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Add unit test cases and Continous Integration. (#113)
Added (i) CMake build scripts, test datasets, and test cases with Catch2 framework and (ii) Github workflow for CI :Build/Test with CMake/CTest and code coverage with codecov. and (iii) Functionality for sanity check (turned off by default), the fix the visual output bug, and test case for multiple references.
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‎.github/workflows/main.yml‎

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name: Build with CMake and Test
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run-name: Build FastANI with CMake and Test by ${{github.actor}}
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on:
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push:
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branches: [ "master" ]
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pull_request:
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branches: [ "master" ]
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# Allows to run this workflow from the Actions tab (w.o. trigger)
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workflow_dispatch:
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env:
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# CMake build type (Release, Debug, RelWithDebInfo, etc.)
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BUILD_TYPE: Debug
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jobs:
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Build-Test:
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# https://docs.github.com/en/actions/using-github-hosted-runners/about-github-hosted-runners
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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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with:
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submodules: recursive
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lfs: true
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- name: Install zlib, gsl, cppcheck and lcov
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run: |
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sudo apt-get update
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sudo apt-get install zlib1g-dev libgsl-dev cppcheck lcov
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# Static Analysis with cppcheck
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- name: cppcheck
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run: cppcheck --enable=all --inconclusive --force --std=c++20 -iext/ -I src/ --output-file=cppcheck_report.txt .
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# uses: deep5050/cppcheck-action@main
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# with:
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# exclude_check: ext/
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# inconcusive: enable
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# force: enable
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# other_options: "--includes-file=src/cgi/include/*.hpp"
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# github_token: ${{ secrets.GITHUB_TOKEN}}
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# - name: publish report
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# uses: mikeal/publish-to-github-action@master
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# env:
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# GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
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# BRANCH_NAME: 'master' # your branch name goes here
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- name: Upload CPPCheck Report as artifact
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uses: actions/upload-artifact@v3
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with:
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name: CPPCheck-Report
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path: ${{github.workspace}}/cppcheck_report.txt
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# Building
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- name: Configure CMake
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# https://cmake.org/cmake/help/latest/variable/CMAKE_BUILD_TYPE.html?highlight=cmake_build_type
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run: cmake -B ${{github.workspace}}/build -DCMAKE_BUILD_TYPE=${{env.BUILD_TYPE}} -DBUILD_TESTING=ON
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- name: Build
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run: cmake --build ${{github.workspace}}/build --config ${{env.BUILD_TYPE}}
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# Testing
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- name: Test
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working-directory: ${{github.workspace}}/build
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# https://cmake.org/cmake/help/latest/manual/ctest.1.html
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run: ctest -C ${{env.BUILD_TYPE}}
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# Run code coverage
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- name: Run lcov to generate coverage
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working-directory: ${{github.workspace}}/build
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run: make lcov2
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# Reporting code coverage
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- name: Report code coverage
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uses: zgosalvez/github-actions-report-lcov@v2
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with:
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working-directory: ${{github.workspace}}/build
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coverage-files: ${{github.workspace}}/build/coverage.info
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artifact-name: code-coverage-report
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github-token: ${{ secrets.GITHUB_TOKEN }}
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# Uploading to Codecov
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- name: Upload coverage reports to codecov.io
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uses: codecov/codecov-action@v3
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with:
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token: ${{ secrets.CODECOV_TOKEN }}
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directory: ${{github.workspace}}/build
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files: ${{github.workspace}}/build/coverage.info
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fail_ci_if_error: true
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verbose: true
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# Uploading to Github Action as artifact
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- name: Upload Coverage Summary as artifact
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uses: actions/upload-artifact@v3
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with:
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name: Coverage-Summary
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path: ${{github.workspace}}/build/coverage_list.txt
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retention-days: 5

‎.gitmodules‎

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[submodule "ext/Catch2"]
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path = ext/Catch2
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url = https://github.com/catchorg/Catch2.git

