Merge branch 'update-build-pipeline' into mgems-release-testing

CMakeLists.txt

@@ -1,5 +1,6 @@
-cmake_minimum_required (VERSION 2.8.12)
+cmake_minimum_required (VERSION 3.11)
 project (mGEMS)
+include(FetchContent)
 
 set(LIBRARY_OUTPUT_PATH ${CMAKE_CURRENT_BINARY_DIR}/lib)
 set(CMAKE_RUNTIME_OUTPUT_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/bin)
@@ -24,161 +25,233 @@ endif()
 ## mGEMS executable
 add_executable(mGEMS ${CMAKE_CURRENT_SOURCE_DIR}/src/mGEMS.cpp)
 
-## Check supported compression types
-find_package(BZip2)
-if (BZIP2_FOUND)
-  include_directories(${BZIP2_INCLUDE_DIRS})
+## mGEMS library
+add_library(libmgems
+${CMAKE_CURRENT_SOURCE_DIR}/src/bin_reads.cpp
+${CMAKE_CURRENT_SOURCE_DIR}/src/extract_bin.cpp
+)
+set_target_properties(libmgems PROPERTIES OUTPUT_NAME mgems)
+
+## Dependencies
+### OpenMP
+find_package(OpenMP)
+if (OPENMP_FOUND)
+  target_link_libraries(mGEMS OpenMP::OpenMP_CXX)
+  target_link_libraries(libmgems OpenMP::OpenMP_CXX)
+  set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -D_GLIBCXX_PARALLEL")
+  set(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} -D_GLIBCXX_PARALLEL")
+  set(CMAKE_SHARED_LINKER_FLAGS "${CMAKE_SHARED_LINKER_FLAGS} -D_GLIBCXX_PARALLEL")
+endif()
+
+### Check supported compression types
+#### zlib
+if ((DEFINED ZLIB_LIBRARY AND DEFINED ZLIB_INCLUDE_DIR) AND (NOT DEFINED ZLIB_FOUND))
+  message(STATUS "zlib library provided in: " ${ZLIB_LIBRARY})
+  message(STATUS "zlib headers provided in: " ${ZLIB_INCLUDE_DIR})
+  include_directories(${ZLIB_INCLUDE_DIR})
+  target_link_libraries(mGEMS ${ZLIB_LIBRARY})
+  target_link_libraries(libmgems ${ZLIB_LIBRARY})
+  set(MGEMS_HAVE_ZLIB 1)
+else()
+  find_package(ZLIB)
+  if (ZLIB_FOUND)
+    include_directories(${ZLIB_INCLUDE_DIR})
+    target_link_libraries(mGEMS ${ZLIB_LIBRARY})
+    target_link_libraries(libmgems ${ZLIB_LIBRARY})
+   set(MGEMS_HAVE_ZLIB 1)
+  else()
+    set(MGEMS_HAVE_ZLIB 0)
+  endif()
+endif()
+
+#### bzip2
+if (DEFINED BZIP2_LIBRARIES AND DEFINED BZIP2_INCLUDE_DIR AND (NOT DEFINED BZIP2_FOUND))
+  message(STATUS "bzip2 library provided in: " ${BZIP2_LIBRARIES})
+  message(STATUS "bzip2 headers provided in: " ${BZIP2_INCLUDE_DIR})
+  include_directories(${BZIP2_INCLUDE_DIR})
   target_link_libraries(mGEMS ${BZIP2_LIBRARIES})
-endif()    
-find_package(LibLZMA)
-if (LIBLZMA_FOUND)
-  include_directories(${LIBLZMA_INCLUDE_DIRS})
-  target_link_libraries(mGEMS ${LIBLZMA_LIBRARIES})
+  target_link_libraries(libmgems ${BZIP2_LIBRARIES})
+  set(MGEMS_HAVE_BZIP2 1)
+else()
+  find_package(BZip2)
+  if (BZIP2_FOUND)
+    include_directories(${BZIP2_INCLUDE_DIR})
+    target_link_libraries(mGEMS ${BZIP2_LIBRARIES})
+    target_link_libraries(libmgems ${BZIP2_LIBRARIES})
+    set(MGEMS_HAVE_BZIP2 1)
+  else()
+    set(MGEMS_HAVE_BZIP2 0)
+  endif()
 endif()
-find_package(ZLIB)
-if (ZLIB_FOUND)
-  include_directories(${ZLIB_INCLUDE_DIRS})
-  target_link_libraries(mGEMS ${ZLIB_LIBRARIES})
+
+#### lzma
+if (DEFINED LIBLZMA_LIBRARY AND DEFINED LIBLZMA_INCLUDE_DIR AND (NOT DEFINED LIBLZMA_FOUND))
+  message(STATUS "liblzma library provided in: " ${LIBLZMA_LIBRARY})
+  message(STATUS "liblzma headers provided in: " ${LIBLZMA_INCLUDE_DIR})
+  include_directories(${LIBLZMA_INCLUDE_DIR})
+  target_link_libraries(mGEMS ${LIBLZMA_LIBRARY})
+  target_link_libraries(libmgems ${LIBLZMA_LIBRARY})
+  set(MGEMS_HAVE_LIBLZMA 1)
+else()
+  find_package(LibLZMA)
+  if (LIBLZMA_FOUND)
+    include_directories(${LIBLZMA_INCLUDE_DIR})
+    target_link_libraries(mGEMS ${LIBLZMA_LIBRARY})
+    target_link_libraries(libmgems ${LIBLZMA_LIBRARY})
+    set(MGEMS_HAVE_LIBLZMA 1)
+  else()
+    set(MGEMS_HAVE_LIBLZMA 0)
+  endif()
 endif()
 
