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Merge pull request #3367 from eseiler/infra/ci
[INFRA] Update CI
2 parents bbae8da + 36fdec1 commit 74a7ed6

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-134
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‎.codecov.yml‎

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# See https://docs.codecov.io/docs/codecovyml-reference
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codecov:
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token: a75b1e95-134c-4ada-adac-5846045f188e
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require_ci_to_pass: no # codecov reports its results independent of whether CI passed
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notify:
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wait_for_ci: no # codecov has not to wait until the CI is finished to post its results

‎.github/workflows/ci_cmake.yml‎

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matrix:
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include:
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- name: "Non-cyclic tests"
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compiler: "gcc-14"
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compiler: "gcc-latest"
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build: unit
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use_include_dependencies: "ON"
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cmake_depends_use_compiler: "OFF"
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- name: "External project"
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compiler: "gcc-14"
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compiler: "gcc-latest"
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build: external_project
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use_include_dependencies: "OFF"
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cmake_depends_use_compiler: "ON"
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container:
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image: ghcr.io/seqan/${{ matrix.compiler }}
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volumes:
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- /home/runner:/home/runner
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steps:
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- name: Checkout
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uses: actions/checkout@v4

‎.github/workflows/ci_coverage.yml‎

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strategy:
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fail-fast: false
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matrix:
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compiler: ["gcc-14"]
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compiler: ["gcc-latest"]
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container:
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image: ghcr.io/seqan/${{ matrix.compiler }}
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volumes:
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- /home/runner:/home/runner
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steps:
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- name: Checkout
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uses: actions/checkout@v4
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--filter ${GITHUB_WORKSPACE}/test/include/seqan3/test \
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--exclude ${GITHUB_WORKSPACE}/include/seqan3/contrib \
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--exclude ${GITHUB_WORKSPACE}/include/seqan3/std \
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--exclude-lines-by-pattern '^\s*$' \
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--exclude-lines-by-pattern '^\s*};$' \
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--exclude-unreachable-branches \
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--exclude-lines-by-pattern '^\s*}|^\s*};' \
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--exclude-throw-branches \
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--exclude-noncode-lines \
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--exclude-unreachable-branches \
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--merge-mode-functions separate \
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-j \
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--cobertura \
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--output ${GITHUB_WORKSPACE}/build/coverage_report.xml
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- name: Submit coverage build
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uses: codecov/codecov-action@v3.1.5
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uses: codecov/codecov-action@v5.4.3
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with:
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files: build/coverage_report.xml
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disable_search: true
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fail_ci_if_error: false
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files: build/coverage_report.xml
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plugins: noop
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token: ${{ secrets.CODECOV_TOKEN }}

‎.github/workflows/ci_license.yml‎

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jobs:
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check:
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name: REUSE Compliance
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runs-on: ubuntu-22.04
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runs-on: ubuntu-latest
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timeout-minutes: 120
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if: github.repository_owner == 'seqan' || github.event_name == 'workflow_dispatch' || github.event.label.name == 'lint'
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steps:

‎.github/workflows/ci_lint.yml‎

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jobs:
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# Cancel other workflows that are dependent on this workflow by adding jobs that have the same concurrency group.
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cancel_linux:
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name: Cancel running Workflows
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cancel_running_workflows:
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name: Cancel ${{ matrix.workflow}}
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strategy:
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fail-fast: false
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matrix:
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workflow: ["linux", "macos", "misc", "coverage", "cmake", "documentation"]
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concurrency:
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group: linux-${{ github.event.pull_request.number }}
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group: ${{ matrix.workflow }}-${{ github.event.pull_request.number }}
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cancel-in-progress: true
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runs-on: ubuntu-22.04
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runs-on: ubuntu-latest
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steps:
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- name: "Cancel Linux"
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run: echo "Cancelling Linux"
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cancel_macos:
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name: Cancel running Workflows
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concurrency:
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group: macos-${{ github.event.pull_request.number }}
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cancel-in-progress: true
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runs-on: ubuntu-22.04
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steps:
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- name: "Cancel macOS"
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run: echo "Cancelling macOS"
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cancel_misc:
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name: Cancel running Workflows
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concurrency:
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group: misc-${{ github.event.pull_request.number }}
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cancel-in-progress: true
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runs-on: ubuntu-22.04
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steps:
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- name: "Cancel Misc"
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run: echo "Cancelling Misc"
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cancel_coverage:
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name: Cancel running Workflows
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concurrency:
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group: coverage-${{ github.event.pull_request.number }}
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cancel-in-progress: true
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runs-on: ubuntu-22.04
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steps:
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- name: "Cancel Coverage"
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run: echo "Cancelling Coverage"
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cancel_cmake:
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name: Cancel running Workflows
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concurrency:
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group: cmake-${{ github.event.pull_request.number }}
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cancel-in-progress: true
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runs-on: ubuntu-22.04
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steps:
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- name: "Cancel CMake"
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run: echo "Cancelling CMake"
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cancel_documentation:
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name: Cancel running Workflows
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concurrency:
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group: documentation-${{ github.event.pull_request.number }}
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cancel-in-progress: true
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runs-on: ubuntu-22.04
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steps:
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- name: "Cancel Documentation"
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run: echo "Cancelling Documentation"
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- name: "Cancel ${{ matrix.workflow }}"
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run: echo "Cancelling ${{ matrix.workflow }}"
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lint:
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name: Lint
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concurrency:
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group: lint-${{ github.event.pull_request.number }}
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cancel-in-progress: true
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needs: [cancel_linux, cancel_macos, cancel_misc, cancel_coverage, cancel_cmake, cancel_documentation]
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runs-on: ubuntu-22.04
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needs: cancel_running_workflows
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runs-on: ubuntu-latest
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timeout-minutes: 15
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steps:
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- name: Run lint

