Refactor code to return interactions as sparse/dense Eigen matrices #847
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| # Copyright (C) 2022 Roberto Rossini (roberros@uio.no) | |
| # SPDX-License-Identifier: MIT | |
| name: MacOS CI | |
| on: | |
| push: | |
| branches: [ main ] | |
| paths: | |
| - ".github/workflows/macos-ci.yml" | |
| - "cmake/**" | |
| - "examples/**" | |
| - "src/**" | |
| - "test/**" | |
| - "CMakeLists.txt" | |
| - "conanfile.py" | |
| tags: | |
| - 'v*.*.*' | |
| pull_request: | |
| paths: | |
| - ".github/workflows/macos-ci.yml" | |
| - "cmake/**" | |
| - "examples/**" | |
| - "src/**" | |
| - "test/**" | |
| - "CMakeLists.txt" | |
| - "conanfile.py" | |
| # https://stackoverflow.com/a/72408109 | |
| concurrency: | |
| group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }} | |
| cancel-in-progress: true | |
| env: | |
| CCACHE_DIR: "${{ github.workspace }}/ccache-cache" | |
| CCACHE_COMPILERCHECK: "content" | |
| CCACHE_COMPRESSLEVEL: "1" | |
| CCACHE_MAXSIZE: "250M" | |
| CONAN_HOME: "${{ github.workspace }}/.conan2" | |
| HOMEBREW_NO_AUTO_UPDATE: "1" | |
| defaults: | |
| run: | |
| shell: bash | |
| jobs: | |
| matrix-factory: | |
| name: Generate job matrix | |
| runs-on: ubuntu-latest | |
| outputs: | |
| matrix: ${{ steps.set-result.outputs.result }} | |
| steps: | |
| - uses: actions/github-script@v7 | |
| id: set-result | |
| with: | |
| script: | | |
| // Documentation | |
| // https://docs.github.com/en/actions/learn-github-actions/contexts#fromjson | |
| // https://github.com/actions/runner/issues/982#issuecomment-809360765 | |
| var includes = [] | |
| includes.push({ compiler_name: 'apple-clang', compiler_version: '14', os: 'macos-12', conan: '2.1.*', cmake: '3.28.*', build_type: 'Release', developer_mode: 'OFF' }) | |
| includes.push({ compiler_name: 'apple-clang', compiler_version: '15', os: 'macos-13', conan: '2.1.*', cmake: '3.28.*', build_type: 'Release', developer_mode: 'OFF' }) | |
| includes.push({ compiler_name: 'apple-clang', compiler_version: '15', os: 'macos-14', conan: '2.1.*', cmake: '3.28.*', build_type: 'Release', developer_mode: 'OFF' }) | |
| includes.push({ compiler_name: 'apple-clang', compiler_version: '15', os: 'macos-13', conan: '2.1.*', cmake: '3.28.*', build_type: 'Debug', developer_mode: 'OFF' }) | |
| includes.push({ compiler_name: 'apple-clang', compiler_version: '15', os: 'macos-14', conan: '2.1.*', cmake: '3.28.*', build_type: 'Debug', developer_mode: 'OFF' }) | |
| return { include: includes } | |
| cache-test-dataset: | |
| uses: paulsengroup/hictk/.github/workflows/cache-test-dataset.yml@main | |
| build-project: | |
| needs: matrix-factory | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| fail-fast: false | |
| matrix: ${{ fromJSON(needs.matrix-factory.outputs.matrix) }} | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Generate requirements.txt for pip | |
| run: | | |
| echo 'conan==${{ matrix.conan }}' > requirements.txt | |
| echo 'cmake==${{ matrix.cmake }}' >> requirements.txt | |
| - uses: actions/setup-python@v5 | |
| with: | |
| python-version: '3.12' | |
| cache: 'pip' | |
| - name: Detect number available CPUs | |
| run: | | |
| ncpus=$(python -c 'import multiprocessing as mp; print(mp.cpu_count())') | |
| echo "CMAKE_BUILD_PARALLEL_LEVEL=$ncpus" >> $GITHUB_ENV | |
| echo "CTEST_PARALLEL_LEVEL=$ncpus" >> $GITHUB_ENV | |
| - name: Install build deps | |
| run: | | |
