Merge pull request #1 from glotzerlab/initial-setup

Initial template

.bumpversion.cfg

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+[bumpversion]
+current_version = 0.0.0
+commit = False
+tag = False
+
+[bumpversion:file:src/version.py]
+
+[bumpversion:file:src/pytest/test_version.py]

.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: "/"
+    target-branch: trunk
+    schedule:
+      interval: "weekly"
+      time: "07:00"
+      timezone: "EST5EDT"
+    pull-request-branch-name:
+      separator: "-"
+    open-pull-requests-limit: 2

.github/release.yaml

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+changelog:
+  exclude:
+    authors:
+      - dependabot
+  categories:
+    - title: Added
+      labels:
+        - enhancement
+    - title: Fixed
+      labels:
+        - bug
+    - title: Changed
+      labels:
+        - "*"

.github/workflows/pre-commit.yaml

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+name: pre-commit
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+on:
+  pull_request:
+  push:
+    branches: [trunk]
+
+  workflow_dispatch:
+
+jobs:
+  pre-commit:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v4
+    - uses: actions/setup-python@v4
+      with:
+        python-version: '3.12'
+    - run: pip install pre-commit
+    - run: pre-commit run --all-files

.github/workflows/release.yaml

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+name: GitHub release
+
+on:
+  pull_request:
+
+  push:
+    branches:
+    - "trunk"
+    tags:
+      - "v*"
+
+  workflow_dispatch:
+
+permissions:
+  contents: write
+
+defaults:
+  run:
+    shell: bash
+
+jobs:
+  release:
+    name: Publish [GitHub]
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Determine version number
+        id: version
+        run: |
+          TAG=${{ github.ref_name }}
+          # Remove v from start of tag name
+          VERSION=${TAG#v}
+          # Replace / with - in merge names
+          VERSION=${VERSION//\//-}
+          echo "version=${VERSION}" >> "$GITHUB_OUTPUT"
+          echo "name=${{ github.event.repository.name }}-${VERSION}" >> "$GITHUB_OUTPUT"
+
+      - name: Checkout
+        uses: actions/checkout@v4
+        with:
+          submodules: true
+          path: ${{ steps.version.outputs.name }}
+
+      - name: Remove .git
+        run: |
+          rm -rf ${{ steps.version.outputs.name }}/.git
+          ls -laR ${{ steps.version.outputs.name }}
+
+      - name: Tar source
+        run: tar --zstd -cvf ${{ steps.version.outputs.name }}.tar.zst ${{ steps.version.outputs.name }}
+
+      - name: Create release
+        uses: softprops/action-gh-release@v1
+        if: startsWith(github.ref, 'refs/tags/v')
+        with:
+          files: "*.tar.zst"
+          name: ${{ steps.version.outputs.version }}
+          generate_release_notes: True
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

.github/workflows/unit-test.yaml

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+name: Unit test
+
+env:
+  # TODO: Set COMPONENT_NAME to the name of your Python package.
+  COMPONENT_NAME: template
+
+  # 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: 4.4.0
+  # 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"
+  # import HOOMD out of the build directory
+  PYTHONPATH: ${{ github.workspace }}/install
+
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+on:
+  pull_request:
+  push:
+    branches: [trunk]
+
+  workflow_dispatch:
+
+defaults:
+  run:
+    shell: bash
+
+jobs:
+  build_test:
+    name: Build and test [${{ matrix.name }}]
+    runs-on: ubuntu-latest
+    container:
+      image: glotzerlab/ci:2023.11.27-cuda120_gcc11_py310
+    strategy:
+      fail-fast: false
+      matrix:
+        include:
+        - name: 'CPU'
+          enable_gpu: 'OFF'
+          enable_mpi: 'OFF'
+        - name: 'CPU, MPI'
+          enable_gpu: 'OFF'
+          enable_mpi: 'ON'
+        - name: 'GPU'
+          enable_gpu: 'ON'
+          enable_mpi: 'OFF'
+        - name: 'GPU, MPI'
+          enable_gpu: 'ON'
+          enable_mpi: 'ON'
+
+    steps:
+    - name: Restore cached HOOMD-blue build
+      id: cache
+      uses: actions/cache/restore@v3
+      with:
+        path: install
+        key: hoomd-blue-${{ env.HOOMD_BLUE_VERSION }}-2023.11.27-cuda120_gcc11_py310-mpi-${{ matrix.enable_mpi }}-gpu-${{ matrix.enable_gpu }}
+    - name: Checkout HOOMD-blue
+      if: steps.cache.outputs.cache-hit != 'true'
+      uses: actions/checkout@v4
+      with:
+        repository: glotzerlab/hoomd-blue
+        path: hoomd-blue
+        submodules: true
+        ref: v${{ env.HOOMD_BLUE_VERSION }}
+    - name: Configure HOOMD-blue
+      if: steps.cache.outputs.cache-hit != 'true'
+      run: |
+        cmake -B build-hoomd-blue -S hoomd-blue \
+              -GNinja \
+              -DCMAKE_BUILD_TYPE=Release \
+              -DENABLE_GPU=${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@v3
+      with:
+        path: install
+        key: hoomd-blue-${{ env.HOOMD_BLUE_VERSION }}-2023.11.27-cuda120_gcc11_py310-mpi-${{ 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: 'trunk'
+  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: v0.2.0
+  hooks:
+  - id: fix-license-header
+    name: Fix license headers (Python)
+    types_or: [python]
+    args:
+    - --license-file=LICENSE
+    - --add=Part of HOOMD-blue, 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
+    - --add=Part of HOOMD-blue, 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
+    - --add=Part of HOOMD-blue, released under the BSD 3-Clause License.
+    - --keep-after=.. include
+    - --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: v0.1.4
+  hooks:
+    - id: ruff-format
+    - id: ruff

.ruff.toml

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+target-version = "py38"
+
+extend-select = [
+    "A",
+    "B",
+    "D",
+    "E501",
+    "EM",
+    "I",
+    "ICN",
+    "ISC",
+    "N",
+    "NPY",
+    "PL",
+    "PT",
+    "RET",
+    "RUF",
+    "UP",
+    "W",
+]
+
+ignore = [
+  "N806", "N803",  # Allow occasional use of uppercase variable and argument names (e.g. N).
+  "D107", # Do not document __init__ separately from the class.
+  "PLR09", # Allow "too many" statements/arguments/etc...
+  "N816", # Allow mixed case names like kT.
+]
+
+[lint.per-file-ignores]
+
+"__init__.py" = ["F401", # __init__.py import submodules for use by the package importer.
+]
+
+[pydocstyle]
+convention = "google"
+
+[format]
+quote-style = "single"
+
+[lint.flake8-import-conventions]
+# Prefer no import aliases
+aliases = {}
+# Always import hoomd without 'from'
+banned-from = ["hoomd"]
+
+# Ban standard import conventions and force common packages to be imported by their actual name.
+[lint.flake8-import-conventions.banned-aliases]
+"numpy" = ["np"]
+"pandas" = ["pd"]
+"matplotlib" = ["mpl"]