Add CI for unit tests, flake8, wheels/sdist. (#2)

.github/actions/boost-cache/action.yml

@@ -0,0 +1,35 @@
+name: Cache Boost
+description: Caches Boost for an OS and a Boost minor version
+inputs:
+  boost_minor:
+    required: true
+  os:
+    required: true
+outputs:
+  cache-hit:
+    description: "Indicates if caching was successful"
+    value: ${{ steps.cache-boost.outputs.cache-hit }}
+  location:
+    description: "The path where Boost ends up"
+    value: "${{ github.workspace }}/boost"
+
+runs:
+  using: "composite"
+  steps:
+  - name: Cache Boost
+    uses: actions/cache@v3
+    id: cache-boost
+    env:
+      cache-name: cache-boost
+    with:
+      path: ${{ github.workspace }}/boost
+      key: ${{ inputs.os }}-boost-${{ inputs.boost_minor }}
+
+  - name: Install Boost
+    if: steps.cache-boost.outputs.cache-hit != 'true'
+    shell: bash
+    run: |
+      wget -qO- https://boostorg.jfrog.io/artifactory/main/release/1.${{ inputs.boost_minor }}.0/source/boost_1_${{ inputs.boost_minor }}_0.tar.bz2 | tar xjf -
+      cd boost_1_${{ inputs.boost_minor }}_0
+      ./bootstrap.sh
+      ./b2 --prefix=../boost --with-serialization --with-filesystem --with-test install

.github/actions/mpi-setup/action.yml

@@ -0,0 +1,14 @@
+name: Set up MPI
+description: Allows to use MPI in Github Actions by configuring oversubscription
+
+runs:
+  using: "composite"
+  steps:
+  - name: Set up MPI for Github Actions
+    shell: bash
+    run: |
+      mkdir -p "$HOME/.openmpi"
+      cat <<EOF > "$HOME/.openmpi/mca-params.conf"
+      rmaps_base_oversubscribe = true
+      rmaps_default_mapping_policy = :oversubscribe
+      EOF

.github/workflows/ctest.yml

@@ -0,0 +1,45 @@
+name: Run C++ tests
+
+on:
+  workflow_call:
+
+jobs:
+  build:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: ["ubuntu-latest", "macos-14"]
+        boost_minor: [85]
+
+    steps:
+    - uses: actions/checkout@v3
+      with:
+        submodules: true
+
+    - name: Install Ubuntu system dependencies
+      if: startsWith(matrix.os, 'ubuntu-')
+      run: |
+        sudo apt-get update
+        sudo apt-get install ninja-build libopenmpi-dev
+
+    - name: Install MacOs system dependencies
+      if: startsWith(matrix.os, 'macos-')
+      run: |
+        brew install ninja openmpi
+
+    - uses: ./.github/actions/boost-cache
+      id: cache-boost
+      with:
+        os: ${{ matrix.os }}
+        boost_minor: ${{ matrix.boost_minor }}
+
+    - name: Configure and build
+      run: |
+        cmake -B build -G Ninja -DCMAKE_PREFIX_PATH=${{ steps.cache-boost.outputs.location }} .
+        cmake --build build
+
+    - uses: ./.github/actions/mpi-setup
+
+    - name: Run CTest
+      run: |
+        ctest --test-dir build --output-on-failure

.github/workflows/main.yml

@@ -0,0 +1,39 @@
+name: Run all tests
+
+on:
+  push:
+    branches: ['main']
+    tags: ['v?[0-9]+.[0-9]+.[0-9]+']
+  pull_request:
+
+jobs:
+  cache_boost:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: ["ubuntu-latest", "macos-14"]
+        boost_minor: [85]
+
+    steps:
+    - uses: actions/checkout@v4
+
+    - uses: ./.github/actions/boost-cache
+      id: cache-boost
+      with:
+        os: ${{ matrix.os }}
+        boost_minor: ${{ matrix.boost_minor }}
+
+  test_cxx:
+    uses: ./.github/workflows/ctest.yml
+    secrets: inherit
+    needs: [cache_boost]
+
+  test_python:
+    uses: ./.github/workflows/test.yml
+    secrets: inherit
+    needs: [cache_boost]
+
+  publish:
+    uses: ./.github/workflows/publish.yml
+    secrets: inherit
+    needs: [cache_boost]

