact@v4.1.7
-      with:
-        name: install-${{ join(matrix.config, '_') }}-${{ github.sha }}
-    - name: Untar install
-      run: tar --use-compress-program='zstd -10 -T0' -xvf install.tar
-
-    - 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(matrix.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(matrix.config[0], '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(matrix.config[0], 'cuda') && contains(matrix.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
-
-    - name: Clean workspace
-      run: ( shopt -s dotglob nullglob; rm -rf ./* )
-      shell: bash
-    - name: Clean HOME
-      run: ( shopt -s dotglob nullglob; rm -rf $HOME/* )
-      shell: bash
-
-
-  ctest:
-    name: Run ctest [${{ join(matrix.config, '_') }}]
-    needs: build
-    runs-on: ${{ matrix.test_runner }}
-    container:
-      image: glotzerlab/ci:2024.06.04-${{ matrix.config[0] }}
-      options: ${{ matrix.test_docker_options }} -e CUDA_VISIBLE_DEVICES
-    strategy:
-      matrix:
-        include:
-        - {config: [clang14_py311, mpi, tbb, llvm], build_runner: [self-hosted,jetstream2,CPU], test_runner: ubuntu-latest, test_docker_options: '' }
-        - {config: [gcc13_py312], build_runner: [self-hosted,jetstream2,CPU], test_runner: ubuntu-latest, test_docker_options: '' }
-        - {config: [gcc13_py312, nomd], build_runner: [self-hosted,jetstream2,CPU], test_runner: ubuntu-latest, test_docker_options: '' }
-        - {config: [gcc13_py312, nohpmc], build_runner: [self-hosted,jetstream2,CPU], test_runner: ubuntu-latest, test_docker_options: '' }
-        - {config: [gcc13_py312, nomd, nohpmc], build_runner: [self-hosted,jetstream2,CPU], test_runner: ubuntu-latest, test_docker_options: '' }
-        - {config: [cuda120_gcc11_py310, mpi, llvm, debug], build_runner: [self-hosted,jetstream2,CPU], test_runner: [self-hosted,GPU], test_docker_options: '--gpus=all --device /dev/nvidia0 --device /dev/nvidia1 --device /dev/nvidia-uvm --device /dev/nvidia-uvm-tools --device /dev/nvidiactl' }
-        - {config: [cuda120_gcc11_py310, mpi, llvm], build_runner: [self-hosted,jetstream2,CPU], test_runner: [self-hosted,GPU], test_docker_options: '--gpus=all --device /dev/nvidia0 --device /dev/nvidia1 --device /dev/nvidia-uvm --device /dev/nvidia-uvm-tools --device /dev/nvidiactl' }
-        - {config: [cuda120_gcc11_py310], build_runner: [self-hosted,jetstream2,CPU], test_runner: [self-hosted,GPU], test_docker_options: '--gpus=all --device /dev/nvidia0 --device /dev/nvidia1 --device /dev/nvidia-uvm --device /dev/nvidia-uvm-tools --device /dev/nvidiactl' }
-        - {config: [gcc9_py39], build_runner: [self-hosted,jetstream2,CPU], test_runner: ubuntu-latest, test_docker_options: '' }
-
-    steps:
-    - name: Clean workspace
-      run: ( shopt -s dotglob nullglob; rm -rf ./* )
-      shell: bash
-    - name: Checkout
-      uses: actions/checkout@v4.1.4
-      with:
-        path: code
-        submodules: true
-
-    - name: Download build
-      uses: actions/download-artifact@v4.1.7
-      with:
-        name: build-${{ join(matrix.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 $HOME/* )
-      shell: bash
-
-
-  validate:
-    name: Validate [${{ join(matrix.config, '_') }}]
-    needs: build
-    runs-on: ${{ matrix.test_runner }}
-    container:
-      image: glotzerlab/ci:2024.06.04-${{ matrix.config[0] }}
-      options: ${{ matrix.test_docker_options }} -e CUDA_VISIBLE_DEVICES
-    strategy:
-      matrix:
-        include:
-        - {config: [clang14_py311, mpi, tbb, llvm], build_runner: [self-hosted,jetstream2,CPU], test_runner: ubuntu-latest, test_docker_options: '' }
-        - {config: [gcc13_py312], build_runner: [self-hosted,jetstream2,CPU], test_runner: ubuntu-latest, test_docker_options: '' }
-        - {config: [cuda120_gcc11_py310, mpi, llvm], build_runner: [self-hosted,jetstream2,CPU], test_runner: [self-hosted,GPU], test_docker_options: '--gpus=all --device /dev/nvidia0 --device /dev/nvidia1 --device /dev/nvidia-uvm --device /dev/nvidia-uvm-tools --device /dev/nvidiactl' }
-        - {config: [cuda120_gcc11_py310], build_runner: [self-hosted,jetstream2,CPU], test_runner: [self-hosted,GPU], test_docker_options: '--gpus=all --device /dev/nvidia0 --device /dev/nvidia1 --device /dev/nvidia-uvm --device /dev/nvidia-uvm-tools --device /dev/nvidiactl' }
-
-    if: ${{ contains(github.event.pull_request.labels.*.name, 'validate') }}
-    steps:
-    - name: Clean workspace
-      run: ( shopt -s dotglob nullglob; rm -rf ./* )
-      shell: bash
-    - name: Checkout
-      uses: actions/checkout@v4.1.4
-      with:
-        path: code
-        submodules: true
-
-    - name: Download install
-      uses: actions/download-artifact@v4.1.7
-      with:
-        name: install-${{ join(matrix.config, '_') }}-${{ github.sha }}
-    - name: Untar install
-      run: tar --use-compress-program='zstd -10 -T0' -xvf install.tar
-
-    - name: Run pytest (serial)
-      if: ${{ !contains(matrix.config, 'mpi') }}
-      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 (mpi)
-      if: ${{ contains(matrix.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 -p hoomd.pytest_plugin_validate -m validate --validate || (( cat pytest.out.1 && exit 1 ))
-    - name: Run howto guides (serial)
-      if: ${{ contains(matrix.config, 'llvm') }}  # 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 $HOME/* )
-      shell: bash
-
-
-  build_release:
-    name: Build [${{ join(matrix.config, '_') }}]
-    runs-on: ${{ matrix.build_runner }}
-    container:
-      image: glotzerlab/ci:2024.06.04-${{ matrix.config[0] }}
-    strategy:
-      matrix:
-        include:
-        - {config: [clang18_py312, mpi], build_runner: [self-hosted,jetstream2,CPU], test_runner: ubuntu-latest, test_docker_options: '' }
-        - {config: [clang17_py312, mpi], build_runner: [self-hosted,jetstream2,CPU], test_runner: ubuntu-latest, test_docker_options: '' }
-        - {config: [clang16_py312, mpi, llvm], build_runner: [self-hosted,jetstream2,CPU], test_runner: ubuntu-latest, test_docker_options: '' }
-        - {config: [clang15_py312, mpi, llvm], build_runner: [self-hosted,jetstream2,CPU], test_runner: ubuntu-latest, test_docker_options: '' }
-        - {config: [clang13_py310, llvm], build_runner: [self-hosted,jetstream2,CPU], test_runner: ubuntu-latest, test_docker_options: '' }
-        - {config: [clang12_py310, llvm], build_runner: [self-hosted,jetstream2,CPU], test_runner: ubuntu-latest, test_docker_options: '' }
-        - {config: [clang11_py310, llvm], build_runner: [self-hosted,jetstream2,CPU], test_runner: ubuntu-latest, test_docker_options: '' }
-        - {config: [gcc14_py312], build_runner: [self-hosted,jetstream2,CPU], test_runner: ubuntu-latest, test_docker_options: '' }
-        - {config: [gcc12_py311], build_runner: [self-hosted,jetstream2,CPU], test_runner: ubuntu-latest, test_docker_options: '' }
-        - {config: [gcc11_py310], build_runner: [self-hosted,jetstream2,CPU], test_runner: ubuntu-latest, test_docker_options: '' }
-        - {config: [gcc10_py310], build_runner: [self-hosted,jetstream2,CPU], test_runner: ubuntu-latest, test_docker_options: '' }
-        - {config: [cuda118_gcc11_py310, mpi, llvm], build_runner: [self-hosted,jetstream2,CPU], test_runner: [self-hosted,GPU], test_docker_options: '--gpus=all --device /dev/nvidia0 --device /dev/nvidia1 --device /dev/nvidia-uvm --device /dev/nvidia-uvm-tools --device /dev/nvidiactl' }
-        - {config: [cuda117_gcc11_py310, mpi, llvm], build_runner: [self-hosted,jetstream2,CPU], test_runner: [self-hosted,GPU], test_docker_options: '--gpus=all --device /dev/nvidia0 --device /dev/nvidia1 --device /dev/nvidia-uvm --device /dev/nvidia-uvm-tools --device /dev/nvidiactl' }
-
-    if: ${{ contains(github.event.pull_request.labels.*.name, 'release') }}
-    steps:
-    - name: Clean workspace
-      run: ( shopt -s dotglob nullglob; rm -rf ./* )
-      shell: bash
-    - name: Checkout
-      uses: actions/checkout@v4.1.4
-      with:
-        path: code
-        submodules: true
-
-    - name: Configure
-      run: |
-        mkdir -p build
-        cd build
-        if [[ ${BUILD_DEBUG} == "true" ]]; then BUILD_TYPE="Debug"; else BUILD_TYPE="Release"; fi
-        echo "BUILD_TYPE=${BUILD_TYPE}"
-        cmake ../code -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(matrix.config[0], 'cuda') }}
-        ENABLE_MPI: ${{ contains(matrix.config, 'mpi') }}
-        ENABLE_TBB: ${{ contains(matrix.config, 'tbb') }}
-        ENABLE_LLVM: ${{ contains(matrix.config, 'llvm') }}
-        BUILD_MD: ${{ !contains(matrix.config, 'nomd') }}
-        BUILD_HPMC: ${{ !contains(matrix.config, 'nohpmc') }}
-        BUILD_DEBUG: ${{ contains(matrix.config, 'debug') }}
-      shell: bash
-    - name: Build
-      run: ninja install -j $(($(getconf _NPROCESSORS_ONLN) + 2))
-      working-directory: build
-    - name: Configure plugins
-      run : |
-        mkdir -p build-example-plugins
-        cd build-example-plugins
-        if [[ ${BUILD_DEBUG} == "true" ]]; then BUILD_TYPE="Debug"; else BUILD_TYPE="Release"; fi
-        echo "BUILD_TYPE=${BUILD_TYPE}"
