Merge pull request #94 from paulsengroup/bump/deps #243
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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/fuzzy-testing.yml" | |
| - "cmake/**" | |
| - "src/**" | |
| - "test/scripts/fuzzy_test.py" | |
| - "test/scripts/link_h5_dataset.py" | |
| - "CMakeLists.txt" | |
| - "conanfile.txt" | |
| tags: | |
| - 'v*.*.*' | |
| pull_request: | |
| paths: | |
| - ".github/workflows/fuzzy-testing.yml" | |
| - "test/scripts/fuzzy_test.py" | |
| - "test/scripts/link_h5_dataset.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: '10000' | |
| 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-project: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| include: | |
| # The .mcool file was generated by using hic2cool followed by cooler balance for all resolutions | |
| # We can't use the version shared by 4DNucleome because the .hic and .mcool files they publish | |
| # differ slightly | |
| - { | |
| title: '.cool', | |
| balance: 'NONE', | |
| url: 'https://www.dropbox.com/s/wq3k09rrpc8smmm/4DNFIPC7P27B.mcool?dl=1', | |
| sha256: '7ead807936afbd02c4a0da93d86dd54de489cc07e87400a691c8e917111749de', | |
| ref-url: 'https://www.dropbox.com/s/wq3k09rrpc8smmm/4DNFIPC7P27B.mcool?dl=1', | |
| ref-sha256: '7ead807936afbd02c4a0da93d86dd54de489cc07e87400a691c8e917111749de' | |
| } | |
| - { | |
| title: '.cool', | |
| balance: 'weight', | |
| url: 'https://www.dropbox.com/s/wq3k09rrpc8smmm/4DNFIPC7P27B.mcool?dl=1', | |
| sha256: '7ead807936afbd02c4a0da93d86dd54de489cc07e87400a691c8e917111749de', | |
| ref-url: 'https://www.dropbox.com/s/wq3k09rrpc8smmm/4DNFIPC7P27B.mcool?dl=1', | |
| ref-sha256: '7ead807936afbd02c4a0da93d86dd54de489cc07e87400a691c8e917111749de' | |
| } | |
| - { | |
| title: '.hic', | |
| balance: 'NONE', | |
| url: 'https://www.dropbox.com/s/gkzxt5ae82dvlrg/4DNFIPC7P27B.hic?dl=1', | |
| sha256: 'b1ba1c942693a5b6e494de7f8da097a1435598a9bb951219929b5a84cb2a6b42', | |
| ref-url: 'https://www.dropbox.com/s/wq3k09rrpc8smmm/4DNFIPC7P27B.mcool?dl=1', | |
| ref-sha256: '7ead807936afbd02c4a0da93d86dd54de489cc07e87400a691c8e917111749de', | |
| } | |
| - { | |
| title: '.hic', | |
| balance: 'KR', | |
| url: 'https://www.dropbox.com/s/gkzxt5ae82dvlrg/4DNFIPC7P27B.hic?dl=1', | |
| sha256: 'b1ba1c942693a5b6e494de7f8da097a1435598a9bb951219929b5a84cb2a6b42', | |
| ref-url: 'https://www.dropbox.com/s/wq3k09rrpc8smmm/4DNFIPC7P27B.mcool?dl=1', | |
| ref-sha256: '7ead807936afbd02c4a0da93d86dd54de489cc07e87400a691c8e917111749de' | |
| } | |
| container: | |
| image: ghcr.io/paulsengroup/ci-docker-images/ubuntu-22.04-cxx-clang-16 | |
| options: "--user=root" | |
| env: | |
| CONAN_HOME: '/root/.conan2' | |
| steps: | |
| - name: Clone hictk | |
| uses: actions/checkout@v4 | |
| - name: Clone hictkpy | |
| uses: actions/checkout@v4 | |
| with: | |
| repository: paulsengroup/hictkpy | |
| ref: main | |
| path: hictkpy | |
| - name: Patch hictkpy | |
| working-directory: hictkpy | |
| if: github.event_name != 'schedule' | |
| run: | | |
| sed -i 's|URL.*\.tar\.xz"|GIT_REPOSITORY https://github.com/paulsengroup/hictk.git|' CMakeLists.txt | |
| sed -i 's|URL_HASH.*|GIT_TAG ${{ github.event.after }}|' CMakeLists.txt | |
| grep 'GIT_TAG' CMakeLists.txt | |
| - name: Patch hictkpy (schedule) | |
| working-directory: hictkpy | |
| if: github.event_name == 'schedule' | |
| run: | | |
| sed -i 's|URL.*\.tar\.xz"|GIT_REPOSITORY https://github.com/paulsengroup/hictk.git|' CMakeLists.txt | |
| sed -i 's|URL_HASH.*|GIT_TAG main|' CMakeLists.txt | |
| - name: Fix permissions | |
| run: | | |
| chown -R $(id -u):$(id -g) $PWD | |
| - name: Generate cache key | |
| id: cache-key | |
| working-directory: hictkpy | |
| run: | | |
| hash="${{ hashFiles('conanfile.txt') }}" | |
| echo "key=fuzzy-testing-$hash" >> $GITHUB_OUTPUT | |
| - name: Install Python | |
| run: | | |
| apt-get update | |
| apt-get install -y python3.11 python3.11-dev | |
| - name: Restore Conan cache | |
| id: cache-conan | |
| uses: actions/cache/restore@v3 | |
| with: | |
| key: conan-${{ steps.cache-key.outputs.key }} | |
| path: ${{ env.CONAN_HOME }} | |