 ## bxzstr
 if (DEFINED CMAKE_BXZSTR_HEADERS)
   message(STATUS "bxzstr headers provided in: ${CMAKE_BXZSTR_HEADERS}")
 else()
-  configure_file(${CMAKE_CURRENT_SOURCE_DIR}/config/CMakeLists-bxzstr.txt.in ${CMAKE_CURRENT_BINARY_DIR}/external/bxzstr-download/CMakeLists.txt)
-  execute_process(COMMAND ${CMAKE_COMMAND} -G "${CMAKE_GENERATOR}" .
-    RESULT_VARIABLE result
-    WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/external/bxzstr-download )
-  if(result)
-    message(FATAL_ERROR "CMake step for bxzstr failed: ${result}")
-  endif()
-  execute_process(COMMAND ${CMAKE_COMMAND} --build .
-    RESULT_VARIABLE result
-    WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/external/bxzstr-download )
-  if(result)
-    message(FATAL_ERROR "Build step for bxzstr failed: ${result}")
-  endif()
-  set(CMAKE_BXZSTR_HEADERS ${CMAKE_CURRENT_BINARY_DIR}/external/bxzstr/include)
+  FetchContent_Declare(bxzstr
+    GIT_REPOSITORY    https://github.com/tmaklin/bxzstr.git
+    GIT_TAG           v1.1.0
+    PREFIX            "external"
+    SOURCE_DIR        "${CMAKE_CURRENT_SOURCE_DIR}/external/bxzstr"
+    BUILD_IN_SOURCE   0
+    CMAKE_ARGS        -D ZSTD_FOUND=0
+                      -D ZLIB_FOUND=${MGEMS_HAVE_ZLIB}
+		      -D BZIP2_FOUND=${MGEMS_HAVE_BZIP2}
+		      -D LIBLZMA_FOUND=${MGEMS_HAVE_LIBLZMA}
+    BUILD_COMMAND     ""
+    CONFIGURE_COMMAND ""
+    INSTALL_COMMAND   ""
+    )
+  FetchContent_MakeAvailable(bxzstr)
+  set(CMAKE_BXZSTR_HEADERS ${CMAKE_CURRENT_SOURCE_DIR}/external/bxzstr/include)
 endif()
 include_directories(${CMAKE_BXZSTR_HEADERS})
 