| pip install -r requirements.txt | |
| brew install ccache | |
| - name: Generate cache key | |
| id: cache-key | |
| run: | | |
| set -u | |
| os="${{ matrix.os }}" | |
| compiler="${{ matrix.compiler_name }}" | |
| compiler_version="${{ matrix.compiler_version }}" | |
| build_type="${{ matrix.build_type }}" | |
| conanfile_hash="${{ hashFiles('conanfile.py') }}" | |
| workflow_hash="${{ hashFiles('.github/workflows/macos-ci.yml') }}" | |
| combined_hash="${{ hashFiles('conanfile.py', '.github/workflows/macos-ci.yml') }}" | |
| # This can be used by to always update a cache entry (useful e.g. for ccache) | |
| current_date="$(date '+%s')" | |
| conan_key_prefix="conan-$os-$compiler-$compiler_version-$conanfile_hash-$build_type" | |
| ccache_key_prefix="ccache-$os-$compiler-$compiler_version-$conanfile_hash-$build_type" | |
| echo "conan-key=$conan_key_prefix" | tee -a $GITHUB_OUTPUT | |
| echo "conan-restore-key=$conan_key_prefix" | tee -a $GITHUB_OUTPUT | |
| echo "ccache-key=${ccache_key_prefix}-${current_date}" | tee -a $GITHUB_OUTPUT | |
| echo "ccache-restore-key=$ccache_key_prefix" | tee -a $GITHUB_OUTPUT | |
| - name: Restore Conan cache | |
| id: cache-conan | |
| uses: actions/cache/restore@v4 | |
| with: | |
| key: conan-${{ steps.cache-key.outputs.conan-restore-key }} | |
| path: ${{ env.CONAN_HOME }} | |
| - name: Configure Conan | |
| if: steps.cache-conan.outputs.cache-hit != 'true' | |
| run: | | |
| conan profile detect --force | |
| - name: Clean Conan cache (pre-build) | |
| if: steps.cache-conan.outputs.cache-hit != 'true' | |
| run: | | |
| conan cache clean "*" --build | |
| conan cache clean "*" --download | |
| conan cache clean "*" --source | |
| conan remove --confirm "*" | |
| - name: Install build dependencies | |
| run: | | |
| conan install . \ | |
| --build=missing \ | |
| -pr default \ | |
| -s "build_type=${{ matrix.build_type }}" \ | |
| -s "compiler=${{ matrix.compiler_name }}" \ | |
| -s "compiler.version=${{ matrix.compiler_version }}" \ | |
| -s compiler.libcxx=libc++ \ | |
| -s compiler.cppstd=17 \ | |
| --output-folder="${{ github.workspace }}/build" | |
| - name: Clean Conan cache (post-build) | |
| if: steps.cache-conan.outputs.cache-hit != 'true' | |
| run: | | |
| conan cache clean "*" --build | |
| conan cache clean "*" --download | |
| conan cache clean "*" --source | |
| - name: Save Conan cache | |
| uses: actions/cache/save@v4 | |
| if: steps.cache-conan.outputs.cache-hit != 'true' | |
| with: | |
| key: conan-${{ steps.cache-key.outputs.conan-key }} | |
| path: ${{ env.CONAN_HOME }} | |
| - name: Cache Ccache folder | |
| uses: actions/cache@v4 | |
| with: | |
| key: ${{ steps.cache-key.outputs.ccache-key }} | |
| restore-keys: ${{ steps.cache-key.outputs.ccache-restore-key }} | |
| path: ${{ env.CCACHE_DIR }} | |
| - name: Configure project | |
| run: | | |
| cmake -DCMAKE_BUILD_TYPE=${{ matrix.build_type }} \ | |
| -DCMAKE_PREFIX_PATH="${{ github.workspace }}/build" \ | |
| -DENABLE_DEVELOPER_MODE=${{ matrix.developer_mode }} \ | |
| -DHICTK_ENABLE_TESTING=ON \ | |
| -DHICTK_BUILD_EXAMPLES=ON \ | |
| -DOPT_ENABLE_CLANG_TIDY=OFF \ | |
| -DOPT_ENABLE_CPPCHECK=OFF \ | |
| -DHICTK_DOWNLOAD_TEST_DATASET=OFF \ | |
| -DHICTK_ENABLE_GIT_VERSION_TRACKING=OFF \ | |
| -DCMAKE_INSTALL_PREFIX=dest \ | |
| -S "${{ github.workspace }}" \ | |
| -B "${{ github.workspace }}/build" | |
| - name: Build project | |
| run: cmake --build ${{ github.workspace }}/build | |
