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added additional github workflows
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‎.github/workflows/documentation.yml‎

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name: Documentation
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on:
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push:
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tags:
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- "*"
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env:
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CPM_SOURCE_CACHE: ${{ github.workspace }}/cpm_modules
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permissions:
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contents: write
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jobs:
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build:
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name: Build and publish documentation
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v3
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- uses: actions/cache@v3
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with:
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path: "**/cpm_modules"
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key: ${{ github.workflow }}-cpm-modules-${{ hashFiles('**/CMakeLists.txt', '**/*.cmake') }}
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- name: Install python dependencies
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run: |
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pip3 install jinja2==3.1.6 Pygments==2.19.1
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- name: Install Doxygen
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uses: ssciwr/doxygen-install@v1
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with:
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version: "1.13.2"
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- name: Build
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run: |
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cmake -S cpp/documentation -Bbuild
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cmake --build build --target GenerateDocs
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- name: Publish
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uses: peaceiris/actions-gh-pages@v4
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with:
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github_token: ${{ secrets.GITHUB_TOKEN }}
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publish_dir: ./build/doxygen/html

‎.github/workflows/install.yml‎

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name: Install
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on:
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push:
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branches:
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- master
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- main
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pull_request:
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branches:
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- master
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- main
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env:
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CTEST_OUTPUT_ON_FAILURE: 1
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CPM_SOURCE_CACHE: ${{ github.workspace }}/cpm_modules
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jobs:
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build:
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v3
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- uses: actions/cache@v3
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with:
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path: "**/cpm_modules"
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key: ${{ github.workflow }}-cpm-modules-${{ hashFiles('**/CMakeLists.txt', '**/*.cmake') }}
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- name: Install build deps
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run: |
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sudo apt-get update
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sudo apt-get install -y libcurl4-openssl-dev
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- name: build and install library
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run: |
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cmake -S cpp -Bbuild -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX="$PWD/local"
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sudo cmake --build build --target install
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- name: configure (tests)
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run: cmake -S cpp/test -Bbuild-test -DTEST_INSTALLED_VERSION=1 -DCMAKE_PREFIX_PATH="$PWD/local"
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- name: build (tests)
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run: cmake --build build-test --config Debug -j4
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- name: test
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run: |
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cd build-test
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ctest --build-config Debug
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- name: cleanup
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run: |
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sudo rm -rf build build-test
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‎.github/workflows/macos.yml‎

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name: MacOS
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on:
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push:
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branches:
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- master
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- main
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pull_request:
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branches:
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- master
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- main
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env:
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CTEST_OUTPUT_ON_FAILURE: 1
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CPM_SOURCE_CACHE: ${{ github.workspace }}/cpm_modules
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jobs:
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build:
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runs-on: macos-latest
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steps:
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- uses: actions/checkout@v3
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- uses: actions/cache@v3
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with:
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path: "**/cpm_modules"
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key: ${{ github.workflow }}-cpm-modules-${{ hashFiles('**/CMakeLists.txt', '**/*.cmake') }}
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- name: Install macOS build dependencies
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run: |
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brew update
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brew install autoconf automake libtool
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- name: configure
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run: cmake -S cpp/test -Bbuild -DCMAKE_BUILD_TYPE=Debug
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- name: build
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run: cmake --build build -j4
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- name: test
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run: |
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cd build
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ctest --build-config Debug

‎.github/workflows/standalone.yml‎

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name: Standalone
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on:
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push:
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branches:
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- master
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- main
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pull_request:
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branches:
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- master
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- main
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env:
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CPM_SOURCE_CACHE: ${{ github.workspace }}/cpm_modules
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jobs:
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build:
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v3
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- uses: actions/cache@v3
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with:
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path: "**/cpm_modules"
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key: ${{ github.workflow }}-cpm-modules-${{ hashFiles('**/CMakeLists.txt', '**/*.cmake') }}
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- name: Install build deps
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run: |
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sudo apt-get update
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sudo apt-get install -y libcurl4-openssl-dev
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- name: configure
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run: cmake -S cpp/standalone -Bbuild -DCMAKE_BUILD_TYPE=Debug
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- name: build
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run: cmake --build build -j4
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- name: run
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run: ./build/Aligncount --help

‎.github/workflows/style.yml‎

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name: Style
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on:
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push:
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branches:
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- master
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- main
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pull_request:
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branches:
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- master
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- main
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env:
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CPM_SOURCE_CACHE: ${{ github.workspace }}/cpm_modules
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jobs:
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build:
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v3
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- uses: actions/cache@v3
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with:
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path: "**/cpm_modules"
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key: ${{ github.workflow }}-cpm-modules-${{ hashFiles('**/CMakeLists.txt', '**/*.cmake') }}
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- name: Install format dependencies
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run: pip3 install clang-format==14.0.6 cmake_format==0.6.11 pyyaml
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- name: configure
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run: cmake -S cpp/test -Bbuild
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- name: check style
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run: cmake --build build --target check-format

‎.github/workflows/ubuntu.yml‎

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name: Ubuntu
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on:
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push:
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branches:
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- master
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- main
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pull_request:
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branches:
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- master
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- main
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env:
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CTEST_OUTPUT_ON_FAILURE: 1
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CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
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CPM_SOURCE_CACHE: ${{ github.workspace }}/cpm_modules
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jobs:
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build:
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v3
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- uses: actions/cache@v3
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with:
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path: "**/cpm_modules"
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key: ${{ github.workflow }}-cpm-modules-${{ hashFiles('**/CMakeLists.txt', '**/*.cmake') }}
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- name: Install build deps
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run: |
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sudo apt-get update
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sudo apt-get install -y libcurl4-openssl-dev
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- name: configure
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run: cmake -S cpp/test -Bbuild -DENABLE_TEST_COVERAGE=1 -DCMAKE_BUILD_TYPE=Debug
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- name: build
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run: cmake --build build -j4
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- name: test
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run: |
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cd build
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ctest --build-config Debug
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- name: collect code coverage
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run: bash <(curl -s https://codecov.io/bash) || echo "Codecov did not collect coverage reports"

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