-        CMAKE_PREFIX_PATH=${GITHUB_WORKSPACE}/install cmake ../code/example_plugins -GNinja -DCMAKE_BUILD_TYPE=${BUILD_TYPE}
-      env:
-        BUILD_DEBUG: ${{ contains(matrix.config, 'debug') }}
-      shell: bash
-    - name: Build plugins
-      run: ninja install -j $(($(getconf _NPROCESSORS_ONLN) + 2))
-      working-directory: build-example-plugins
-
-    - name: Remove object files
-      run: find build -type f -name '*.o' -delete
-    # Tar the build directory to preserve permissions and reduce HTTP requests on upload.
-    - 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
-    # Upload the tarballs. Retain the file for a limited time in case developers need to download
-    # and run tests locally for further debugging.
-    - name: 'Upload build'
-      uses: actions/upload-artifact@v4.3.3
-      with:
-        name: build-${{ join(matrix.config, '_') }}-${{ github.sha }}
-        path: build.tar
-        retention-days: 7
-    - name: 'Upload install'
-      uses: actions/upload-artifact@v4.3.3
-      with:
-        name: install-${{ join(matrix.config, '_') }}-${{ 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 $HOME/* )
-      shell: bash
-
-
-  pytest_release:
-    name: Run pytest [${{ join(matrix.config, '_') }}]
-    needs: build_release
-    runs-on: ${{ matrix.test_runner }}
-    container:
-      image: glotzerlab/ci:2024.06.04-${{ matrix.config[0] }}
-      options: ${{ matrix.test_docker_options }} -e CUDA_VISIBLE_DEVICES
-    strategy:
-      matrix:
-        include:
-        - {config: [clang18_py312, mpi], build_runner: [self-hosted,jetstream2,CPU], test_runner: ubuntu-latest, test_docker_options: '' }
-        - {config: [clang17_py312, mpi], build_runner: [self-hosted,jetstream2,CPU], test_runner: ubuntu-latest, test_docker_options: '' }
-        - {config: [clang16_py312, mpi, llvm], build_runner: [self-hosted,jetstream2,CPU], test_runner: ubuntu-latest, test_docker_options: '' }
-        - {config: [clang15_py312, mpi, llvm], build_runner: [self-hosted,jetstream2,CPU], test_runner: ubuntu-latest, test_docker_options: '' }
-        - {config: [clang13_py310, llvm], build_runner: [self-hosted,jetstream2,CPU], test_runner: ubuntu-latest, test_docker_options: '' }
-        - {config: [clang12_py310, llvm], build_runner: [self-hosted,jetstream2,CPU], test_runner: ubuntu-latest, test_docker_options: '' }
-        - {config: [clang11_py310, llvm], build_runner: [self-hosted,jetstream2,CPU], test_runner: ubuntu-latest, test_docker_options: '' }
-        - {config: [gcc14_py312], build_runner: [self-hosted,jetstream2,CPU], test_runner: ubuntu-latest, test_docker_options: '' }
-        - {config: [gcc12_py311], build_runner: [self-hosted,jetstream2,CPU], test_runner: ubuntu-latest, test_docker_options: '' }
-        - {config: [gcc11_py310], build_runner: [self-hosted,jetstream2,CPU], test_runner: ubuntu-latest, test_docker_options: '' }
-        - {config: [gcc10_py310], build_runner: [self-hosted,jetstream2,CPU], test_runner: ubuntu-latest, test_docker_options: '' }
-        - {config: [cuda118_gcc11_py310, mpi, llvm], build_runner: [self-hosted,jetstream2,CPU], test_runner: [self-hosted,GPU], test_docker_options: '--gpus=all --device /dev/nvidia0 --device /dev/nvidia1 --device /dev/nvidia-uvm --device /dev/nvidia-uvm-tools --device /dev/nvidiactl' }
-        - {config: [cuda117_gcc11_py310, mpi, llvm], build_runner: [self-hosted,jetstream2,CPU], test_runner: [self-hosted,GPU], test_docker_options: '--gpus=all --device /dev/nvidia0 --device /dev/nvidia1 --device /dev/nvidia-uvm --device /dev/nvidia-uvm-tools --device /dev/nvidiactl' }
-
-    if: ${{ contains(github.event.pull_request.labels.*.name, 'release') }}
-    steps:
-    - name: Clean workspace
-      run: ( shopt -s dotglob nullglob; rm -rf ./* )
-      shell: bash
-    - name: Checkout
-      uses: actions/checkout@v4.1.4
-      with:
-        path: code
-        submodules: true
-
-    - name: Download install
-      uses: actions/download-artifact@v4.1.7
-      with:
-        name: install-${{ join(matrix.config, '_') }}-${{ github.sha }}
-    - name: Untar install
-      run: tar --use-compress-program='zstd -10 -T0' -xvf install.tar
-
-    - 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(matrix.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(matrix.config[0], '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(matrix.config[0], 'cuda') && contains(matrix.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
-
-    - name: Clean workspace
-      run: ( shopt -s dotglob nullglob; rm -rf ./* )
-      shell: bash
-    - name: Clean HOME
-      run: ( shopt -s dotglob nullglob; rm -rf $HOME/* )
-      shell: bash
-
-
-  ctest_release:
-    name: Run ctest [${{ join(matrix.config, '_') }}]
-    needs: build_release
-    runs-on: ${{ matrix.test_runner }}
-    container:
-      image: glotzerlab/ci:2024.06.04-${{ matrix.config[0] }}
-      options: ${{ matrix.test_docker_options }} -e CUDA_VISIBLE_DEVICES
-    strategy:
-      matrix:
-        include:
-        - {config: [clang18_py312, mpi], build_runner: [self-hosted,jetstream2,CPU], test_runner: ubuntu-latest, test_docker_options: '' }
-        - {config: [clang17_py312, mpi], build_runner: [self-hosted,jetstream2,CPU], test_runner: ubuntu-latest, test_docker_options: '' }
-        - {config: [clang16_py312, mpi, llvm], build_runner: [self-hosted,jetstream2,CPU], test_runner: ubuntu-latest, test_docker_options: '' }
-        - {config: [clang15_py312, mpi, llvm], build_runner: [self-hosted,jetstream2,CPU], test_runner: ubuntu-latest, test_docker_options: '' }
-        - {config: [clang13_py310, llvm], build_runner: [self-hosted,jetstream2,CPU], test_runner: ubuntu-latest, test_docker_options: '' }
-        - {config: [clang12_py310, llvm], build_runner: [self-hosted,jetstream2,CPU], test_runner: ubuntu-latest, test_docker_options: '' }
-        - {config: [clang11_py310, llvm], build_runner: [self-hosted,jetstream2,CPU], test_runner: ubuntu-latest, test_docker_options: '' }
-        - {config: [gcc14_py312], build_runner: [self-hosted,jetstream2,CPU], test_runner: ubuntu-latest, test_docker_options: '' }
-        - {config: [gcc12_py311], build_runner: [self-hosted,jetstream2,CPU], test_runner: ubuntu-latest, test_docker_options: '' }
-        - {config: [gcc11_py310], build_runner: [self-hosted,jetstream2,CPU], test_runner: ubuntu-latest, test_docker_options: '' }
-        - {config: [gcc10_py310], build_runner: [self-hosted,jetstream2,CPU], test_runner: ubuntu-latest, test_docker_options: '' }
-        - {config: [cuda118_gcc11_py310, mpi, llvm], build_runner: [self-hosted,jetstream2,CPU], test_runner: [self-hosted,GPU], test_docker_options: '--gpus=all --device /dev/nvidia0 --device /dev/nvidia1 --device /dev/nvidia-uvm --device /dev/nvidia-uvm-tools --device /dev/nvidiactl' }
-        - {config: [cuda117_gcc11_py310, mpi, llvm], build_runner: [self-hosted,jetstream2,CPU], test_runner: [self-hosted,GPU], test_docker_options: '--gpus=all --device /dev/nvidia0 --device /dev/nvidia1 --device /dev/nvidia-uvm --device /dev/nvidia-uvm-tools --device /dev/nvidiactl' }
-
-    if: ${{ contains(github.event.pull_request.labels.*.name, 'release') }}
-    steps:
-    - name: Clean workspace
-      run: ( shopt -s dotglob nullglob; rm -rf ./* )
-      shell: bash
-    - name: Checkout
-      uses: actions/checkout@v4.1.4
-      with:
-        path: code
-        submodules: true
-
-    - name: Download build
-      uses: actions/download-artifact@v4.1.7
-      with:
-        name: build-${{ join(matrix.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
-
-
-  # This job is used to provide a single requirement for branch merge conditions. GitHub considers
-  # the check passing even if it is skipped, so this job raises errors when required jobs were not
-  # run.
-  unit_tests_complete:
-    name: Unit test
-    needs: [pytest, ctest, validate]
-    if: ${{ always() && github.event_name == 'pull_request' }}
-    runs-on: ubuntu-latest
-
-    steps:
-      - name: Error if pytest did not succeed
-        if: needs.pytest.result != 'success'
-        run: echo "::error ::pytest tests failed." && exit 1
-      - name: Error if ctest did not succeed
-        if: needs.ctest.result != 'success'
-        run: echo "::error ::ctest tests failed." && exit 1
-      - name: Warn if validate did not run
-        if: needs.validate.result == 'skipped'
-        run: echo "::warning ::Skipped validation tests." && exit 1
-      - name: Error if validate did not succeed
-        if: needs.validate.result != 'success'
-        run: echo "::error ::Validation tests failed." && exit 1
-      - run: echo "Done!"
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index d09aceccb4..dac91ebd24 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -11,13 +11,6 @@ exclude: (?x)(
 repos:
 - repo: local
   hooks:
-  - id: make_workflows
-    name: make_workflows
-    language: python
-    entry: python3 .github/workflows/make_workflows.py
-    pass_filenames: false
-    always_run: true
-    additional_dependencies: [jinja2==3.1.2, pyyaml==6.0.1]
   - id: check-maintainer
     name: Check for maintainer comments
     description: 'Enforce that `maintainer` comments are removed.'