‎CMakeLists.txt‎

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cmake_minimum_required(VERSION 3.20)
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project(FastANI
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VERSION 1.34
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DESCRIPTION "Fast computation of whole-genome Average Nucleotide Identity (ANI)."
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LANGUAGES CXX)
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#
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# Main executable
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add_executable(FastANI src/cgi/core_genome_identity.cpp src/cgi/main.cpp)
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target_include_directories(FastANI PUBLIC "src/")
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#
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# by default, static linking
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option(GSL_SHARED "Build using shared libraries" OFF)
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option(BUILD_TESTING "Build tests" ON) # build tests
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#
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# zlib dependency
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find_package(ZLIB 1.1 REQUIRED)
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if(${ZLIB_FOUND})
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message("Using zlib library v${ZLIB_VERSION_STRING}")
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endif(${ZLIB_FOUND})
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target_link_libraries(FastANI PUBLIC ZLIB::ZLIB)
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#
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# openmp dependency
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find_package(OpenMP)
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if(${OpenMP_CXX_FOUND})
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message("Using OpenMP_CXX v${OpenMP_CXX_VERSION}")
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target_link_libraries(FastANI PUBLIC ${OpenMP_CXX_LIBRARIES})
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target_include_directories(FastANI PUBLIC ${OpenMP_CXX_INCLUDE_DIRS})
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target_compile_options(FastANI PUBLIC ${OpenMP_CXX_FLAGS})
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else()
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message("NOTE: OpenMP not found; Compiling as a single threaded app...")
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endif(${OpenMP_CXX_FOUND})
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#
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# GSL or Boost math
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find_package(GSL 1.6)
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if(${GSL_FOUND})
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message("GSL v${GSL_VERSION} Found: ${GSL_LIBDIR}")
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if(${GSL_SHARED})
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target_link_libraries(FastANI PUBLIC ${GSL_LIBRARIES})
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else()
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# GSL_LIBDIR is not documented
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target_link_libraries(FastANI PUBLIC
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${GSL_LIBDIR}/libgsl.a
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${GSL_LIBDIR}/libgslcblas.a)
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endif(${GSL_SHARED})
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target_include_directories(FastANI PUBLIC ${GSL_INCLUDE_DIRS})
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else()
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set(Boost_USE_STATIC_LIBS ON) # only find static libs
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set(Boost_USE_DEBUG_LIBS OFF) # ignore debug libs and
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set(Boost_USE_RELEASE_LIBS ON) # only find release libs
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set(Boost_USE_MULTITHREADED ON)
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find_package(Boost 1.45 REQUIRED COMPONENTS math_c99)
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target_link_libraries(FastANI PUBLIC ${Boost_MATCH_C99_LIBRARY})
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target_include_directories(FastANI PUBLIC ${Boost_INCLUDE_DIRS})
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target_compile_definitions(FastANI PUBLIC USE_BOOST=1)
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endif(${GSL_FOUND})
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#
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#
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if(${BUILD_TESTING})
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add_subdirectory(ext/Catch2)
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include(CTest)
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include(Catch)
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add_executable(FastANITest tests/fastani_tests.cpp src/cgi/core_genome_identity.cpp)
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target_include_directories(FastANITest PUBLIC "src/"
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${OpenMP_CXX_INCLUDE_DIRS})
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target_compile_options(FastANITest PUBLIC
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--coverage -g -O0 -fprofile-arcs -ftest-coverage ${OpenMP_CXX_FLAGS})
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target_link_libraries(FastANITest PRIVATE
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Catch2::Catch2 Catch2::Catch2WithMain
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ZLIB::ZLIB GSL::gsl GSL::gslcblas
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${OpenMP_CXX_LIBRARIES}
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gcov)
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catch_discover_tests(FastANITest)
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file(COPY data DESTINATION ${CMAKE_CURRENT_BINARY_DIR})
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add_custom_target(lcov lcov -c -d .. -o FastANITest.out
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COMMAND genhtml -o ../lcov/ FastANITest.out
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DEPENDS FastANITest)
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add_custom_target(lcov2 lcov -c -d ./ -o FastANITest.info
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COMMAND lcov -e FastANITest.info "*/FastANI/src/*/*.cpp" "*/FastANI/src/*/*.hpp" > coverage.info
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COMMAND lcov --list coverage.info |tee coverage_list.txt
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COMMAND lcov --summary coverage.info |tee coverage_summary.txt
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DEPENDS FastANITest)
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endif(${BUILD_TESTING})
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set(CPACK_GENERATOR "TGZ")
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set(CPACK_SOURCE_GENERATOR "TGZ")
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set(CPACK_PACKAGE_DIRECTORY ${PROJECT_BINARY_DIR}/package)
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set(CPACK_SOURCE_IGNORE_FILES .git/ .github/
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.vscode/ .cache/ .mypy_cache/
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.idea/ complie_comands.json
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lcov/ lcov0/ lcov2/ data/ cmake-build-debug/
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_CPack_Packages/ build.sh/ build/ build.clang/
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${CMAKE_BINARY_DIR}/ ${PROJECT_BINARY_DIR}/)
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include(CPack)