.github/workflows/publish.yml

@@ -0,0 +1,142 @@
+name: Publish wheels and sdist tarball to PyPi
+
+on:
+  workflow_call:
+
+jobs:
+  build_sdist:
+    name: Build source distribution
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v3
+      with:
+        submodules: true
+        fetch-depth: 0
+
+    - name: Set up Python 3.12
+      uses: actions/setup-python@v4
+      with:
+        python-version: 3.12
+
+    - name: Build a source tarball
+      run: |
+        python -m pip install build
+        python -m build -s
+
+    - name: Store sdist as artifact
+      uses: actions/upload-artifact@v3
+      with:
+        name: dist
+        path: dist/*.tar.gz
+
+  test_sdist:
+    name: Test source distribution
+
+    runs-on: ubuntu-latest
+    needs: [build_sdist]
+
+    steps:
+    - uses: actions/checkout@v3
+      with:
+        submodules: true
+
+    - name: Set up Python 3.12
+      uses: actions/setup-python@v4
+      with:
+        python-version: 3.12
+
+    - name: Download artifacts produced during the build_wheels and build_sdist jobs
+      uses: actions/download-artifact@v3
+      with:
+        name: dist
+        path: dist/
+
+    - uses: ./.github/actions/boost-cache
+      id: cache-boost
+      with:
+        os: ubuntu-latest
+        boost_minor: 85
+
+    - name: Install system dependencies
+      run: |
+        sudo apt-get update
+        sudo apt-get install -y libopenmpi-dev
+
+    - uses: ./.github/actions/mpi-setup
+
+    - name: Install package, clean local directory
+      run: |
+        export CMAKE_PREFIX_PATH=${{ steps.cache-boost.outputs.location }}
+        export SKBUILD_CMAKE_DEFINE="CMAKE_INSTALL_RPATH_USE_LINK_PATH=ON"
+        python -m pip install dist/*
+        python -m pip install mock mpi4py pytest pytest-mpi pytest-xdist
+
+    - name: Run tests
+      run: |
+        pytest -n 3 tests
+
+  build_wheels:
+    name: Build wheels on ${{ matrix.os }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ubuntu-latest]
+
+    steps:
+    - uses: actions/checkout@v4
+      with:
+        submodules: true
+        fetch-depth: 0
+
+    # Used to host cibuildwheel
+    - uses: actions/setup-python@v5
+
+    - name: Install cibuildwheel
+      run: python -m pip install cibuildwheel==2.18.1
+
+    - name: Build wheels
+      run: python -m cibuildwheel --output-dir dist
+      env:
+        CIBW_TEST_COMMAND: "pytest {project}/tests"
+
+    - uses: actions/upload-artifact@v4
+      with:
+        name: cibw-wheels-${{ matrix.os }}-${{ strategy.job-index }}
+        path: ./dist/*.whl
+
+  publish:
+    name: Publish package to PyPI
+    if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags')
+
+    runs-on: ubuntu-latest
+    needs: [build_wheels, build_sdist, test_sdist]
+
+    environment:
+      name: publish_pypi
+      url: https://pypi.org/p/brain-indexer
+
+    permissions:
+      id-token: write  # IMPORTANT: this permission is mandatory for trusted publishing
+
+    steps:
+    - name: Download artifacts produced by the build_sdist job
+      uses: actions/download-artifact@v3
+      with:
+        name: dist
+        path: dist/
+
+    - name: Download artifacts produced by the build_wheels job
+      uses: actions/download-artifact@v3
+      with:
+        pattern: cibw-wheels-*
+        path: dist/
+        merge-multiple: true
+
+    - name: Display structure of downloaded files
+      run: ls -R
+      working-directory: dist
+
+    - name: Publish source distribution package to PyPI
+      uses: pypa/gh-action-pypi-publish@release/v1
+      with:
+        packages_dir: dist/

