Improve compilation times #1162
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) 2022 Roberto Rossini (roberros@uio.no) | |
| # SPDX-License-Identifier: MIT | |
| name: Ubuntu CI | |
| on: | |
| push: | |
| branches: [main] | |
| paths: | |
| - ".github/workflows/ubuntu-ci.yml" | |
| - "cmake/**" | |
| - "examples/**" | |
| - "src/**" | |
| - "test/integration/**" | |
| - "test/units/**" | |
| - "CMakeLists.txt" | |
| - "conanfile.py" | |
| tags: | |
| - "v*.*.*" | |
| pull_request: | |
| paths: | |
| - ".github/workflows/ubuntu-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 | |
| defaults: | |
| run: | |
| shell: bash | |
| jobs: | |
| matrix-factory: | |
| runs-on: ubuntu-latest | |
| outputs: | |
| matrix: ${{ steps.set-result.outputs.result }} | |
| steps: | |
| - name: Checkout repo | |
| uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 0 | |
| ref: ${{ github.event.after }} | |
| - name: Detect CI type | |
| id: ci-type | |
| run: | | |
| if git log --format=%B -n 1 ${{ github.event.after }} | grep -qF '[ci full]'; then | |
| echo "type=full" | tee -a "$GITHUB_OUTPUT" | |
| else | |
| echo "type=short" | tee -a "$GITHUB_OUTPUT" | |
| fi | |
| - name: Generate matrix | |
| uses: actions/github-script@v7 | |
| id: set-result | |
| with: | |
| script: | | |
| // Documentation | |
| // https://docs.github.com/en/actions/learn-github-actions/contexts#fromjson | |
| // https://github.com/actions/runner/issues/982#issuecomment-809360765 | |
| var ci_short = "${{ steps.ci-type.outputs.type }}" === "short" | |
| var includes = [] | |
| // Debug builds (short CI) | |
| includes.push({ compiler: 'gcc-8', os: 'ubuntu-20.04', generator: 'Ninja', cmake: '3.29.*', conan: '2.4.*', build_type: 'Debug', developer_mode: 'OFF' }) | |
| includes.push({ compiler: 'gcc-14', os: 'ubuntu-24.04', generator: 'Ninja', cmake: '3.29.*', conan: '2.4.*', build_type: 'Debug', developer_mode: 'ON' }) | |
| includes.push({ compiler: 'clang-8', os: 'ubuntu-20.04', generator: 'Ninja', cmake: '3.29.*', conan: '2.4.*', build_type: 'Debug', developer_mode: 'OFF' }) | |
| includes.push({ compiler: 'clang-18', os: 'ubuntu-24.04', generator: 'Ninja', cmake: '3.29.*', conan: '2.4.*', build_type: 'Debug', developer_mode: 'ON' }) | |
| // Release builds (short CI) | |
| includes.push({ compiler: 'gcc-14', os: 'ubuntu-24.04', generator: 'Ninja', cmake: '3.29.*', conan: '2.4.*', build_type: 'Release', developer_mode: 'ON' }) | |
| includes.push({ compiler: 'clang-18', os: 'ubuntu-24.04', generator: 'Ninja', cmake: '3.29.*', conan: '2.4.*', build_type: 'Release', developer_mode: 'ON' }) | |
| if (ci_short) { | |
| return { include: includes } | |
| } | |
| // Debug builds (long CI) | |
| includes.push({ compiler: 'gcc-9', os: 'ubuntu-22.04', generator: 'Ninja', cmake: '3.29.*', conan: '2.4.*', build_type: 'Debug', developer_mode: 'OFF' }) | |
| includes.push({ compiler: 'gcc-10', os: 'ubuntu-24.04', generator: 'Ninja', cmake: '3.29.*', conan: '2.4.*', build_type: 'Debug', developer_mode: 'OFF' }) | |
| includes.push({ compiler: 'gcc-11', os: 'ubuntu-24.04', generator: 'Ninja', cmake: '3.29.*', conan: '2.4.*', build_type: 'Debug', developer_mode: 'OFF' }) | |
| includes.push({ compiler: 'gcc-12', os: 'ubuntu-24.04', generator: 'Ninja', cmake: '3.29.*', conan: '2.4.*', build_type: 'Debug', developer_mode: 'OFF' }) | |
| includes.push({ compiler: 'gcc-13', os: 'ubuntu-24.04', generator: 'Ninja', cmake: '3.29.*', conan: '2.4.*', build_type: 'Debug', developer_mode: 'OFF' }) | |
