Add native support to write .hic files #656
Workflow file for this run
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| # Copyright (C) 2023 Roberto Rossini (roberros@uio.no) | |
| # SPDX-License-Identifier: MIT | |
| name: Windows CI | |
| on: | |
| push: | |
| branches: [ main ] | |
| paths: | |
| - ".github/workflows/windows-ci.yml" | |
| - "cmake/**" | |
| - "examples/**" | |
| - "src/**" | |
| - "test/**" | |
| - "CMakeLists.txt" | |
| - "conanfile.txt" | |
| tags: | |
| - 'v*.*.*' | |
| pull_request: | |
| paths: | |
| - ".github/workflows/windows-ci.yml" | |
| - "cmake/**" | |
| - "examples/**" | |
| - "src/**" | |
| - "test/**" | |
| - "CMakeLists.txt" | |
| - "conanfile.txt" | |
| # 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" | |
| defaults: | |
| run: | |
| shell: bash | |
| jobs: | |
| cache-test-dataset: | |
| uses: paulsengroup/hictk/.github/workflows/cache-test-dataset.yml@main | |
| build-project: | |
| needs: cache-test-dataset | |
| runs-on: windows-latest | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| include: | |
| - { compiler-name: msvc, os: 'windows-2022', conan-ver: '2.0.*', cmake-ver: '3.26.*', build_type: Debug, developer_mode: OFF } | |
| - { compiler-name: msvc, os: 'windows-2022', conan-ver: '2.0.*', cmake-ver: '3.26.*', build_type: Release, developer_mode: OFF } | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Generate requirements.txt for pip | |
| run: | | |
| echo 'conan==${{ matrix.conan-ver }}' > requirements.txt | |
| echo 'cmake==${{ matrix.cmake-ver }}' >> requirements.txt | |
| - uses: actions/setup-python@v5 | |
| with: | |
| python-version: '3.11' | |
| 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" >> $GITHUB_ENV | |
| - name: Install deps | |
| run: | | |
| pip install -r requirements.txt | |
| choco install ccache | |
| - name: Generate cache key | |
| id: cache-key | |
| run: | | |
| set -u | |
| os="${{ matrix.os }}" | |
| compiler="${{ matrix.compiler-name }}" | |
| build_type="${{ matrix.build_type }}" | |
| conanfile_hash="${{ hashFiles('conanfile.txt') }}" | |
| workflow_hash="${{ hashFiles('.github/workflows/windows-ci.yml') }}" | |
| combined_hash="${{ hashFiles('conanfile.txt', '.github/workflows/windows-ci.yml') }}" | |
| # This can be used by to always update a cache entry (useful e.g. for ccache) | |
| current_date="$(date '+%s')" | |
| conan_key_prefix="conan-$os-$compiler-$conanfile_hash-$build_type" | |
| ccache_key_prefix="ccache-$os-$compiler-$conanfile_hash-$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: ${{ env.CONAN_HOME }} | |
| - name: Configure Conan | |
| if: steps.cache-conan.outputs.cache-hit != 'true' | |
| run: | | |
| conan profile detect --force | |
| - name: Clean Conan cache (pre-build) | |
| if: steps.cache-conan.outputs.cache-hit != 'true' | |
| run: | | |
| conan cache clean "*" --build | |
| conan cache clean "*" --download | |
| conan cache clean "*" --source | |
| conan remove --confirm "*" | |
| - name: Install build dependencies | |
| run: | | |
| conan install . \ | |
| --build=missing \ | |
| -pr:h default \ | |
| -pr:b default \ | |
| -s "compiler=${{ matrix.compiler-name }}" \ | |
| -s "build_type=${{ matrix.build_type }}" \ | |
| -s "compiler.runtime_type=${{ matrix.build_type }}" \ | |
| -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: 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 \ | |
| -DHICTK_DOWNLOAD_TEST_DATASET=OFF \ | |
| -DHICTK_ENABLE_GIT_VERSION_TRACKING=OFF \ | |
| -DOPT_ENABLE_CLANG_TIDY=OFF \ | |
| -DOPT_ENABLE_CPPCHECK=OFF \ | |
| -S . \ | |
| -B build | |
| - name: Build project | |
| run: cmake --build build --config ${{ matrix.build_type }} | |
| - 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 | |
| enableCrossOsArchive: 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 \ | |
| --exclude-regex 'Cooler: dataset large read\/write.*' \ | |
| --exclude-regex 'HiC: HiCFileWriter' |& | |
| tail -n 1000 | |
| windows-ci-status-check: | |
| name: Status Check (Windows CI) | |
| if: ${{ always() }} | |
| runs-on: ubuntu-latest | |
| needs: | |
| - build-project | |
| steps: | |
| - name: Collect job results | |
| if: needs.build-project.result != 'success' | |
| run: exit 1 |