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Merge pull request #70 from sys-bio/develop
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Release 2.13.2
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@luciansmith
luciansmith authored Jul 1, 2022
2 parents 97e6b59 + 6f520e4 commit 0db49fd
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Showing 81 changed files with 181 additions and 146 deletions.
127 changes: 79 additions & 48 deletions CMakeLists.txt
View file
Original file line number Diff line number Diff line change
Expand Up @@ -12,7 +12,7 @@ project(libantimony)
#
SET(LIBANTIMONY_VERSION_MAJOR 2)
SET(LIBANTIMONY_VERSION_MINOR 13)
SET(LIBANTIMONY_VERSION_PATCH ".1")
SET(LIBANTIMONY_VERSION_PATCH ".2")
SET(LIBANTIMONY_VERSION_RELEASE "")


Expand Down Expand Up @@ -53,9 +53,18 @@ SET(CPACK_PACKAGE_VERSION_PATCH "${LIBANTIMONY_VERSION_PATCH}")
SET(CPACK_PACKAGE_VERSION_RELEASE "${LIBANTIMONY_VERSION_RELEASE}")
INCLUDE(CPack)

SET(LIBANTIMONY_VERSION_STRING "v${LIBANTIMONY_VERSION_MAJOR}.${LIBANTIMONY_VERSION_MINOR}${LIBANTIMONY_VERSION_PATCH}${LIBANTIMONY_VERSION_RELEASE}")


option(BUILD_SHARED_LIBS "Build shared library (Set to OFF to build static libraries)" ON)
set(CMAKE_BUILD_TYPE "RelWithDebInfo" CACHE STRING "Choose the type of build, options are: None (CMAKE_CXX_FLAGS or CMAKE_C_FLAGS are used), Debug, Release, RelWithDebInfo, MinSizeRel" )

set(USE_UNIVERSAL_BINARIES "ON" CACHE BOOL "Build and link to universal binaries on MacOS")

if (USE_UNIVERSAL_BINARIES)
set(CMAKE_OSX_ARCHITECTURES "arm64;x86_64" CACHE INTERNAL "Compile for intel and M1 chips on apple" FORCE)
message(STATUS "building on mac with universal binaries")
endif()

####################################################################
#
Expand All @@ -65,10 +74,10 @@ set(CMAKE_BUILD_TYPE "RelWithDebInfo" CACHE STRING "Choose the type of build, op
# which language bindings should be build
option(WITH_SBML "Generate SBML translations" ON )
if (WITH_SBML)
option(WITH_STATIC_SBML "Use the static version of the libsbml library" OFF )
option(WITH_STATIC_SBML "Use the static version of the libsbml library" ON )
option(WITH_COMP_SBML "Use the hierarchical composition package API" ON )
OPTION(WITH_LIBSBML_EXPAT "Set if libsbml was compiled with a separate expat library." OFF)
OPTION(WITH_LIBSBML_LIBXML "Set if libsbml was compiled with a separate libxml library." ON)
OPTION(WITH_LIBSBML_EXPAT "Set if libsbml was compiled with a separate expat library." ON)
OPTION(WITH_LIBSBML_LIBXML "Set if libsbml was compiled with a separate libxml library." OFF)
OPTION(WITH_LIBSBML_XERCES "Set if libsbml was compiled with a separate xerces library." OFF)
OPTION(WITH_LIBSBML_COMPRESSION "Set if libsbml was compiled with separate zdll and bzip libraries." ON)
endif()
Expand Down Expand Up @@ -98,7 +107,6 @@ endif()



SET(LIBANTIMONY_VERSION_STRING "v${LIBANTIMONY_VERSION_MAJOR}.${LIBANTIMONY_VERSION_MINOR}${LIBANTIMONY_VERSION_PATCH}${LIBANTIMONY_VERSION_RELEASE}")
add_definitions( -DLIBANTIMONY_VERSION_STRING="${LIBANTIMONY_VERSION_STRING}" )


