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Merge pull request #87 from mphowardlab/azplugins-v1
Release azplugins v1
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‎.clang-format

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

‎.github/dependabot.yml

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

‎.github/workflows/test.yml

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‎.github/workflows/unit-test.yaml

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name: Unit test
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env:
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COMPONENT_NAME: azplugins
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# Most components should not modify the rest of this file. When needed, merge in updates from
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# https://github.com/glotzerlab/hoomd-component-template/
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#############################################################################################
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# HOOMD-blue version to build.
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HOOMD_BLUE_VERSION: v4.8.2
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# prevent deadlocked MPI tests from causing the job to cancel
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MPIEXEC_TIMEOUT: 3000
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# allow mpirun to execute as root in the tests
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OMPI_ALLOW_RUN_AS_ROOT: 1
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OMPI_ALLOW_RUN_AS_ROOT_CONFIRM: 1
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# allow openmpi to oversubscribe cores
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PRTE_MCA_rmaps_default_mapping_policy: ":oversubscribe"
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OMPI_MCA_rmaps_base_oversubscribe: "true"
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# prevent errors from mis-configured openib systems
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OMPI_MCA_btl: "vader,self"
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concurrency:
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group: ${{ github.workflow }}-${{ github.ref }}
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cancel-in-progress: true
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on:
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pull_request:
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push:
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branches: [main]
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workflow_dispatch:
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defaults:
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run:
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shell: bash
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jobs:
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build_test:
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name: Build and test [${{ matrix.name }}]
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runs-on: ubuntu-24.04
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container:
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image: nvidia/cuda:12.5.0-devel-ubuntu22.04
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strategy:
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fail-fast: false
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matrix:
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include:
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- name: "CPU"
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enable_gpu: "OFF"
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enable_mpi: "OFF"
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- name: "CPU, MPI"
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enable_gpu: "OFF"
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enable_mpi: "ON"
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- name: "GPU"
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enable_gpu: "ON"
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enable_mpi: "OFF"
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- name: "GPU, MPI"
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enable_gpu: "ON"
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enable_mpi: "ON"
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steps:
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- name: Restore cached HOOMD-blue build
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id: cache
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uses: actions/cache/restore@v4
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with:
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path: install
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key: hoomd-blue-${{ env.HOOMD_BLUE_VERSION }}-${{ matrix.enable_mpi }}-gpu-${{ matrix.enable_gpu }}
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- name: Install git
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run: |
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apt-get update
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apt-get install git --yes
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- name: Checkout HOOMD-blue
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uses: actions/checkout@v4
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with:
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repository: glotzerlab/hoomd-blue
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path: hoomd-blue
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submodules: true
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ref: ${{ env.HOOMD_BLUE_VERSION }}
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- name: Create Python Environment
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uses: mamba-org/setup-micromamba@v1
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with:
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environment-name: test
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environment-file: hoomd-blue/.github/workflows/environments/py312-conda-lock.yml
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micromamba-root-path: ${{ github.workspace }}/micromamba
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- name: Configure conda environment variables
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run: |
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echo "PYTHONPATH=$GITHUB_WORKSPACE/install" >> $GITHUB_ENV
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echo "CONDA_PREFIX=$MAMBA_ROOT_PREFIX/envs/test" >> $GITHUB_ENV
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echo "CMAKE_PREFIX_PATH=$MAMBA_ROOT_PREFIX/envs/test" >> $GITHUB_ENV
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echo "$MAMBA_ROOT_PREFIX/envs/test/bin" >> $GITHUB_PATH
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- name: Configure HOOMD-blue
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if: steps.cache.outputs.cache-hit != 'true'
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run: |
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cmake -B build-hoomd-blue -S hoomd-blue \
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-GNinja \
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-DCMAKE_BUILD_TYPE=Release \
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-DENABLE_GPU=${ENABLE_GPU} \
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-DENABLE_MPI=${ENABLE_MPI} \
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-DCUDA_ARCH_LIST="70" \
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-DBUILD_TESTING=OFF \
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-DPLUGINS="" \
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-DCMAKE_INSTALL_PREFIX=${GITHUB_WORKSPACE}/install
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env:
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ENABLE_GPU: ${{ matrix.enable_gpu }}
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ENABLE_MPI: ${{ matrix.enable_mpi }}
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- name: Build HOOMD-blue
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if: steps.cache.outputs.cache-hit != 'true'
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run: ninja install -j $(($(getconf _NPROCESSORS_ONLN) + 2))
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working-directory: build-hoomd-blue
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- name: Cache HOOMD-blue build
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if: steps.cache.outputs.cache-hit != 'true'
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uses: actions/cache/save@v4
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with:
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path: install
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key: hoomd-blue-${{ env.HOOMD_BLUE_VERSION }}-${{ matrix.enable_mpi }}-gpu-${{ matrix.enable_gpu }}
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- name: Checkout component
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uses: actions/checkout@v4
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with:
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path: component
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- name: Configure component
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run: CMAKE_PREFIX_PATH=${GITHUB_WORKSPACE}/install cmake -S component -B build-component -GNinja -DCMAKE_BUILD_TYPE=Release
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- name: Build component
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run: ninja install -j $(($(getconf _NPROCESSORS_ONLN) + 2))
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working-directory: build-component
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- name: Run pytest (serial)
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run: python3 -m pytest --pyargs hoomd.${COMPONENT_NAME} -x -v -ra --durations=0 --durations-min=0.1
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- name: Run pytest (MPI)
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if: ${{ matrix.enable_mpi == 'ON' }}
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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:
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autoupdate_schedule: quarterly
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autoupdate_branch: 'main'
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autofix_prs: false
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repos:
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- repo: https://github.com/pre-commit/pre-commit-hooks
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rev: 'v4.4.0'
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hooks:
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- id: end-of-file-fixer
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exclude_types: [svg]
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- id: trailing-whitespace
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exclude_types: [svg]
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- id: check-json
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- id: check-yaml
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- id: check-case-conflict
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- id: fix-encoding-pragma
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args:
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- --remove
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- id: mixed-line-ending
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- repo: https://github.com/glotzerlab/fix-license-header
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rev: v0.3.2
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hooks:
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- id: fix-license-header
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name: Fix license headers (Python)
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types_or: [python]
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args:
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- --license-file=LICENSE
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- --num=2
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- --add=Part of azplugins, released under the BSD 3-Clause License.
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- --keep-before=#!
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- id: fix-license-header
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name: Fix license headers (C)
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types_or: [c, c++, cuda, inc]
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args:
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- --license-file=LICENSE
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- --num=2
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- --add=Part of azplugins, released under the BSD 3-Clause License.
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- --comment-prefix=//
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- id: fix-license-header
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name: Fix license headers (reStructuredText)
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types_or: [rst]
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args:
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- --license-file=LICENSE
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- --num=2
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- --add=Part of azplugins, released under the BSD 3-Clause License.
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- --keep-after=.. include
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- --keep-after=.. automodule
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- --comment-prefix=..
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- repo: https://github.com/pre-commit/mirrors-clang-format
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rev: v16.0.6
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hooks:
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- id: clang-format
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types_or: [c, c++, cuda, inc]
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- repo: https://github.com/astral-sh/ruff-pre-commit
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rev: v0.2.2
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hooks:
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- id: ruff-format
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- id: ruff

‎.readthedocs.yaml

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

‎.readthedocs.yml

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