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eseilereseiler
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Merge pull request #8 from eseiler/infra/cron
Add cron jobs
2 parents 619fb7b + c94ede8 commit be8cffe

29 files changed

+538
-87
lines changed

‎.github/config/codechecker.skip‎

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# SPDX-FileCopyrightText: 2006-2025, Knut Reinert & Freie Universität Berlin
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# SPDX-FileCopyrightText: 2016-2025, Knut Reinert & MPI für molekulare Genetik
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# SPDX-License-Identifier: CC0-1.0
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-${GITHUB_WORKSPACE}/include/fpgalign/contrib/*
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+${GITHUB_WORKSPACE}/*
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-*

‎.github/config/codechecker.yml‎

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# SPDX-FileCopyrightText: 2006-2025, Knut Reinert & Freie Universität Berlin
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# SPDX-FileCopyrightText: 2016-2025, Knut Reinert & MPI für molekulare Genetik
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# SPDX-License-Identifier: CC0-1.0
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analyze:
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- --enable=performance
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- --enable=bugprone
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- --enable=prefix:clang-diagnostic-shadow
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- --disable=bugprone-easily-swappable-parameters
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- --disable=clang-diagnostic-implicit-int-float-conversion
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- --disable=clang-diagnostic-float-conversion
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- --disable=clang-diagnostic-implicit-int-conversion
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- --disable=bugprone-exception-escape
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- --disable=bugprone-narrowing-conversions
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- --disable=deadcode.DeadStores
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- --skip=${GITHUB_WORKSPACE}/.github/config/codechecker.skip
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- --clean
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parse:
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- --export=html
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- --output=./html
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- --skip=${GITHUB_WORKSPACE}/.github/config/codechecker.skip
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- --trim-path-prefix=${GITHUB_WORKSPACE}/

‎.github/config/custom.imp‎

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# SPDX-FileCopyrightText: 2006-2025, Knut Reinert & Freie Universität Berlin
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# SPDX-FileCopyrightText: 2016-2025, Knut Reinert & MPI für molekulare Genetik
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# SPDX-License-Identifier: CC0-1.0
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[
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{ "include": [ "<seqan3/contrib/std/detail/adaptor_base.hpp>", "public", "<hibf/contrib/std/detail/adaptor_base.hpp>", "public"] }
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]

‎.github/workflows/cron_codechecker.yml‎

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# SPDX-FileCopyrightText: 2006-2025, Knut Reinert & Freie Universität Berlin
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# SPDX-FileCopyrightText: 2016-2025, Knut Reinert & MPI für molekulare Genetik
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# SPDX-License-Identifier: CC0-1.0
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name: CodeChecker
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on:
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schedule:
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- cron: "0 4 * * MON"
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workflow_dispatch:
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concurrency:
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group: codechecker-actions
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cancel-in-progress: true
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env:
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TZ: Europe/Berlin
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defaults:
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run:
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shell: bash -Eexuo pipefail {0}
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jobs:
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build:
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name: CodeChecker
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runs-on: ubuntu-latest
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if: github.repository_owner == 'seqan' || github.event_name == 'workflow_dispatch'
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container:
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image: ghcr.io/seqan/codechecker
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steps:
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- name: Run CodeChecker
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uses: seqan/actions/codechecker@main
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with:
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deploy_host: ${{ secrets.DEPLOY_HOST }}
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deploy_user: ${{ secrets.DEPLOY_USER }}
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deploy_ssh_key: ${{ secrets.DEPLOY_SSH_KEY }}
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deploy_path: ${{ secrets.DEPLOY_CODECHECKER_PATH }}

‎.github/workflows/cron_codeql.yml‎

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# SPDX-FileCopyrightText: 2006-2025 Knut Reinert & Freie Universität Berlin
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# SPDX-FileCopyrightText: 2016-2025 Knut Reinert & MPI für molekulare Genetik
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# SPDX-License-Identifier: CC0-1.0
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name: CodeQL
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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: codeql-${{ github.ref }}
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cancel-in-progress: true
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env:
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CODEQL_EXTRACTOR_CPP_AUTOINSTALL_DEPENDENCIES: false
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SHARG_NO_VERSION_CHECK: 1
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TZ: Europe/Berlin
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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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codeql:
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name: CodeQL
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runs-on: ubuntu-latest
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permissions:
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security-events: write
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container:
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image: ghcr.io/seqan/gcc-second-latest
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steps:
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- name: Checkout
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uses: actions/checkout@v4
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- name: Initialize CodeQL
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uses: github/codeql-action/init@v3
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with:
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languages: cpp
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- name: Autobuild
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uses: github/codeql-action/autobuild@v3
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- name: Perform CodeQL Analysis
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uses: github/codeql-action/analyze@v3
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with:
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category: "/language:cpp"