| includes.push({ compiler: 'clang-9', os: 'ubuntu-20.04', generator: 'Ninja', cmake: '3.29.*', conan: '2.4.*', build_type: 'Debug', developer_mode: 'OFF' }) | |
| includes.push({ compiler: 'clang-10', os: 'ubuntu-20.04', generator: 'Ninja', cmake: '3.29.*', conan: '2.4.*', build_type: 'Debug', developer_mode: 'OFF' }) | |
| includes.push({ compiler: 'clang-11', os: 'ubuntu-22.04', generator: 'Ninja', cmake: '3.29.*', conan: '2.4.*', build_type: 'Debug', developer_mode: 'OFF' }) | |
| includes.push({ compiler: 'clang-12', os: 'ubuntu-22.04', generator: 'Ninja', cmake: '3.29.*', conan: '2.4.*', build_type: 'Debug', developer_mode: 'OFF' }) | |
| includes.push({ compiler: 'clang-13', os: 'ubuntu-22.04', generator: 'Ninja', cmake: '3.29.*', conan: '2.4.*', build_type: 'Debug', developer_mode: 'OFF' }) | |
| includes.push({ compiler: 'clang-14', os: 'ubuntu-24.04', generator: 'Ninja', cmake: '3.29.*', conan: '2.4.*', build_type: 'Debug', developer_mode: 'OFF' }) | |
| includes.push({ compiler: 'clang-15', os: 'ubuntu-24.04', generator: 'Ninja', cmake: '3.29.*', conan: '2.4.*', build_type: 'Debug', developer_mode: 'OFF' }) | |
| includes.push({ compiler: 'clang-16', os: 'ubuntu-24.04', generator: 'Ninja', cmake: '3.29.*', conan: '2.4.*', build_type: 'Debug', developer_mode: 'OFF' }) | |
| includes.push({ compiler: 'clang-17', os: 'ubuntu-24.04', generator: 'Ninja', cmake: '3.29.*', conan: '2.4.*', build_type: 'Debug', developer_mode: 'OFF' }) | |
| // Release builds (long CI) | |
| includes.push({ compiler: 'gcc-8', os: 'ubuntu-20.04', generator: 'Ninja', cmake: '3.29.*', conan: '2.4.*', build_type: 'Release', developer_mode: 'OFF' }) | |
| includes.push({ compiler: 'gcc-9', os: 'ubuntu-22.04', generator: 'Ninja', cmake: '3.29.*', conan: '2.4.*', build_type: 'Release', developer_mode: 'OFF' }) | |
| includes.push({ compiler: 'gcc-10', os: 'ubuntu-24.04', generator: 'Ninja', cmake: '3.29.*', conan: '2.4.*', build_type: 'Release', developer_mode: 'OFF' }) | |
| includes.push({ compiler: 'gcc-11', os: 'ubuntu-24.04', generator: 'Ninja', cmake: '3.29.*', conan: '2.4.*', build_type: 'Release', developer_mode: 'OFF' }) | |
| includes.push({ compiler: 'gcc-12', os: 'ubuntu-24.04', generator: 'Ninja', cmake: '3.29.*', conan: '2.4.*', build_type: 'Release', developer_mode: 'OFF' }) | |
| includes.push({ compiler: 'gcc-13', os: 'ubuntu-24.04', generator: 'Ninja', cmake: '3.29.*', conan: '2.4.*', build_type: 'Release', developer_mode: 'OFF' }) | |
| includes.push({ compiler: 'clang-8', os: 'ubuntu-20.04', generator: 'Ninja', cmake: '3.29.*', conan: '2.4.*', build_type: 'Release', developer_mode: 'OFF' }) | |
| includes.push({ compiler: 'clang-9', os: 'ubuntu-20.04', generator: 'Ninja', cmake: '3.29.*', conan: '2.4.*', build_type: 'Release', developer_mode: 'OFF' }) | |
| includes.push({ compiler: 'clang-10', os: 'ubuntu-20.04', generator: 'Ninja', cmake: '3.29.*', conan: '2.4.*', build_type: 'Release', developer_mode: 'OFF' }) | |
| includes.push({ compiler: 'clang-11', os: 'ubuntu-22.04', generator: 'Ninja', cmake: '3.29.*', conan: '2.4.*', build_type: 'Release', developer_mode: 'OFF' }) | |
| includes.push({ compiler: 'clang-12', os: 'ubuntu-22.04', generator: 'Ninja', cmake: '3.29.*', conan: '2.4.*', build_type: 'Release', developer_mode: 'OFF' }) | |
| includes.push({ compiler: 'clang-13', os: 'ubuntu-22.04', generator: 'Ninja', cmake: '3.29.*', conan: '2.4.*', build_type: 'Release', developer_mode: 'OFF' }) | |
