Update the docs #1152
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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/integration/**" | |
| - "test/units/**" | |
| - "CMakeLists.txt" | |
| - "conanfile.py" | |
| tags: | |
| - "v*.*.*" | |
| pull_request: | |
| paths: | |
| - ".github/workflows/windows-ci.yml" | |
| - "cmake/**" | |
| - "examples/**" | |
| - "src/**" | |
| - "test/integration/**" | |
| - "test/units/**" | |
| - "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: | |
| CONAN_HOME: "${{ github.workspace }}\\.conan2" | |
| HICTK_CI: "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: 'msvc', os: 'windows-2022', conan: '2.4.*', cmake: '3.29.*', build_type: 'Debug', developer_mode: 'OFF' }) | |
| includes.push({ compiler_name: 'msvc', os: 'windows-2022', conan: '2.4.*', cmake: '3.29.*', build_type: 'Release', developer_mode: 'OFF' }) | |
| return { include: includes } | |
| cache-test-dataset: | |
| uses: paulsengroup/hictk/.github/workflows/cache-test-dataset.yml@main | |
| name: Cache test dataset | |
| build-project: | |
| needs: matrix-factory | |
| runs-on: windows-latest | |
| 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" >> $GITHUB_ENV | |
| - name: Install deps | |
| run: pip install -r requirements.txt | |
| - name: Generate cache key | |
| id: cache-key | |
| run: | | |
| set -u | |
| os="${{ matrix.os }}" | |
| compiler="${{ matrix.compiler_name }}" | |
| build_type="${{ matrix.build_type }}" | |
| conanfile_hash="${{ hashFiles('conanfile.py') }}" | |
| conan_key_prefix="conan-$os-$compiler-$conanfile_hash-$build_type" | |
| echo "conan-key=$conan_key_prefix" | tee -a $GITHUB_OUTPUT | |
| - name: Restore Conan cache | |
| id: cache-conan | |
| uses: actions/cache/restore@v4 | |
| with: | |
| key: ${{ steps.cache-key.outputs.conan-key }} | |
| path: ${{ env.CONAN_HOME }}\p | |
| - name: Configure Conan | |
| run: | | |
| conan profile detect --force | |
| conan_profile="$(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/' "$conan_profile" | |
| - name: Clean Conan cache (pre-build) | |
| if: steps.cache-conan.outputs.cache-hit != 'true' | |
| run: | | |
| conan cache clean "*" --build | |
| conan cache clean "*" --download | |
| conan cache clean "*" --source | |
| conan remove --confirm "*" | |
| - name: Compile build dependencies | |
| if: steps.cache-conan.outputs.cache-hit != 'true' | |
| run: | | |
| conan install . \ | |
| --build=missing \ | |
| --build="b2/*" \ | |
| --build="catch2/*" \ | |
| -pr:h default \ | |
| -pr:b default \ | |
| -s:h "compiler=${{ 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=${{ matrix.build_type }}" \ | |
| -s:b compiler.cppstd=17 | |
| - name: Install build dependencies | |
| run: | | |
| conan install . \ | |
| -pr:h default \ | |
| -pr:b default \ | |
| -s:h "compiler=${{ 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: ${{ steps.cache-key.outputs.conan-key }} | |
| path: ${{ env.CONAN_HOME }}\p | |
| env: | |
| ZSTD_CLEVEL: 19 | |
| - name: Configure project | |
| run: | | |
| cmake -DCMAKE_BUILD_TYPE=${{ 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 \ | |
| -DCMAKE_INSTALL_PREFIX=dest \ | |
| -S "${{ github.workspace }}" \ | |
| -B "${{ github.workspace }}/build" | |
| - name: Build project | |
| run: cmake --build build --config ${{ matrix.build_type }} | |
| - name: Package binaries | |
| run: | | |
| cmake --install build | |
| tar -cf - -C dest/ bin | zstd -T0 -13 -o binaries.tar.zst | |
| - name: Package unit tests | |
| run: | | |
| rm -r build/src | |
| tar -cf - build/ | zstd -T0 -13 -o unit-tests.tar.zst | |
| - name: Upload unit tests | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: "unit-tests-${{ matrix.os }}-\ | |
| ${{ matrix.compiler_name }}-\ | |
| ${{ matrix.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.build_type }}-\ | |
| ${{ matrix.developer_mode }}" | |
| path: binaries.tar.zst | |
| if-no-files-found: error | |
| retention-days: 1 | |
| 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: Restore test dataset | |
| uses: actions/cache/restore@v4 | |
| with: | |
| key: ${{ needs.cache-test-dataset.outputs.cache-key }} | |
| path: test/data/hictk_test_data.tar.zst | |
| fail-on-cache-miss: true | |
| enableCrossOsArchive: true | |
| - name: Download unit tests artifact | |
| uses: actions/download-artifact@v4 | |
| with: | |
| name: "unit-tests-${{ matrix.os }}-\ | |
| ${{ matrix.compiler_name }}-\ | |
| ${{ matrix.build_type }}-\ | |
| ${{ matrix.developer_mode }}" | |
| - name: Extract binaries test dataset | |
| run: | | |
| tar -xf unit-tests.tar.zst | |
| tar -xf test/data/hictk_test_data.tar.zst | |
| - name: Generate requirements.txt for pip | |
| run: | | |
| echo 'cmake==${{ 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 (Debug) | |
| if: matrix.build_type == 'Debug' | |
| run: | | |
