Refactor code to return interactions as sparse/dense Eigen matrices #833
Workflow file for this run
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| # Copyright (C) 2023 Roberto Rossini (roberros@uio.no) | |
| # SPDX-License-Identifier: MIT | |
| name: Run Codecov | |
| on: | |
| push: | |
| branches: [ main ] | |
| paths: | |
| - ".github/codecov.yml" | |
| - ".github/workflows/codecov.yml" | |
| - "cmake/**" | |
| - "examples/**" | |
| - "src/**" | |
| - "test/**" | |
| - "CMakeLists.txt" | |
| - "conanfile.py" | |
| tags: | |
| - 'v*.*.*' | |
| pull_request: | |
| paths: | |
| - ".github/codecov.yml" | |
| - ".github/workflows/codecov.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 | |
| defaults: | |
| run: | |
| shell: bash | |
| env: | |
| CCACHE_DIR: "/opt/ccache-cache" | |
| CCACHE_COMPILERCHECK: "content" | |
| CCACHE_COMPRESSLEVEL: "13" | |
| CCACHE_MAXSIZE: "200M" | |
| CONAN_HOME: "/opt/conan/" | |
| jobs: | |
| cache-test-dataset: | |
| uses: paulsengroup/hictk/.github/workflows/cache-test-dataset.yml@main | |
| run-codecov: | |
| name: Codecov | |
| needs: cache-test-dataset | |
| runs-on: ubuntu-latest | |
| container: | |
| image: ghcr.io/paulsengroup/ci-docker-images/ubuntu-24.04-cxx-gcc-14 | |
| options: '--user=root' | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Fix permissions | |
| run: | | |
| chown -R $(id -u):$(id -g) $PWD | |
| - name: Generate cache key | |
| id: cache-key | |
| run: | | |
| hash="${{ hashFiles('conanfile.py', '.github/workflows/codecov.yml') }}" | |
| # This can be used by to always update a cache entry (useful e.g. for ccache) | |
| current_date="$(date '+%s')" | |
| ccache_key_prefix="codecov-ccache-$hash" | |
| echo "conan-key=codecov-$hash" >> $GITHUB_OUTPUT | |
| echo "ccache-key=${ccache_key_prefix}-${current_date}" >> $GITHUB_OUTPUT | |
| echo "ccache-restore-key=$ccache_key_prefix" >> $GITHUB_OUTPUT | |
| - name: Restore Conan cache | |
| id: cache-conan | |
| uses: actions/cache/restore@v4 | |
| with: | |
| key: conan-${{ steps.cache-key.outputs.conan-key }} | |
| path: ${{ env.CONAN_HOME }} | |
| - name: Clean Conan cache (pre-build) | |
| if: steps.cache-conan.outputs.cache-hit != 'true' | |
| run: | | |
| conan cache clean "*" --build | |
| conan cache clean "*" --download | |
| conan cache clean "*" --source | |
| conan remove --confirm "*" | |
| - name: Copy Conan settings | |
| run: cp "/root/.conan2/settings.yml" "$CONAN_HOME" | |
| - name: Install build dependencies | |
| run: | | |
| conan install . \ | |
| --build=missing \ | |
| -pr:b="$CONAN_DEFAULT_PROFILE_PATH" \ | |
| -pr:h="$CONAN_DEFAULT_PROFILE_PATH" \ | |
| -s build_type=Debug \ | |
| -s compiler.libcxx=libstdc++11 \ | |
| -s compiler.cppstd=17 \ | |
| --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: 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: ${{ env.CONAN_HOME }} | |
| - name: Configure project | |
| run: | | |
| cmake -DCMAKE_BUILD_TYPE=Debug \ | |
| -DCMAKE_PREFIX_PATH="$PWD/build" \ | |
| -DENABLE_DEVELOPER_MODE=ON \ | |
| -DOPT_ENABLE_COVERAGE=ON \ | |