From 9e970fb1f326e7e38a1ea931c6827b327f5c245c Mon Sep 17 00:00:00 2001
From: "Joshua A. Anderson" <joaander@umich.edu>
Date: Thu, 6 Jun 2024 14:17:26 -0400
Subject: [PATCH 16/32] Switch to shared stale bot configuration.

---
 .github/workflows/stale.yaml | 11 ++++++++++
 .github/workflows/stale.yml  | 39 ------------------------------------
 2 files changed, 11 insertions(+), 39 deletions(-)
 create mode 100644 .github/workflows/stale.yaml
 delete mode 100644 .github/workflows/stale.yml

diff --git a/.github/workflows/stale.yaml b/.github/workflows/stale.yaml
new file mode 100644
index 0000000000..2a8cdf75af
--- /dev/null
+++ b/.github/workflows/stale.yaml
@@ -0,0 +1,11 @@
+name: Close stale issues and PRs
+
+on:
+  schedule:
+    - cron: '0 19 * * *'
+
+  workflow_dispatch:
+
+jobs:
+  stale:
+    uses: glotzerlab/workflows/.github/workflows/stale.yaml@5cfac9da9cb78e16ae97a9119b6fd13c1c2d6f5e # 0.1.0
diff --git a/.github/workflows/stale.yml b/.github/workflows/stale.yml
deleted file mode 100644
index e3c8161c7b..0000000000
--- a/.github/workflows/stale.yml
+++ /dev/null
@@ -1,39 +0,0 @@
-name: Close stale issues and PRs
-
-on:
-  schedule:
-    - cron: '0 19 * * *'
-
-  # Trigger on request.
-  workflow_dispatch:
-
-jobs:
-  stale:
-    runs-on: ubuntu-latest
-    steps:
-    - name: Run stale action
-      uses: actions/stale@v9.0.0
-      with:
-        operations-per-run: 120
-        delete-branch: true
-        days-before-close: 10
-        stale-issue-label: stale
-        stale-pr-label: stale
-        exempt-issue-labels: essential
-        exempt-pr-labels: essential
-
-        days-before-issue-stale: 260
-        stale-issue-message: >
-          This issue has been automatically marked as stale because it has not had
-          recent activity. It will be closed if no further activity occurs.
-        close-issue-message: >
-          This issue has been automatically closed because it has not had
-          recent activity.
-
-        days-before-pr-stale: 20
-        stale-pr-message: >
-          This pull request has been automatically marked as stale because it has not had
-          recent activity. It will be closed if no further activity occurs.
-        close-pr-message: >
-          This pull request has been automatically closed because it has not had
-          recent activity.

From 8566a854fc15e0127c20ae11ba44051dce269c73 Mon Sep 17 00:00:00 2001
From: "Joshua A. Anderson" <joaander@umich.edu>
Date: Thu, 6 Jun 2024 14:22:24 -0400
Subject: [PATCH 17/32] Refactor release workflow.

---
 .github/workflows/release.yaml | 95 ++++++++++++++++++++++++++++++++
 .github/workflows/release.yml  | 98 ----------------------------------
 2 files changed, 95 insertions(+), 98 deletions(-)
 create mode 100644 .github/workflows/release.yaml
 delete mode 100644 .github/workflows/release.yml

diff --git a/.github/workflows/release.yaml b/.github/workflows/release.yaml
new file mode 100644
index 0000000000..0802c287e3
--- /dev/null
+++ b/.github/workflows/release.yaml
@@ -0,0 +1,95 @@
+name: GitHub Release
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+on:
+  pull_request:
+
+  push:
+    branches:
+    - "trunk-*"
+    tags:
+      - "v*"
+
+  workflow_dispatch:
+
+
+env:
+  name: hoomd
+
+defaults:
+  run:
+    shell: bash
+
+
+jobs:
+  release:
+    name: Build release tarball
+    runs-on: ubuntu-latest
+
+    steps:
+    - name: Checkout
+      uses: actions/checkout@a5ac7e51b41094c92402da3b24376905380afc29 # v4.1.6
+      with:
+        fetch-depth: 0
+        submodules: true
+        path: code
+
+    - name: Install tools
+      run: sudo apt-get install pcregrep pandoc
+
+    - name: Determine last tag via git describe
+      if: ${{ ! startsWith(github.ref, 'refs/tags/v') }}
+      run: echo "tag=$(git describe --abbrev=0)" >> $GITHUB_ENV
+      working-directory: code
+
+    # git describe does not return the current tag in tag pushes on GitHub Actions, use GITHUB_REF instead
+    - name: Determine tag from GITHUB_REF
+      if:  startsWith(github.ref, 'refs/tags/v')
+      run: echo "tag=$(echo ${GITHUB_REF} | sed  -e 's/refs\/tags\///g')" >> $GITHUB_ENV
+
+    - name: Write version change log
+      run: .github/workflows/make-changelog-md.sh  ${tag:1} | tee ${GITHUB_WORKSPACE}/changelog.md
+      working-directory: code
+
+    - name: Copy source
+      run: cp -R code ${name}-${tag:1}
+
+    - name: Remove .git
+      run: rm -rf ${name}-${tag:1}/.git && ls -laR ${name}-${tag:1}
+
+    - name: Tar source
+      run: tar -cvzf ${name}-${tag:1}.tar.gz ${name}-${tag:1}
+
+    - name: Tar source
+      run: tar -cvJf ${name}-${tag:1}.tar.xz ${name}-${tag:1}
+
+    - name: Upload release files
+      uses: actions/upload-artifact@65462800fd760344b1a7b4382951275a0abb4808 # v4.3.3
+      with:
+        name: release
+        path: |
+          *.tar.gz
+          changelog.md
+
+  publish:
+    name: Publish [GitHub]
+    needs: [release]
+    runs-on: ubuntu-latest
+
+    steps:
+    - name: Download artifacts
+      uses: actions/download-artifact@65a9edc5881444af0b9093a5e628f2fe47ea3b2e # v4.1.7
+      with:
+        name: release
+
+    - name: Create release
+      uses: softprops/action-gh-release@69320dbe05506a9a39fc8ae11030b214ec2d1f87 # v2.0.5
+      if: startsWith(github.ref, 'refs/tags/v')
+      with:
+        files: "*.tar.*"
+        body_path: changelog.md
+      env:
+        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml
deleted file mode 100644
index 2a31363a83..0000000000
--- a/.github/workflows/release.yml
+++ /dev/null
@@ -1,98 +0,0 @@
-# Edit `release.yml` in `.github/workflows/templates` and run `make_workflows.py` to update the
-# workflow.
-name: GitHub Release
-
-concurrency:
-  group: ${{ github.workflow }}-${{ github.ref }}
-  cancel-in-progress: true
-
-on:
-  # Trigger on pull requests.
-  pull_request:
-
-  # Trigger on pushes to the trunk branches. This prevents building commits twice when the pull
-  # request source branch is in the same repository.
-  push:
-    branches:
-    - "trunk-*"
-    # Trigger on tags. Tag builds create GitHub releases with the change log and source tarball.
-    tags:
-      - "v*"
-
-  # Trigger on request.
-  workflow_dispatch:
-
-
-env:
-  name: hoomd
-
-defaults:
-  run:
-    shell: bash
-
-
-jobs:
-  release:
-    name: Build release tarball
-    runs-on: ubuntu-latest
-    container:
-      image: glotzerlab/ci:2024.06.04-ubuntu20.04
-
-    steps:
-      - name: Checkout
-        uses: actions/checkout@v4.1.4
-        with:
-          fetch-depth: 0
-          submodules: true
-          path: code
-
-      - name: Determine last tag via git describe
-        if: ${{ ! startsWith(github.ref, 'refs/tags/v') }}
-        run: echo "tag=$(git describe --abbrev=0)" >> $GITHUB_ENV
-        working-directory: code
-
-      # git describe does not return the current tag in tag pushes on GitHub Actions, use GITHUB_REF instead
-      - name: Determine tag from GITHUB_REF
-        if:  startsWith(github.ref, 'refs/tags/v')
-        run: echo "tag=$(echo ${GITHUB_REF} | sed  -e 's/refs\/tags\///g')" >> $GITHUB_ENV
-
-      - name: Write version change log
-        run: .github/workflows/make-changelog-md.sh  ${tag:1} | tee ${GITHUB_WORKSPACE}/changelog.md
-        working-directory: code
-
-      - name: Copy source
-        run: cp -R code ${name}-${tag:1}
-
-      - name: Remove .git
-        run: rm -rf ${name}-${tag:1}/.git && ls -laR ${name}-${tag:1}
-
-      - name: Tar source
-        run: tar -cvzf ${name}-${tag:1}.tar.gz ${name}-${tag:1}
-
-      - name: Upload release files
-        uses: actions/upload-artifact@v4.3.3
-        with:
-          name: release
-          path: |
-            *.tar.gz
-            changelog.md
-
-  publish:
-    name: Publish [GitHub]
-    needs: [release]
-    runs-on: ubuntu-latest
-
-    steps:
-      - name: Download artifacts
-        uses: actions/download-artifact@v4.1.7
-        with:
-          name: release
-
-      - name: Create release
-        uses: softprops/action-gh-release@v2.0.2
-        if: startsWith(github.ref, 'refs/tags/v')
-        with:
-          files: "*.tar.gz"
-          body_path: changelog.md
-        env:
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

From ea3e878ab29b3ad4173040bbf670a83605a379a4 Mon Sep 17 00:00:00 2001
From: "Joshua A. Anderson" <joaander@umich.edu>
Date: Thu, 6 Jun 2024 14:24:30 -0400
Subject: [PATCH 18/32] Remove debug code.