.github/workflows/test.yml

@@ -0,0 +1,56 @@
+name: Run Python tests and lint
+
+on:
+  workflow_call:
+
+jobs:
+  build:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: ["ubuntu-latest", "macos-14"]
+        boost_minor: [85]
+        python-version: ['3.11', '3.12']
+        toxenv: ['py3']
+        include:
+          - os: 'ubuntu-latest'
+            python-version: '3.12'
+            toxenv: 'flake8'
+
+    steps:
+    - uses: actions/checkout@v3
+      with:
+        submodules: true
+
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v4
+      with:
+        python-version: ${{ matrix.python-version }}
+
+    - name: Install Ubuntu system dependencies
+      if: startsWith(matrix.os, 'ubuntu-')
+      run: |
+        sudo apt-get update
+        sudo apt-get install libopenmpi-dev
+
+    - name: Install MacOs system dependencies
+      if: startsWith(matrix.os, 'macos-')
+      run: |
+        brew install openmpi
+
+    - uses: ./.github/actions/boost-cache
+      id: cache-boost
+      with:
+        os: ${{ matrix.os }}
+        boost_minor: ${{ matrix.boost_minor }}
+
+    - name: Install Python dependencies
+      run: |
+        python -m pip install --upgrade pip
+        python -m pip install tox
+
+    - name: Test with tox
+      run: |
+        export CMAKE_PREFIX_PATH=${{ steps.cache-boost.outputs.location }}
+        export SKBUILD_CMAKE_DEFINE="CMAKE_INSTALL_RPATH_USE_LINK_PATH=ON"
+        tox -e ${{ matrix.toxenv }}

pyproject.toml

@@ -2,7 +2,7 @@
 name = "brain-indexer"
 description = "A spatial index implementation for spheres, morphologies and synapses"
 authors = [{ name="Blue Brain Project", email = "bbp-ou-hpc@epfl.ch" } ]
-license = {text = "Blue Brain Project Licence"}
+license = {"file" = "LICENSE.txt"}
 # maintainer is the field chosen for docs `contributors`
 maintainers = [{name="Fernando Pereira"}, {name="Antonio Bellotta"}, {name="Luc Dominic Grosheintz-Laval"}]
 dynamic = ["version"]
@@ -68,14 +68,27 @@ SI_UNIT_TESTS="OFF"
 [tool.setuptools_scm]
 
 [tool.cibuildwheel]
-skip = ["pp*", "*-win32", "*-manylinux_i686", "*-musllinux_i686", "*-musllinux_x86_64", "*-musllinux_aarch64"]
+skip = ["cp3{6,7,8,9}-*", "pp*", "*-win32", "*-manylinux_i686", "*-musllinux_i686", "*-musllinux_x86_64", "*-musllinux_aarch64"]
 test-requires = ["pytest", "pytest-mpi"]
 test-command = ["python -m pytest {project}/tests"]
 
 [tool.cibuildwheel.config-settings]
 # for redistributable wheels, MPI support should not be enabled (until MPI settles on a standard ABI: https://github.com/mpi-forum/mpi-issues/issues/751)
 "cmake.define.SI_MPI"="OFF"
 
+[tool.cibuildwheel.linux]
+before-all = """
+yum install -y wget
+wget -qO- https://boostorg.jfrog.io/artifactory/main/release/1.85.0/source/boost_1_85_0.tar.bz2 | tar xjf -
+cd boost_1_85_0
+./bootstrap.sh
+./b2 --prefix=/opt/boost --with-serialization --with-filesystem --with-test install
+"""
+
+[tool.cibuildwheel.linux.environment]
+CMAKE_PREFIX_PATH = "/opt/boost"
+SKBUILD_CMAKE_DEFINE = "CMAKE_INSTALL_RPATH_USE_LINK_PATH=ON"
+
 [tool.cibuildwheel.macos]
 environment = { MACOSX_DEPLOYMENT_TARGET = "10.15" }