Commit 2f658923 authored by Andreas Tille's avatar Andreas Tille
Browse files

New upstream version 5.17.0+dfsg

parent 2b3044cb

CMakeLists.txt

+17 −11
Original line number Diff line number Diff line
@@ -59,6 +59,17 @@ include (CheckCCompilerFlag) 
include (CheckCSourceRuns)

include (CheckSymbolExists)

include (CheckTypeSize)

if (${CMAKE_VERSION} VERSION_GREATER 2.8.4)

	include(GNUInstallDirs)

else ()

	set (CMAKE_INSTALL_DATADIR "share/libsbml/")

	set (CMAKE_INSTALL_LIBDIR "lib")

	set (CMAKE_INSTALL_INCLUDEDIR "include")

	set (CMAKE_INSTALL_BINDIR "bin")

	set (CMAKE_INSTALL_DATADIR "share")

	set (CMAKE_INSTALL_FULL_LIBDIR "${CMAKE_INSTALL_PREFIX}/lib")

	set (CMAKE_INSTALL_FULL_INCLUDEDIR "${CMAKE_INSTALL_PREFIX}/include")

endif ()



###############################################################################

#
@@ -94,7 +105,7 @@ MATH(EXPR LIBSBML_VERSION_NUMERIC "${LIBSBML_VERSION_MAJOR} * 10000 + ${LIBSBML_ 
set(PACKAGE_VERSION "${LIBSBML_VERSION_MAJOR}.${LIBSBML_VERSION_MINOR}.${LIBSBML_VERSION_PATCH}${LIBSBML_VERSION_RELEASE}")

set(PACKAGE_NAME "libSBML")



set(PACKAGE_CONFIG_DIR lib/cmake CACHE PATH

set(PACKAGE_CONFIG_DIR "${CMAKE_INSTALL_LIBDIR}/cmake" CACHE PATH

    "Path into which the cmake config files should be installed")
@@ -864,10 +875,10 @@ set( MISC_PREFIX ) 
if(UNIX OR CYGWIN)

    set(PATH_SEP "/")

    set(FILE_SEP ":")

    set( MISC_PREFIX "share/libsbml/" )

    set( MISC_PREFIX "${CMAKE_INSTALL_DATADIR}/libsbml/" )

    set(LIBSBML_LIBRARY sbml)

else()

    set( MISC_PREFIX "" )

    set( MISC_PREFIX "." )

    set(PATH_SEP "\\")

    set(FILE_SEP ";")

    if(MINGW)
@@ -1178,7 +1189,7 @@ set(DOCUMENTATION_FILES 
        VERSION.txt

)



install(FILES ${DOCUMENTATION_FILES} DESTINATION ${MISC_PREFIX}.)

install(FILES ${DOCUMENTATION_FILES} DESTINATION ${MISC_PREFIX})



###############################################################################

#
@@ -1202,19 +1213,14 @@ if (WITH_XERCES) 
set (PRIVATE_LIBS "${XERCES_LIBRARY} ${PRIVATE_LIBS}")

endif()



SET (PC_LIBDIR ${CMAKE_INSTALL_LIBDIR})

if ("${CMAKE_INSTALL_LIBDIR}" STREQUAL "lib")

SET (PC_LIBDIR ${CMAKE_INSTALL_PREFIX}/${CMAKE_INSTALL_LIBDIR})

endif()



file(WRITE  "${CMAKE_CURRENT_BINARY_DIR}/libsbml.pc" "Name: ${PACKAGE_NAME}\n")

file(APPEND "${CMAKE_CURRENT_BINARY_DIR}/libsbml.pc" "Description: A library for reading/writing/manipulating SBML\n")

file(APPEND "${CMAKE_CURRENT_BINARY_DIR}/libsbml.pc" "URL: http://sbml.org/Software/libSBML\n")

file(APPEND "${CMAKE_CURRENT_BINARY_DIR}/libsbml.pc" "Version: ${PACKAGE_VERSION}\n")

file(APPEND "${CMAKE_CURRENT_BINARY_DIR}/libsbml.pc" "\n")

file(APPEND "${CMAKE_CURRENT_BINARY_DIR}/libsbml.pc" "prefix=${CMAKE_INSTALL_PREFIX}\n")

file(APPEND "${CMAKE_CURRENT_BINARY_DIR}/libsbml.pc" "libdir=${PC_LIBDIR}\n")

file(APPEND "${CMAKE_CURRENT_BINARY_DIR}/libsbml.pc" "includedir=${CMAKE_INSTALL_PREFIX}/include\n")

file(APPEND "${CMAKE_CURRENT_BINARY_DIR}/libsbml.pc" "libdir=${CMAKE_INSTALL_FULL_LIBDIR}\n")

file(APPEND "${CMAKE_CURRENT_BINARY_DIR}/libsbml.pc" "includedir=${CMAKE_INSTALL_FULL_INCLUDEDIR}\n")

file(APPEND "${CMAKE_CURRENT_BINARY_DIR}/libsbml.pc" "\n")

file(APPEND "${CMAKE_CURRENT_BINARY_DIR}/libsbml.pc" "Libs: -L\${libdir} -lsbml\n")

file(APPEND "${CMAKE_CURRENT_BINARY_DIR}/libsbml.pc" "Libs.private:        ${PRIVATE_LIBS}\n")