---
 .github/workflows/build_and_test.yaml | 12 ------------
 1 file changed, 12 deletions(-)

diff --git a/.github/workflows/build_and_test.yaml b/.github/workflows/build_and_test.yaml
index 06ad4c3a88..3cda6bae51 100644
--- a/.github/workflows/build_and_test.yaml
+++ b/.github/workflows/build_and_test.yaml
@@ -42,18 +42,6 @@ env:
   PYTHONPATH: ${{ github.workspace }}/install
 
 jobs:
-  debug:
-    runs-on: ubuntu-latest
-    steps:
-      - name: build_runner
-        run: echo '${{ inputs.build_runner }}'
-      - name: build_runner_from_json
-        run: echo '${{ fromJson(inputs.build_runner) }}'
-      - name: test_runner
-        run: echo '${{ inputs.test_runner }}'
-      - name: test_runner_from_json
-        run: echo '${{ fromJson(inputs.test_runner) }}'
-
   build:
     runs-on: ${{ fromJson(inputs.build_runner) }}
     container:

From 084019349c7d7a851a3623c2404c84e39f15f281 Mon Sep 17 00:00:00 2001
From: "Joshua A. Anderson" <joaander@umich.edu>
Date: Thu, 6 Jun 2024 14:25:39 -0400
Subject: [PATCH 19/32] Update GitHub actions with dependabot.

---
 .github/dependabot.yaml | 21 +++++++++++++++++++++
 1 file changed, 21 insertions(+)

diff --git a/.github/dependabot.yaml b/.github/dependabot.yaml
index e55f6a0839..87985bd108 100644
--- a/.github/dependabot.yaml
+++ b/.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

From 882f17e3608559b2ffaee212f27c2499a289ff03 Mon Sep 17 00:00:00 2001
From: "Joshua A. Anderson" <joaander@umich.edu>
Date: Thu, 6 Jun 2024 14:26:55 -0400
Subject: [PATCH 20/32] Run pre-commit.

---
 .github/workflows/build_and_test.yaml | 14 +++++++-------
 .github/workflows/test.yaml           |  6 +++---
 2 files changed, 10 insertions(+), 10 deletions(-)

diff --git a/.github/workflows/build_and_test.yaml b/.github/workflows/build_and_test.yaml
index 3cda6bae51..8150e64ad6 100644
--- a/.github/workflows/build_and_test.yaml
+++ b/.github/workflows/build_and_test.yaml
@@ -23,7 +23,7 @@ on:
       validate:
         type: string
         required: false
-      
+
 env:
   # prevent deadlocked MPI tests from causing the job to cancel
   MPIEXEC_TIMEOUT: 3000
@@ -87,11 +87,11 @@ jobs:
         BUILD_HPMC: ${{ !contains(inputs.config, 'nohpmc') }}
         BUILD_DEBUG: ${{ contains(inputs.config, 'debug') }}
       shell: bash
-      
+
     - name: Build
       run: ninja install -j $(($(getconf _NPROCESSORS_ONLN) + 2))
       working-directory: build
-      
+
     - name: Configure plugins
       run : |
         if [[ ${BUILD_DEBUG} == "true" ]]; then BUILD_TYPE="Debug"; else BUILD_TYPE="Release"; fi
@@ -100,20 +100,20 @@ jobs:
       env:
         BUILD_DEBUG: ${{ contains(inputs.config, 'debug') }}
       shell: bash
-      
+
     - name: Build plugins
       run: ninja install -j $(($(getconf _NPROCESSORS_ONLN) + 2))
       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:
diff --git a/.github/workflows/test.yaml b/.github/workflows/test.yaml
index c25139e03a..7ed0558870 100644
--- a/.github/workflows/test.yaml
+++ b/.github/workflows/test.yaml
@@ -56,11 +56,11 @@ jobs:
           validate: 'true'
 
         - config: [gcc13_py312, nomd]
-        
+
         - config: [gcc13_py312, nohpmc]
-        
+
         - config: [gcc13_py312, nomd, nohpmc]
-        
+
         - config: [cuda120_gcc11_py310, mpi, llvm, debug]
           test_runner: [self-hosted,GPU]
           test_docker_options: '--gpus=all --device /dev/nvidia0 --device /dev/nvidia1 --device /dev/nvidia-uvm --device /dev/nvidia-uvm-tools --device /dev/nvidiactl'

From feeedea5bc4b97e6b884a5c5b2cc0df2336081a6 Mon Sep 17 00:00:00 2001
From: "Joshua A. Anderson" <joaander@umich.edu>
Date: Thu, 6 Jun 2024 14:42:34 -0400
Subject: [PATCH 21/32] Pass full image name to reusable workflow.

---
 .github/workflows/build_and_test.yaml | 8 ++++----
 .github/workflows/test.yaml           | 4 ++--
 2 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/.github/workflows/build_and_test.yaml b/.github/workflows/build_and_test.yaml
index 8150e64ad6..b0822af312 100644
--- a/.github/workflows/build_and_test.yaml
+++ b/.github/workflows/build_and_test.yaml
@@ -6,7 +6,7 @@ on:
       config:
         type: string
         required: true
-      container_prefix:
+      image:
         type: string
         required: true
       build_runner:
@@ -45,7 +45,7 @@ jobs:
   build:
     runs-on: ${{ fromJson(inputs.build_runner) }}
     container:
-      image: glotzerlab/ci:2024.06.04-${{ inputs.container_prefix }}
+      image: ${{ inputs.image == '' && null || inputs.image }}
 
     steps:
     - name: Set Werror on recent compilers
@@ -139,7 +139,7 @@ jobs:
     needs: build
     runs-on: ${{ fromJson(inputs.test_runner) }}
     container:
-      image: glotzerlab/ci:2024.06.04-${{ inputs.container_prefix }}
+      image: ${{ inputs.image == '' && null || inputs.image }}
       options: ${{ inputs.test_docker_options }} -e CUDA_VISIBLE_DEVICES
 
     steps:
@@ -205,7 +205,7 @@ jobs:
     needs: build
     runs-on: ${{ fromJson(inputs.test_runner) }}
     container:
-      image: glotzerlab/ci:2024.06.04-${{ inputs.container_prefix }}
+      image: ${{ inputs.image == '' && null || inputs.image }}
       options: ${{ inputs.test_docker_options }} -e CUDA_VISIBLE_DEVICES
 
     steps:
diff --git a/.github/workflows/test.yaml b/.github/workflows/test.yaml
index 7ed0558870..d3fedbd0eb 100644
--- a/.github/workflows/test.yaml
+++ b/.github/workflows/test.yaml
@@ -26,7 +26,7 @@ jobs:
     uses: ./.github/workflows/build_and_test.yaml
     with:
       config: ${{ join(matrix.config, '_') }}
-      container_prefix: ${{ matrix.config[0] }}
+      image: glotzerlab/ci:2024.06.04-${{ matrix.config[0] }}
       # Use self-hosted runners or fall back to GitHub hosted runners when self-hosted are offline
       build_runner: ${{ needs.start_action_runners.outputs.active == '0' && toJson('ubuntu-latest') || '["self-hosted","jetstream2","CPU"]' }}
       # Default to ubuntu-latest when unset
@@ -74,7 +74,7 @@ jobs:
     uses: ./.github/workflows/build_and_test.yaml
     with:
       config: ${{ join(matrix.config, '_') }}
-      container_prefix: ${{ matrix.config[0] }}
+      image: glotzerlab/ci:2024.06.04-${{ matrix.config[0] }}
       # Use self-hosted runners or fall back to GitHub hosted runners when self-hosted are offline
       build_runner: ${{ needs.start_action_runners.outputs.active == '0' && toJson('ubuntu-latest') || '["self-hosted","jetstream2","CPU"]' }}
       # Default to ubuntu-latest when unset

From e39b0135ebce6e18897d28bdcd7e50b8a7351f83 Mon Sep 17 00:00:00 2001
From: "Joshua A. Anderson" <joaander@umich.edu>
Date: Thu, 6 Jun 2024 14:49:34 -0400
Subject: [PATCH 22/32] Document currently tested compilers.

---
 BUILDING.rst | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/BUILDING.rst b/BUILDING.rst
index 364554c03b..ee53f21856 100644
--- a/BUILDING.rst
+++ b/BUILDING.rst
@@ -77,7 +77,7 @@ Install prerequisites
 
 **General requirements:**
 
-- C++17 capable compiler (tested with ``gcc`` 9 - 13 and ``clang`` 10 - 16)
+- C++17 capable compiler (tested with ``gcc`` 9 - 14 and ``clang`` 10 - 18)
 - Python >= 3.9
 - NumPy >= 1.19
 - pybind11 >= 2.12

From bd5d505e245f3a293c0534db03ebf017f5fb1592 Mon Sep 17 00:00:00 2001
From: "Joshua A. Anderson" <joaander@umich.edu>
Date: Thu, 6 Jun 2024 15:22:40 -0400
Subject: [PATCH 23/32] Remove template specifier on constructors and
 destructors.

---
 hoomd/md/PotentialExternal.h | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/hoomd/md/PotentialExternal.h b/hoomd/md/PotentialExternal.h
index d637aca31c..700ae00c14 100644
--- a/hoomd/md/PotentialExternal.h
+++ b/hoomd/md/PotentialExternal.h
@@ -37,8 +37,8 @@ template<class evaluator> class PotentialExternal : public ForceCompute
     {
     public:
     //! Constructs the compute
-    PotentialExternal<evaluator>(std::shared_ptr<SystemDefinition> sysdef);
-    virtual ~PotentialExternal<evaluator>();
+    PotentialExternal(std::shared_ptr<SystemDefinition> sysdef);
+    virtual ~PotentialExternal();
 
     //! type of external potential parameters
     typedef typename evaluator::param_type param_type;

From ebd5581e860ebb90a648fd7726eae4adde3b4d57 Mon Sep 17 00:00:00 2001
From: "Joshua A. Anderson" <joaander@umich.edu>
Date: Thu, 6 Jun 2024 15:52:15 -0400
Subject: [PATCH 24/32] Use std::vector for variable MPI request arrays.