| skip_labels=( | |
| '.*dataset large read\/write.*' | |
| '.*HiCFileWriter.*' | |
| '.*VectorOfAtomicDecimals.*' | |
| ) | |
| pattern="$(IFS='|' ; echo "${skip_labels[*]}")" | |
| ctest --test-dir build \ | |
| --schedule-random \ | |
| --output-on-failure \ | |
| --no-tests=error \ | |
| --timeout 360 \ | |
| --exclude-regex "$pattern" |& | |
| tail -n 1000 | |
| - name: Run unit tests (Release) | |
| if: matrix.build_type == 'Release' | |
| run: | | |
| ctest --test-dir build \ | |
| --schedule-random \ | |
| --output-on-failure \ | |
| --no-tests=error \ | |
| --timeout 120 |& | |
| tail -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 | |
| - uses: actions/setup-python@v5 | |
| with: | |
| python-version: "3.12" | |
| cache-dependency-path: "test/integration/pyproject.toml" | |
| cache: "pip" | |
| - name: Restore test dataset | |
| uses: actions/cache/restore@v4 | |
| with: | |
| key: ${{ needs.cache-test-dataset.outputs.cache-key }} | |
| path: test/data/hictk_test_data.tar.zst | |
| fail-on-cache-miss: true | |
| enableCrossOsArchive: true | |
| - name: Download binaries artifact | |
| uses: actions/download-artifact@v4 | |
| with: | |
| name: "binaries-${{ matrix.os }}-\ | |
| ${{ matrix.compiler_name }}-\ | |
| ${{ matrix.build_type }}-\ | |
| ${{ matrix.developer_mode }}" | |
| - name: Extract binaries test dataset | |
| run: | | |
| tar -xf binaries.tar.zst | |
| tar -xf test/data/hictk_test_data.tar.zst | |
| - name: Install test suite | |
| run: | | |
| python.exe -m venv venv --upgrade | |
| venv/Scripts/pip.exe install test/integration | |
| - name: Detect number available CPUs | |
| run: | | |
| ncpus=$(python -c 'import multiprocessing as mp; print(mp.cpu_count())') | |
| echo "NPROC=$ncpus" | tee -a $GITHUB_ENV | |
| - name: Test hictk balance | |
| run: | | |
| venv/Scripts/hictk_integration_suite.exe \ | |
| bin/hictk.exe \ | |
| test/integration/config.toml \ | |
| --data-dir test/data \ | |
| --threads "$NPROC" \ | |
| --result-file integration-test-report.balance.json \ | |
| --suites=balance | |
| - name: Test hictk convert | |
| run: | | |
| venv/Scripts/hictk_integration_suite.exe \ | |
| bin/hictk.exe \ | |
| test/integration/config.toml \ | |
| --data-dir test/data \ | |
| --threads "$NPROC" \ | |
| --result-file integration-test-report.convert.json \ | |
| --suites=convert | |
| - name: Test hictk dump | |
| run: | | |
| venv/Scripts/hictk_integration_suite.exe \ | |
| bin/hictk.exe \ | |
| test/integration/config.toml \ | |
| --data-dir test/data \ | |
| --threads "$NPROC" \ | |
| --result-file integration-test-report.dump.json \ | |
| --suites=dump | |
| - name: Test hictk fix-mcool | |
| run: | | |
| venv/Scripts/hictk_integration_suite.exe \ | |
| bin/hictk.exe \ | |
| test/integration/config.toml \ | |
| --data-dir test/data \ | |
| --threads "$NPROC" \ | |
| --result-file integration-test-report.fix-mcool.json \ | |
| --suites=fix-mcool | |
| - name: Test hictk load | |
| run: | | |
| venv/Scripts/hictk_integration_suite.exe \ | |
| bin/hictk.exe \ | |
| test/integration/config.toml \ | |
| --data-dir test/data \ | |
| --threads "$NPROC" \ | |
| --result-file integration-test-report.load.json \ | |
| --suites=load | |
| - name: Test hictk merge | |
| run: | | |
| venv/Scripts/hictk_integration_suite.exe \ | |
| bin/hictk.exe \ | |
| test/integration/config.toml \ | |
| --data-dir test/data \ | |
| --threads "$NPROC" \ | |
| --result-file integration-test-report.merge.json \ | |
| --suites=merge | |
| - name: Test hictk metadata | |
| run: | | |
| venv/Scripts/hictk_integration_suite.exe \ | |
| bin/hictk.exe \ | |
| test/integration/config.toml \ | |
| --data-dir test/data \ | |
| --threads "$NPROC" \ | |
| --result-file integration-test-report.metadata.json \ | |
| --suites=metadata | |
| - name: Test hictk rename-chromosomes | |
| run: | | |
| venv/Scripts/hictk_integration_suite.exe \ | |
| bin/hictk.exe \ | |
| test/integration/config.toml \ | |
| --data-dir test/data \ | |
| --threads "$NPROC" \ | |
| --result-file integration-test-report.rename-chromosomes.json \ | |
| --suites=rename-chromosomes | |
| - name: Test hictk validate | |
| run: | | |
| venv/Scripts/hictk_integration_suite.exe \ | |
| bin/hictk.exe \ | |
| test/integration/config.toml \ | |
| --data-dir test/data \ | |
| --threads "$NPROC" \ | |
| --result-file integration-test-report.validate.json \ | |
| --suites=validate | |
| - name: Test hictk zoomify | |
| run: | | |
| venv/Scripts/hictk_integration_suite.exe \ | |
| bin/hictk.exe \ | |
| test/integration/config.toml \ | |
| --data-dir test/data \ | |
| --threads "$NPROC" \ | |
| --result-file integration-test-report.zoomify.json \ | |
| --suites=zoomify | |
| windows-ci-status-check: | |
| name: Status Check (Windows 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 |