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CMakeLists.txt
View file @ a547decd
......@@ -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
View file @ a547decd
......@@ -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
View file @ a547decd
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_PACKAGES.ac
View file @ a547decd
......@@ -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
# -----------------------------------------------------------------------------
......
config/bzip2.m4
View file @ a547decd
......@@ -9,7 +9,7 @@ dnl <!-------------------------------------------------------------------------
dnl This file is part of libSBML. Please visit http://sbml.org for more
dnl information about SBML, and the latest version of libSBML.
dnl
dnl Copyright (C) 2013-2017 jointly by the following organizations:
dnl Copyright (C) 2013-2018 jointly by the following organizations:
dnl 1. California Institute of Technology, Pasadena, CA, USA
dnl 2. EMBL European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
dnl 3. University of Heidelberg, Heidelberg, Germany
......
config/chk_swig_version.sh.in
View file @ a547decd
......@@ -7,7 +7,7 @@
# This file is part of libSBML. Please visit http://sbml.org for more
# information about SBML, and the latest version of libSBML.
#
# Copyright (C) 2013-2017 jointly by the following organizations:
# Copyright (C) 2013-2018 jointly by the following organizations:
# 1. California Institute of Technology, Pasadena, CA, USA
# 2. EMBL European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
# 3. University of Heidelberg, Heidelberg, Germany
......
config/csharp.m4
View file @ a547decd
......@@ -9,7 +9,7 @@ dnl <!-------------------------------------------------------------------------
dnl This file is part of libSBML. Please visit http://sbml.org for more
dnl information about SBML, and the latest version of libSBML.
dnl
dnl Copyright (C) 2013-2017 jointly by the following organizations:
dnl Copyright (C) 2013-2018 jointly by the following organizations:
dnl 1. California Institute of Technology, Pasadena, CA, USA
dnl 2. EMBL European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
dnl 3. University of Heidelberg, Heidelberg, Germany
......
config/doxygen.m4
View file @ a547decd
......@@ -7,7 +7,7 @@ dnl ---------------------------------------------------------------------------
dnl This file is part of libSBML. Please visit http://sbml.org for more
dnl information about SBML, and the latest version of libSBML.
dnl
dnl Copyright (C) 2013-2017 jointly by the following organizations:
dnl Copyright (C) 2013-2018 jointly by the following organizations:
dnl 1. California Institute of Technology, Pasadena, CA, USA
dnl 2. EMBL European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
dnl 3. University of Heidelberg, Heidelberg, Germany
......
config/expat.m4
View file @ a547decd
......@@ -9,7 +9,7 @@ dnl ---------------------------------------------------------------------------
dnl This file is part of libSBML. Please visit http://sbml.org for more
dnl information about SBML, and the latest version of libSBML.
dnl
dnl Copyright (C) 2013-2017 jointly by the following organizations:
dnl Copyright (C) 2013-2018 jointly by the following organizations:
dnl 1. California Institute of Technology, Pasadena, CA, USA
dnl 2. EMBL European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
dnl 3. University of Heidelberg, Heidelberg, Germany
......
config/java.m4
View file @ a547decd
......@@ -9,7 +9,7 @@ dnl <!-------------------------------------------------------------------------
dnl This file is part of libSBML. Please visit http://sbml.org for more
dnl information about SBML, and the latest version of libSBML.
dnl
dnl Copyright (C) 2013-2017 jointly by the following organizations:
dnl Copyright (C) 2013-2018 jointly by the following organizations:
dnl 1. California Institute of Technology, Pasadena, CA, USA
dnl 2. EMBL European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
dnl 3. University of Heidelberg, Heidelberg, Germany
......
config/libcheck.m4
View file @ a547decd
......@@ -6,7 +6,7 @@ dnl ---------------------------------------------------------------------------
dnl This file is part of libSBML. Please visit http://sbml.org for more
dnl information about SBML, and the latest version of libSBML.
dnl
dnl Copyright (C) 2013-2017 jointly by the following organizations:
dnl Copyright (C) 2013-2018 jointly by the following organizations:
dnl 1. California Institute of Technology, Pasadena, CA, USA
dnl 2. EMBL European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
dnl 3. University of Heidelberg, Heidelberg, Germany
......
config/machine.m4
View file @ a547decd
......@@ -6,7 +6,7 @@ dnl ---------------------------------------------------------------------------
dnl This file is part of libSBML. Please visit http://sbml.org for more
dnl information about SBML, and the latest version of libSBML.
