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Merge pull request #267 from eseiler/infra/codechecker_codeql
[INFRA] Add CodeChecker and CodeQL
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‎.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}/*
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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=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/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/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 8 * * MON"
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workflow_dispatch:
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concurrency:
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group: codechecker-${{ github.ref }}
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cancel-in-progress: true
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env:
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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 -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/clang-19
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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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configure_path: ../test/analyse
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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 21 * * MON"
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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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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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if: github.repository_owner == 'seqan' || github.event_name == 'workflow_dispatch'
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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-14
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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: 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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build-mode: manual
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trap-caching: false
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- name: Build tests
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run: |
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cmake test/analyse -DCMAKE_BUILD_TYPE=Release \
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-DCMAKE_EXPORT_COMPILE_COMMANDS=ON
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make -k
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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/lint.yml‎

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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_running_workflows
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runs-on: ubuntu-22.04
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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/readme_snippet.yml‎

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push:
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branches:
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- 'main'
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workflow_dispatch:
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concurrency:
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group: readme-snippet-${{ github.ref }}
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cancel-in-progress: true
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env:
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TZ: Europe/Berlin
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jobs:
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readme-snippet:
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name: Update README
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concurrency:
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group: readme-snippet-${{ github.ref }}
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cancel-in-progress: false
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runs-on: ubuntu-22.04
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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: Checkout Sharg
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uses: actions/checkout@v4

‎.github/workflows/update_cookbook.yml‎

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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: Sharg lint
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name: Sharg Cookbook
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on:
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push:
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branches:
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- 'main'
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workflow_dispatch:
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concurrency:
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group: update-cookbook-${{ github.ref }}
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cancel-in-progress: true
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env:
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jobs:
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update-cookbook:
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name: Update Cookbook
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concurrency:
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group: update-cookbook-${{ github.ref }}
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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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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: Checkout Sharg
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uses: actions/checkout@v4

‎test/analyse/CMakeLists.txt‎

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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: BSD-3-Clause
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cmake_minimum_required (VERSION 3.20...3.31)
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project (sharg_test_analyze CXX)
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include (../sharg-test.cmake)
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enable_testing ()
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add_subdirectory (../snippet snippet)
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add_subdirectory (../unit unit)

‎test/sharg-test.cmake‎

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set (CMAKE_CXX_EXTENSIONS OFF)
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endif ()
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set (SHARG_TEST_CPM_DIR
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"${CMAKE_CURRENT_LIST_DIR}/../cmake/"
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CACHE STRING "Path to directory containing CPM.cmake.")
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set (CPM_INDENT "CMake Package Manager CPM: ")
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include ("${SHARG_TEST_CPM_DIR}/CPM.cmake")
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CPMUsePackageLock ("${SHARG_TEST_CPM_DIR}/package-lock.cmake")
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include (${CMAKE_CURRENT_LIST_DIR}/cmake/sharg_require_ccache.cmake)
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# require Sharg package
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find_package (Sharg REQUIRED HINTS ${CMAKE_CURRENT_LIST_DIR}/../cmake)
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enable_testing ()
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set (CPM_INDENT "CMake Package Manager CPM: ")
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CPMUsePackageLock ("${CMAKE_CURRENT_LIST_DIR}/../cmake/package-lock.cmake")
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include (CheckCXXSourceCompiles)
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include (FindPackageHandleStandardArgs)
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include (FindPackageMessage)
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include (sharg_test_component)
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include (sharg_test_files)
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include (sharg_require_ccache)
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include (add_subdirectories)

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