| includes.push({ compiler: 'clang-14', os: 'ubuntu-24.04', generator: 'Ninja', cmake: '3.29.*', conan: '2.4.*', build_type: 'Release', developer_mode: 'OFF' }) | |
| includes.push({ compiler: 'clang-15', os: 'ubuntu-24.04', generator: 'Ninja', cmake: '3.29.*', conan: '2.4.*', build_type: 'Release', developer_mode: 'OFF' }) | |
| includes.push({ compiler: 'clang-16', os: 'ubuntu-24.04', generator: 'Ninja', cmake: '3.29.*', conan: '2.4.*', build_type: 'Release', developer_mode: 'OFF' }) | |
| includes.push({ compiler: 'clang-17', os: 'ubuntu-24.04', generator: 'Ninja', cmake: '3.29.*', conan: '2.4.*', build_type: 'Release', developer_mode: 'OFF' }) | |
| // Make sure project builds with CMake 3.25 | |
| includes.push({ compiler: 'clang-18', os: 'ubuntu-24.04', generator: 'Ninja', cmake: '3.25.2', conan: '2.4.*', build_type: 'Release', developer_mode: 'OFF' }) | |
| // Make sure project builds with make | |
| includes.push({ compiler: 'clang-18', os: 'ubuntu-24.04', generator: 'Unix Makefiles', cmake: '3.29.*', conan: '2.4.*', 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: | |
| name: Build project | |
| needs: matrix-factory | |
| runs-on: ubuntu-latest | |
| strategy: | |
| fail-fast: false | |
| matrix: ${{ fromJSON(needs.matrix-factory.outputs.matrix) }} | |
| container: | |
| image: ghcr.io/paulsengroup/ci-docker-images/${{ matrix.os }}-cxx-${{ matrix.compiler }}:latest | |
| options: "--user=root" | |
| env: | |
| CCACHE_DIR: "/opt/ccache-cache" | |
| CCACHE_COMPILERCHECK: "content" | |
| CCACHE_COMPRESSLEVEL: "1" | |
| CCACHE_MAXSIZE: "500M" | |
| CONAN_HOME: "/opt/conan/" | |
| outputs: | |
| ccache-old-cache-key: ${{ steps.cache-ccache.outputs.cache-matched-key }} | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Fix permissions | |
| run: | | |
| chown -R $(id -u):$(id -g) $PWD | |
| - name: Check build deps are up-to-date | |
| id: build-deps-outdated | |
| run: | | |
| pattern='[[:digit:]]\+\.[[:digit:]]\+\.[[:digit:]]\+$' | |
| flag=false | |
| if [[ $(cmake --version | grep -o "$pattern") != ${{ matrix.cmake }} || | |
| $(conan --version | grep -o "$pattern") != ${{ matrix.conan }} ]]; then | |
| flag=true | |
| fi | |
| echo "outdated=$flag" | tee -a "$GITHUB_OUTPUT" | |
| - name: Update build deps | |
| if: ${{ steps.buld-deps-outdated.outputs.outdated }} | |
| run: | | |
| apt-get update | |
| apt-get install -y --no-install-recommends python3-pip | |
| python3 -m pip install \ | |
| "cmake==${{ matrix.cmake }}" \ | |
| "conan==${{ matrix.conan }}" | |
| - name: Generate cache keys | |
| id: cache-key | |
| run: | | |
| set -u | |
| os="${{ matrix.os }}" | |
| compiler="${{ matrix.compiler }}" | |
| generator="${{ matrix.generator }}" | |
| build_type="${{ matrix.build_type }}" | |
| dev_mode="${{ matrix.developer_mode }}" | |
| conanfile_hash="${{ hashFiles('conanfile.py') }}" | |
| # This can be used by to always update a cache entry (useful e.g. for ccache) | |
| current_date="$(date '+%s')" | |
| conan_key_prefix="conan-$os-$compiler-$conanfile_hash-$build_type-$generator-$dev_mode" | |
| ccache_key_prefix="ccache-$os-$compiler-$GITHUB_REF-$conanfile_hash-$build_type-$generator-$dev_mode" | |
| echo "conan-key=$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: ${{ steps.cache-key.outputs.conan-key }} | |
| path: ${{ env.CONAN_HOME }}/p | |
| - name: Clean Conan cache (pre-build) | |
| if: steps.cache-conan.outputs.cache-hit != 'true' | |
| run: | | |
| conan cache clean "*" --build | |
