Fix S3 bugs and test writing to S3 #17
Workflow file for this run
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| name: Tests | |
| on: | |
| push: | |
| branches: | |
| - main | |
| pull_request: | |
| branches: | |
| - main | |
| env: | |
| BUILD_TYPE: Release | |
| concurrency: | |
| group: ${{ github.workflow }}-${{ github.ref }} | |
| cancel-in-progress: ${{ github.ref != 'refs/heads/main' }} | |
| jobs: | |
| test: | |
| name: Test on ${{ matrix.platform }} | |
| runs-on: ${{ matrix.platform }} | |
| timeout-minutes: 20 | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| platform: | |
| - "ubuntu-latest" | |
| - "windows-latest" | |
| - "macos-latest" | |
| include: | |
| - platform: "ubuntu-latest" | |
| vcpkg_triplet: "x64-linux" | |
| - platform: "windows-latest" | |
| vcpkg_triplet: "x64-windows-static" | |
| - platform: "macos-latest" | |
| vcpkg_triplet: "arm64-osx" | |
| permissions: | |
| actions: write | |
| steps: | |
| - uses: actions/checkout@v3 | |
| with: | |
| submodules: true | |
| ref: ${{ github.event.pull_request.head.sha }} | |
| - name: Install vcpkg | |
| run: | | |
| git clone https://github.com/microsoft/vcpkg.git | |
| cd vcpkg && ./bootstrap-vcpkg.sh | |
| echo "VCPKG_ROOT=${{github.workspace}}/vcpkg" >> $GITHUB_ENV | |
| echo "${{github.workspace}}/vcpkg" >> $GITHUB_PATH | |
| ./vcpkg integrate install | |
| shell: bash | |
| - name: Configure CMake | |
| run: | | |
| cmake --preset=default -DVCPKG_TARGET_TRIPLET=${{matrix.vcpkg_triplet}} | |
| cmake -B ${{github.workspace}}/build -DCMAKE_BUILD_TYPE=${{env.BUILD_TYPE}} | |
| - name: Build | |
| run: cmake --build ${{github.workspace}}/build --config ${{env.BUILD_TYPE}} | |
| - name: Test | |
| working-directory: ${{github.workspace}}/build | |
| run: ctest -C ${{env.BUILD_TYPE}} -L acquire-zarr --output-on-failure | |
| test_s3: | |
| name: Test S3 | |
| runs-on: ubuntu-latest | |
| env: | |
| MINIO_ROOT_USER: admin | |
| MINIO_ROOT_PASSWORD: password | |
| MINIO_URL: http://localhost:9000 | |
| MINIO_ALIAS: myminio | |
| MINIO_BUCKET: acquire-test | |
| MINIO_ACCESS_KEY: acquire | |
| MINIO_SECRET_KEY: 12345678 | |
| steps: | |
| - uses: actions/checkout@v3 | |
| with: | |
| submodules: true | |
| ref: ${{ github.event.pull_request.head.sha }} | |
| - name: Install minio and mcli | |
| run: | | |
| apt update && apt install -y tmux wget | |
| wget https://dl.min.io/server/minio/release/linux-amd64/minio -O /usr/local/bin/minio | |
| wget https://dl.min.io/client/mc/release/linux-amd64/mc -O /usr/local/bin/mcli | |
| chmod +x /usr/local/bin/minio | |
| chmod +x /usr/local/bin/mcli | |
| - name: Start minio in tmux | |
| run: | | |
| tmux new -d -s minio | |
| tmux send-keys -t minio "MINIO_ROOT_USER=$MINIO_ROOT_USER MINIO_ROOT_PASSWORD=$MINIO_ROOT_PASSWORD minio server /tmp/minio --console-address :9001" Enter | |
| sleep 5 | |
| mcli alias set $MINIO_ALIAS $MINIO_URL $MINIO_ROOT_USER $MINIO_ROOT_PASSWORD | |
| mcli admin user svcacct add --access-key $MINIO_ACCESS_KEY --secret-key $MINIO_SECRET_KEY $MINIO_ALIAS $MINIO_ROOT_USER | |
| - name: Create a bucket | |
| run: | | |
| mcli mb $MINIO_ALIAS/$MINIO_BUCKET | |
| - name: Install vcpkg | |
| run: | | |
| git clone https://github.com/microsoft/vcpkg.git | |
