From a8d36e7b5f6606f1c43b5ff4a47fa0158c438611 Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Fri, 18 Oct 2019 09:58:02 +0100 Subject: [PATCH] Updates for the 2019.2.1 release. --- CHANGELOG | 7 +++++- corelib/CMakeLists.txt | 50 +++++++++++++++++++++--------------------- wrapper/CMakeLists.txt | 2 +- 3 files changed, 32 insertions(+), 27 deletions(-) diff --git a/CHANGELOG b/CHANGELOG index 64421eae3..ba1bb3cff 100644 --- a/CHANGELOG +++ b/CHANGELOG @@ -3,7 +3,12 @@ SIRE changelog devel branch: - [2019.2.0] Sep 2019 - Updated the Gromacs topology writer to support + [2019.2.1] October 2019 - Updated the Conda recipe to pin the dependencies + of dependencies that are used at run time since Conda doesn't + automatically do this for you. Added instructions detailing the + Azure Pipeline build process and how to create a new release. + + [2019.2.0] September 2019 - Updated the Gromacs topology writer to support perturbable molecules containing a variable number of bonds. Created a Docker container for building wrappers and updated to using CastXML. Added support for running background diff --git a/corelib/CMakeLists.txt b/corelib/CMakeLists.txt index 0bd65bd15..3b6a899e6 100644 --- a/corelib/CMakeLists.txt +++ b/corelib/CMakeLists.txt @@ -8,7 +8,7 @@ set (S_VERSION_MAJOR "2019") set (S_VERSION_MINOR "2") -set (S_VERSION_PATCH "0") +set (S_VERSION_PATCH "1") set (SIRE_VERSION "${S_VERSION_MAJOR}.${S_VERSION_MINOR}.${S_VERSION_PATCH}") @@ -48,8 +48,8 @@ endif() set( CMAKE_INSTALL_MESSAGE "NEVER" ) # Option used to control the number of cores for the compile -set ( BUILD_NCORES "0" - CACHE STRING +set ( BUILD_NCORES "0" + CACHE STRING "The number of cores used to compile Sire. Leave this at 0 to automatically work this out." ) string(REGEX MATCH "[0-9]+" NCORES ${BUILD_NCORES}) @@ -163,7 +163,7 @@ else() "Install directory for Sire. This directory can be moved after compilation" ) set(CMAKE_INSTALL_PREFIX "${SIRE_INSTALL_PREFIX}" CACHE INTERNAL - "Prefix prepended to install directories" FORCE ) + "Prefix prepended to install directories" FORCE ) endif() endif() @@ -174,7 +174,7 @@ message( STATUS "sire.app root directory is ${SIRE_APP}" ) # Absolutely can't run cmake in the source directory! if ( CMAKE_BINARY_DIR STREQUAL CMAKE_SOURCE_DIR ) message( STATUS "${CMAKE_BINARY_DIR} | ${CMAKE_SOURCE_DIR}" ) - message( FATAL_ERROR "You must run CMake in a different directory to the source!" ) + message( FATAL_ERROR "You must run CMake in a different directory to the source!" ) endif() # name the project @@ -195,7 +195,7 @@ macro( SAVE_SIRE_VARIABLE _var _value ) "set( ${_var} \"${_value}\" )\n") endmacro (SAVE_SIRE_VARIABLE) -math (EXPR SIRE_VERSION_NUMBER +math (EXPR SIRE_VERSION_NUMBER "${S_VERSION_MAJOR}*100000 + ${S_VERSION_MINOR}*100 + ${S_VERSION_PATCH}") set (SIRE_VERSION_STRING "${S_VERSION_MAJOR}_${S_VERSION_MINOR}_${S_VERSION_PATCH}") @@ -260,12 +260,12 @@ set (CMAKE_SKIP_BUILD_RPATH