Expand Down Expand Up @@ -273,6 +281,7 @@ if(WITH_LIBSBML_LIBXML)
${CMAKE_SOURCE_DIR}
${CMAKE_SOURCE_DIR}/dependencies/lib
${LIBSBML_INCLUDE_DIR}/../lib
${LIBSBML_INSTALL_DIR}/lib
)
set(LIBANTIMONY_LIBS ${LIBANTIMONY_LIBS} ${ZDLL_LIBRARY} )

Expand Down Expand Up @@ -309,20 +318,22 @@ endif()

if(WITH_LIBSBML_COMPRESSION)
find_library(ZDLL_LIBRARY
NAMES zdll.lib zdll.so zdll.dylib zdll z
NAMES zdll.lib zdll.so zdll.dylib zdll z zlibd.lib zlibstaticd.lib zlibmd.lib zlibstatic.lib
PATHS /usr/lib /usr/local/lib
${CMAKE_SOURCE_DIR}
${CMAKE_SOURCE_DIR}/dependencies/lib
${LIBSBML_INCLUDE_DIR}/../lib
${LIBSBML_INSTALL_DIR}/lib
)
set(LIBANTIMONY_LIBS ${LIBANTIMONY_LIBS} ${ZDLL_LIBRARY} )

find_library(BZIP_LIBRARY
NAMES bzip2.lib bzip2.so bzip2.dylib bzip2 bz2 bz2d
NAMES bzip2.lib bzip2.so bzip2.dylib bzip2 bz2 bz2d bz2md bz2mdd
PATHS /usr/lib /usr/local/lib
${CMAKE_SOURCE_DIR}
${CMAKE_SOURCE_DIR}/dependencies/lib
${LIBSBML_INCLUDE_DIR}/../lib
${LIBSBML_INSTALL_DIR}/lib
)
set(LIBANTIMONY_LIBS ${LIBANTIMONY_LIBS} ${BZIP_LIBRARY} )
endif()
Expand All @@ -337,18 +348,8 @@ if(WITH_SWIG)
PATHS
"c:/Program Files (x86)/Swig"
c:/Program Files/Swig
c:/swigwin-2.0.11
c:/swigwin-2.0.10
c:/swigwin-2.0.9
c:/swigwin-2.0.8
c:/swigwin-2.0.7
c:/swigwin-2.0.6
c:/swigwin-2.0.5
c:/swigwin-2.0.4
c:/swigwin-2.0.3
c:/swigwin-2.0.2
c:/swigwin-2.0.1
c:/swigwin-2.0.0
c:/Program Files/swigwin-3.0.10
c:/Program Files/swigwin-4.0.2
/usr/local/bin
/opt/local/bin
/usr/bin
Expand Down Expand Up @@ -762,6 +763,34 @@ file(GLOB QTANTIMONY_RESOURCES
${QTANTIMONY_SRC_DIR}antimonyicon.rc
${QTANTIMONY_SRC_DIR}antimony.qrc
)

## https://stackoverflow.com/questions/32183975/how-to-print-all-the-properties-of-a-target-in-cmake/56738858#56738858
## https://stackoverflow.com/a/56738858/3743145

## Get all properties that cmake supports
execute_process(COMMAND cmake --help-property-list OUTPUT_VARIABLE CMAKE_PROPERTY_LIST)
## Convert command output into a CMake list
STRING(REGEX REPLACE ";" "\\\\;" CMAKE_PROPERTY_LIST "${CMAKE_PROPERTY_LIST}")
STRING(REGEX REPLACE "\n" ";" CMAKE_PROPERTY_LIST "${CMAKE_PROPERTY_LIST}")

list(REMOVE_DUPLICATES CMAKE_PROPERTY_LIST)

function(print_target_properties tgt)
if(NOT TARGET ${tgt})
message("There is no target named '${tgt}'")
return()
endif()

foreach (prop ${CMAKE_PROPERTY_LIST})
string(REPLACE "<CONFIG>" "${CMAKE_BUILD_TYPE}" prop ${prop})
get_target_property(propval ${tgt} ${prop})
if (propval)
message ("${tgt} ${prop} = ${propval}")
endif()
endforeach(prop)
endfunction(print_target_properties)