| - name: Clean Conan cache (pre-build) | |
| if: steps.cache-conan.outputs.cache-hit != 'true' | |
| run: | | |
| conan cache clean "*" --build | |
| conan cache clean "*" --download | |
| conan cache clean "*" --source | |
| conan remove --confirm "*" | |
| - name: Install build dependencies | |
| run: | | |
| conan install . \ | |
| --build=missing \ | |
| -pr:b="$CONAN_DEFAULT_PROFILE_PATH" \ | |
| -pr:h="$CONAN_DEFAULT_PROFILE_PATH" \ | |
| -s build_type=Release \ | |
| -s compiler.libcxx=libstdc++11 \ | |
| -s compiler.cppstd=17 \ | |
| -o '*/*:shared=True' \ | |
| --output-folder=build | |
| conan install hictkpy \ | |
| --build=missing \ | |
| -pr:b="$CONAN_DEFAULT_PROFILE_PATH" \ | |
| -pr:h="$CONAN_DEFAULT_PROFILE_PATH" \ | |
| -s build_type=Release \ | |
| -s compiler.libcxx=libstdc++11 \ | |
| -s compiler.cppstd=17 \ | |
| -o '*/*:shared=True' \ | |
| --output-folder=build | |
| - name: Clean Conan cache (post-build) | |
| if: steps.cache-conan.outputs.cache-hit != 'true' | |
| run: | | |
| conan cache clean "*" --build | |
| conan cache clean "*" --download | |
| conan cache clean "*" --source | |
| - name: Install Python bindings | |
| working-directory: hictkpy | |
| run: | | |
| pip install --upgrade pip setuptools wheel pybind11 | |
| env CC=clang-16 \ | |
| CXX=clang++-16 \ | |
| CMAKE_ARGS="-DCMAKE_PREFIX_PATH=$PWD/../build" \ | |
| HICTKPY_SETUP_SKIP_CONAN=1 \ | |
| pip install . -v | |
| - name: Save Conan cache | |
| uses: actions/cache/save@v3 | |
| if: steps.cache-conan.outputs.cache-hit != 'true' | |
| with: | |
| key: conan-${{ steps.cache-key.outputs.key }} | |
| path: ${{ env.CONAN_HOME }} | |
| - name: Install test dependencies | |
| run: | | |
| apt-get update | |
| apt-get install -y curl zstd | |
| pip install --no-cache-dir 'cooler>=0.9.2' | |
| - 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" >> $GITHUB_OUTPUT | |
| else | |
| echo "type=short" >> $GITHUB_OUTPUT | |
| fi | |
| - name: Prepare for test | |
| id: test-params | |
| env: | |
| PYTHONHASHSEED: 0 | |
| run: | | |
| seed="$(python3 -c 'import random; print(random.randint(0, 2**32))')" | |
| duration=600 | |
| if [[ ${{ github.event_name }} == 'workflow_dispatch' ]]; then | |
| duration='${{ inputs.duration }}' | |
| elif [[ ${{ steps.ci-type.outputs.type }} == 'full' ]]; then | |
| duration=3600 | |
| fi | |
| resolution=10000 | |
| if [[ ${{ github.event_name }} == 'workflow_dispatch' ]]; then | |
| resolution='${{ inputs.resolution }}' | |
| fi | |
| 2>&1 echo "Seed: ${seed}" | |
| 2>&1 echo "Duration: ${duration}" | |
| 2>&1 echo "Resolution: ${resolution}" | |
| echo "seed=$seed" >> $GITHUB_OUTPUT | |
| echo "duration=$duration" >> $GITHUB_OUTPUT | |
| echo "resolution=$resolution" >> $GITHUB_OUTPUT | |
| - name: Clone hictk | |
| uses: actions/checkout@v4 | |
| with: | |
| path: hictk | |
| - name: Fix permissions | |
| run: | | |
| chown -R $(id -u):$(id -g) $PWD | |
| - name: Download test datasets | |
| working-directory: hictk | |
| run: | | |
| resolution="${{ steps.test-params.outputs.resolution }}" | |
| echo "${{ matrix.ref-sha256 }} reference.mcool" | tee checksums.sha256 | |
| curl -L "${{ matrix.ref-url }}" -o reference.mcool | |
| sha256sum -c checksums.sha256 | |
| cooler cp "reference.mcool::/resolutions/$resolution" reference.cool | |
| rm reference.mcool | |
| if [[ ${{ matrix.ref-sha256 }} == ${{ matrix.sha256 }} ]]; then | |
| ln -s reference.cool test.matrix | |
| else | |
| echo "${{ matrix.sha256 }} test.matrix" | tee checksums.sha256 | |
| curl -L "${{ matrix.url }}" -o test.matrix | |
| sha256sum -c checksums.sha256 | |
| if [[ ${{ matrix.title }} == .cool ]]; then | |
| cooler cp "test.matrix::/resolutions/$resolution" test.matrix.tmp | |
| mv test.matrix.tmp test.matrix | |
| fi | |
| fi | |
| - name: Run test | |
| working-directory: hictk | |
| run: | | |
| test/scripts/fuzzy_test.py \ | |
| --seed '${{ steps.test-params.outputs.seed }}' \ | |
| --duration '${{ steps.test-params.outputs.duration }}' \ | |
| --balance ${{ matrix.balance }} \ | |
| test.matrix \ | |
| reference.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 |