FALSE) if (APPLE) # make sure that all libraries are named "@rpath/library.dylib". This will allow - # the library to be found as long as the executable can substitute @rpath with the + # the library to be found as long as the executable can substitute @rpath with the # path to the library set (CMAKE_INSTALL_NAME_DIR "@rpath") # Add the two passed directories to the @rpaths to search for libraries. @executable_path - # is the directory containing the executable, so the libraries are included in + # is the directory containing the executable, so the libraries are included in # @exeutable_path/../${SIRE_LIBS} and @exeutable_path/../${SIRE_BUNDLED_LIBS} set (SIRE_INSTALL_RPATH "@executable_path/.:@executable_path/../${SIRE_LIBS}:@executable_path/../${SIRE_BUNDLED_LIBS}") else() @@ -363,7 +363,7 @@ check_function_exists( cbrt HAVE_CUBEROOT ) check_symbol_exists( backtrace "execinfo.h" HAVE_BACKTRACE ) #create config.h -configure_file(${CMAKE_CURRENT_SOURCE_DIR}/build/cmake/sire_config.h.in +configure_file(${CMAKE_CURRENT_SOURCE_DIR}/build/cmake/sire_config.h.in ${CMAKE_CURRENT_BINARY_DIR}/sire_config.h) # We need to get the compiler flags for different options @@ -506,13 +506,13 @@ if ( ${SIRE_CXX_COMPILER_ID} MATCHES "GNU" ) OUTPUT_VARIABLE exe_output ) # These two regexps are copied from the Chicken CMake - # files (which provide a very useful cmake tutorial - thanks :-) + # files (which provide a very useful cmake tutorial - thanks :-) SET( VERSION_BUILD_REGEX "^([0-9]+)[.]([0-9]+).*$" ) STRING( REGEX REPLACE ${VERSION_BUILD_REGEX} "\\1" GCC_MAJOR_VERSION ${exe_output} ) STRING( REGEX REPLACE ${VERSION_BUILD_REGEX} "\\2" GCC_MINOR_VERSION ${exe_output} ) - + message( STATUS "Using GCC version " "${GCC_MAJOR_VERSION}.${GCC_MINOR_VERSION}" ) @@ -582,7 +582,7 @@ elseif ( ${SIRE_CXX_COMPILER_ID} MATCHES "CLANG" ) set ( SIRE_WARNALL_FLAGS "-Wall" ) set ( SIRE_DEBUG_FLAGS "-g" ) - # an old incompatibility between clang and gcc means that some + # an old incompatibility between clang and gcc means that some # distributions will fail if use -ffast-math set(CMAKE_OLD_REQUIRED_FLAGS ${CMAKE_REQUIRED_FLAGS}) set(CMAKE_REQUIRED_FLAGS "-O3 -ffast-math") @@ -595,7 +595,7 @@ elseif ( ${SIRE_CXX_COMPILER_ID} MATCHES "CLANG" ) return 0; }" CAN_USE_FFAST_MATH) - set(CMAKE_REQUIRED_FLAGS ${CMAKE_OLD_REQUIRED_FLAGS}) + set(CMAKE_REQUIRED_FLAGS ${CMAKE_OLD_REQUIRED_FLAGS}) if (CAN_USE_FFAST_MATH) set ( SIRE_RELEASE_FLAGS "-O3 -ffast-math" ) @@ -628,7 +628,7 @@ elseif( ${CMAKE_CXX_COMPILER} MATCHES "icpc" ) set ( SIRE_WARNALL_FLAGS "-w1" ) set ( SIRE_RELEASE_FLAGS "-O3 -finline -finline-functions -ansi-alias -fargument-noalias-global -ip -g -simd" ) set ( SIRE_DEBUG_FLAGS "-g" ) - set ( SIRE_VISIBILITY_FLAGS "-DSIRE_NO_VISIBILITY_AVAILABLE" ) + set ( SIRE_VISIBILITY_FLAGS "-DSIRE_NO_VISIBILITY_AVAILABLE" ) set ( SIRE_SHARE_LINK_FLAGS "-shared" ) set ( SIRE_STATIC_LINK_FLAGS "-static" ) @@ -672,7 +672,7 @@ elseif (MSVC) set ( SIRE_EXE_LINK_FLAGS "/LTCG /OPT:REF /OPT:ICF" ) set ( SIRE_PLATFORM_FLAGS "/DSIRE_ALWAYS_INLINE=__forceinline" ) - + else() message( STATUS "CMAKE_SYSTEM_NAME == ${CMAKE_SYSTEM_NAME}" ) message( STATUS "CMAKE_C_COMPILER == ${CMAKE_C_COMPILER}" ) @@ -710,7 +710,7 @@ else() option( SIRE_BUNDLE_BLASLAPACK "Whether Sire should use its bundled copy of BLAS and LAPACK" ON ) option( SIRE_BUNDLE_QT "Whether Sire should use its bundled copy of Qt" ON ) option( SIRE_BUNDLE_OPENMM "Whether Sire should use its bundled copy of OpenMM" OFF ) - + save_sire_variable( "SIRE_ENABLE_BUNDLING" "${SIRE_ENABLE_BUNDLING}" ) save_sire_variable( "SIRE_BUNDLE_TBB" "${SIRE_BUNDLE_TBB}" ) save_sire_variable( "SIRE_BUNDLE_CPUID" "${SIRE_BUNDLE_CPUID}" ) @@ -725,7 +725,7 @@ else() set (SIRE_FOUND_BOOST FALSE) set (SIRE_FOUND_BLASLAPACK FALSE) set (SIRE_FOUND_QT FALSE) - set (SIRE_FOUND_OPENMM FALSE) + set (SIRE_FOUND_OPENMM FALSE) set (SIRE_FOUND_NETCDF FALSE) set (SIRE_FOUND_CPUID FALSE) @@ -747,11 +747,11 @@ else() if (NOT EXISTS "${BUNDLE_STAGEDIR}") file(MAKE_DIRECTORY ${BUNDLE_STAGEDIR}) endif() - + if (NOT EXISTS "${BUNDLE_STAGEDIR}/lib") file(MAKE_DIRECTORY ${BUNDLE_STAGEDIR}/lib) endif() - + if (NOT EXISTS "${BUNDLE_STAGEDIR}/include") file(MAKE_DIRECTORY ${BUNDLE_STAGEDIR}/include) endif() @@ -787,7 +787,7 @@ else() if ( NOT ${BUNDLE_STAGEDIR} STREQUAL "${CMAKE_INSTALL_PREFIX}/${SIRE_BUNDLED_DIR}" ) # All of the bundled objects are built into the directory ${CMAKE_BINARY_DIR}/bundled # This directory must be installed into the sire.app/ directory - install( DIRECTORY ${BUNDLE_STAGEDIR} + install( DIRECTORY ${BUNDLE_STAGEDIR} DESTINATION ${CMAKE_INSTALL_PREFIX} USE_SOURCE_PERMISSIONS ) endif() @@ -878,7 +878,7 @@ if (NOT ${SIRE_FOUND_BOOST}) save_sire_variable( "SIRE_BOOST_INCLUDE_DIR" "${Boost_INCLUDE_DIR}" ) else() message(FATAL_ERROR "Cannot find the boost libraries.") - endif() + endif() endif() if (NOT ${SIRE_FOUND_GSL}) @@ -887,11 +887,11 @@ if (NOT ${SIRE_FOUND_GSL}) message( STATUS "GSL paths ${GSL_LINK_DIRECTORIES} " "${GSL_LIBRARIES} | ${GSL_INCLUDE_DIR}" ) - + list(APPEND SIREMATHS_EXTRA_LIBRARIES ${GSL_LIBRARIES}) - + include_directories( BEFORE ${GSL_INCLUDE_DIR}) - + save_sire_variable( "SIRE_GSL_INCLUDE_PATH" "${GSL_INCLUDE_DIR}" ) endif() @@ -1072,7 +1072,7 @@ add_subdirectory (src/apps) include( GetGitVersion ) # install the extra includes file in the Sire/cmake directory -install (FILES ${SIRE_VARIABLES_FILE} +install (FILES ${SIRE_VARIABLES_FILE} DESTINATION ${SIRE_CMAKEFILES} ) diff --git a/wrapper/CMakeLists.txt b/wrapper/CMakeLists.txt index 090c8ffc7..5274a470b 100644 --- a/wrapper/CMakeLists.txt +++ b/wrapper/CMakeLists.txt @@ -10,7 +10,7 @@ # project version set (SIRE_VERSION_MAJOR "2019") set (SIRE_VERSION_MINOR "2") -set (SIRE_VERSION_PATCH "0") +set (SIRE_VERSION_PATCH "1") set (SIRE_VERSION "${SIRE_VERSION_MAJOR}.${SIRE_VERSION_MINOR}.${SIRE_VERSION_PATCH}")