if (WITH_QTANTIMONY)
set(CMAKE_AUTOMOC ON)
set(CMAKE_AUTORCC ON)
Expand Down Expand Up @@ -789,34 +818,36 @@ if (WITH_QTANTIMONY)
install(TARGETS QTAntimony DESTINATION bin)
install(FILES ${QTANTIMONY_SRC_DIR}antimony.ico ${QTANTIMONY_SRC_DIR}antimony_ico.png DESTINATION bin)

set_target_properties(QTAntimony PROPERTIES RUNTIME_OUTPUT_DIRECTORY "${CMAKE_BINARY_DIR}/QTAntimony/$<0:>")

message(STATUS "QT dir: ${Qt5_DIR}")
message(STATUS "Binary dir: ${CMAKE_BINARY_DIR}")
message(STATUS "Runtime output dir: ${RUNTIME_OUTPUT_DIRECTORY}")
message(STATUS "CMake install dir: ${CMAKE_INSTALL_PREFIX}")
#print_target_properties(QTAntimony)
if (WIN32)
add_custom_command(TARGET QTAntimony POST_BUILD
COMMAND dir
WORKING_DIRECTORY ${CMAKE_BINARY_DIR}
COMMENT "get directory contents.")
add_custom_command(TARGET QTAntimony POST_BUILD
COMMAND ${Qt5_DIR}/../../../bin/windeployqt.exe QTAntimony.exe
WORKING_DIRECTORY ${CMAKE_BINARY_DIR}/QTAntimony
COMMENT "Running windeployqt on QTAntimony to copy DLLs.")
install(CODE "execute_process(COMMAND ${Qt5_DIR}/../../../bin/windeployqt.exe ${CMAKE_INSTALL_PREFIX}/bin/QTAntimony.exe)")
endif(WIN32)


endif(WITH_QTANTIMONY)


####################################################################
#
# Set up remaining variables, add option for universal binaries
#
if(UNIX)
if(APPLE)
add_definitions(-DMACOSX)
#create universal binaries
option(ENABLE_UNIVERSAL "Create Universal Binaries" OFF)

set(CMAKE_OSX_ARCHITECTURES "${CMAKE_OSX_ARCHITECTURES}" CACHE STRING "A semicolon separated list of build architectures to be used")
if(ENABLE_UNIVERSAL)
# if universal binaries are requested and none defined so far
# overwrite them with all three common architectures. If the user
# specified their own list of architectures do not touch!
if (CMAKE_OSX_ARCHITECTURES STREQUAL "")
set(CMAKE_OSX_ARCHITECTURES "i386;ppc;x86_64" CACHE STRING "A semicolon separated list of build architectures to be used" FORCE)
endif()
endif(ENABLE_UNIVERSAL)
else(APPLE)
add_definitions(-DLINUX)
endif(APPLE)
# add_definitions( -DPACKAGE_VERSION=\"${PACKAGE_VERSION}\" -DPACKAGE_NAME="${PROJECT_NAME}")

else(UNIX)


if(NOT UNIX)
add_definitions(-DWIN32 -DLIBANTIMONY_EXPORTS -DLIBLAX_EXPORTS)
if(MSVC)
add_definitions(-D_CRT_SECURE_NO_WARNINGS)
Expand All @@ -841,14 +872,14 @@ endif(UNIX)
#
# Install win32 dependencies
#
if (NOT UNIX)
file(GLOB win_dependencies "${CMAKE_SOURCE_DIR}/win32/*.dll" "${CMAKE_CURRENT_SOURCE_DIR}/win32/README.txt")
if (NOT WITH_STATIC_SBML)
list(APPEND win_dependencies ${LIBSBML_DLL})
endif()
install(FILES ${win_dependencies} DESTINATION bin/)
install(FILES "${CMAKE_SOURCE_DIR}/win32/platforms/qwindows.dll" DESTINATION bin/platforms/)
endif()
#if (NOT UNIX)
# file(GLOB win_dependencies "${CMAKE_SOURCE_DIR}/win32/*.dll" "${CMAKE_CURRENT_SOURCE_DIR}/win32/README.txt")
# if (NOT WITH_STATIC_SBML)
# list(APPEND win_dependencies ${LIBSBML_DLL})
# endif()
# install(FILES ${win_dependencies} DESTINATION bin/)
# install(FILES "${CMAKE_SOURCE_DIR}/win32/platforms/qwindows.dll" DESTINATION bin/platforms/)
#endif()