---
 .github/workflows/test.yaml |  2 +-
 hoomd/Communicator.cc       | 18 +++++++++---------
 hoomd/CommunicatorGPU.cc    | 30 +++++++++++++++---------------
 hoomd/HOOMDMPI.h            |  1 +
 hoomd/LoadBalancer.cc       | 10 +++++-----
 5 files changed, 31 insertions(+), 30 deletions(-)

diff --git a/.github/workflows/test.yaml b/.github/workflows/test.yaml
index d3fedbd0eb..65e1afecc1 100644
--- a/.github/workflows/test.yaml
+++ b/.github/workflows/test.yaml
@@ -94,7 +94,7 @@ jobs:
         - config: [clang13_py310, llvm]
         - config: [clang12_py310, llvm]
         - config: [clang11_py310, llvm]
-        - config: [gcc14_py312]
+        - config: [gcc14_py312, mpi]
         - config: [gcc12_py311]
         - config: [gcc11_py310]
         - config: [gcc10_py310]
diff --git a/hoomd/Communicator.cc b/hoomd/Communicator.cc
index 3b1165d2b3..67a8b0b30d 100644
--- a/hoomd/Communicator.cc
+++ b/hoomd/Communicator.cc
@@ -254,9 +254,9 @@ void Communicator::GroupCommunicator<group_data>::migrateGroups(bool incomplete,
         /*
          * communicate rank information (phase 1)
          */
-        unsigned int n_send_groups[m_comm.m_n_unique_neigh];
-        unsigned int n_recv_groups[m_comm.m_n_unique_neigh];
-        unsigned int offs[m_comm.m_n_unique_neigh];
+        std::vector<unsigned int> n_send_groups(m_comm.m_n_unique_neigh);
+        std::vector<unsigned int> n_recv_groups(m_comm.m_n_unique_neigh);
+        std::vector<unsigned int> offs(m_comm.m_n_unique_neigh);
         unsigned int n_recv_tot = 0;
 
             {
@@ -272,8 +272,8 @@ void Communicator::GroupCommunicator<group_data>::migrateGroups(bool incomplete,
             for (unsigned int ineigh = 0; ineigh < m_comm.m_n_unique_neigh; ineigh++)
                 n_send_groups[ineigh] = h_end.data[ineigh] - h_begin.data[ineigh];
 
-            MPI_Request req[2 * m_comm.m_n_unique_neigh];
-            MPI_Status stat[2 * m_comm.m_n_unique_neigh];
+            std::vector<MPI_Request> req(2 * m_comm.m_n_unique_neigh);
+            std::vector<MPI_Status> stat(2 * m_comm.m_n_unique_neigh);
 
             unsigned int nreq = 0;
 
@@ -299,7 +299,7 @@ void Communicator::GroupCommunicator<group_data>::migrateGroups(bool incomplete,
                           &req[nreq++]);
                 } // end neighbor loop
 
-            MPI_Waitall(nreq, req, stat);
+            MPI_Waitall(nreq, req.data(), stat.data());
 
             // sum up receive counts
             for (unsigned int ineigh = 0; ineigh < m_comm.m_n_unique_neigh; ineigh++)
@@ -601,8 +601,8 @@ void Communicator::GroupCommunicator<group_data>::migrateGroups(bool incomplete,
             for (unsigned int ineigh = 0; ineigh < m_comm.m_n_unique_neigh; ineigh++)
                 n_send_groups[ineigh] = h_end.data[ineigh] - h_begin.data[ineigh];
 
-            MPI_Request req[2 * m_comm.m_n_unique_neigh];
-            MPI_Status stat[2 * m_comm.m_n_unique_neigh];
+            std::vector<MPI_Request> req(2 * m_comm.m_n_unique_neigh);
+            std::vector<MPI_Status> stat(2 * m_comm.m_n_unique_neigh);
 
             unsigned int nreq = 0;
 
@@ -628,7 +628,7 @@ void Communicator::GroupCommunicator<group_data>::migrateGroups(bool incomplete,
                           &req[nreq++]);
                 } // end neighbor loop
 
-            MPI_Waitall(nreq, req, stat);
+            MPI_Waitall(nreq, req.data(), stat.data());
 
             // sum up receive counts
             for (unsigned int ineigh = 0; ineigh < m_comm.m_n_unique_neigh; ineigh++)
diff --git a/hoomd/CommunicatorGPU.cc b/hoomd/CommunicatorGPU.cc
index 6e14af15b2..b8f67b2a93 100644
--- a/hoomd/CommunicatorGPU.cc
+++ b/hoomd/CommunicatorGPU.cc
@@ -704,8 +704,8 @@ void CommunicatorGPU::GroupCommunicatorGPU<group_data>::migrateGroups(bool incom
             for (unsigned int ineigh = 0; ineigh < m_gpu_comm.m_n_unique_neigh; ineigh++)
                 n_send_groups[ineigh] = h_end.data[ineigh] - h_begin.data[ineigh];
 
-            MPI_Request req[2 * m_gpu_comm.m_n_unique_neigh];
-            MPI_Status stat[2 * m_gpu_comm.m_n_unique_neigh];
+            std::vector<MPI_Request> req(2 * m_gpu_comm.m_n_unique_neigh);
+            std::vector<MPI_Status> stat(2 * m_gpu_comm.m_n_unique_neigh);
 
             unsigned int nreq = 0;
 
@@ -733,7 +733,7 @@ void CommunicatorGPU::GroupCommunicatorGPU<group_data>::migrateGroups(bool incom
                 recv_bytes += (unsigned int)sizeof(unsigned int);
                 } // end neighbor loop
 
-            MPI_Waitall(nreq, req, stat);
+            MPI_Waitall(nreq, req.data(), stat.data());
 
             // sum up receive counts
             for (unsigned int ineigh = 0; ineigh < m_gpu_comm.m_n_unique_neigh; ineigh++)
@@ -1059,8 +1059,8 @@ void CommunicatorGPU::GroupCommunicatorGPU<group_data>::migrateGroups(bool incom
             for (unsigned int ineigh = 0; ineigh < m_gpu_comm.m_n_unique_neigh; ineigh++)
                 n_send_groups[ineigh] = h_end.data[ineigh] - h_begin.data[ineigh];
 
-            MPI_Request req[2 * m_gpu_comm.m_n_unique_neigh];
-            MPI_Status stat[2 * m_gpu_comm.m_n_unique_neigh];
+            std::vector<MPI_Request> req(2 * m_gpu_comm.m_n_unique_neigh);
+            std::vector<MPI_Status> stat(2 * m_gpu_comm.m_n_unique_neigh);
 
             unsigned int nreq = 0;
 
@@ -1088,7 +1088,7 @@ void CommunicatorGPU::GroupCommunicatorGPU<group_data>::migrateGroups(bool incom
                 recv_bytes += (unsigned int)sizeof(unsigned int);
                 } // end neighbor loop
 
-            MPI_Waitall(nreq, req, stat);
+            MPI_Waitall(nreq, req.data(), stat.data());
 
             // sum up receive counts
             for (unsigned int ineigh = 0; ineigh < m_gpu_comm.m_n_unique_neigh; ineigh++)
@@ -1488,8 +1488,8 @@ void CommunicatorGPU::GroupCommunicatorGPU<group_data>::exchangeGhostGroups(
                         = h_ghost_group_end.data[ineigh + stage * m_gpu_comm.m_n_unique_neigh]
                           - h_ghost_group_begin.data[ineigh + stage * m_gpu_comm.m_n_unique_neigh];
 
-                MPI_Request req[2 * m_gpu_comm.m_n_unique_neigh];
-                MPI_Status stat[2 * m_gpu_comm.m_n_unique_neigh];
+                std::vector<MPI_Request> req(2 * m_gpu_comm.m_n_unique_neigh);
+                std::vector<MPI_Status> stat(2 * m_gpu_comm.m_n_unique_neigh);
 
                 unsigned int nreq = 0;
 
@@ -1526,7 +1526,7 @@ void CommunicatorGPU::GroupCommunicatorGPU<group_data>::exchangeGhostGroups(
                     recv_bytes += (unsigned int)sizeof(unsigned int);
                     }
 
-                MPI_Waitall(nreq, req, stat);
+                MPI_Waitall(nreq, req.data(), stat.data());
 
                 // total up receive counts
                 for (unsigned int ineigh = 0; ineigh < m_gpu_comm.m_n_unique_neigh; ineigh++)
@@ -1902,8 +1902,8 @@ void CommunicatorGPU::migrateParticles()
             for (unsigned int ineigh = 0; ineigh < m_n_unique_neigh; ineigh++)
                 n_send_ptls[ineigh] = h_end.data[ineigh] - h_begin.data[ineigh];
 
-            MPI_Request req[2 * m_n_unique_neigh];
-            MPI_Status stat[2 * m_n_unique_neigh];
+            std::vector<MPI_Request> req(2 * m_n_unique_neigh);
+            std::vector<MPI_Status> stat(2 * m_n_unique_neigh);
 
             unsigned int nreq = 0;
 
@@ -1939,7 +1939,7 @@ void CommunicatorGPU::migrateParticles()
                 recv_bytes += (unsigned int)sizeof(unsigned int);
                 } // end neighbor loop
 
-            MPI_Waitall(nreq, req, stat);
+            MPI_Waitall(nreq, req.data(), stat.data());
 
             // sum up receive counts
             for (unsigned int ineigh = 0; ineigh < m_n_unique_neigh; ineigh++)
@@ -2405,8 +2405,8 @@ void CommunicatorGPU::exchangeGhosts()
                     = h_ghost_end.data[ineigh + stage * m_n_unique_neigh]
                       - h_ghost_begin.data[ineigh + stage * m_n_unique_neigh];
 
-            MPI_Request req[2 * m_n_unique_neigh];
-            MPI_Status stat[2 * m_n_unique_neigh];
+            std::vector<MPI_Request> req(2 * m_n_unique_neigh);
+            std::vector<MPI_Status> stat(2 * m_n_unique_neigh);
 
             unsigned int nreq = 0;
 
@@ -2443,7 +2443,7 @@ void CommunicatorGPU::exchangeGhosts()
                 recv_bytes += (unsigned int)sizeof(unsigned int);
                 }
 
-            MPI_Waitall(nreq, req, stat);
+            MPI_Waitall(nreq, req.data(), stat.data());
 
