Merge pull request #87 from mphowardlab/azplugins-v1

Release azplugins v1

.clang-format

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+---
+BasedOnStyle: WebKit
+AccessModifierOffset: 0
+AlignAfterOpenBracket: Align
+AlignEscapedNewlines: 'Left'
+AlignOperands: 'true'
+AlignTrailingComments: 'true'
+AllowAllArgumentsOnNextLine: 'false'
+AllowAllParametersOfDeclarationOnNextLine: 'false'
+AllowShortFunctionsOnASingleLine: Empty
+AllowShortIfStatementsOnASingleLine: 'false'
+AllowShortLoopsOnASingleLine: 'false'
+BinPackArguments: 'false'
+BinPackParameters: 'false'
+BreakBeforeBraces: Whitesmiths
+BreakConstructorInitializers: BeforeColon
+ColumnLimit: '100'
+CompactNamespaces: 'true'
+Cpp11BracedListStyle: 'true'
+FixNamespaceComments: 'true'
+IndentWidth: '4'
+KeepEmptyLinesAtTheStartOfBlocks: false
+Language: Cpp
+NamespaceIndentation: None
+PointerAlignment: Left
+SortIncludes: 'true'
+SpaceAfterCStyleCast: 'false'
+SpaceAfterTemplateKeyword: 'false'
+SpaceBeforeParens: ControlStatements
+SpacesInAngles: 'false'
+SpaceInEmptyParentheses: false
+Standard: Cpp11
+TabWidth: '4'
+UseTab: Never
+
+...

.github/dependabot.yml

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+version: 2
+updates:
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      interval: "weekly"

.github/workflows/unit-test.yaml

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+name: Unit test
+
+env:
+  COMPONENT_NAME: azplugins
+
+  # Most components should not modify the rest of this file. When needed, merge in updates from
+  # https://github.com/glotzerlab/hoomd-component-template/
+
+  #############################################################################################
+  # HOOMD-blue version to build.
+  HOOMD_BLUE_VERSION: v4.8.2
+  # 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
+  PRTE_MCA_rmaps_default_mapping_policy: ":oversubscribe"
+  OMPI_MCA_rmaps_base_oversubscribe: "true"
+  # prevent errors from mis-configured openib systems
+  OMPI_MCA_btl: "vader,self"
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+on:
+  pull_request:
+  push:
+    branches: [main]
+
+  workflow_dispatch:
+
+defaults:
+  run:
+    shell: bash
+
+jobs:
+  build_test:
+    name: Build and test [${{ matrix.name }}]
+    runs-on: ubuntu-24.04
+    container:
+      image: nvidia/cuda:12.5.0-devel-ubuntu22.04
+    strategy:
+      fail-fast: false
+      matrix:
+        include:
+          - name: "CPU"
+            enable_gpu: "OFF"
+            enable_mpi: "OFF"
+          - name: "CPU, MPI"
+            enable_gpu: "OFF"
+            enable_mpi: "ON"
+          - name: "GPU"
+            enable_gpu: "ON"
+            enable_mpi: "OFF"
+          - name: "GPU, MPI"
+            enable_gpu: "ON"
+            enable_mpi: "ON"
+
+    steps:
+      - name: Restore cached HOOMD-blue build
+        id: cache
+        uses: actions/cache/restore@v4
+        with:
+          path: install
+          key: hoomd-blue-${{ env.HOOMD_BLUE_VERSION }}-${{ matrix.enable_mpi }}-gpu-${{ matrix.enable_gpu }}
+      - name: Install git
+        run: |
+          apt-get update
+          apt-get install git --yes
+      - name: Checkout HOOMD-blue
+        uses: actions/checkout@v4
+        with:
+          repository: glotzerlab/hoomd-blue
+          path: hoomd-blue
+          submodules: true
+          ref: ${{ env.HOOMD_BLUE_VERSION }}
+      - name: Create Python Environment
+        uses: mamba-org/setup-micromamba@v1
+        with:
+          environment-name: test
+          environment-file: hoomd-blue/.github/workflows/environments/py312-conda-lock.yml
+          micromamba-root-path: ${{ github.workspace }}/micromamba
+
+      - name: Configure conda environment variables
+        run: |
+          echo "PYTHONPATH=$GITHUB_WORKSPACE/install" >> $GITHUB_ENV
+          echo "CONDA_PREFIX=$MAMBA_ROOT_PREFIX/envs/test" >> $GITHUB_ENV
+          echo "CMAKE_PREFIX_PATH=$MAMBA_ROOT_PREFIX/envs/test" >> $GITHUB_ENV
+          echo "$MAMBA_ROOT_PREFIX/envs/test/bin" >> $GITHUB_PATH
+
+      - name: Configure HOOMD-blue
+        if: steps.cache.outputs.cache-hit != 'true'
+        run: |
+          cmake -B build-hoomd-blue -S hoomd-blue \
+                -GNinja \
+                -DCMAKE_BUILD_TYPE=Release \
+                -DENABLE_GPU=${ENABLE_GPU} \
+                -DENABLE_MPI=${ENABLE_MPI} \
+                -DCUDA_ARCH_LIST="70" \
+                -DBUILD_TESTING=OFF \
+                -DPLUGINS="" \
+                -DCMAKE_INSTALL_PREFIX=${GITHUB_WORKSPACE}/install
+        env:
+          ENABLE_GPU: ${{ matrix.enable_gpu }}
+          ENABLE_MPI: ${{ matrix.enable_mpi }}
+      - name: Build HOOMD-blue
+        if: steps.cache.outputs.cache-hit != 'true'
+        run: ninja install -j $(($(getconf _NPROCESSORS_ONLN) + 2))
+        working-directory: build-hoomd-blue
+      - name: Cache HOOMD-blue build
+        if: steps.cache.outputs.cache-hit != 'true'
+        uses: actions/cache/save@v4
+        with:
+          path: install
+          key: hoomd-blue-${{ env.HOOMD_BLUE_VERSION }}-${{ matrix.enable_mpi }}-gpu-${{ matrix.enable_gpu }}
+
+      - name: Checkout component
+        uses: actions/checkout@v4
+        with:
+          path: component
+      - name: Configure component
+        run: CMAKE_PREFIX_PATH=${GITHUB_WORKSPACE}/install cmake -S component -B build-component -GNinja -DCMAKE_BUILD_TYPE=Release
+      - name: Build component
+        run: ninja install -j $(($(getconf _NPROCESSORS_ONLN) + 2))
+        working-directory: build-component
+
+      - name: Run pytest (serial)
+        run: python3 -m pytest --pyargs hoomd.${COMPONENT_NAME} -x -v -ra --durations=0 --durations-min=0.1
+      - name: Run pytest (MPI)
+        if: ${{ matrix.enable_mpi == 'ON' }}
+        run: mpirun -n 2 ${GITHUB_WORKSPACE}/install/hoomd/pytest/pytest-openmpi.sh --pyargs hoomd.${COMPONENT_NAME} -x -v -ra --durations=0 --durations-min=0.1 || (( cat pytest.out.1 && exit 1 ))