 ## cxxargs
 if (DEFINED CMAKE_CXXARGS_HEADERS)
   message(STATUS "cxxargs headers provided in: ${CMAKE_CXXARGS_HEADERS}")
 else()
-  configure_file(${CMAKE_CURRENT_SOURCE_DIR}/config/CMakeLists-cxxargs.txt.in ${CMAKE_CURRENT_BINARY_DIR}/external/cxxargs-download/CMakeLists.txt)
-  execute_process(COMMAND ${CMAKE_COMMAND} -G "${CMAKE_GENERATOR}" .
-    RESULT_VARIABLE result
-    WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/external/cxxargs-download )
-  if(result)
-    message(FATAL_ERROR "CMake step for cxxargs failed: ${result}")
-  endif()
-  execute_process(COMMAND ${CMAKE_COMMAND} --build .
-    RESULT_VARIABLE result
-    WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/external/cxxargs-download )
-  if(result)
-    message(FATAL_ERROR "Build step for cxxargs failed: ${result}")
-  endif()
-  set(CMAKE_CXXARGS_HEADERS ${CMAKE_CURRENT_BINARY_DIR}/external/cxxargs/include)
+  FetchContent_Declare(cxxargs
+    GIT_REPOSITORY    https://github.com/tmaklin/cxxargs.git
+    GIT_TAG           v1.1.4
+    PREFIX            "external"
+    SOURCE_DIR        "${CMAKE_CURRENT_SOURCE_DIR}/external/cxxargs"
+    BUILD_IN_SOURCE   0
+    BUILD_COMMAND     ""
+    CONFIGURE_COMMAND ""
+    INSTALL_COMMAND   ""
+    )
+  FetchContent_MakeAvailable(cxxargs)
+  set(CMAKE_CXXARGS_HEADERS ${CMAKE_CURRENT_SOURCE_DIR}/external/cxxargs/include)
 endif()
 include_directories("${CMAKE_CXXARGS_HEADERS}")
 
+## Check dependencies and download them if not given
 ## cxxio
 if (DEFINED CMAKE_CXXIO_HEADERS)
   message(STATUS "cxxio headers provided in: ${CMAKE_CXXIO_HEADERS}")
 else()
-  configure_file(${CMAKE_CURRENT_SOURCE_DIR}/config/CMakeLists-cxxio.txt.in ${CMAKE_CURRENT_BINARY_DIR}/external/cxxio-download/CMakeLists.txt)
-  execute_process(COMMAND ${CMAKE_COMMAND} -G "${CMAKE_GENERATOR}" .
-    RESULT_VARIABLE result
-    WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/external/cxxio-download )
-  if(result)
-    message(FATAL_ERROR "CMake step for cxxio failed: ${result}")
-  endif()
-  execute_process(COMMAND ${CMAKE_COMMAND} --build .
-    RESULT_VARIABLE result
-    WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/external/cxxio-download )
-  if(result)
-    message(FATAL_ERROR "Build step for cxxio failed: ${result}")
-  endif()
-  set(CMAKE_CXXIO_HEADERS ${CMAKE_CURRENT_BINARY_DIR}/external/cxxio/include)
+  FetchContent_Declare(cxxio
+    GIT_REPOSITORY    https://github.com/tmaklin/cxxio.git
+    GIT_TAG           v0.1.0
+    PREFIX            "external"
+    SOURCE_DIR        "${CMAKE_CURRENT_SOURCE_DIR}/external/cxxio"
+    BUILD_IN_SOURCE   0
+    BUILD_COMMAND     ""
+    CONFIGURE_COMMAND ""
+    INSTALL_COMMAND   ""
+    )
+  FetchContent_MakeAvailable(cxxio)
+  set(CMAKE_CXXIO_HEADERS ${CMAKE_CURRENT_SOURCE_DIR}/external/cxxio/include)
 endif()
 include_directories("${CMAKE_CXXIO_HEADERS}")
 