| -DOPT_ENABLE_SANITIZER_ADDRESS=OFF \ | |
| -DOPT_ENABLE_SANITIZER_UNDEFINED_BEHAVIOR=OFF \ | |
| -DOPT_ENABLE_CLANG_TIDY=OFF \ | |
| -DHICTK_BUILD_EXAMPLES=OFF \ | |
| -DHICTK_ENABLE_TESTING=ON \ | |
| -DHICTK_DOWNLOAD_TEST_DATASET=OFF \ | |
| -DHICTK_ENABLE_GIT_VERSION_TRACKING=OFF \ | |
| -S . \ | |
| -B build | |
| - 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: Build project | |
| run: cmake --build build -j $(nproc) | |
| - name: Print Ccache statistics | |
| run: ccache -s | |
| - 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: Extract test dataset | |
| run: tar -xf test/data/hictk_test_data.tar.xz | |
| - name: Run unit tests | |
| run: | | |
| ctest --test-dir build/ \ | |
| --schedule-random \ | |
| --output-on-failure \ | |
| --no-tests=error \ | |
| --timeout 240 \ | |
| -j $(nproc) |& | |
| head -n 1000 | |
| - name: Install test dependencies | |
| run: | | |
| apt-get update | |
| apt-get install -y --no-install-recommends python3-pip xz-utils | |
| python3 -m pip install 'cooler>=0.9.3' | |
| - name: Run integration tests | |
| run: | | |
| test/scripts/hictk_balance_ice.sh build/src/hictk/hictk | |
| test/scripts/hictk_balance_scale.sh build/src/hictk/hictk | |
| test/scripts/hictk_balance_vc.sh build/src/hictk/hictk | |
| test/scripts/hictk_convert_hic2cool.sh build/src/hictk/hictk | |
| test/scripts/hictk_convert_cool2hic.sh build/src/hictk/hictk | |
| test/scripts/hictk_dump_chroms.sh build/src/hictk/hictk | |
| test/scripts/hictk_dump_bins.sh build/src/hictk/hictk | |
| test/scripts/hictk_dump_resolutions.sh build/src/hictk/hictk | |
| test/scripts/hictk_dump_normalizations.sh build/src/hictk/hictk | |
| test/scripts/hictk_dump_cells.sh build/src/hictk/hictk | |
| test/scripts/hictk_dump_gw.sh build/src/hictk/hictk | |
| test/scripts/hictk_dump_cis.sh build/src/hictk/hictk | |
| test/scripts/hictk_dump_trans.sh build/src/hictk/hictk | |
| test/scripts/hictk_dump_balanced.sh build/src/hictk/hictk | |
| test/scripts/hictk_fix_mcool.sh build/src/hictk/hictk | |
| test/scripts/hictk_load_coo.sh build/src/hictk/hictk sorted | |
| test/scripts/hictk_load_coo.sh build/src/hictk/hictk unsorted | |
| test/scripts/hictk_load_bg2.sh build/src/hictk/hictk sorted | |
| test/scripts/hictk_load_bg2.sh build/src/hictk/hictk unsorted | |
| test/scripts/hictk_load_4dn.sh build/src/hictk/hictk | |
| test/scripts/hictk_merge.sh build/src/hictk/hictk | |
| test/scripts/hictk_rename_chromosomes.sh build/src/hictk/hictk | |
| test/scripts/hictk_validate.sh build/src/hictk/hictk | |
| test/scripts/hictk_zoomify.sh build/src/hictk/hictk | |
| - name: Upload coverage reports to Codecov | |
| uses: codecov/codecov-action@v3 | |
| with: | |
| fail_ci_if_error: true | |
| gcov: true | |
| gcov_executable: gcov-14 | |
| os: linux | |
| token: ${{ secrets.CODECOV_TOKEN }} | |
| verbose: true | |
| codecov-status-check: | |
| name: Status Check (Codecov) | |
| if: ${{ always() }} | |
| runs-on: ubuntu-latest | |
| needs: | |
| - run-codecov | |
| steps: | |
| - name: Collect job results | |
| if: needs.run-codecov.result != 'success' | |
| run: exit 1 |