‎Makefile.in‎

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CFLAGS += -include src/common/memcpyLink.h
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endif
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SOURCES=src/cgi/core_genome_identity.cpp
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SOURCES=src/cgi/core_genome_identity.cpp src/cgi/main.cpp
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all : fastANI
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‎README.md‎

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[![Apache 2.0 License](https://img.shields.io/badge/license-Apache%20v2.0-blue.svg)](LICENSE)
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[![BioConda Install](https://img.shields.io/conda/dn/bioconda/fastani.svg?style=flag&label=BioConda%20install)](https://anaconda.org/bioconda/fastani)
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[![GitHub Downloads](https://img.shields.io/github/downloads/ParBLiSS/FastANI/total.svg?style=social&logo=github&label=Download)](https://github.com/ParBLiSS/FastANI/releases)
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![Build with CMake and Test](https://github.com/ParBLiSS/FastANI/actions/workflows/main.yml/badge.svg)
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[![codecov](https://codecov.io/gh/ParBLiSS/FastANI/branch/master/graph/badge.svg?token=B7YFZ56BW2)](https://codecov.io/gh/srirampc/FastANI)
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FastANI is developed for fast alignment-free computation of whole-genome Average Nucleotide Identity (ANI). ANI is defined as mean nucleotide identity of orthologous gene pairs shared between two microbial genomes. FastANI supports pairwise comparison of both complete and draft genome assemblies. Its underlying procedure follows a similar workflow as described by [Goris et al. 2007](http://www.ncbi.nlm.nih.gov/pubmed/17220447). However, it avoids expensive sequence alignments and uses [Mashmap](https://github.com/marbl/MashMap) as its MinHash based sequence mapping engine to compute the orthologous mappings and alignment identity estimates. Based on our experiments with complete and draft genomes, its accuracy is on par with [BLAST-based ANI solver](http://enve-omics.ce.gatech.edu/ani/) and it achieves two to three orders of magnitude speedup. Therefore, it is useful for pairwise ANI computation of large number of genome pairs. More details about its speed, accuracy and potential applications are described here: "[High Throughput ANI Analysis of 90K Prokaryotic Genomes Reveals Clear Species Boundaries](https://doi.org/10.1038/s41467-018-07641-9)".
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‎configure.ac‎

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AC_INIT(src/cgi/core_genome_identity.cpp)
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AC_INIT
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AC_CONFIG_SRCDIR([src/cgi/core_genome_identity.cpp])
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AC_CONFIG_SRCDIR([src/cgi/main.cpp])
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AC_ARG_WITH(gsl, [ --with-gsl=<path/to/gsl> GNU Scientific Library install dir (default: /usr/local/)])
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AC_ARG_ENABLE(static-gsl, [ --enable-static-gsl])
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AC_SUBST(amcppflags, "-DUSE_BOOST")
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fi
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AC_OUTPUT(Makefile)
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AC_CONFIG_FILES([Makefile])
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AC_OUTPUT

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