‎.github/workflows/ci_linux.yml‎

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strategy:
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fail-fast: false
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matrix:
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compiler: ["clang-19", "clang-18", "clang-17", "gcc-14", "gcc-13", "gcc-12", "intel"]
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include:
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- compiler: "intel"
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cxx_flags: "-fp-model=strict -Wno-overriding-option"
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compiler: ["clang-latest", "clang-second-latest", "clang-third-latest", "gcc-latest", "gcc-second-latest", "gcc-third-latest", "intel"]
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container:
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image: ghcr.io/seqan/${{ matrix.compiler }}
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volumes:
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- /home/runner:/home/runner
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steps:
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- name: Checkout
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uses: actions/checkout@v4
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$CXX --version || true
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cmake --version || true
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mkdir build && cd build
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cmake ../test/unit -DCMAKE_BUILD_TYPE=Release \
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-DCMAKE_CXX_FLAGS="${{ matrix.cxx_flags }}"
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cmake ../test/unit -DCMAKE_BUILD_TYPE=Release
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make gtest_main
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- name: Build tests

‎.github/workflows/ci_macos.yml‎

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jobs:
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build:
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name: ${{ matrix.compiler }}
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runs-on: macos-14
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runs-on: macos-latest
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if: github.repository_owner == 'seqan' || github.event_name == 'workflow_dispatch' || github.event.label.name == 'lint'
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strategy:
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fail-fast: false
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matrix:
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compiler: ["clang-19", "clang-18", "clang-17", "gcc-14", "gcc-13", "gcc-12"]
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compiler: ["clang-latest", "clang-second-latest", "clang-third-latest", "gcc-latest", "gcc-second-latest", "gcc-third-latest"]
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steps:
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- name: Checkout
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uses: actions/checkout@v4

‎.github/workflows/ci_misc.yml‎

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strategy:
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fail-fast: false
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matrix:
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compiler: ["clang-19", "gcc-14", "gcc-12", "intel"]
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compiler: ["clang-latest", "gcc-latest", "gcc-third-latest", "intel"]
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build: ["snippet", "performance", "header"]
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include:
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- compiler: "intel"
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cxx_flags: "-fp-model=strict -Wno-overriding-option"
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container:
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image: ghcr.io/seqan/${{ matrix.compiler }}
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volumes:
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- /home/runner:/home/runner
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steps:
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- name: Checkout
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uses: actions/checkout@v4
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run: |
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mkdir build && cd build
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cmake ../test/${{ matrix.build }} -DCMAKE_BUILD_TYPE=Release \
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-DCMAKE_CXX_FLAGS="${{ matrix.cxx_flags }}" \
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-DSEQAN3_BENCHMARK_MIN_TIME=0.01s
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case "${{ matrix.build }}" in
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snippet) make gtest_main;;

‎.github/workflows/ci_update_cookbook.yml‎

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jobs:
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update-cookbook:
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name: Update Cookbook
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runs-on: ubuntu-22.04
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runs-on: ubuntu-latest
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if: github.repository_owner == 'seqan'
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timeout-minutes: 15
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steps:

‎.github/workflows/cron_api.yml‎

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strategy:
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fail-fast: false
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matrix:
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compiler: ["gcc-14", "gcc-13", "gcc-12"]
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compiler: ["gcc-latest", "gcc-second-latest", "gcc-third-latest"]
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container:
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image: ghcr.io/seqan/${{ matrix.compiler }}
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volumes:
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- /home/runner:/home/runner
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steps:
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- name: Checkout
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uses: actions/checkout@v4
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- name: Configure tests
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run: |
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mkdir build && cd build
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cmake ../test/api_stability -DCMAKE_BUILD_TYPE=Release \
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-DCMAKE_CXX_FLAGS="${{ matrix.cxx_flags }}"
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cmake ../test/api_stability -DCMAKE_BUILD_TYPE=Release
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- name: Build tests
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working-directory: build

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