             // total up receive counts
             for (unsigned int ineigh = 0; ineigh < m_n_unique_neigh; ineigh++)
diff --git a/hoomd/HOOMDMPI.h b/hoomd/HOOMDMPI.h
index 58115e52b3..3cedc49212 100644
--- a/hoomd/HOOMDMPI.h
+++ b/hoomd/HOOMDMPI.h
@@ -20,6 +20,7 @@
 
 #include <mpi.h>
 
+#include <algorithm>
 #include <numeric>
 #include <queue>
 #include <sstream>
diff --git a/hoomd/LoadBalancer.cc b/hoomd/LoadBalancer.cc
index 38f9fce00a..1b4bde01e6 100644
--- a/hoomd/LoadBalancer.cc
+++ b/hoomd/LoadBalancer.cc
@@ -564,12 +564,12 @@ void LoadBalancer::computeOwnedParticles()
         }
     countParticlesOffRank(cnts);
 
-    MPI_Request req[2 * m_comm->getNUniqueNeighbors()];
-    MPI_Status stat[2 * m_comm->getNUniqueNeighbors()];
+    std::vector<MPI_Request> req(2 * m_comm->getNUniqueNeighbors());
+    std::vector<MPI_Status> stat(2 * m_comm->getNUniqueNeighbors());
     unsigned int nreq = 0;
 
-    unsigned int n_send_ptls[m_comm->getNUniqueNeighbors()];
-    unsigned int n_recv_ptls[m_comm->getNUniqueNeighbors()];
+    std::vector<unsigned int> n_send_ptls(m_comm->getNUniqueNeighbors());
+    std::vector<unsigned int> n_recv_ptls(m_comm->getNUniqueNeighbors());
     for (unsigned int cur_neigh = 0; cur_neigh < m_comm->getNUniqueNeighbors(); ++cur_neigh)
         {
         unsigned int neigh_rank = h_unique_neigh.data[cur_neigh];
@@ -590,7 +590,7 @@ void LoadBalancer::computeOwnedParticles()
                   m_mpi_comm,
                   &req[nreq++]);
         }
-    MPI_Waitall(nreq, req, stat);
+    MPI_Waitall(nreq, req.data(), stat.data());
 
     // reduce the particles sent to me
     int N_own = m_pdata->getN();

From 2d6e6cef62aa02978bba10989d1fbf95661a55a7 Mon Sep 17 00:00:00 2001
From: "Joshua A. Anderson" <joaander@umich.edu>
Date: Thu, 6 Jun 2024 16:21:49 -0400
Subject: [PATCH 25/32] Fix more variable arrays.

---
 .github/workflows/build_and_test.yaml | 4 ++--
 hoomd/md/NeighborList.cc              | 2 +-
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/build_and_test.yaml b/.github/workflows/build_and_test.yaml
index b0822af312..4a506a84df 100644
--- a/.github/workflows/build_and_test.yaml
+++ b/.github/workflows/build_and_test.yaml
@@ -89,7 +89,7 @@ jobs:
       shell: bash
 
     - name: Build
-      run: ninja install -j $(($(getconf _NPROCESSORS_ONLN) + 2))
+      run: ninja install -j $(($(getconf _NPROCESSORS_ONLN) + 2)) -k 0
       working-directory: build
 
     - name: Configure plugins
@@ -102,7 +102,7 @@ jobs:
       shell: bash
 
     - name: Build plugins
-      run: ninja install -j $(($(getconf _NPROCESSORS_ONLN) + 2))
+      run: ninja install -j $(($(getconf _NPROCESSORS_ONLN) + 2)) -k 0
       working-directory: build-example-plugins
 
     - name: Remove object files
diff --git a/hoomd/md/NeighborList.cc b/hoomd/md/NeighborList.cc
index f6d0ccd5bc..0a67d5db3c 100644
--- a/hoomd/md/NeighborList.cc
+++ b/hoomd/md/NeighborList.cc
@@ -750,7 +750,7 @@ pybind11::list NeighborList::getExclusions()
  */
 void NeighborList::countExclusions()
     {
-    unsigned int MAX_COUNT_EXCLUDED = 16;
+    constexpr unsigned int MAX_COUNT_EXCLUDED = 16;
     unsigned int excluded_count[MAX_COUNT_EXCLUDED + 2];
     unsigned int num_excluded, max_num_excluded;
 

From 43e20cd7df41c98df7110986410cb9bcb9c1e71b Mon Sep 17 00:00:00 2001
From: "Joshua A. Anderson" <joaander@umich.edu>
Date: Thu, 6 Jun 2024 16:32:04 -0400
Subject: [PATCH 26/32] Fix an uninitialized variable warning.

---
 hoomd/mpcd/test/communicator_mpi_test.cc | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/hoomd/mpcd/test/communicator_mpi_test.cc b/hoomd/mpcd/test/communicator_mpi_test.cc
index 118f1862e9..3a8af9bc02 100644
--- a/hoomd/mpcd/test/communicator_mpi_test.cc
+++ b/hoomd/mpcd/test/communicator_mpi_test.cc
@@ -480,7 +480,8 @@ void test_communicator_migrate(communicator_creator comm_creator,
     comm->migrateParticles(2);
         {
         unsigned int tag(0xffffffff), type(0xffffffff);
-        Scalar3 pos, vel;
+        Scalar3 pos = make_scalar3(0,0,0);
+        Scalar3 vel = make_scalar3(0,0,0);
 
         if (pdata->getN())
             {

From 0d7b90933086694e40ea23ac8e7cbb99d996020d Mon Sep 17 00:00:00 2001
From: "Joshua A. Anderson" <joaander@umich.edu>
Date: Thu, 6 Jun 2024 17:53:42 -0400
Subject: [PATCH 27/32] Fix more uses of VLAs.

---
 hoomd/hpmc/ShapeConvexPolyhedron.h |  2 ++
 hoomd/hpmc/ShapeUnion.h            |  6 +++---
 hoomd/hpmc/UpdaterMuVT.h           | 12 ++++++------
 3 files changed, 11 insertions(+), 9 deletions(-)

diff --git a/hoomd/hpmc/ShapeConvexPolyhedron.h b/hoomd/hpmc/ShapeConvexPolyhedron.h
index 561fcdf004..ee6e87f046 100644
--- a/hoomd/hpmc/ShapeConvexPolyhedron.h
+++ b/hoomd/hpmc/ShapeConvexPolyhedron.h
@@ -229,6 +229,8 @@ struct PolyhedronVertices : ShapeParams
     /// Z coordinate of vertices
     ManagedArray<ShortReal> z;
 
+    /// TODO: store aligned copy of d here for use in the support function.
+
     /** List of triangles hull_verts[3*i], hull_verts[3*i+1], hull_verts[3*i+2] making up the convex
         hull
     */
diff --git a/hoomd/hpmc/ShapeUnion.h b/hoomd/hpmc/ShapeUnion.h
index bfff2da48d..3967e4faf8 100644
--- a/hoomd/hpmc/ShapeUnion.h
+++ b/hoomd/hpmc/ShapeUnion.h
@@ -1124,13 +1124,13 @@ DEVICE inline bool sample_narrow_phase(RNG& rng,
                                                            r,
                                                            dim,
                                                            detail::SamplingMethod::accurate);
-    typename Shape::depletion_storage_type temp[ntemp];
+    std::vector<typename Shape::depletion_storage_type> temp(ntemp);
     unsigned int nelem = initializeDepletionTemporaryStorage(shape_i,
                                                              shape_j,
                                                              r_ij,
                                                              r,
                                                              dim,
-                                                             temp,
+                                                             temp.data(),
                                                              V,
                                                              detail::SamplingMethod::accurate);
 
@@ -1143,7 +1143,7 @@ DEVICE inline bool sample_narrow_phase(RNG& rng,
                                             p,
                                             dim,
                                             nelem,
-                                            temp,
+                                            temp.data(),
                                             detail::SamplingMethod::accurate))
         return false;
 
diff --git a/hoomd/hpmc/UpdaterMuVT.h b/hoomd/hpmc/UpdaterMuVT.h
index ccf4be40e0..f9b342e87e 100644
--- a/hoomd/hpmc/UpdaterMuVT.h
+++ b/hoomd/hpmc/UpdaterMuVT.h
@@ -1010,15 +1010,15 @@ template<class Shape> void UpdaterMuVT<Shape>::update(uint64_t timestep)
                              0,
                              m_exec_conf->getHOOMDWorldMPICommunicator(),
                              &stat);
-                    char s[n];
-                    MPI_Recv(s,
+                    std::vector<char> s(n);
+                    MPI_Recv(s.data(),
                              n,
                              MPI_CHAR,
                              m_gibbs_other,
                              0,
                              m_exec_conf->getHOOMDWorldMPICommunicator(),
                              &stat);
-                    type_name = std::string(s);
+                    type_name = std::string(s.data());
 
                     // resolve type name
                     type = m_pdata->getTypeByName(type_name);
@@ -1245,9 +1245,9 @@ template<class Shape> void UpdaterMuVT<Shape>::update(uint64_t timestep)
                              m_gibbs_other,
                              0,
                              m_exec_conf->getHOOMDWorldMPICommunicator());
-                    char s[n];
-                    memcpy(s, type_name.c_str(), n);
-                    MPI_Send(s,
+                    std::vector<char> s(n);
+                    memcpy(s.data(), type_name.c_str(), n);
+                    MPI_Send(s.data(),
                              n,
                              MPI_CHAR,
                              m_gibbs_other,

From c03d8cb63769c3760ff4e5e657001bc173c0bca5 Mon Sep 17 00:00:00 2001
From: "Joshua A. Anderson" <joaander@umich.edu>
Date: Mon, 10 Jun 2024 11:08:28 -0400
Subject: [PATCH 28/32] Inline much of the convex polyhedron overlap code.

