Add C++ DynamicArrays in Brian2 for runtime mode
#1525
Workflow file for this run
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| name: TestSuite | |
| on: [push, pull_request] | |
| jobs: | |
| get_python_versions: | |
| name: "Determine Python versions" | |
| runs-on: ubuntu-latest | |
| outputs: | |
| min-python: ${{ steps.nep29.outputs.min-python }} | |
| max-python: ${{ steps.nep29.outputs.max-python }} | |
| steps: | |
| - name: "calculate versions according to NEP29" | |
| id: nep29 | |
| uses: mstimberg/github-calc-nep29@a73481e4e8488a5fa0b3be70a385cc5206a261ba # v0.7 | |
| with: | |
| token: ${{ secrets.GITHUB_TOKEN }} | |
| pre-commit: | |
| name: Run linters with pre-commit | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4.2.2 | |
| with: | |
| persist-credentials: false | |
| - uses: actions/setup-python@a26af69be951a213d495a4c3e4e4022e16d87065 # v5.6.0 | |
| with: | |
| python-version: '3.12' | |
| cache: 'pip' | |
| cache-dependency-path: .devcontainer/dev-requirements.txt | |
| - name: Install deps | |
| run: pip3 install -r .devcontainer/dev-requirements.txt | |
| - name: Run pre-commit hooks | |
| run: pre-commit run --all-files --show-diff-on-failure | |
| testing: | |
| needs: [get_python_versions, pre-commit] | |
| name: "Python ${{ matrix.python-version }} on ${{ matrix.os.image }} (standalone: ${{ matrix.standalone }}, 32bit: ${{ matrix.float_dtype_32 }})" | |
| runs-on: ${{ matrix.os.image }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: [{image: ubuntu-24.04, triplet: x64-linux}, | |
| {image: windows-2022, triplet: x64-windows}, | |
| {image: macOS-13, triplet: x64-osx}, | |
| {image: macOS-14, triplet: arm64-osx}] | |
| standalone: [false, true] | |
| float_dtype_32: [false, true] | |
| python-version: ["${{ needs.get_python_versions.outputs.max-python }}"] | |
| include: | |
| - os: {image: ubuntu-24.04, triplet: x64-linux} | |
| standalone: false | |
| python-version: "${{ needs.get_python_versions.outputs.min-python }} < 3.11.9 || ${{ needs.get_python_versions.outputs.min-python }} >= 3.12" | |
| float_dtype_32: false | |
| - os: {image: ubuntu-24.04, triplet: x64-linux} | |
| standalone: true | |
| python-version: "${{ needs.get_python_versions.outputs.min-python }} < 3.11.9 || ${{ needs.get_python_versions.outputs.min-python }} >= 3.12" | |
| float_dtype_32: false | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| steps: | |
| - name: Checkout Repository | |
| uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4.2.2 | |
| with: | |
| fetch-depth: 0 | |
| persist-credentials: false | |
| - name: Install GSL | |
| uses: johnwason/vcpkg-action@ff71808de10afc0e3160fd079353c69ba0d7dd60 # v7.0.0 | |
| id: vcpkg | |
| with: | |
| pkgs: gsl | |
| triplet: ${{ matrix.os.triplet }} | |
| cache-key: gsl-${{ matrix.os.triplet }} | |
| revision: master | |
| token: ${{ github.token }} | |
| - name: Set GSL preference for vcpkg | |
| shell: bash | |
| run: | | |
| mkdir ~/.brian/ | |
| # Replaces backslashes with forward slashes | |
| echo "GSL.directory=\"${{ github.workspace }}\\vcpkg\\installed\${{ matrix.os.triplet }}\\include"\" | tr '\\' '/' > ~/.brian/user_preferences | |
| cat ~/.brian/user_preferences | |
| - name: Install Python | |
| id: python | |
| uses: actions/setup-python@a26af69be951a213d495a4c3e4e4022e16d87065 # v5.6.0 | |
