Add read for neurodata_types, e.g., Container, TimeSeries #353
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| name: Run tests | |
| on: | |
| push: | |
| branches: | |
| - main | |
| pull_request: | |
| #branches: | |
| #- main | |
| workflow_dispatch: | |
| jobs: | |
| test: | |
| defaults: | |
| run: | |
| shell: bash | |
| concurrency: | |
| group: ${{ github.workflow }}-${{ github.ref }}-${{ matrix.os }} | |
| cancel-in-progress: true | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: [macos-latest, ubuntu-latest] | |
| runs-on: ${{ matrix.os }} | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v4 | |
| - name: Install dependencies - ubuntu | |
| if: matrix.os == 'ubuntu-latest' | |
| run: | | |
| sudo apt-get update | |
| sudo apt-get install -y libhdf5-dev libboost-all-dev | |
| git clone https://github.com/catchorg/Catch2.git | |
| cd Catch2 | |
| git checkout "v3.5.3" | |
| cmake -Bbuild -H. -DBUILD_TESTING=OFF | |
| sudo cmake --build build/ --target install | |
| - name: Install dependencies - macos | |
| if: matrix.os == 'macos-latest' | |
| run: brew install hdf5 boost catch2 | |
| - name: Configure | |
| shell: pwsh | |
| run: cmake "--preset=ci-$("${{ matrix.os }}".split("-")[0])" | |
| - name: Build | |
| run: cmake --build build --config Release -j 2 | |
| - name: Install | |
| run: cmake --install build --config Release --prefix prefix | |
| - name: Test | |
| working-directory: build | |
| run: ctest --output-on-failure --no-tests=error -C Release -j 2 | |
| - name: Upload artifacts | |
| uses: actions/upload-artifact@v3 | |
| with: | |
| name: test-files-${{ matrix.os }} | |
| path: | | |
| build/tests/data/*.nwb | |
| sanitize: | |
| needs: test | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v4 | |
| - name: Install dependencies | |
| run: | | |
| sudo apt-get update | |
| sudo apt-get install -y libhdf5-dev libboost-all-dev | |
| git clone https://github.com/catchorg/Catch2.git | |
| cd Catch2 | |
| git checkout "v3.5.3" | |
| cmake -Bbuild -H. -DBUILD_TESTING=OFF | |
| sudo cmake --build build/ --target install | |
| - name: Configure | |
| run: cmake --preset=ci-sanitize | |
| - name: Build | |
| run: cmake --build build/sanitize -j 2 | |
| - name: Test | |
| working-directory: build/sanitize | |
| env: | |
| ASAN_OPTIONS: "strict_string_checks=1:\ | |
| detect_stack_use_after_return=1:\ | |
| check_initialization_order=1:\ | |
| strict_init_order=1:\ | |
| detect_leaks=1:\ | |
| halt_on_error=1" | |
| UBSAN_OPTIONS: "print_stacktrace=1:\ | |
| halt_on_error=1" | |
| run: ctest --output-on-failure --no-tests=error -j 2 | |
| validate: | |
| needs: [test, sanitize] | |
| defaults: | |
| run: | |
| shell: bash | |
| concurrency: | |
| group: ${{ github.workflow }}-${{ github.ref }}-${{ matrix.os }} | |
| cancel-in-progress: true | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: [macos-latest, ubuntu-latest] | |
| runs-on: ${{ matrix.os }} | |
| steps: | |
| - name: Download test files | |
| uses: actions/download-artifact@v3 | |
| with: | |
| name: test-files-${{ matrix.os }} | |
| path: nwb_files | |
| - name: Set up Python | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: '3.12' | |
| - name: Install pynwb and run validation | |
| run: | | |
| python -m pip install --upgrade pip | |
| python -m pip install nwbinspector | |
| nwbinspector nwb_files --threshold BEST_PRACTICE_VIOLATION |