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eseilereseiler
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Merge pull request #3321 from eseiler/fix/tsan
[INFRA] Sanitizer CI
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‎.clang-format‎

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@@ -274,4 +274,5 @@ WhitespaceSensitiveMacros:
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- STRINGIZE
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- SEQAN3_WORKAROUND_GCC_BOGUS_MEMCPY_START
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- SEQAN3_WORKAROUND_GCC_BOGUS_MEMCPY_STOP
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- reduction
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...

‎.github/workflows/ci_misc.yml‎

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@@ -60,7 +60,7 @@ jobs:
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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=0.01
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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;;
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performance) make benchmark_main;;

‎.github/workflows/ci_sanitizer.yml‎

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# SPDX-FileCopyrightText: 2006-2024, Knut Reinert & Freie Universität Berlin
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# SPDX-FileCopyrightText: 2016-2024, Knut Reinert & MPI für molekulare Genetik
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# SPDX-License-Identifier: CC0-1.0
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name: Sanitizer
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on:
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schedule:
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- cron: "0 6 * * SAT"
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workflow_dispatch:
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concurrency:
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group: sanitizer-actions
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cancel-in-progress: true
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env:
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SEQAN3_NO_VERSION_CHECK: 1
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TZ: Europe/Berlin
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TSAN_OPTIONS: ignore_noninstrumented_modules=1
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UBSAN_OPTIONS: print_stacktrace=1
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defaults:
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run:
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shell: bash -Eeuxo pipefail {0}
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jobs:
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build:
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name: ${{ matrix.name }} ${{ matrix.build_type }} ${{ matrix.os }}
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runs-on: ${{ matrix.os }}
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if: github.repository_owner == 'seqan' || github.event_name == 'workflow_dispatch'
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env:
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ASAN_OPTIONS: strict_string_checks=1:detect_stack_use_after_return=1:check_initialization_order=1:strict_init_order=1:detect_leaks=${{ contains(matrix.os, 'macos') && '0' || '1' }}
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strategy:
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fail-fast: false
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matrix:
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name: [ASan, TSan, UBSan]
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os: [ubuntu-latest, macos-14]
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build_type: [Release, RelWithDebInfo, Debug]
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exclude:
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# macOS llvm packages do not contain libarcher, which is required for TSan to handle OpenMP.
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# TSan runs on ubuntu with clang. Packages there contain libarcher.
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- name: "TSan"
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os: macos-14
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include:
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- os: macos-14
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compiler: clang-19
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- os: ubuntu-latest
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compiler: gcc-14
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image: ghcr.io/seqan/gcc-14
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- name: "TSan"
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os: ubuntu-latest
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compiler: clang-19
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image: ghcr.io/seqan/clang-19
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cxx_flags: "-fsanitize=thread"
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ctest_excludes: "-E async_input_buffer_snippet"
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- name: "ASan"
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os: ubuntu-latest
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cxx_flags: "-fsanitize=address -Wno-maybe-uninitialized"
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- name: "ASan"
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os: macos-14
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cxx_flags: "-fsanitize=address"
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- name: "UBSan"
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os: ubuntu-latest
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cxx_flags: "-fsanitize=undefined,float-divide-by-zero -Wno-maybe-uninitialized -Wno-stringop-overflow"
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- name: "UBSan"
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os: macos-14
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cxx_flags: "-fsanitize=undefined,float-divide-by-zero,local-bounds,nullability"
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ctest_excludes: "-E tmp_directory_snippet_cmp_output"
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container:
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# If an image is defined for a matrix entry, use it.
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# Otherwise, use the "empty"/'' image which means do not use a container at all.
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image: ${{ matrix.image || '' }}
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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: Setup compiler
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if: contains(matrix.os, 'macos')
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uses: seqan/actions/setup-compiler@main
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with:
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compiler: ${{ matrix.compiler }}
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- name: Configure tests
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run: |
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mkdir build && cd build
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cmake ../test/analyse -DCMAKE_BUILD_TYPE=${{ matrix.build_type }} \
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-DCMAKE_CXX_FLAGS="-fno-omit-frame-pointer ${{ matrix.cxx_flags }} -fno-sanitize-recover=all" \
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-DSEQAN3_BENCHMARK_MIN_TIME=0.01s \
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-DSEQAN3_WITH_SEQAN2_CI=OFF
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make gtest_main benchmark_main
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- name: Build tests
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working-directory: build
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run: make -k
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- name: Run tests
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working-directory: build
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continue-on-error: true
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id: test
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run: ctest . -j --output-on-failure --no-tests=error ${{ matrix.ctest_excludes }}
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# Rerun failed tests with **one** thread. Some snippets touch the same file and fail in parallel.
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- name: Rerun failed tests
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if: steps.test.outcome == 'failure'
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working-directory: build
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run: ctest . -j1 --output-on-failure --no-tests=error --rerun-failed