| - name: Package binaries | |
| run: | | |
| cmake --install build | |
| gtar -cf - -C dest/ bin | | |
| zstd -T0 -13 -o binaries.tar.zst | |
| - name: Package unit tests | |
| run: | | |
| gtar -cf - build/ | zstd -T0 -13 -o unit-tests.tar.zst | |
| - name: Upload unit tests | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: > | |
| unit-tests-${{ matrix.os }}- | |
| ${{ matrix.compiler_name }}- | |
| ${{ matrix.compiler_version }}- | |
| ${{ matrix.build_type }}- | |
| ${{ matrix.developer_mode }} | |
| path: unit-tests.tar.zst | |
| if-no-files-found: error | |
| retention-days: 1 | |
| - name: Upload binaries | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: > | |
| binaries-${{ matrix.os }}- | |
| ${{ matrix.compiler_name }}- | |
| ${{ matrix.compiler_version }}- | |
| ${{ matrix.build_type }}- | |
| ${{ matrix.developer_mode }} | |
| path: binaries.tar.zst | |
| if-no-files-found: error | |
| retention-days: 1 | |
| - name: Print Ccache statistics | |
| run: ccache -s | |
| run-unit-tests: | |
| name: Run unit tests | |
| needs: [ matrix-factory, cache-test-dataset, build-project ] | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| fail-fast: false | |
| matrix: ${{ fromJSON(needs.matrix-factory.outputs.matrix) }} | |
| steps: | |
| - name: Checkout repo | |
| uses: actions/checkout@v4 | |
| - name: Fix permissions | |
| run: | | |
| chown -R $(id -u):$(id -g) $PWD | |
| - name: Restore test dataset | |
| uses: actions/cache/restore@v4 | |
| with: | |
| key: ${{ needs.cache-test-dataset.outputs.cache-key }} | |
| path: test/data/hictk_test_data.tar.xz | |
| fail-on-cache-miss: true | |
| - name: Download unit tests artifact | |
| uses: actions/download-artifact@v4 | |
| with: | |
| name: > | |
| unit-tests-${{ matrix.os }}- | |
| ${{ matrix.compiler_name }}- | |
| ${{ matrix.compiler_version }}- | |
| ${{ matrix.build_type }}- | |
| ${{ matrix.developer_mode }} | |
| - name: Extract binaries test dataset | |
| run: | | |
| zstd -dcf unit-tests.tar.zst | gtar -xf - | |
| gtar -xf test/data/hictk_test_data.tar.xz | |
| - name: Generate requirements.txt for pip | |
| run: | | |
| echo 'cmake==${{ matrix.cmake }}' > requirements.txt | |
| - uses: actions/setup-python@v5 | |
| with: | |
| python-version: '3.12' | |
| cache: 'pip' | |
| - name: Install test dependencies | |
| run: pip install -r requirements.txt | |
| - name: Run unit tests | |
| run: | | |
| ctest --test-dir build/ \ | |
| --schedule-random \ | |
| --output-on-failure \ | |
| --no-tests=error \ | |
| --timeout 360 2>&1 | | |
| head -n 1000 | |
| run-integration-tests: | |
| name: Run integration tests | |
| needs: [ matrix-factory, cache-test-dataset, build-project ] | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| fail-fast: false | |
| matrix: ${{ fromJSON(needs.matrix-factory.outputs.matrix) }} | |
| steps: | |
| - name: Checkout repo | |
| uses: actions/checkout@v4 | |
| - name: Fix permissions | |
| run: | | |
| chown -R $(id -u):$(id -g) $PWD | |
| - name: Generate requirements.txt for pip | |
| run: echo 'cooler>=0.9.3' > requirements.txt | |
| - uses: actions/setup-python@v5 | |
| with: | |
| python-version: '3.12' | |
| cache: 'pip' | |
| - name: Install test dependencies | |
| run: pip install -r requirements.txt | |
| - name: Restore test dataset | |
| uses: actions/cache/restore@v4 | |
| with: | |
| key: ${{ needs.cache-test-dataset.outputs.cache-key }} | |
