Refactor FileStream and HiCFileWriter to be more robust against data races #619
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| # Copyright (C) 2023 Roberto Rossini <roberros@uio.no> | |
| # SPDX-License-Identifier: MIT | |
| name: Run fuzzy tests | |
| on: | |
| push: | |
| branches: [main] | |
| paths: | |
| - ".github/workflows/build-conan-deps.yml" | |
| - ".github/workflows/fuzzy-testing.yml" | |
| - "cmake/**" | |
| - "src/**" | |
| - "test/fuzzer/**" | |
| - "CMakeLists.txt" | |
| - "conanfile.py" | |
| pull_request: | |
| paths: | |
| - ".github/workflows/build-conan-deps.yml" | |
| - ".github/workflows/fuzzy-testing.yml" | |
| - "cmake/**" | |
| - "src/**" | |
| - "test/fuzzer/**" | |
| - "CMakeLists.txt" | |
| - "conanfile.py" | |
| schedule: | |
| # Run weekly | |
| - cron: "15 3 * * 0" | |
| workflow_dispatch: | |
| inputs: | |
| duration: | |
| description: "Test duration in seconds" | |
| required: true | |
| default: "600" | |
| type: string | |
| resolution: | |
| description: "Matrix resolution to use for testing" | |
| required: true | |
| default: "random" | |
| type: string | |
| # https://stackoverflow.com/a/72408109 | |
| concurrency: | |
| group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }} | |
| cancel-in-progress: true | |
| defaults: | |
| run: | |
| shell: bash | |
| jobs: | |
| build-conan-deps: | |
| name: Build Conan deps | |
| uses: paulsengroup/hictk/.github/workflows/build-conan-deps.yml@main | |
| with: | |
| os: ubuntu-20.04 | |
| build-project: | |
| name: Build project | |
| needs: build-conan-deps | |
| runs-on: ubuntu-latest | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| include: | |
| - { | |
| dataset: "4DNFIYECESRC", | |
| format: "cool", | |
| normalization: "NONE", | |
| bin-type: "fixed", | |
| } | |
| - { | |
| dataset: "4DNFIYECESRC", | |
| format: "cool", | |
| normalization: "weight", | |
| bin-type: "fixed", | |
| } | |
| - { | |
| dataset: "4DNFIYECESRC", | |
| format: "cool", | |
| normalization: "VC", | |
| bin-type: "fixed", | |
| } | |
| - { | |
| dataset: "4DNFIYECESRC", | |
| format: "cool", | |
| normalization: "NONE", | |
| bin-type: "variable", | |
| } | |
| - { | |
| dataset: "4DNFIYECESRC", | |
| format: "hic8", | |
| normalization: "NONE", | |
| bin-type: "fixed", | |
| } | |
| - { | |
| dataset: "4DNFIYECESRC", | |
| format: "hic8", | |
| normalization: "KR", | |
| bin-type: "fixed", | |
| } | |
| - { | |
| dataset: "4DNFIYECESRC", | |
| format: "hic9", | |
| normalization: "NONE", | |
| bin-type: "fixed", | |
| } | |
| - { | |
| dataset: "4DNFIYECESRC", | |
| format: "hic9", | |
| normalization: "SCALE", | |
| bin-type: "fixed", | |
| } | |
| - { | |
| dataset: "4DNFIYECESRC", | |
| format: "hic9", | |
| normalization: "VC", | |
| bin-type: "fixed", | |
| } | |
| container: | |
| image: ghcr.io/paulsengroup/ci-docker-images/ubuntu-24.04-cxx-clang-18 | |
| options: "--user=root" | |
| env: | |
| CCACHE_DISABLE: "1" | |
| CONAN_HOME: "/opt/conan/" | |
| HICTK_CI: "1" | |
| steps: | |
| - name: Clone hictk | |
| uses: actions/checkout@v4 | |
| - name: Fix permissions | |
| run: | | |
| chown -R $(id -u):$(id -g) $PWD | |
| - name: Install Python | |
| run: | | |
| apt-get update | |
| apt-get install -y python3.12 python3.12-dev | |
| - name: Restore Conan cache | |
| uses: actions/cache/restore@v4 | |
| with: | |
| key: ${{ needs.build-conan-deps.outputs.conan-key }} | |
| path: ${{ env.CONAN_HOME }}/p | |
| fail-on-cache-miss: true | |
| - name: Restore CMake configs | |
| uses: actions/cache/restore@v4 | |
| with: | |
| key: ${{ needs.build-conan-deps.outputs.cmake-prefix-release-key }} | |
| path: /tmp/cmake-prefix-rel.tar | |
| fail-on-cache-miss: true | |