 ## alignment-writer
-if (DEFINED CMAKE_ALIGNMENT_WRITER_HEADERS)
+if (DEFINED CMAKE_ALIGNMENT_WRITER_HEADERS AND DEFINED CMAKE_ALIGNMENT_WRITER_LIBRARY)
   message(STATUS "alignment-writer headers provided in: ${CMAKE_ALIGNMENT_WRITER_HEADERS}")
+  message(STATUS "alignment-writer library provided in: ${CMAKE_ALIGNMENT_WRITER_LIBRARY}")
 else()
-  configure_file(${CMAKE_CURRENT_SOURCE_DIR}/config/CMakeLists-alignment-writer.txt.in ${CMAKE_BINARY_DIR}/external/alignment-writer-download/CMakeLists.txt)
-  execute_process(COMMAND ${CMAKE_COMMAND} -G "${CMAKE_GENERATOR}" .
-    RESULT_VARIABLE result
-    WORKING_DIRECTORY ${CMAKE_BINARY_DIR}/external/alignment-writer-download )
-  if(result)
-    message(FATAL_ERROR "CMake step for alignment-writer failed: ${result}")
-  endif()
-  execute_process(COMMAND ${CMAKE_COMMAND} --build .
-    RESULT_VARIABLE result
-    WORKING_DIRECTORY ${CMAKE_BINARY_DIR}/external/alignment-writer-download )
-  if(result)
-    message(FATAL_ERROR "Build step for alignment-writer failed: ${result}")
-  endif()
-  add_subdirectory(${CMAKE_CURRENT_BINARY_DIR}/external/alignment-writer
-                   ${CMAKE_CURRENT_BINARY_DIR}/external/alignment-writer/build)
+  FetchContent_Declare(alignment-writer
+    GIT_REPOSITORY    https://github.com/tmaklin/alignment-writer.git
+    GIT_TAG           v0.5.0
+    PREFIX            "external"
+    SOURCE_DIR        "${CMAKE_CURRENT_SOURCE_DIR}/external/alignment-writer"
+    BINARY_DIR        "${CMAKE_CURRENT_BINARY_DIR}/external/alignment-writer"
+    BUILD_IN_SOURCE   0
+    CMAKE_ARGS      -D CMAKE_BXZSTR_HEADERS=${CMAKE_BXZSTR_HEADERS}
+		    -D CMAKE_CXXARGS_HEADERS=${CMAKE_CXXARGS_HEADERS}
+		    -D CMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE}
+		    -D "CMAKE_C_FLAGS=${CMAKE_C_FLAGS}"
+		    -D "CMAKE_CXX_FLAGS=${CMAKE_CXX_FLAGS}"
+		    -D "CMAKE_C_COMPILER=${CMAKE_C_COMPILER}"
+		    -D "CMAKE_CXX_COMPILER=${CMAKE_CXX_COMPILER}"
+    INSTALL_COMMAND   ""
+    )
+  FetchContent_MakeAvailable(alignment-writer)
+  add_dependencies(mGEMS libalignmentwriter)
   set_target_properties(alignment-writer PROPERTIES EXCLUDE_FROM_ALL 1)
-  set(CMAKE_ALIGNMENT_WRITER_HEADERS ${CMAKE_CURRENT_BINARY_DIR}/external/alignment-writer/include)
+  set(CMAKE_ALIGNMENT_WRITER_HEADERS ${CMAKE_CURRENT_SOURCE_DIR}/external/alignment-writer/include)
+  set(CMAKE_ALIGNMENT_WRITER_LIBRARY ${CMAKE_CURRENT_BINARY_DIR}/lib/libalignment-writer.a)
 endif()
 include_directories(${CMAKE_ALIGNMENT_WRITER_HEADERS})
+target_link_libraries(mGEMS ${CMAKE_ALIGNMENT_WRITER_LIBRARY})
+target_link_libraries(libmgems ${CMAKE_ALIGNMENT_WRITER_LIBRARY})
 