if(WIN32 AND INSTALL_SYSTEM_RUNTIMES)
include(InstallRequiredSystemLibraries)
Expand Down
10 changes: 7 additions & 3 deletions azure-pipelines.yml
View file
Original file line number Diff line number Diff line change
Expand Up @@ -48,11 +48,13 @@ stages:
CheckFile: check-release.zip
CheckURL: https://github.com/sys-bio/antimony/releases/download/libcheck/check-release.zip
PythonCMake: -DWITH_PYTHON=ON -DPython_ROOT_DIR=$(PythonRoot)
expatlib: libexpatmd.lib
64-bit Windows Debug:
BuildType: Debug
CheckFile: check-debug.zip
CheckURL: https://github.com/sys-bio/antimony/releases/download/libcheck/check-debug.zip
PythonCMake: -DWITH_PYTHON=OFF
expatlib: libexpatmdd.lib
steps:
- script: |
echo "SOURCE_DIR $(SOURCE_DIR)"
Expand Down Expand Up @@ -151,7 +153,7 @@ stages:
mkdir $(BUILD_DIR)
echo "CD to build dir: $(BUILD_DIR)"
cd $(BUILD_DIR)
cmake -DCMAKE_PREFIX_PATH=/usr/local/opt/qt@5/lib -DLIBSBML_INSTALL_DIR=$(DEPS_INSTALL_PREFIX) -DWITH_QTANTIMONY=ON -DWITH_STATIC_SBML=ON -DCMAKE_INSTALL_PREFIX=$(INSTALL_DIR) -DCMAKE_BUILD_TYPE=$(BuildType) -DWITH_CHECK=ON -DLIBCHECK_INCLUDE_DIR=$(CHECK_INSTALL_PREFIX)/include/ -DLIBCHECK_LIBRARY=$(CHECK_INSTALL_PREFIX)/lib/libcheck.lib -DQt5_DIR=$(QT_INSTALL_PREFIX)/Qt5/5.15.2/msvc2019_64/lib/cmake/Qt5 -DEXTRA_LIBS=wsock32.lib $(PythonCMake) ..
cmake -DCMAKE_PREFIX_PATH=/usr/local/opt/qt@5/lib -DLIBSBML_INSTALL_DIR=$(DEPS_INSTALL_PREFIX) -DWITH_QTANTIMONY=ON -DWITH_LIBSBML_EXPAT=ON -DEXPAT_LIBRARY=$(DEPS_INSTALL_PREFIX)/lib/$(expatlib) -DWITH_LIBSBML_LIBXML=OFF -DWITH_STATIC_SBML=ON -DCMAKE_INSTALL_PREFIX=$(INSTALL_DIR) -DCMAKE_BUILD_TYPE=$(BuildType) -DWITH_CHECK=ON -DLIBCHECK_INCLUDE_DIR=$(CHECK_INSTALL_PREFIX)/include/ -DLIBCHECK_LIBRARY=$(CHECK_INSTALL_PREFIX)/lib/libcheck.lib -DQt5_DIR=$(QT_INSTALL_PREFIX)/Qt5/5.15.2/msvc2019_64/lib/cmake/Qt5 -DEXTRA_LIBS=wsock32.lib $(PythonCMake) ..
displayName: Run CMake Configure Command
- script: |
echo "less -N $(BUILD_DIR)/source/CMakeFiles/antimony.dir/build.make"
Expand Down Expand Up @@ -350,7 +352,9 @@ stages:
mkdir $(BUILD_DIR)
echo "CD to build dir: $(BUILD_DIR)"
cd $(BUILD_DIR)