‎.github/workflows/cron_cpm.yml‎

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# SPDX-FileCopyrightText: 2006-2025 Knut Reinert & Freie Universität Berlin
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# SPDX-FileCopyrightText: 2016-2025 Knut Reinert & MPI für molekulare Genetik
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# SPDX-License-Identifier: CC0-1.0
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name: Update CPM
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on:
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schedule:
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- cron: "0 12 * * SAT"
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workflow_dispatch:
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env:
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TZ: Europe/Berlin
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concurrency:
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group: update-cpm-actions
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cancel-in-progress: true
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jobs:
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update_cpm:
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name: Update CPM
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runs-on: ubuntu-latest
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timeout-minutes: 15
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if: github.repository_owner == 'seqan' || github.event_name == 'workflow_dispatch'
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steps:
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- name: Run update CPM
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uses: seqan/actions/update_cpm_package_lock@main
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with:
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token: ${{ secrets.SEQAN_ACTIONS_PAT }}
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gpg_key: ${{ secrets.SEQAN_ACTIONS_GPG_KEY }}
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gpg_passphrase: ${{ secrets.SEQAN_ACTIONS_GPG_PASSPHRASE }}
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package_lock_file: cmake/package-lock.cmake

‎.github/workflows/cron_iwyu.yml‎

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# SPDX-FileCopyrightText: 2006-2025, Knut Reinert & Freie Universität Berlin
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# SPDX-FileCopyrightText: 2016-2025, Knut Reinert & MPI für molekulare Genetik
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# SPDX-License-Identifier: CC0-1.0
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name: IWYU
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on:
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schedule:
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- cron: "0 4 * * MON"
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workflow_dispatch:
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concurrency:
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group: iwyu-actions
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cancel-in-progress: true
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env:
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TZ: Europe/Berlin
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defaults:
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run:
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shell: bash -Eexuo pipefail {0}
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jobs:
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build:
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name: IWYU
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runs-on: ubuntu-latest
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if: github.repository_owner == 'seqan' || github.event_name == 'workflow_dispatch'
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container:
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image: ghcr.io/seqan/iwyu
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steps:
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- name: Run IWYU
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uses: seqan/actions/iwyu@main
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with:
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configure_path: .
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token: ${{ secrets.SEQAN_ACTIONS_PAT }}
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gpg_key: ${{ secrets.SEQAN_ACTIONS_GPG_KEY }}
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gpg_passphrase: ${{ secrets.SEQAN_ACTIONS_GPG_PASSPHRASE }}

‎.github/workflows/cron_sanitizer.yml‎

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# SPDX-FileCopyrightText: 2006-2025, Knut Reinert & Freie Universität Berlin
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# SPDX-FileCopyrightText: 2016-2025, 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 4 * * 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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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-latest]
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build_type: [Release, RelWithDebInfo, Debug]
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exclude:
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- name: "TSan"
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os: macos-latest
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include:
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- name: "ASan"
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cxx_flags: "-fno-omit-frame-pointer -fsanitize=address"
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- name: "TSan"
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cxx_flags: "-fno-omit-frame-pointer -fsanitize=thread"
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- name: "UBSan"
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os: macos-latest
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cxx_flags: "-fno-omit-frame-pointer -fsanitize=undefined,float-divide-by-zero,implicit-conversion,local-bounds,nullability -Wno-pass-failed"
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- name: "UBSan"
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os: macos-latest
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build_type: Release
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ctest_excludes: "-E tmp_directory_snippet_cmp_output"
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- name: "UBSan"
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os: macos-latest
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build_type: RelWithDebInfo
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ctest_excludes: "-E tmp_directory_snippet_cmp_output"
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- name: "UBSan"
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os: ubuntu-latest
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cxx_flags: "-fno-omit-frame-pointer -fsanitize=undefined,float-divide-by-zero"
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- os: macos-latest
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compiler: clang-latest
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- os: ubuntu-latest
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compiler: gcc-latest
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image: ghcr.io/seqan/gcc-latest
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- name: "TSan"
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os: ubuntu-latest
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compiler: clang-latest
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image: ghcr.io/seqan/clang-latest
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container:
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image: ${{ matrix.image || '' }}
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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: ${{ matrix.compiler }}
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- name: Configure tests
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run: |
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mkdir build && cd build
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cmake .. -DCMAKE_BUILD_TYPE=${{ matrix.build_type }} \
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-DCMAKE_CXX_FLAGS="${{ matrix.cxx_flags }}"
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make gtest_main
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- name: Build and run tests
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working-directory: build
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run: make -k check

‎cmake/package-lock.cmake‎

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# thresholding
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CPMDeclarePackage (thresholding
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NAME thresholding
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URL "${PROJECT_SOURCE_DIR}/contrib/threshold.tar.gz"
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URL "${PROJECT_SOURCE_DIR}/contrib/threshold.tar.gz" # main
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URL_HASH SHA256=4990c7fb9778a2fb8a19794b966d57496ca77bcd708b4cee3c93eea6e5b67d80
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SYSTEM TRUE
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EXCLUDE_FROM_ALL TRUE

‎include/fpgalign/argument_parsing.hpp‎

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#pragma once
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#include <string>
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#include <vector>
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#include <cstdint> // for uint8_t
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#include <string> // for string
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#include <vector> // for vector
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#include <fpgalign/config.hpp>
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#include <fpgalign/config.hpp> // for config
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enum class subcommand : uint8_t
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{

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