-## Check dependencies and download them if not given
 ## telescope
-if (DEFINED CMAKE_TELESCOPE_HEADERS)
-  target_link_libraries(mGEMS libtelescope)
+if (DEFINED CMAKE_TELESCOPE_LIBRARY AND DEFINED CMAKE_TELESCOPE_HEADERS)
+  message(STATUS "telescope headers provided in: ${CMAKE_TELESCOPE_HEADERS}")
+  message(STATUS "telescope library provided in: ${CMAKE_TELESCOPE_LIBRARY}")
 else()
-  configure_file(${CMAKE_CURRENT_SOURCE_DIR}/config/CMakeLists-telescope.txt.in ${CMAKE_CURRENT_BINARY_DIR}/external/telescope-download/CMakeLists.txt)
-  execute_process(COMMAND ${CMAKE_COMMAND} -G "${CMAKE_GENERATOR}" .
-    RESULT_VARIABLE result
-    WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/external/telescope-download )
-  if(result)
-    message(FATAL_ERROR "CMake step for telescope failed: ${result}")
-  endif()
-  execute_process(COMMAND ${CMAKE_COMMAND} --build .
-    RESULT_VARIABLE result
-    WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/external/telescope-download )
-  if(result)
-    message(FATAL_ERROR "Build step for telescope failed: ${result}")
-  endif()
-  add_subdirectory(${CMAKE_CURRENT_BINARY_DIR}/external/telescope
-                   ${CMAKE_CURRENT_BINARY_DIR}/external/telescope/build)
+  FetchContent_Declare(telescope
+    GIT_REPOSITORY    https://github.com/tmaklin/telescope.git
+    GIT_TAG           v0.7.0-prerelease
+    PREFIX            "external"
+    SOURCE_DIR        "${CMAKE_CURRENT_SOURCE_DIR}/external/telescope"
+    BINARY_DIR        "${CMAKE_CURRENT_BINARY_DIR}/external/telescope"
+    BUILD_IN_SOURCE   0
+    CMAKE_ARGS      -D CMAKE_BXZSTR_HEADERS=${CMAKE_BXZSTR_HEADERS}
+		    -D CMAKE_CXXARGS_HEADERS=${CMAKE_CXXARGS_HEADERS}
+		    -D CMAKE_CXXIO_HEADERS=${CMAKE_CXXIO_HEADERS}
+		    -D CMAKE_ALIGNMENT_WRITER_HEADERS=${CMAKE_ALIGNMENT_WRITER_HEADERS}
+		    -D CMAKE_ALIGNMENT_WRITER_LIBRARY=${CMAKE_ALIGNMENT_WRITER_LIBRARY}
+		    -D CMAKE_BITMAGIC_HEADERS=${CMAKE_CURRENT_SOURCE_DIR}/external/telescope/external/BitMagic-7.12.3/src
+		    -D CMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE}
+		    -D "CMAKE_C_FLAGS=${CMAKE_C_FLAGS}"
+		    -D "CMAKE_CXX_FLAGS=${CMAKE_CXX_FLAGS}"
+		    -D "CMAKE_C_COMPILER=${CMAKE_C_COMPILER}"
+		    -D "CMAKE_CXX_COMPILER=${CMAKE_CXX_COMPILER}"
+    INSTALL_COMMAND   ""
+    )
+  FetchContent_MakeAvailable(telescope)
+  add_dependencies(mGEMS libalignmentwriter)
+  add_dependencies(telescope libalignmentwriter)
+  add_dependencies(mGEMS telescope)
   set_target_properties(telescope PROPERTIES EXCLUDE_FROM_ALL 1)
-  target_link_libraries(mGEMS libtelescope libalignmentwriter)
-  set(CMAKE_TELESCOPE_HEADERS ${CMAKE_CURRENT_BINARY_DIR}/external/telescope/include ${CMAKE_CURRENT_BINARY_DIR}/external/telescope/build/include)
-  if (NOT DEFINED CMAKE_BITMAGIC_HEADERS)
-    set(CMAKE_BITMAGIC_HEADERS ${CMAKE_CURRENT_BINARY_DIR}/external/telescope/external/BitMagic-7.12.3/src)
-  endif()
+  set(CMAKE_TELESCOPE_HEADERS ${CMAKE_CURRENT_SOURCE_DIR}/external/telescope/include)
+  set(CMAKE_TELESCOPE_LIBRARY ${CMAKE_CURRENT_BINARY_DIR}/lib/libtelescope.a)
+  set(CMAKE_BITMAGIC_HEADERS ${CMAKE_CURRENT_SOURCE_DIR}/external/telescope/external/BitMagic-7.12.3/src)
 endif()
-
 include_directories(${CMAKE_TELESCOPE_HEADERS} ${CMAKE_BITMAGIC_HEADERS})
+target_link_libraries(mGEMS ${CMAKE_TELESCOPE_LIBRARY})
+target_link_libraries(libmgems ${CMAKE_TELESCOPE_LIBRARY})
 