‎.github/workflows/cron_avx2.yml‎

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@@ -51,7 +51,7 @@ jobs:
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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="-mavx2 ${{ matrix.cxx_flags }}" \
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-DSEQAN3_BENCHMARK_MIN_TIME=0.01
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-DSEQAN3_BENCHMARK_MIN_TIME=0.01s
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case "${{ matrix.build }}" in
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unit) make gtest_main;;
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snippet) make gtest_main;;

‎.github/workflows/cron_latest_libraries.yml‎

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@@ -59,7 +59,7 @@ jobs:
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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=0.01
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-DSEQAN3_BENCHMARK_MIN_TIME=0.01s
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case "${{ matrix.build }}" in
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unit) make gtest_main;;
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snippet) make gtest_main;;

‎include/seqan3/core/debug_stream/debug_stream_type.hpp‎

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@@ -28,7 +28,7 @@ namespace seqan3
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//!\ingroup core_debug_stream
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//!\implements seqan3::enum_bitwise_operators
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//!\sa seqan3::enum_bitwise_operators enables combining enum values.
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enum fmtflags2
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enum class fmtflags2 : int8_t
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{
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none = 0, //!< No flag is set.
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utf8 = 1, //!< Enables use of non-ASCII UTF8 characters in formatted output.

‎include/seqan3/io/structure_file/format_vienna.hpp‎

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@@ -200,8 +200,14 @@ class format_vienna
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using alph_type = typename std::ranges::range_value_t<structure_type>::structure_alphabet_type;
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// We need the structure_length parameter to count the length of the structure while reading
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// because we cannot infer it from the (already resized) structure_seq object.
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auto res = std::ranges::copy(read_structure<alph_type>(stream_view), std::ranges::begin(structure));
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auto range = read_structure<alph_type>(stream_view);
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// Use std::views::take to avoid going out of bounds if the structure is longer than the sequence.
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auto res = std::ranges::copy(range | std::views::take(std::ranges::distance(seq)),
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std::ranges::begin(structure));
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structure_length = std::ranges::distance(std::ranges::begin(structure), res.out);
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// If the structure is longer than the sequence, there are characters left.
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// std::ranges::distance will also consume the characters in the stream.
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structure_length += std::ranges::distance(range);
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if constexpr (!detail::decays_to_ignore_v<bpp_type>)
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detail::bpp_from_rna_structure<alph_type>(bpp, structure);

‎include/seqan3/utility/math.hpp‎

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@@ -123,9 +123,25 @@ base_t pow(base_t base, exp_t exp)
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if (base == 0)
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return 0;
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auto check = [base](base_t result)
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{
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if (base > 0)
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{
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return result > std::numeric_limits<base_t>::max() / base;
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}
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else if (result < 0) // and base < 0
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{
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return result < std::numeric_limits<base_t>::max() / base;
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}
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else // base < 0 and result > 0
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{
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return base < std::numeric_limits<base_t>::min() / result;
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}
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};
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for (exp_t i = 0; i < exp; ++i)
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{
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if ((base < 0 ? std::numeric_limits<base_t>::min() : std::numeric_limits<base_t>::max()) / base < result)
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if (check(result))
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{
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std::string error_message{"Calculating " + std::to_string(base) + '^' + std::to_string(exp)
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+ " will result in an "

‎test/performance/CMakeLists.txt‎

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@@ -10,7 +10,7 @@ include (../seqan3-test.cmake)
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CPMGetPackage (benchmark)
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set (SEQAN3_BENCHMARK_MIN_TIME
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"1"
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"1s"
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CACHE STRING "Set --benchmark_min_time= for each bechmark. Timings are unreliable in CI.")
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macro (seqan3_benchmark benchmark_cpp)

‎test/performance/alignment/global_affine_alignment_parallel_benchmark.cpp‎

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@@ -113,7 +113,7 @@ void seqan3_affine_dna4_omp_for(benchmark::State & state)
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int64_t total = 0;
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for (auto _ : state)
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{
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# pragma omp parallel for num_threads(std::thread::hardware_concurrency()) schedule(guided)
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# pragma omp parallel for num_threads(std::thread::hardware_concurrency()) schedule(guided) reduction(+:total)
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for (size_t i = 0; i < zip.size(); ++i)
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{
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auto rng = align_pairwise(zip[i], affine_cfg | result_t{});
@@ -182,7 +182,7 @@ void seqan2_affine_dna4_omp_for(benchmark::State & state)
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int64_t total = 0;
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for (auto _ : state)
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{
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# pragma omp parallel for num_threads(std::thread::hardware_concurrency()) schedule(guided)
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# pragma omp parallel for num_threads(std::thread::hardware_concurrency()) schedule(guided) reduction(+:total)
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for (size_t i = 0; i < seqan2::length(vec1); ++i)
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{
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if constexpr (score_only)

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