| conan cache clean "*" --download | |
| conan cache clean "*" --source | |
| conan remove --confirm "*" | |
| - name: Copy Conan settings | |
| run: | | |
| if [ ! -f "$CONAN_HOME/settings.yml" ]; then | |
| cp "/root/.conan2/settings.yml" "$CONAN_HOME" | |
| fi | |
| - name: Install build dependencies | |
| run: | | |
| conan install . \ | |
| --build=missing \ | |
| -pr:b="$CONAN_DEFAULT_PROFILE_PATH" \ | |
| -pr:h="$CONAN_DEFAULT_PROFILE_PATH" \ | |
| -s build_type="${{ matrix.build_type }}" \ | |
| -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: ${{ steps.cache-key.outputs.conan-key }} | |
| path: ${{ env.CONAN_HOME }}/p | |
| env: | |
| ZSTD_CLEVEL: 19 | |
| - name: Restore Ccache folder | |
| id: cache-ccache | |
| uses: actions/cache/restore@v4 | |
| with: | |
| key: ${{ steps.cache-key.outputs.ccache-restore-key }} | |
| path: ${{ env.CCACHE_DIR }} | |
| - name: Reset Ccache stats | |
| run: ccache --zero-stats | |
| - name: Configure project | |
| run: | | |
| cmake -DCMAKE_BUILD_TYPE=${{ matrix.build_type }} \ | |
| -DCMAKE_PREFIX_PATH="$PWD/build" \ | |
| -DENABLE_DEVELOPER_MODE=${{ matrix.developer_mode }} \ | |
| -DOPT_ENABLE_CLANG_TIDY=OFF \ | |
| -DOPT_ENABLE_CPPCHECK=OFF \ | |
| -DHICTK_ENABLE_TESTING=ON \ | |
| -DHICTK_BUILD_EXAMPLES=ON \ | |
| -DHICTK_DOWNLOAD_TEST_DATASET=OFF \ | |
| -DHICTK_ENABLE_GIT_VERSION_TRACKING=OFF \ | |
| -DCMAKE_INSTALL_PREFIX=dest \ | |
| -S . \ | |
| -B build | |
| - name: Build project | |
| run: cmake --build build -j $(nproc) | |
| - name: Package binaries | |
| run: | | |
| cmake --install build | |
| tar -cf - -C dest/ bin | zstd -T0 -13 -o binaries.tar.zst | |
| - name: Package unit tests | |
| run: | | |
| rm -r build/src | |
| tar -cf - build/ | zstd -T0 -13 -o unit-tests.tar.zst | |
| - name: Upload unit tests | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: "unit-tests-${{ matrix.os }}-\ | |
| ${{ matrix.compiler }}-\ | |
| ${{ matrix.generator }}-\ | |
| ${{ 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 }}-\ | |
| ${{ matrix.generator }}-\ | |
| ${{ matrix.build_type }}-\ | |
| ${{ matrix.developer_mode }}" | |
| path: binaries.tar.zst | |
| if-no-files-found: error | |
| retention-days: 1 | |
| - name: Print Ccache statistics (pre-cleanup) | |
| run: | | |
| ccache --show-stats \ | |
| --show-compression \ | |
| --verbose | |
| - name: Cleanup Ccache folder | |
| run: | | |
| ccache --evict-older-than=14400s # 4h | |
| ccache --recompress=19 --recompress-threads="$(nproc)" | |
| ccache --cleanup | |
| - name: Print Ccache statistics (post-cleanup) | |
| run: | | |
| ccache --show-stats \ | |
| --show-compression \ | |
| --verbose | |
| - name: Save Ccache folder | |
| uses: actions/cache/save@v4 | |
| with: | |
| key: ${{ steps.cache-key.outputs.ccache-key }} | |
| path: ${{ env.CCACHE_DIR }} | |
| env: | |
| ZSTD_CLEVEL: 1 | |
| clean-stale-cache: | |
| needs: [build-project] | |
| uses: paulsengroup/hictk/.github/workflows/evict-gha-cache.yml@main | |
| name: Clean stale Ccache cache | |
| permissions: | |
| actions: write | |
| if: needs.build-project.outputs.ccache-old-cache-key != '' | |
| with: | |
| cache-key: "${{ needs.build-project.outputs.ccache-old-cache-key }}" | |
| run-unit-tests: | |
| name: Run unit tests | |
| needs: [matrix-factory, cache-test-dataset, build-project] | |
| runs-on: ubuntu-latest | |
| strategy: | |
| fail-fast: false | |
| matrix: ${{ fromJSON(needs.matrix-factory.outputs.matrix) }} | |