| - name: Extract CMake configs | |
| run: | | |
| mkdir conan-env | |
| tar -xf /tmp/cmake-prefix-rel.tar -C conan-env/ --strip-components=1 | |
| - name: Configure project | |
| run: | | |
| cmake -DCMAKE_BUILD_TYPE=Release \ | |
| -DCMAKE_PREFIX_PATH="$PWD/conan-env" \ | |
| -DENABLE_DEVELOPER_MODE=ON \ | |
| -DOPT_ENABLE_CLANG_TIDY=OFF \ | |
| -DOPT_ENABLE_CPPCHECK=OFF \ | |
| -DHICTK_ENABLE_TESTING=ON \ | |
| -DHICTK_ENABLE_FUZZY_TESTING=ON \ | |
| -DHICTK_BUILD_EXAMPLES=OFF \ | |
| -DHICTK_DOWNLOAD_TEST_DATASET=OFF \ | |
| -S . \ | |
| -B build | |
| - name: Build hictk_fuzzer | |
| run: cmake --build build -j $(nproc) -t hictk_fuzzer | |
| - name: Install test dependencies | |
| run: | | |
| pip install --no-cache-dir 'cooler==0.10.*' 'numpy<2' | |
| - name: Detect CI type | |
| id: ci-type | |
| run: | | |
| if git log --format=%B -n 1 ${{ github.event.after }} | grep -qF '[ci full]'; then | |
| echo "type=full" | tee -a "$GITHUB_OUTPUT" | |
| else | |
| echo "type=short" | tee -a "$GITHUB_OUTPUT" | |
| fi | |
| - name: Prepare for test | |
| id: test-params | |
| run: | | |
| duration=120 | |
| if [[ ${{ github.event_name }} == 'workflow_dispatch' ]]; then | |
| duration='${{ inputs.duration }}' | |
| elif [[ '${{ steps.ci-type.outputs.type }}' == 'full' ]]; then | |
| duration=3600 | |
| fi | |
| resolution=50000 | |
| if [[ ${{ github.event_name }} == 'workflow_dispatch' ]]; then | |
| if [[ '${{ inputs.resolution }}' == 'random' ]]; then | |
| resolution="$( | |
| python3 -c 'import random; import sys; print(random.choice([int(x) for x in sys.argv[1:]]))' \ | |
| 1000 5000 10000 50000 100000 500000 | |
| )" | |
| else | |
| resolution='${{ inputs.resolution }}' | |
| fi | |
| fi | |
| if [[ '${{ matrix.bin-type }}' == variable ]]; then | |
| resolution=0 | |
| fi | |
| 2>&1 echo "Duration: ${duration}" | |
| 2>&1 echo "Resolution: ${resolution}" | |
| echo "duration=$duration" | tee -a "$GITHUB_OUTPUT" | |
| echo "resolution=$resolution" | tee -a "$GITHUB_OUTPUT" | |
| - name: Download test datasets | |
| run: | | |
| test/fuzzer/scripts/download_test_datasets.py \ | |
| test/fuzzer/test_files.json \ | |
| . \ | |
| --format cool "${{ matrix.format }}" \ | |
| --resolution "${{ steps.test-params.outputs.resolution }}" \ | |
| --dataset "${{ matrix.dataset }}" \ | |
| --nproc 2 | |
| - name: Run test (df) | |
| run: | | |
| build/test/fuzzer/src/hictk_fuzzer fuzz \ | |
| --resolution ${{ steps.test-params.outputs.resolution }} \ | |
| --duration '${{ steps.test-params.outputs.duration }}' \ | |
| --normalization ${{ matrix.normalization }} \ | |
| --nproc $(nproc) \ | |
| --format df \ | |
| *".${{ matrix.format }}" \ | |
| *.cool | |
| - name: Run test (dense) | |
| run: | | |
| build/test/fuzzer/src/hictk_fuzzer fuzz \ | |
| --resolution ${{ steps.test-params.outputs.resolution }} \ | |
| --duration '${{ steps.test-params.outputs.duration }}' \ | |
| --normalization ${{ matrix.normalization }} \ | |
| --nproc $(nproc) \ | |
| --format dense \ | |
| *".${{ matrix.format }}" \ | |
| *.cool | |
| - name: Run test (sparse) | |
| run: | | |
| build/test/fuzzer/src/hictk_fuzzer fuzz \ | |
| --resolution ${{ steps.test-params.outputs.resolution }} \ | |
| --duration '${{ steps.test-params.outputs.duration }}' \ | |
| --normalization ${{ matrix.normalization }} \ | |
| --nproc $(nproc) \ | |
| --format sparse \ | |
| *".${{ matrix.format }}" \ | |
| *.cool | |
| fuzzy-testing-status-check: | |
| name: Status Check (fuzzy-testing) | |
| if: ${{ always() }} | |
| runs-on: ubuntu-latest | |
| needs: | |
| - build-project | |
| steps: | |
| - name: Collect job results | |
| if: needs.build-project.result != 'success' | |
| run: exit 1 |