cmake -DCMAKE_PREFIX_PATH=/usr/local/opt/qt@5/lib -DQt5_DIR=$(brew --prefix qt5)/lib/cmake/Qt5 -DLIBSBML_INSTALL_DIR=$(DEPS_INSTALL_PREFIX) -DWITH_QTANTIMONY=ON -DWITH_STATIC_SBML=ON -DCMAKE_INSTALL_PREFIX=$(INSTALL_DIR) -DCMAKE_BUILD_TYPE=$(BuildType) -DWITH_CHECK=ON -DWITH_PYTHON=ON -DPython_ROOT_DIR=$(PythonRoot) ..
#Can't make universal binaries with QT, at least not yet.
#cmake -DCMAKE_PREFIX_PATH=/usr/local/opt/qt@5/lib -DQt5_DIR=$(brew --prefix qt5)/lib/cmake/Qt5 -DWITH_LIBSBML_EXPAT=ON -DWITH_LIBSBML_LIBXML=OFF -DLIBSBML_INSTALL_DIR=$(DEPS_INSTALL_PREFIX) -DWITH_QTANTIMONY=ON -DWITH_STATIC_SBML=ON -DCMAKE_INSTALL_PREFIX=$(INSTALL_DIR) -DCMAKE_BUILD_TYPE=$(BuildType) -DWITH_CHECK=ON -DWITH_PYTHON=ON -DPython_ROOT_DIR=$(PythonRoot) ..
cmake -DCMAKE_PREFIX_PATH=/usr/local/opt/qt@5/lib -DQt5_DIR=$(brew --prefix qt5)/lib/cmake/Qt5 -DWITH_LIBSBML_EXPAT=ON -DWITH_LIBSBML_LIBXML=OFF -DLIBSBML_INSTALL_DIR=$(DEPS_INSTALL_PREFIX) -DWITH_QTANTIMONY=ON -DUSE_UNIVERSAL_BINARIES=OFF -DWITH_STATIC_SBML=ON -DCMAKE_INSTALL_PREFIX=$(INSTALL_DIR) -DCMAKE_BUILD_TYPE=$(BuildType) -DWITH_CHECK=ON -DWITH_PYTHON=ON -DPython_ROOT_DIR=$(PythonRoot) ..
displayName: Run CMake Configure Command
- script: |
echo "less -N $(BUILD_DIR)/source/CMakeFiles/antimony.dir/build.make"
Expand Down Expand Up @@ -512,7 +516,7 @@ stages:
mkdir $(BUILD_DIR)
echo "CD to build dir: $(BUILD_DIR)"
cd $(BUILD_DIR)
cmake -DCMAKE_PREFIX_PATH=/usr/local/opt/qt@5/lib -DLIBSBML_INSTALL_DIR=$(DEPS_INSTALL_PREFIX) -DLIBXML_LIBRARY=${DEPS_INSTALL_PREFIX}/lib64/libxml2.a -DWITH_QTANTIMONY=OFF -DWITH_STATIC_SBML=ON -DCMAKE_INSTALL_PREFIX=$(INSTALL_DIR) -DCMAKE_BUILD_TYPE=$(BuildType) -DWITH_CHECK=OFF -DWITH_PYTHON=ON -DPython_ROOT_DIR=$(PythonRoot) ..
cmake -DCMAKE_PREFIX_PATH=/usr/local/opt/qt@5/lib -DLIBSBML_INSTALL_DIR=$(DEPS_INSTALL_PREFIX) -DWITH_LIBSBML_EXPAT=ON -DWITH_LIBSBML_LIBXML=OFF -DLIBEXPAT_LIBRARY=${DEPS_INSTALL_PREFIX}/lib64/libexpat.a -DWITH_QTANTIMONY=OFF -DWITH_STATIC_SBML=ON -DCMAKE_INSTALL_PREFIX=$(INSTALL_DIR) -DCMAKE_BUILD_TYPE=$(BuildType) -DWITH_CHECK=OFF -DWITH_PYTHON=ON -DPython_ROOT_DIR=$(PythonRoot) ..
displayName: Run CMake Configure Command
- script: |
echo "less -N $(BUILD_DIR)/source/CMakeFiles/antimony.dir/build.make"
Expand Down
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