| path: test/data/hictk_test_data.tar.xz | |
| fail-on-cache-miss: true | |
| - name: Download binaries artifact | |
| uses: actions/download-artifact@v4 | |
| with: | |
| name: > | |
| binaries-${{ matrix.os }}- | |
| ${{ matrix.compiler_name }}- | |
| ${{ matrix.compiler_version }}- | |
| ${{ matrix.build_type }}- | |
| ${{ matrix.developer_mode }} | |
| - name: Extract binaries test dataset | |
| run: | | |
| zstd -dcf binaries.tar.zst | tar -xf - | |
| tar -xf test/data/hictk_test_data.tar.xz | |
| - name: Test hictk balance | |
| run: | | |
| test/scripts/hictk_balance_ice.sh bin/hictk | |
| test/scripts/hictk_balance_scale.sh bin/hictk | |
| test/scripts/hictk_balance_vc.sh bin/hictk | |
| - name: Test hictk convert (hic2cool) | |
| run: | | |
| test/scripts/hictk_convert_hic2cool.sh bin/hictk | |
| - name: Test hictk convert (cool2hic) | |
| run: | | |
| test/scripts/hictk_convert_cool2hic.sh bin/hictk | |
| - name: Test hictk dump chroms | |
| run: | | |
| test/scripts/hictk_dump_chroms.sh bin/hictk | |
| - name: Test hictk dump bins | |
| run: | | |
| test/scripts/hictk_dump_bins.sh bin/hictk | |
| - name: Test hictk dump resolutions | |
| run: | | |
| test/scripts/hictk_dump_resolutions.sh bin/hictk | |
| - name: Test hictk dump normalizations | |
| run: | | |
| test/scripts/hictk_dump_normalizations.sh bin/hictk | |
| - name: Test hictk dump cells | |
| run: | | |
| test/scripts/hictk_dump_cells.sh bin/hictk | |
| - name: Test hictk dump genome-wide | |
| run: | | |
| test/scripts/hictk_dump_gw.sh bin/hictk | |
| - name: Test hictk dump cis | |
| run: | | |
| test/scripts/hictk_dump_cis.sh bin/hictk | |
| - name: Test hictk dump trans | |
| run: | | |
| test/scripts/hictk_dump_trans.sh bin/hictk | |
| - name: Test hictk dump balanced | |
| run: | | |
| test/scripts/hictk_dump_balanced.sh bin/hictk | |
| - name: Test hictk fix-mcool | |
| run: | | |
| test/scripts/hictk_fix_mcool.sh bin/hictk | |
| - name: Test hictk load coo sorted | |
| run: | | |
| test/scripts/hictk_load_coo.sh bin/hictk sorted | |
| - name: Test hictk load coo unsorted | |
| run: | | |
| test/scripts/hictk_load_coo.sh bin/hictk unsorted | |
| - name: Test hictk load bg2 sorted | |
| run: | | |
| test/scripts/hictk_load_bg2.sh bin/hictk sorted | |
| - name: Test hictk load bg2 unsorted | |
| run: | | |
| test/scripts/hictk_load_bg2.sh bin/hictk unsorted | |
| - name: Test hictk load 4dn | |
| run: | | |
| test/scripts/hictk_load_4dn.sh bin/hictk | |
| - name: Test hictk merge | |
| run: | | |
| test/scripts/hictk_merge.sh bin/hictk | |
| - name: Test hictk rename-chroms | |
| run: | | |
| test/scripts/hictk_rename_chromosomes.sh bin/hictk | |
| - name: Test hictk validate | |
| run: | | |
| test/scripts/hictk_validate.sh bin/hictk | |
| - name: Test hictk zoomify | |
| run: | | |
| test/scripts/hictk_zoomify.sh bin/hictk | |
| macos-ci-status-check: | |
| name: Status Check (MacOS CI) | |
| if: ${{ always() }} | |
| runs-on: ubuntu-latest | |
| needs: | |
| - matrix-factory | |
| - cache-test-dataset | |
| - build-project | |
| - run-unit-tests | |
| - run-integration-tests | |
| steps: | |
| - name: Collect job results | |
| if: | | |
| needs.matrix-factory.result != 'success' || | |
| needs.cache-test-dataset.result != 'success' || | |
| needs.build-project.result != 'success' || | |
| needs.run-unit-tests.result != 'success' || | |
| needs.run-integration-tests.result != 'success' | |
| run: exit 1 |