| cd vcpkg && ./bootstrap-vcpkg.sh | |
| echo "VCPKG_ROOT=${{github.workspace}}/vcpkg" >> $GITHUB_ENV | |
| echo "${{github.workspace}}/vcpkg" >> $GITHUB_PATH | |
| ./vcpkg integrate install | |
| shell: bash | |
| - name: Configure CMake | |
| run: | | |
| cmake --preset=default | |
| cmake -B ${{github.workspace}}/build -DCMAKE_BUILD_TYPE=${{env.BUILD_TYPE}} | |
| - name: Build | |
| run: cmake --build ${{github.workspace}}/build --config ${{env.BUILD_TYPE}} | |
| - name: Test | |
| working-directory: ${{github.workspace}}/build | |
| env: | |
| ZARR_S3_ENDPOINT: ${{ env.MINIO_URL }} | |
| ZARR_S3_BUCKET_NAME: ${{ env.MINIO_BUCKET }} | |
| ZARR_S3_ACCESS_KEY_ID: ${{ env.MINIO_ACCESS_KEY }} | |
| ZARR_S3_SECRET_ACCESS_KEY: ${{ env.MINIO_SECRET_KEY }} | |
| run: ctest -C ${{env.BUILD_TYPE}} -L s3 --output-on-failure | |
| test_python: | |
| name: Test Python on ${{ matrix.platform }} | |
| runs-on: ${{ matrix.platform }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| platform: | |
| - "ubuntu-latest" | |
| - "windows-latest" | |
| - "macos-latest" | |
| env: | |
| MINIO_ROOT_USER: admin | |
| MINIO_ROOT_PASSWORD: password | |
| MINIO_URL: http://localhost:9000 | |
| MINIO_ALIAS: myminio | |
| MINIO_BUCKET: acquire-test | |
| MINIO_ACCESS_KEY: acquire | |
| MINIO_SECRET_KEY: 12345678 | |
| steps: | |
| - uses: actions/checkout@v3 | |
| with: | |
| submodules: true | |
| ref: ${{ github.event.pull_request.head.sha }} | |
| - name: Set up Python 3.10 | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: "3.10" | |
| - name: Install minio and mcli | |
| run: | | |
| apt update && apt install -y tmux wget | |
| wget https://dl.min.io/server/minio/release/linux-amd64/minio -O /usr/local/bin/minio | |
| wget https://dl.min.io/client/mc/release/linux-amd64/mc -O /usr/local/bin/mcli | |
| chmod +x /usr/local/bin/minio | |
| chmod +x /usr/local/bin/mcli | |
| - name: Start minio in tmux | |
| run: | | |
| tmux new -d -s minio | |
| tmux send-keys -t minio "MINIO_ROOT_USER=$MINIO_ROOT_USER MINIO_ROOT_PASSWORD=$MINIO_ROOT_PASSWORD minio server /tmp/minio --console-address :9001" Enter | |
| sleep 5 | |
| mcli alias set $MINIO_ALIAS $MINIO_URL $MINIO_ROOT_USER $MINIO_ROOT_PASSWORD | |
| mcli admin user svcacct add --access-key $MINIO_ACCESS_KEY --secret-key $MINIO_SECRET_KEY $MINIO_ALIAS $MINIO_ROOT_USER | |
| - name: Create a bucket | |
| run: | | |
| mcli mb $MINIO_ALIAS/$MINIO_BUCKET | |
| - name: Install vcpkg | |
| run: | | |
| git clone https://github.com/microsoft/vcpkg.git | |
| cd vcpkg && ./bootstrap-vcpkg.sh | |
| echo "VCPKG_ROOT=${{github.workspace}}/vcpkg" >> $GITHUB_ENV | |
| echo "${{github.workspace}}/vcpkg" >> $GITHUB_PATH | |
| ./vcpkg integrate install | |
| shell: bash | |
| - name: Install dependencies | |
| run: python -m pip install -U pip "pybind11[global]" cmake build numpy pytest | |
| - name: Build and install Python bindings | |
| run: python -m pip install ".[testing]" | |
| - name: Run tests | |
| env: | |
| ZARR_S3_ENDPOINT: ${{ env.MINIO_URL }} | |
| ZARR_S3_BUCKET_NAME: ${{ env.MINIO_BUCKET }} | |
| ZARR_S3_ACCESS_KEY_ID: ${{ env.MINIO_ACCESS_KEY }} | |
| ZARR_S3_SECRET_ACCESS_KEY: ${{ env.MINIO_SECRET_KEY }} | |
| run: python -m pytest -v |