| container: | |
| image: ghcr.io/paulsengroup/ci-docker-images/${{ matrix.os }}-cxx-${{ matrix.compiler }}:latest | |
| options: "--user=root" | |
| env: | |
| HICTK_CI: "1" | |
| steps: | |
| - name: Checkout repo | |
| uses: actions/checkout@v4 | |
| - name: Restore test dataset | |
| uses: actions/cache/restore@v4 | |
| with: | |
| key: ${{ needs.cache-test-dataset.outputs.cache-key }} | |
| path: test/data/hictk_test_data.tar.zst | |
| fail-on-cache-miss: true | |
| - name: Download unit tests artifact | |
| uses: actions/download-artifact@v4 | |
| with: | |
| name: "unit-tests-${{ matrix.os }}-\ | |
| ${{ matrix.compiler }}-\ | |
| ${{ matrix.generator }}-\ | |
| ${{ matrix.build_type }}-\ | |
| ${{ matrix.developer_mode }}" | |
| - name: Extract binaries and test dataset | |
| run: | | |
| zstd -dcf unit-tests.tar.zst | tar -xf - | |
| tar -xf test/data/hictk_test_data.tar.zst | |
| - name: Add test user | |
| run: useradd devel | |
| - name: Fix permissions | |
| run: | | |
| chown -R devel:devel build/ | |
| - name: Setup dependencies | |
| run: | | |
| apt-get update | |
| apt-get install -q -y --no-install-recommends \ | |
| python3-pip \ | |
| sudo | |
| python3 -m pip install "cmake==${{ matrix.cmake }}" | |
| - name: Run unit tests | |
| run: | | |
| sudo -u devel -E env "PATH=$PATH" \ | |
| ctest --test-dir build/ \ | |
| --schedule-random \ | |
| --output-on-failure \ | |
| --no-tests=error \ | |
| --timeout 360 \ | |
| -j $(nproc) |& | |
| head -n 1000 | |
| run-integration-tests: | |
| name: Run integration tests | |
| needs: [matrix-factory, cache-test-dataset, build-project] | |
| runs-on: ubuntu-latest | |
| strategy: | |
| fail-fast: false | |
| matrix: ${{ fromJSON(needs.matrix-factory.outputs.matrix) }} | |
| container: | |
| image: ubuntu:24.04 | |
| options: "--user=root" | |
| env: | |
| HICTK_CI: "1" | |
| DEBIAN_FRONTEND: "noninteractive" | |
| TZ: "Etc/UTC" | |
| steps: | |
| - name: Install dependencies | |
| run: | | |
| apt-get update | |
| apt-get install -q -y --no-install-recommends \ | |
| curl \ | |
| git \ | |
| python3.12 \ | |
| python3.12-venv \ | |
| python3-pip \ | |
| sudo \ | |
| tar \ | |
| zip \ | |
| zstd | |
| if [ "${{ matrix.developer_mode }}" = ON ]; then | |
| apt-get install -q -y --no-install-recommends \ | |
| libasan8 \ | |
| libubsan1 | |
| fi | |
| - name: Checkout repo | |
| uses: actions/checkout@v4 | |
| - name: Restore test dataset | |
| uses: actions/cache/restore@v4 | |
| with: | |
| key: ${{ needs.cache-test-dataset.outputs.cache-key }} | |
| path: test/data/hictk_test_data.tar.zst | |
| fail-on-cache-miss: true | |
| - name: Download binaries artifact | |
| uses: actions/download-artifact@v4 | |
| with: | |
| name: "binaries-${{ matrix.os }}-\ | |
| ${{ matrix.compiler }}-\ | |
| ${{ matrix.generator }}-\ | |
| ${{ matrix.build_type }}-\ | |
| ${{ matrix.developer_mode }}" | |
| - name: Extract binaries and test dataset | |
| run: | | |
| tar -xf binaries.tar.zst | |
| tar -xf test/data/hictk_test_data.tar.zst | |
| - name: Install test suite | |
| run: | | |
| python3.12 -m venv venv --upgrade | |
| venv/bin/pip install test/integration | |
| - name: Add test user | |
| run: useradd devel | |
| - name: Test hictk balance | |
| run: | | |
| sudo -u devel -E env "PATH=$PATH" \ | |
| venv/bin/hictk_integration_suite \ | |
| bin/hictk \ | |
| test/integration/config.toml \ | |
| --data-dir test/data \ | |
| --threads "$(nproc)" \ | |