---
 hoomd/VectorMath.h                 | 2 +-
 hoomd/hpmc/MinkowskiMath.h         | 2 +-
 hoomd/hpmc/ShapeConvexPolyhedron.h | 6 +++---
 hoomd/hpmc/XenoCollide3D.h         | 2 +-
 4 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/hoomd/VectorMath.h b/hoomd/VectorMath.h
index ec32096a9a..d570f299b9 100644
--- a/hoomd/VectorMath.h
+++ b/hoomd/VectorMath.h
@@ -1187,7 +1187,7 @@ template<class Real> struct rotmat3
 
     Multiplication is matrix multiplication, where the vector is represented as a column vector.
 */
-template<class Real> DEVICE inline vec3<Real> operator*(const rotmat3<Real>& A, const vec3<Real>& b)
+template<class Real> DEVICE inline __attribute__((always_inline)) vec3<Real> operator*(const rotmat3<Real>& A, const vec3<Real>& b)
     {
     return vec3<Real>(dot(A.row0, b), dot(A.row1, b), dot(A.row2, b));
     }
diff --git a/hoomd/hpmc/MinkowskiMath.h b/hoomd/hpmc/MinkowskiMath.h
index b4a14cddd4..72100a98c5 100644
--- a/hoomd/hpmc/MinkowskiMath.h
+++ b/hoomd/hpmc/MinkowskiMath.h
@@ -65,7 +65,7 @@ template<class SupportFuncA, class SupportFuncB> class CompositeSupportFunc3D
         \returns S_B(n) - S_A(n) in world space coords (transformations put n into local coords for
        S_A and S_b)
     */
-    DEVICE vec3<ShortReal> operator()(const vec3<ShortReal>& n) const
+    DEVICE inline __attribute__((always_inline)) vec3<ShortReal> operator()(const vec3<ShortReal>& n) const
         {
             // translation/rotation formula comes from pg 168 of "Games Programming Gems 7"
 #ifdef __HIPCC__
diff --git a/hoomd/hpmc/ShapeConvexPolyhedron.h b/hoomd/hpmc/ShapeConvexPolyhedron.h
index ee6e87f046..0e4ffe8527 100644
--- a/hoomd/hpmc/ShapeConvexPolyhedron.h
+++ b/hoomd/hpmc/ShapeConvexPolyhedron.h
@@ -270,7 +270,7 @@ class SupportFuncConvexPolyhedron
         Note that for performance it is assumed that unused vertices (beyond N) have already
         been set to zero.
     */
-    DEVICE SupportFuncConvexPolyhedron(const PolyhedronVertices& _verts,
+    DEVICE inline SupportFuncConvexPolyhedron(const PolyhedronVertices& _verts,
                                        ShortReal extra_sweep_radius = ShortReal(0.0))
         : verts(_verts), sweep_radius(extra_sweep_radius)
         {
@@ -281,7 +281,7 @@ class SupportFuncConvexPolyhedron
         @param n Normal vector input (in the local frame)
         @returns Local coords of the point furthest in the direction of n
     */
-    DEVICE vec3<ShortReal> operator()(const vec3<ShortReal>& n) const
+    DEVICE inline __attribute__((always_inline)) vec3<ShortReal> operator()(const vec3<ShortReal>& n) const
         {
         ShortReal max_dot = -(verts.diameter * verts.diameter);
         unsigned int max_idx = 0;
@@ -791,7 +791,7 @@ struct ShapeConvexPolyhedron
     @returns true when *a* and *b* overlap, and false when they are disjoint
 */
 template<>
-DEVICE inline bool test_overlap(const vec3<Scalar>& r_ab,
+DEVICE inline __attribute__((always_inline)) bool test_overlap(const vec3<Scalar>& r_ab,
                                 const ShapeConvexPolyhedron& a,
                                 const ShapeConvexPolyhedron& b,
                                 unsigned int& err)
diff --git a/hoomd/hpmc/XenoCollide3D.h b/hoomd/hpmc/XenoCollide3D.h
index fca8bc6814..80f0923c72 100644
--- a/hoomd/hpmc/XenoCollide3D.h
+++ b/hoomd/hpmc/XenoCollide3D.h
@@ -70,7 +70,7 @@ const unsigned int XENOCOLLIDE_3D_MAX_ITERATIONS = 1024;
     \ingroup minkowski
 */
 template<class SupportFuncA, class SupportFuncB>
-DEVICE inline bool xenocollide_3d(const SupportFuncA& sa,
+DEVICE inline __attribute__((always_inline)) bool xenocollide_3d(const SupportFuncA& sa,
                                   const SupportFuncB& sb,
                                   const vec3<ShortReal>& ab_t,
                                   const quat<ShortReal>& q,

From d1dbc61fc5df4de64d26b5c9f27fd3933149d35f Mon Sep 17 00:00:00 2001
From: "Joshua A. Anderson" <joaander@umich.edu>
Date: Mon, 10 Jun 2024 11:37:22 -0400
Subject: [PATCH 29/32] Replace scratchpad array with statically sized one.

The maximum size is 4096 vertices. I doubt any user is attempting such
a large vertex count polyhedron.
---
 hoomd/hpmc/ShapeConvexPolyhedron.h | 12 ++++++++++--
 1 file changed, 10 insertions(+), 2 deletions(-)

diff --git a/hoomd/hpmc/ShapeConvexPolyhedron.h b/hoomd/hpmc/ShapeConvexPolyhedron.h
index 0e4ffe8527..99ceaa3eef 100644
--- a/hoomd/hpmc/ShapeConvexPolyhedron.h
+++ b/hoomd/hpmc/ShapeConvexPolyhedron.h
@@ -43,6 +43,8 @@ namespace detail
 */
 struct PolyhedronVertices : ShapeParams
     {
+    static constexpr unsigned int MAX_VERTS = 4096;
+    
     /// Default constructor initializes zero values.
     DEVICE PolyhedronVertices()
         : n_hull_verts(0), N(0), diameter(ShortReal(0)), sweep_radius(ShortReal(0)), ignore(0)
@@ -81,6 +83,12 @@ struct PolyhedronVertices : ShapeParams
                   bool managed = false)
         {
         N = (unsigned int)verts.size();
+
+        if (N > MAX_VERTS)
+            {
+            throw std::domain_error("Too many vertices in polyhedron.");
+            }
+        
         diameter = 0;
         sweep_radius = sweep_radius_;
 
@@ -295,7 +303,7 @@ class SupportFuncConvexPolyhedron
             __m256 ny_v = _mm256_broadcast_ss(&n.y);
             __m256 nz_v = _mm256_broadcast_ss(&n.z);
             __m256 max_dot_v = _mm256_broadcast_ss(&max_dot);
-            float d_s[verts.x.size()] __attribute__((aligned(32)));
+            float d_s[PolyhedronVertices::MAX_VERTS] __attribute__((aligned(32)));
 
             for (unsigned int i = 0; i < verts.N; i += 8)
                 {
@@ -347,7 +355,7 @@ class SupportFuncConvexPolyhedron
             __m128 ny_v = _mm_load_ps1(&n.y);
             __m128 nz_v = _mm_load_ps1(&n.z);
             __m128 max_dot_v = _mm_load_ps1(&max_dot);
-            float d_s[verts.x.size()] __attribute__((aligned(16)));
+            float d_s[PolyhedronVertices::MAX_VERTS] __attribute__((aligned(16)));
 
             for (unsigned int i = 0; i < verts.N; i += 4)
                 {

From b16a9e9d560b60a1852552f39255d5590cc90d80 Mon Sep 17 00:00:00 2001
From: "Joshua A. Anderson" <joaander@umich.edu>
Date: Mon, 10 Jun 2024 11:38:30 -0400
Subject: [PATCH 30/32] Run pre-commit.

---
 hoomd/VectorMath.h                       |  4 +++-
 hoomd/hpmc/MinkowskiMath.h               |  3 ++-
 hoomd/hpmc/ShapeConvexPolyhedron.h       | 15 ++++++++-------
 hoomd/hpmc/XenoCollide3D.h               | 10 +++++-----
 hoomd/mpcd/test/communicator_mpi_test.cc |  4 ++--
 5 files changed, 20 insertions(+), 16 deletions(-)

diff --git a/hoomd/VectorMath.h b/hoomd/VectorMath.h
index d570f299b9..b1714c8a56 100644
--- a/hoomd/VectorMath.h
+++ b/hoomd/VectorMath.h
@@ -1187,7 +1187,9 @@ template<class Real> struct rotmat3
 
     Multiplication is matrix multiplication, where the vector is represented as a column vector.
 */
-template<class Real> DEVICE inline __attribute__((always_inline)) vec3<Real> operator*(const rotmat3<Real>& A, const vec3<Real>& b)
+template<class Real>
+DEVICE inline __attribute__((always_inline)) vec3<Real> operator*(const rotmat3<Real>& A,
+                                                                  const vec3<Real>& b)
     {
     return vec3<Real>(dot(A.row0, b), dot(A.row1, b), dot(A.row2, b));
     }
diff --git a/hoomd/hpmc/MinkowskiMath.h b/hoomd/hpmc/MinkowskiMath.h
index 72100a98c5..f0a1ea549c 100644
--- a/hoomd/hpmc/MinkowskiMath.h
+++ b/hoomd/hpmc/MinkowskiMath.h
@@ -65,7 +65,8 @@ template<class SupportFuncA, class SupportFuncB> class CompositeSupportFunc3D
         \returns S_B(n) - S_A(n) in world space coords (transformations put n into local coords for
        S_A and S_b)
     */
-    DEVICE inline __attribute__((always_inline)) vec3<ShortReal> operator()(const vec3<ShortReal>& n) const
+    DEVICE inline __attribute__((always_inline)) vec3<ShortReal>
+    operator()(const vec3<ShortReal>& n) const
         {
             // translation/rotation formula comes from pg 168 of "Games Programming Gems 7"
 #ifdef __HIPCC__
diff --git a/hoomd/hpmc/ShapeConvexPolyhedron.h b/hoomd/hpmc/ShapeConvexPolyhedron.h
index 99ceaa3eef..5f591fce59 100644
--- a/hoomd/hpmc/ShapeConvexPolyhedron.h
+++ b/hoomd/hpmc/ShapeConvexPolyhedron.h
@@ -44,7 +44,7 @@ namespace detail
 struct PolyhedronVertices : ShapeParams
     {
     static constexpr unsigned int MAX_VERTS = 4096;
-    
+
     /// Default constructor initializes zero values.
     DEVICE PolyhedronVertices()
         : n_hull_verts(0), N(0), diameter(ShortReal(0)), sweep_radius(ShortReal(0)), ignore(0)
@@ -88,7 +88,7 @@ struct PolyhedronVertices : ShapeParams
             {
             throw std::domain_error("Too many vertices in polyhedron.");
             }
-        
+
         diameter = 0;
         sweep_radius = sweep_radius_;
 