 ## seamat
 if (DEFINED CMAKE_SEAMAT_HEADERS)
   message(STATUS "seamat headers provided in: ${CMAKE_SEAMAT_HEADERS}")
 else()
-  configure_file(${CMAKE_CURRENT_SOURCE_DIR}/config/CMakeLists-seamat.txt.in ${CMAKE_BINARY_DIR}/external/seamat-download/CMakeLists.txt)
-  execute_process(COMMAND ${CMAKE_COMMAND} -G "${CMAKE_GENERATOR}" .
-    RESULT_VARIABLE result
-    WORKING_DIRECTORY ${CMAKE_BINARY_DIR}/external/seamat-download )
-  if(result)
-    message(FATAL_ERROR "CMake step for seamat failed: ${result}")
-  endif()
-  execute_process(COMMAND ${CMAKE_COMMAND} --build .
-    RESULT_VARIABLE result
-    WORKING_DIRECTORY ${CMAKE_BINARY_DIR}/external/seamat-download )
-  if(result)
-    message(FATAL_ERROR "Build step for seamat failed: ${result}")
-  endif()
-  add_subdirectory(${CMAKE_CURRENT_BINARY_DIR}/external/seamat
-                   ${CMAKE_CURRENT_BINARY_DIR}/external/seamat/build)
-  target_link_libraries(mGEMS)
-  set(CMAKE_SEAMAT_HEADERS ${CMAKE_CURRENT_BINARY_DIR}/external/seamat/include)
+  FetchContent_Declare(seamat
+    GIT_REPOSITORY    https://github.com/tmaklin/seamat.git
+    GIT_TAG           v0.2.2
+    PREFIX            "external"
+    SOURCE_DIR        "${CMAKE_CURRENT_SOURCE_DIR}/external/seamat"
+    BUILD_IN_SOURCE   0
+    CMAKE_ARGS        -D CMAKE_BUILD_TESTS=0
+    BUILD_COMMAND     ""
+    CONFIGURE_COMMAND ""
+    INSTALL_COMMAND   ""
+    )
+  FetchContent_MakeAvailable(seamat)
+  set(CMAKE_SEAMAT_HEADERS ${CMAKE_CURRENT_SOURCE_DIR}/external/seamat/include ${CMAKE_CURRENT_BINARY_DIR}/_deps/seamat-build/include)
 endif()
 include_directories(${CMAKE_SEAMAT_HEADERS})
 
@@ -192,7 +265,7 @@ if(GIT_FOUND)
     ERROR_QUIET
     OUTPUT_STRIP_TRAILING_WHITESPACE
   )
-  message( STATUS "mSWEEP-assembly plugin version: ${_BUILD_VERSION}")
+  message( STATUS "mGEMS version: ${_BUILD_VERSION}")
 else()
   message(STATUS "GIT not found, version numbering disabled")
   set(_BUILD_VERSION "unknown")
@@ -204,12 +277,5 @@ configure_file(${CMAKE_CURRENT_SOURCE_DIR}/include/version.h.in ${CMAKE_CURRENT_
 
 include_directories(${CMAKE_CURRENT_SOURCE_DIR}/include)
 
-## mGEMS library
-add_library(libmgems
-${CMAKE_CURRENT_SOURCE_DIR}/src/bin_reads.cpp
-${CMAKE_CURRENT_SOURCE_DIR}/src/extract_bin.cpp
-)
-set_target_properties(libmgems PROPERTIES OUTPUT_NAME mgems)
-
 # Link libraries
 target_link_libraries(mGEMS libmgems)