dnl
dnl Copyright (C) 2013-2017 jointly by the following organizations:
dnl Copyright (C) 2013-2018 jointly by the following organizations:
dnl 1. California Institute of Technology, Pasadena, CA, USA
dnl 2. EMBL European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
dnl 3. University of Heidelberg, Heidelberg, Germany
......
config/makefile-common-actions.mk
View file @ a547decd
......@@ -8,7 +8,7 @@
## This file is part of libSBML. Please visit http://sbml.org for more
## information about SBML, and the latest version of libSBML.
##
## Copyright (C) 2013-2017 jointly by the following organizations:
## Copyright (C) 2013-2018 jointly by the following organizations:
## 1. California Institute of Technology, Pasadena, CA, USA
## 2. EMBL European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
## 3. University of Heidelberg, Heidelberg, Germany
......
config/makefile-common-vars.mk.in
View file @ a547decd
......@@ -10,7 +10,7 @@
## This file is part of libSBML. Please visit http://sbml.org for more
## information about SBML, and the latest version of libSBML.
##
## Copyright (C) 2013-2017 jointly by the following organizations:
## Copyright (C) 2013-2018 jointly by the following organizations:
## 1. California Institute of Technology, Pasadena, CA, USA
## 2. EMBL European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
## 3. University of Heidelberg, Heidelberg, Germany
......@@ -175,6 +175,7 @@ USE_LAYOUT = @USE_LAYOUT@
USE_QUAL = @USE_QUAL@
USE_GROUPS = @USE_GROUPS@
USE_MULTI = @USE_MULTI@
USE_RENDER = @USE_RENDER@
USE_SWIG = @USE_SWIG@
SWIG = @SWIG@
......
config/matlab.m4
View file @ a547decd
......@@ -8,7 +8,7 @@ dnl <!-------------------------------------------------------------------------
dnl This file is part of libSBML. Please visit http://sbml.org for more
dnl information about SBML, and the latest version of libSBML.
dnl
dnl Copyright (C) 2013-2017 jointly by the following organizations:
dnl Copyright (C) 2013-2018 jointly by the following organizations:
dnl 1. California Institute of Technology, Pasadena, CA, USA
dnl 2. EMBL European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
dnl 3. University of Heidelberg, Heidelberg, Germany
......
config/octave.m4
View file @ a547decd
......@@ -8,7 +8,7 @@ dnl <!-------------------------------------------------------------------------
dnl This file is part of libSBML. Please visit http://sbml.org for more
dnl information about SBML, and the latest version of libSBML.
dnl
dnl Copyright (C) 2013-2017 jointly by the following organizations:
dnl Copyright (C) 2013-2018 jointly by the following organizations:
dnl 1. California Institute of Technology, Pasadena, CA, USA
dnl 2. EMBL European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
dnl 3. University of Heidelberg, Heidelberg, Germany
......
config/perl.m4
View file @ a547decd
......@@ -9,7 +9,7 @@ dnl <!-------------------------------------------------------------------------
dnl This file is part of libSBML. Please visit http://sbml.org for more
dnl information about SBML, and the latest version of libSBML.
dnl
dnl Copyright (C) 2013-2017 jointly by the following organizations:
dnl Copyright (C) 2013-2018 jointly by the following organizations:
dnl 1. California Institute of Technology, Pasadena, CA, USA
dnl 2. EMBL European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
dnl 3. University of Heidelberg, Heidelberg, Germany
......
config/platform.m4
View file @ a547decd
......@@ -6,7 +6,7 @@ dnl ---------------------------------------------------------------------------
dnl This file is part of libSBML. Please visit http://sbml.org for more
dnl information about SBML, and the latest version of libSBML.
dnl
dnl Copyright (C) 2013-2017 jointly by the following organizations:
dnl Copyright (C) 2013-2018 jointly by the following organizations:
dnl 1. California Institute of Technology, Pasadena, CA, USA
dnl 2. EMBL European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
dnl 3. University of Heidelberg, Heidelberg, Germany
......
config/printJavaDataModel.java
View file @ a547decd
......@@ -7,7 +7,7 @@
* This file is part of libSBML. Please visit http://sbml.org for more
* information about SBML, and the latest version of libSBML.
*
* Copyright (C) 2013-2017 jointly by the following organizations:
* Copyright (C) 2013-2018 jointly by the following organizations:
* 1. California Institute of Technology, Pasadena, CA, USA
* 2. EMBL European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
* 3. University of Heidelberg, Heidelberg, Germany
......