.pre-commit-config.yaml

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+ci:
+  autoupdate_schedule: quarterly
+  autoupdate_branch: 'main'
+  autofix_prs: false
+
+repos:
+- repo: https://github.com/pre-commit/pre-commit-hooks
+  rev: 'v4.4.0'
+  hooks:
+  - id: end-of-file-fixer
+    exclude_types: [svg]
+  - id: trailing-whitespace
+    exclude_types: [svg]
+  - id: check-json
+  - id: check-yaml
+  - id: check-case-conflict
+  - id: fix-encoding-pragma
+    args:
+    - --remove
+  - id: mixed-line-ending
+- repo: https://github.com/glotzerlab/fix-license-header
+  rev: v0.3.2
+  hooks:
+  - id: fix-license-header
+    name: Fix license headers (Python)
+    types_or: [python]
+    args:
+    - --license-file=LICENSE
+    - --num=2
+    - --add=Part of azplugins, released under the BSD 3-Clause License.
+    - --keep-before=#!
+  - id: fix-license-header
+    name: Fix license headers (C)
+    types_or: [c, c++, cuda, inc]
+    args:
+    - --license-file=LICENSE
+    - --num=2
+    - --add=Part of azplugins, released under the BSD 3-Clause License.
+    - --comment-prefix=//
+  - id: fix-license-header
+    name: Fix license headers (reStructuredText)
+    types_or: [rst]
+    args:
+    - --license-file=LICENSE
+    - --num=2
+    - --add=Part of azplugins, released under the BSD 3-Clause License.
+    - --keep-after=.. include
+    - --keep-after=.. automodule
+    - --comment-prefix=..
+- repo: https://github.com/pre-commit/mirrors-clang-format
+  rev: v16.0.6
+  hooks:
+  - id: clang-format
+    types_or: [c, c++, cuda, inc]
+- repo: https://github.com/astral-sh/ruff-pre-commit
+  rev: v0.2.2
+  hooks:
+    - id: ruff-format
+    - id: ruff

.readthedocs.yaml

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+version: 2
+
+sphinx:
+  configuration: doc/conf.py
+  fail_on_warning: true
+
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "mambaforge-22.9"
+  jobs:
+    post_install:
+      - wget https://github.com/glotzerlab/hoomd-blue/releases/download/v4.8.2/hoomd-4.8.2.tar.gz
+      - tar -xzvf hoomd-4.8.2.tar.gz
+      - python doc/mock_install.py hoomd-4.8.2/hoomd src
+
+conda:
+  environment: doc/environment.yaml