| --result-file integration-test-report.balance.json \ | |
| --suites=balance | |
| - name: Test hictk convert | |
| run: | | |
| sudo -u devel -E env "PATH=$PATH" \ | |
| venv/bin/hictk_integration_suite \ | |
| bin/hictk \ | |
| test/integration/config.toml \ | |
| --data-dir test/data \ | |
| --threads "$(nproc)" \ | |
| --result-file integration-test-report.convert.json \ | |
| --suites=convert | |
| - name: Test hictk dump | |
| run: | | |
| sudo -u devel -E env "PATH=$PATH" \ | |
| venv/bin/hictk_integration_suite \ | |
| bin/hictk \ | |
| test/integration/config.toml \ | |
| --data-dir test/data \ | |
| --threads "$(nproc)" \ | |
| --result-file integration-test-report.dump.json \ | |
| --suites=dump | |
| - name: Test hictk fix-mcool | |
| run: | | |
| sudo -u devel -E env "PATH=$PATH" \ | |
| venv/bin/hictk_integration_suite \ | |
| bin/hictk \ | |
| test/integration/config.toml \ | |
| --data-dir test/data \ | |
| --threads "$(nproc)" \ | |
| --result-file integration-test-report.fix-mcool.json \ | |
| --suites=fix-mcool | |
| - name: Test hictk load | |
| run: | | |
| sudo -u devel -E env "PATH=$PATH" \ | |
| venv/bin/hictk_integration_suite \ | |
| bin/hictk \ | |
| test/integration/config.toml \ | |
| --data-dir test/data \ | |
| --threads "$(nproc)" \ | |
| --result-file integration-test-report.load.json \ | |
| --suites=load | |
| - name: Test hictk merge | |
| run: | | |
| sudo -u devel -E env "PATH=$PATH" \ | |
| venv/bin/hictk_integration_suite \ | |
| bin/hictk \ | |
| test/integration/config.toml \ | |
| --data-dir test/data \ | |
| --threads "$(nproc)" \ | |
| --result-file integration-test-report.merge.json \ | |
| --suites=merge | |
| - name: Test hictk metadata | |
| run: | | |
| sudo -u devel -E env "PATH=$PATH" \ | |
| venv/bin/hictk_integration_suite \ | |
| bin/hictk \ | |
| test/integration/config.toml \ | |
| --data-dir test/data \ | |
| --threads "$(nproc)" \ | |
| --result-file integration-test-report.metadata.json \ | |
| --suites=metadata | |
| - name: Test hictk rename-chromosomes | |
| run: | | |
| sudo -u devel -E env "PATH=$PATH" \ | |
| venv/bin/hictk_integration_suite \ | |
| bin/hictk \ | |
| test/integration/config.toml \ | |
| --data-dir test/data \ | |
| --threads "$(nproc)" \ | |
| --result-file integration-test-report.rename-chromosomes.json \ | |
| --suites=rename-chromosomes | |
| - name: Test hictk validate | |
| run: | | |
| sudo -u devel -E env "PATH=$PATH" \ | |
| venv/bin/hictk_integration_suite \ | |
| bin/hictk \ | |
| test/integration/config.toml \ | |
| --data-dir test/data \ | |
| --threads "$(nproc)" \ | |
| --result-file integration-test-report.validate.json \ | |
| --suites=validate | |
| - name: Test hictk zoomify | |
| run: | | |
| sudo -u devel -E env "PATH=$PATH" \ | |
| venv/bin/hictk_integration_suite \ | |
| bin/hictk \ | |
| test/integration/config.toml \ | |
| --data-dir test/data \ | |
| --threads "$(nproc)" \ | |
| --result-file integration-test-report.zoomify.json \ | |
| --suites=zoomify | |
| - name: Upload integration test results | |
| if: ${{ always() }} | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: "integration-test-reports-\ | |
| ${{ matrix.os }}-\ | |
| ${{ matrix.compiler }}-\ | |
| ${{ matrix.generator }}-\ | |
| ${{ matrix.build_type }}-\ | |
| ${{ matrix.developer_mode }}" | |
| path: integration-test-report*.json | |
| retention-days: 7 | |
| ubuntu-ci-status-check: | |
| name: Status Check (Ubuntu 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 |