@@ -279,7 +279,7 @@ class SupportFuncConvexPolyhedron
         been set to zero.
     */
     DEVICE inline SupportFuncConvexPolyhedron(const PolyhedronVertices& _verts,
-                                       ShortReal extra_sweep_radius = ShortReal(0.0))
+                                              ShortReal extra_sweep_radius = ShortReal(0.0))
         : verts(_verts), sweep_radius(extra_sweep_radius)
         {
         }
@@ -289,7 +289,8 @@ class SupportFuncConvexPolyhedron
         @param n Normal vector input (in the local frame)
         @returns Local coords of the point furthest in the direction of n
     */
-    DEVICE inline __attribute__((always_inline)) vec3<ShortReal> operator()(const vec3<ShortReal>& n) const
+    DEVICE inline __attribute__((always_inline)) vec3<ShortReal>
+    operator()(const vec3<ShortReal>& n) const
         {
         ShortReal max_dot = -(verts.diameter * verts.diameter);
         unsigned int max_idx = 0;
@@ -800,9 +801,9 @@ struct ShapeConvexPolyhedron
 */
 template<>
 DEVICE inline __attribute__((always_inline)) bool test_overlap(const vec3<Scalar>& r_ab,
-                                const ShapeConvexPolyhedron& a,
-                                const ShapeConvexPolyhedron& b,
-                                unsigned int& err)
+                                                               const ShapeConvexPolyhedron& a,
+                                                               const ShapeConvexPolyhedron& b,
+                                                               unsigned int& err)
     {
     vec3<ShortReal> dr(r_ab);
 
diff --git a/hoomd/hpmc/XenoCollide3D.h b/hoomd/hpmc/XenoCollide3D.h
index 80f0923c72..6d5ca06ca4 100644
--- a/hoomd/hpmc/XenoCollide3D.h
+++ b/hoomd/hpmc/XenoCollide3D.h
@@ -71,11 +71,11 @@ const unsigned int XENOCOLLIDE_3D_MAX_ITERATIONS = 1024;
 */
 template<class SupportFuncA, class SupportFuncB>
 DEVICE inline __attribute__((always_inline)) bool xenocollide_3d(const SupportFuncA& sa,
-                                  const SupportFuncB& sb,
-                                  const vec3<ShortReal>& ab_t,
-                                  const quat<ShortReal>& q,
-                                  const ShortReal R,
-                                  unsigned int& err_count)
+                                                                 const SupportFuncB& sb,
+                                                                 const vec3<ShortReal>& ab_t,
+                                                                 const quat<ShortReal>& q,
+                                                                 const ShortReal R,
+                                                                 unsigned int& err_count)
     {
     // This implementation of XenoCollide is hand-written from the description of the algorithm on
     // page 171 of _Games Programming Gems 7_
diff --git a/hoomd/mpcd/test/communicator_mpi_test.cc b/hoomd/mpcd/test/communicator_mpi_test.cc
index 3a8af9bc02..77c3767f02 100644
--- a/hoomd/mpcd/test/communicator_mpi_test.cc
+++ b/hoomd/mpcd/test/communicator_mpi_test.cc
@@ -480,8 +480,8 @@ void test_communicator_migrate(communicator_creator comm_creator,
     comm->migrateParticles(2);
         {
         unsigned int tag(0xffffffff), type(0xffffffff);
-        Scalar3 pos = make_scalar3(0,0,0);
-        Scalar3 vel = make_scalar3(0,0,0);
+        Scalar3 pos = make_scalar3(0, 0, 0);
+        Scalar3 vel = make_scalar3(0, 0, 0);
 
         if (pdata->getN())
             {

From e6eaf30bc22cb2bd858c661e3b469504e921b653 Mon Sep 17 00:00:00 2001
From: "Joshua A. Anderson" <joaander@umich.edu>
Date: Mon, 10 Jun 2024 12:01:35 -0400
Subject: [PATCH 31/32] Fix VLA usage in PotentialTersoff.h.

---
 hoomd/md/PotentialTersoff.h | 16 +++++++++-------
 1 file changed, 9 insertions(+), 7 deletions(-)

diff --git a/hoomd/md/PotentialTersoff.h b/hoomd/md/PotentialTersoff.h
index 225f403555..398465746b 100644
--- a/hoomd/md/PotentialTersoff.h
+++ b/hoomd/md/PotentialTersoff.h
@@ -135,6 +135,9 @@ template<class evaluator> class PotentialTersoff : public ForceCompute
     // r_cut (not squared) given to the neighborlist
     std::shared_ptr<GlobalArray<Scalar>> m_r_cut_nlist;
 
+    // scratch pad memory per type
+    std::vector<Scalar> m_phi_ab;
+
     //! Actually compute the forces
     virtual void computeForces(uint64_t timestep);
     };
@@ -145,7 +148,8 @@ template<class evaluator> class PotentialTersoff : public ForceCompute
 template<class evaluator>
 PotentialTersoff<evaluator>::PotentialTersoff(std::shared_ptr<SystemDefinition> sysdef,
                                               std::shared_ptr<NeighborList> nlist)
-    : ForceCompute(sysdef), m_nlist(nlist), m_typpair_idx(m_pdata->getNTypes())
+    : ForceCompute(sysdef), m_nlist(nlist), m_typpair_idx(m_pdata->getNTypes()),
+      m_phi_ab(m_pdata->getNTypes())
     {
     this->m_exec_conf->msg->notice(5) << "Constructing PotentialTersoff" << std::endl;
 
@@ -605,12 +609,10 @@ template<class evaluator> void PotentialTersoff<evaluator>::computeForces(uint64
             Scalar viriali_yz(0.0);
             Scalar viriali_zz(0.0);
 
-            Scalar phi_ab[ntypes];
-
             // reset phi
             for (unsigned int typ_b = 0; typ_b < ntypes; ++typ_b)
                 {
-                phi_ab[typ_b] = Scalar(0.0);
+                m_phi_ab[typ_b] = Scalar(0.0);
                 }
 
             // all neighbors of this particle
@@ -645,7 +647,7 @@ template<class evaluator> void PotentialTersoff<evaluator>::computeForces(uint64
 
                     // evaluate the scalar per-neighbor contribution
                     evaluator eval(rij_sq, rcutsq, param);
-                    eval.evalPhi(phi_ab[typej]);
+                    eval.evalPhi(m_phi_ab[typej]);
                     }
 
                 // self-energy
@@ -656,7 +658,7 @@ template<class evaluator> void PotentialTersoff<evaluator>::computeForces(uint64
                     Scalar rcutsq = h_rcutsq.data[typpair_idx];
                     evaluator eval(Scalar(0.0), rcutsq, param);
                     Scalar energy(0.0);
-                    eval.evalSelfEnergy(energy, phi_ab[typ_b]);
+                    eval.evalSelfEnergy(energy, m_phi_ab[typ_b]);
                     pei += energy;
                     }
                 }
@@ -760,7 +762,7 @@ template<class evaluator> void PotentialTersoff<evaluator>::computeForces(uint64
                     Scalar force_divr = Scalar(0.0);
                     Scalar potential_eng = Scalar(0.0);
                     Scalar bij = Scalar(0.0);
-                    eval.evalForceij(fR, fA, chi, phi_ab[typej], bij, force_divr, potential_eng);
+                    eval.evalForceij(fR, fA, chi, m_phi_ab[typej], bij, force_divr, potential_eng);
 
                     // add this force to particle i
                     fi += force_divr * dxij;

From 5adc61c2aa08c310965bde45b7b5a8c1b10a2a40 Mon Sep 17 00:00:00 2001
From: "Joshua A. Anderson" <joaander@umich.edu>
Date: Mon, 10 Jun 2024 13:12:56 -0400
Subject: [PATCH 32/32] Test the latest compilers in the typical build
 configurations.

---
 .github/workflows/test.yaml | 11 ++++++-----
 1 file changed, 6 insertions(+), 5 deletions(-)

diff --git a/.github/workflows/test.yaml b/.github/workflows/test.yaml
index 65e1afecc1..3f809d189f 100644
--- a/.github/workflows/test.yaml
+++ b/.github/workflows/test.yaml
@@ -39,7 +39,7 @@ jobs:
       fail-fast: false
       matrix:
         include:
-        - config: [clang14_py311, mpi, tbb, llvm]
+        - config: [clang18_py312, mpi, tbb]
           validate: 'true'
 
         - config: [gcc13_py312]
@@ -55,11 +55,11 @@ jobs:
           test_docker_options: '--gpus=all --device /dev/nvidia0 --device /dev/nvidia1 --device /dev/nvidia-uvm --device /dev/nvidia-uvm-tools --device /dev/nvidiactl'
           validate: 'true'
 
-        - config: [gcc13_py312, nomd]
+        - config: [gcc14_py312, nomd]
 
-        - config: [gcc13_py312, nohpmc]
+        - config: [gcc14_py312, nohpmc]
 
-        - config: [gcc13_py312, nomd, nohpmc]
+        - config: [gcc14_py312, nomd, nohpmc]
 
         - config: [cuda120_gcc11_py310, mpi, llvm, debug]
           test_runner: [self-hosted,GPU]
@@ -91,10 +91,11 @@ jobs:
         - config: [clang17_py312, mpi]
         - config: [clang16_py312, mpi, llvm]
         - config: [clang15_py312, mpi, llvm]
+        - config: [clang14_py311, mpi, tbb, llvm]
         - config: [clang13_py310, llvm]
         - config: [clang12_py310, llvm]
         - config: [clang11_py310, llvm]
-        - config: [gcc14_py312, mpi]
+        - config: [gcc13_py312, mpi]
         - config: [gcc12_py311]
         - config: [gcc11_py310]
         - config: [gcc10_py310]