Makefile.in

+1 −0
Original line number Diff line number Diff line
@@ -287,6 +287,7 @@ examples = \ 
  examples/python/printUnits.py                                     \

  examples/python/promoteParameters.py                              \

  examples/python/readSBML.py                                       \

  examples/python/renameSId.py                                      \

  examples/python/stringInput.py                                    \

  examples/python/setIdFromNames.py                                 \

  examples/python/translateMath.py                                  \

NEWS.txt

+101 −1
Original line number Diff line number Diff line 
           libSBML NEWS -- History of user-visible changes



====================================================================

5.17.0 (2018-05-09)

====================================================================



STABLE RELEASE



* Render



  - The first official version of the specification of the Render

    package is now available, and thus the 

    libSBML code for 'render' is now included in the stable release of 

    libSBML.  This means that all prebuilt binaries for the stable 

    release will include the 'render' package code. The src archive 

    containing libSBML core code will continue to be available, with

    additional src archives available in the stable branch: one

    containing libSBML core plus all stable packages and additional

    archives of the individual package code.

    

    NOTE: The libSBML GNU make-based build system has not been updated

          for packages. Thus, to build from src, it is necessary to

          use the CMake build system.





* New features



  - The libSBML-matlab interface function TranslateSBML has been

    optimized for speed.



  - The libSBML-matlab interface function OutputSBML can now be called

    with an output argument and no inputs to return information about 

    the libSBML version and enabled packages used to build the 

    binary files.



  - A new function getDefaultSBMLStruct has been added to the 

    libSBML-matlab interface. This function takes a string name of the

    element with level and version information and returns the relevant

    MATLAB-SBML structure for the element. Many thanks go to Thomas Pfau

    for supplying this function.



  - On occasion the functions 'getDerivedUnitDefinition' that return

    calculated units were reporting incorrect units without flagging

    any issues. This has been made less ambiguous and a derived 

    UnitDefinition will not contain any units if it cannot be correctly 

    determined.



  - Unit validation has been optimized and significantly speeded up for

    larger models. 

  

  - 'comp' package-specific updates:



    - The C API for comp has been completed.



  - 'fbc' package-specific updates:



    - SourceForge Tracker item #455: Error messages have been improved.

        

  - 'multi' package-specific updates:



    - The C API for multi has been completed.



  - 'qual' package-specific updates:



    - SourceForge Tracker item #455: Error messages have been improved.



  - 'render' package-specific updates:



    - A full C API for the render package has been added.



* Bug fixes



  - SourceForge Tracker item #459: An error in the function that

    converts libsbml-infix to matlab infix was failing when log

    functions were failing. This is fixed. Thanks to Sven Thiele

    for reporting the issue.



  - The validation check for duplicate values of the 'metaid'

    attribute was not being extended to all packages. This has

    been fixed. 



  - Python examples have been updated to work with Python v3.



  - 'qual' package-specific bug fixes:



    - SourceForge Tracker item #457: Validation of rule qual-20311

      was producing an error when it should have been a warning.

      Thanks to Justin McManus for reporting the problem.





EXPERIMENTAL RELEASE



* New features



  - 'distrib' package-specific updates:



    - The 'distrib' package has undergone significant changes.

      The code has been fully updated to match this. We have also 

      used a Distrib prefix on all classes to prevent clashes with

      other packages or even other libraries. We welcome feedback 

      on this approach.





====================================================================

5.16.0 (2017-12-07)

VERSION.txt

+1 −1
Original line number Diff line number Diff line 
5.16.0
 
5.17.0

VERSION_PACKAGES.ac

+9 −0
Original line number Diff line number Diff line
@@ -94,6 +94,15 @@ AC_SUBST(PACKAGE_LAYOUT_RELEASE, 1) 
AC_SUBST(PACKAGE_LAYOUT_SPEC_URL, [http://identifiers.org/combine.specifications/sbml.level-3.version-1.layout.version-1.release-1])

AC_SUBST(PACKAGE_LAYOUT_ERRATA_URL, [http://sbml.org/Documents/Specifications/SBML_Level_3/Packages/Layout_%28layout%29/Confirmed_issues_in_the_Layout_package_specification])



# -----------------------------------------------------------------------------

# 'render' package

# -----------------------------------------------------------------------------



AC_SUBST(PACKAGE_RENDER_VERSION, 1)

AC_SUBST(PACKAGE_RENDER_RELEASE, 1)

AC_SUBST(PACKAGE_RENDER_SPEC_URL, [http://identifiers.org/combine.specifications/sbml.level-3.version-1.render.version-1.release-1])

AC_SUBST(PACKAGE_RENDER_ERRATA_URL, [http://sbml.org/Documents/Specifications/SBML_Level_3/Packages/Render_%28render%29/Confirmed_issues_in_the_Render_package_specification])



# -----------------------------------------------------------------------------

# 'qual' package

# -----------------------------------------------------------------------------