Fix division by zero when fetching pixels from coolers with bin tables with variable bin size #1035
Workflow file for this run
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| # 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.py" | |
| tags: | |
| - "v*.*.*" | |
| pull_request: | |
| paths: | |
| - ".github/workflows/windows-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" | |
| HICTK_CI: "1" | |
| 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: | |
| # prettier-ignore | |
| - { compiler-name: msvc, os: 'windows-2022', conan-ver: '2.4.*', cmake-ver: '3.29.*', build_type: Debug, developer_mode: OFF } | |
| # prettier-ignore | |
| - { compiler-name: msvc, os: 'windows-2022', conan-ver: '2.4.*', cmake-ver: '3.29.*', 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: "3.12" | |
| 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" >> $GITHUB_ENV | |
| - name: Install deps | |
| run: | | |
| pip install -r requirements.txt | |
| choco install ccache | |
| - name: Generate cache key | |
| id: cache-key | |
| run: | | |
| set -u | |
| os="${{ matrix.os }}" | |
| compiler="${{ matrix.compiler-name }}" | |
| build_type="${{ matrix.build_type }}" | |
| conanfile_hash="${{ hashFiles('conanfile.py') }}" | |
| workflow_hash="${{ hashFiles('.github/workflows/windows-ci.yml') }}" | |
| combined_hash="${{ hashFiles('conanfile.py', '.github/workflows/windows-ci.yml') }}" | |
| # This can be used by to always update a cache entry (useful e.g. for ccache) | |
| current_date="$(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: ${{ env.CONAN_HOME }} | |
| - name: Configure Conan | |
| if: steps.cache-conan.outputs.cache-hit != 'true' | |
| run: | | |
| conan profile detect --force | |
| conan_profile="$(conan profile path default)" | |
| sed -i 's/build_type=Release/build_type=${{ matrix.build_type }}/' "$conan_profile" | |
| sed -i 's/compiler\.cppstd=.*/compiler.cppstd=17/' "$conan_profile" | |
| - name: Clean Conan cache (pre-build) | |
| if: steps.cache-conan.outputs.cache-hit != 'true' | |
| run: | | |
| conan cache clean "*" --build | |
| conan cache clean "*" --download | |
| conan cache clean "*" --source | |
| conan remove --confirm "*" | |
| - name: Install build dependencies | |
| run: | | |
| conan install . \ | |
| --build=missing \ | |
| --build="b2/*" \ | |
| --build="catch2/*" \ | |
| -pr:h default \ | |
| -pr:b default \ | |
| -s:h "compiler=${{ matrix.compiler-name }}" \ | |
| -s:h "build_type=${{ matrix.build_type }}" \ | |
| -s:h "compiler.runtime_type=${{ matrix.build_type }}" \ | |
| -s:h compiler.cppstd=17 \ | |
| -s:b "compiler=${{ matrix.compiler-name }}" \ | |
| -s:b "build_type=${{ matrix.build_type }}" \ | |
| -s:b "compiler.runtime_type=${{ matrix.build_type }}" \ | |
| -s:b compiler.cppstd=17 \ | |
| --output-folder=build | |
| - name: Clean Conan cache (post-build) | |
| if: steps.cache-conan.outputs.cache-hit != 'true' | |
| run: | | |
| conan cache clean "*" --build | |
| conan cache clean "*" --download | |
| conan cache clean "*" --source | |
| - name: Save Conan cache | |
| uses: actions/cache/save@v4 | |
| if: steps.cache-conan.outputs.cache-hit != 'true' | |
| with: | |
| key: conan-${{ 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 '.*(dataset large read\/write|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 |