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CMakeLists.txt
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cmake_minimum_required(VERSION 3.1)
project(pastaq VERSION "0.9.0")
# Set project properties.
set(CMAKE_CXX_STANDARD 17)
set(CMAKE_CXX_STANDARD_REQUIRED ON)
set(CMAKE_EXPORT_COMPILE_COMMANDS ON)
set(CMAKE_POSITION_INDEPENDENT_CODE ON)
# Set up compiler options based on platform.
if (CMAKE_COMPILER_IS_GNUCXX)
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wall -Wextra -Wpedantic")
endif()
if (MSVC)
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} /W4")
endif()
# Build the pastaqlib c++ library.
# ------------------------------
# Threads.
find_package(Threads REQUIRED)
# Zlib
find_package(ZLIB REQUIRED)
# Eigen.
add_subdirectory("${CMAKE_CURRENT_SOURCE_DIR}/ext/eigen" ${CMAKE_CURRENT_BINARY_DIR}/eigen)
# Build pastaqs library.
add_library(pastaqlib
"${CMAKE_CURRENT_SOURCE_DIR}/src/lib/centroid/centroid.cpp"
"${CMAKE_CURRENT_SOURCE_DIR}/src/lib/centroid/centroid_serialize.cpp"
"${CMAKE_CURRENT_SOURCE_DIR}/src/lib/feature_detection/feature_detection.cpp"
"${CMAKE_CURRENT_SOURCE_DIR}/src/lib/feature_detection/feature_detection_serialize.cpp"
"${CMAKE_CURRENT_SOURCE_DIR}/src/lib/grid/grid.cpp"
"${CMAKE_CURRENT_SOURCE_DIR}/src/lib/grid/grid_serialize.cpp"
"${CMAKE_CURRENT_SOURCE_DIR}/src/lib/link/link.cpp"
"${CMAKE_CURRENT_SOURCE_DIR}/src/lib/link/link_serialize.cpp"
"${CMAKE_CURRENT_SOURCE_DIR}/src/lib/metamatch/metamatch.cpp"
"${CMAKE_CURRENT_SOURCE_DIR}/src/lib/metamatch/metamatch_serialize.cpp"
"${CMAKE_CURRENT_SOURCE_DIR}/src/lib/protein_inference/protein_inference.cpp"
"${CMAKE_CURRENT_SOURCE_DIR}/src/lib/protein_inference/protein_inference_serialize.cpp"
"${CMAKE_CURRENT_SOURCE_DIR}/src/lib/raw_data/raw_data.cpp"
"${CMAKE_CURRENT_SOURCE_DIR}/src/lib/raw_data/raw_data_serialize.cpp"
"${CMAKE_CURRENT_SOURCE_DIR}/src/lib/raw_data/xml_reader.cpp"
"${CMAKE_CURRENT_SOURCE_DIR}/src/lib/utils/base64.cpp"
"${CMAKE_CURRENT_SOURCE_DIR}/src/lib/utils/compression.cpp"
"${CMAKE_CURRENT_SOURCE_DIR}/src/lib/utils/interpolation.cpp"
"${CMAKE_CURRENT_SOURCE_DIR}/src/lib/utils/search.cpp"
"${CMAKE_CURRENT_SOURCE_DIR}/src/lib/utils/serialization.cpp"
"${CMAKE_CURRENT_SOURCE_DIR}/src/lib/warp2d/warp2d.cpp"
"${CMAKE_CURRENT_SOURCE_DIR}/src/lib/warp2d/warp2d_serialize.cpp"
)
target_include_directories(pastaqlib PUBLIC src/lib)
target_link_libraries(pastaqlib ${CMAKE_THREAD_LIBS_INIT} Eigen3::Eigen ZLIB::ZLIB)
# Build the python bindings.
# --------------------------
# PyBind.
add_subdirectory("${CMAKE_CURRENT_SOURCE_DIR}/ext/pybind11" ${CMAKE_CURRENT_BINARY_DIR}/pybind11)
pybind11_add_module(pastaq src/python-bindings/pastaq/bindings.cpp)
target_link_libraries(pastaq PRIVATE pastaqlib)
# Include tests if testing library is present.
# --------------------------------------------
if(${CMAKE_CURRENT_SOURCE_DIR} STREQUAL ${CMAKE_SOURCE_DIR} AND (${PASTAQ_ENABLE_TESTS}))
unset(DOCTEST_LIBRARY_PATH CACHE)
find_path(
DOCTEST_LIBRARY_PATH
"doctest.h"
PATHS "${CMAKE_CURRENT_SOURCE_DIR}"
PATH_SUFFIX "${CMAKE_CURRENT_SOURCE_DIR}/ext/doctest/doctest"
)
if (DOCTEST_LIBRARY_PATH)
# Add the testing library.
add_library(doctest INTERFACE)
target_include_directories(doctest
INTERFACE
"${CMAKE_CURRENT_SOURCE_DIR}/ext/doctest/doctest")
enable_testing()
# Add tests.
add_executable(
pastaqlib_test
tests/centroid_test.cpp
tests/feature_detection_test.cpp
tests/grid_test.cpp
tests/main.cpp
tests/metamatch_test.cpp
tests/mock_stream_test.cpp
tests/serialization_test.cpp
tests/warp2d_test.cpp
tests/xml_reader_test.cpp
)
add_test(NAME pastaqlib_test COMMAND pastaqlib_test)
target_link_libraries(pastaqlib_test stdc++ doctest pastaqlib)
else()
message("-- [${PROJECT_NAME}] Testing library not found. Ignoring tests...")
endif()
endif()