| with: | |
| cache: 'pip' | |
| python-version: ${{ matrix.python-version }} | |
| - name: Install Brian2 and dependencies | |
| env: | |
| PYTHON_BINARY: ${{ steps.python.outputs.python-path }} | |
| run: | | |
| "$PYTHON_BINARY" -m pip install .[test] | |
| - name: Determine Cython cache dir | |
| id: cython-cache | |
| run: | | |
| cd $GITHUB_WORKSPACE/.. # move out of the workspace to avoid direct import | |
| CACHE_DIR=$("$PYTHON_BINARY" -c 'from brian2.codegen.runtime.cython_rt.extension_manager import get_cython_cache_dir; print(get_cython_cache_dir())') | |
| echo "Cython cache dir: $CACHE_DIR" | |
| echo "cachedir=$CACHE_DIR" >> "$GITHUB_OUTPUT" | |
| env: | |
| PYTHON_BINARY: ${{ steps.python.outputs.python-path }} | |
| - name: restore Cython cache | |
| uses: actions/cache@5a3ec84eff668545956fd18022155c47e93e2684 # v4.2.3 | |
| if: ${{ ! matrix.standalone }} | |
| with: | |
| key: cython-extensions-${{ matrix.os.image }}-${{ matrix.python-version }}-32bit-${{ matrix.float_dtype_32 }} | |
| path: ${{ steps.cython-cache.outputs.cachedir }} | |
| - name: Run Tests | |
| run: | | |
| cd $GITHUB_WORKSPACE/.. && \ | |
| "$PYTHON_BINARY" $GITHUB_WORKSPACE/$SCRIPT_NAME && \ | |
| cp coverage.xml $GITHUB_WORKSPACE/ | |
| env: | |
| SCRIPT_NAME: dev/continuous-integration/run_test_suite.py | |
| SPHINX_DIR: ${{ github.workspace }}/docs_sphinx | |
| AGENT_OS: ${{runner.os}} | |
| STANDALONE: ${{ matrix.standalone }} | |
| FLOAT_DTYPE_32: ${{ matrix.float_dtype_32 }} | |
| PYTHON_BINARY: ${{ steps.python.outputs.python-path }} | |
| DO_NOT_RESET_PREFERENCES: true # Make sure that GSL setting is used | |
| - name: Send coverage to Coveralls (parallel) | |
| if: ${{ startsWith(matrix.os.image, 'ubuntu-') && matrix.python-version == needs.get_python_versions.outputs.max-python }} | |
| uses: coverallsapp/github-action@648a8eb78e6d50909eff900e4ec85cab4524a45b # v2.3.6 | |
| with: | |
| parallel: true | |
| flag-name: run ${{ join(matrix.*, ' - ') }} | |
| coveralls: | |
| name: Indicate completion to coveralls.io | |
| needs: testing | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Close parallel build | |
| uses: coverallsapp/github-action@648a8eb78e6d50909eff900e4ec85cab4524a45b # v2.3.6 | |
| with: | |
| parallel-finished: true | |
| test_doc_build: | |
| needs: get_python_versions | |
| name: Test building the documentation | |
| runs-on: ubuntu-latest | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| steps: | |
| - name: Checkout Repository | |
| uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4.2.2 | |
| with: | |
| fetch-depth: 0 | |
| persist-credentials: false | |
| submodules: true | |
| - name: Setup Conda and Python | |
| uses: conda-incubator/setup-miniconda@835234971496cad1653abb28a638a281cf32541f # v3.2.0 | |
| with: | |
| conda-remove-defaults: true | |
| auto-update-conda: true | |
| auto-activate-base: false | |
| miniforge-version: latest | |
| activate-environment: 'test_env' | |
| python-version: "${{ needs.get_python_versions.outputs.max-python }}" | |
| - name: Install dependencies | |
| run: pip install -r rtd-requirements.txt | |
| - name: Install brian2 | |
| run: pip install . | |
| - name: Build HTML documentation | |
| run: | | |
| cd docs_sphinx | |
| sphinx-build -b html . ../docs | |
| env: | |
| READTHEDOCS: True |