Commit d383beb7 authored by Andreas Tille's avatar Andreas Tille
Browse files

New upstream version 5.17.2+dfsg

parent 2f658923

CMakeLists.txt

+13 −11
Original line number Diff line number Diff line
@@ -172,12 +172,6 @@ include(CPack) 
# Here we have the main configuration options for libsbml.

#



option(LIBSBML_USE_LEGACY_MATH

"Use libSBML's legacy math implementation of ASTs, instead of the one

introduced in libSBML 5.10 for better support of SBML Level 3 packages." OFF)

mark_as_advanced(LIBSBML_USE_LEGACY_MATH)





# Build static / shared library

# option(BUILD_SHARED_LIBS  "Build shared library. (Set to OFF to build static libraries.)" OFF)
@@ -331,6 +325,10 @@ if("${LIBSBML_DEPENDENCY_DIR}" STREQUAL "") 
(Particularly important on Windows.)" FORCE)

endif()



if (WITH_PYTHON)

    # add option to enable Python API2 (with warnings)

    option(PYTHON_USE_API2_WARNINGS   "Enable the new Python API2 with warnings."    OFF)

endif (WITH_PYTHON)



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

#
@@ -1048,6 +1046,10 @@ else(UNIX) 
                endif(${flag_var} MATCHES "/Zi")



            endforeach(flag_var)

        # add /bigobj to allow debug builds to work with swig and packages

        ADD_DEFINITIONS(/bigobj)

        SET(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} /bigobj")

        SET(CMAKE_CXX_FLAGS_RELWITHDEBINFO "${CMAKE_CXX_FLAGS_RELWITHDEBINFO} /bigobj")

    endif()



        file(GLOB WIN32_BINARIES ${LIBSBML_DEPENDENCY_DIR}/bin/*.dll)
@@ -1372,11 +1374,11 @@ else() 
endif()



message(STATUS "")

if(LIBSBML_USE_LEGACY_MATH)

  message(STATUS "     Use Legacy Math                 = yes")

else()

  message(STATUS "     Use Legacy Math                 = no")

endif()



if(PYTHON_USE_API2_WARNINGS)

  message(STATUS "")

  message(STATUS "     Using Python API2 warnings      = yes")

endif(PYTHON_USE_API2_WARNINGS)



if (LIBSBML_PACKAGE_SUMMARY)

  message(STATUS "")

LICENSE.html

+1 −1
Original line number Diff line number Diff line
@@ -9,7 +9,7 @@ The majority of libSBML is copyrighted as follows: 


<ul>



<li> Copyright &copy; 2013-2017 jointly by the following organizations:<br>

<li> Copyright &copy; 2013-2018 jointly by the following organizations:<br>

    1. California Institute of Technology, Pasadena, CA, USA<br>

    2. EMBL European Bioinformatics Institute (EBML-EBI), Hinxton, UK<br>

    3. University of Heidelberg, Heidelberg, Germany<br>

LICENSE.txt

+1 −1
Original line number Diff line number Diff line
@@ -2,7 +2,7 @@ 


The majority of libSBML is copyrighted as follows:



* 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

Makefile.in

+20 −0
Original line number Diff line number Diff line
@@ -297,6 +297,7 @@ examples = \ 
  examples/python/inlineInitialAssignments.py                       \

  examples/python/replaceOneFD.py                                   \

  examples/python/evaluateCustomMath.py                             \

  examples/python/inlineFunctionDefinitions.py                       \

  examples/php/createExampleSBML.php                                \

  examples/php/echoSBML.php                                         \

  examples/php/validateSBML.php                                     \
@@ -396,20 +397,26 @@ rbindings = \ 
  src/bindings/r/NAMESPACE                            \

  src/bindings/r/libsbml.i                            \

  src/bindings/r/local-downcast-extension-layout.cpp  \

  src/bindings/r/local-downcast-extension-l3v2extendedmath.cpp  \

  src/bindings/r/local-downcast-astplugins-l3v2extendedmath.cpp     \

  src/bindings/r/local-downcast-astplugins.cpp.in     \

  src/bindings/r/local-downcast-extension.cpp.in      \

  src/bindings/r/local-downcast-namespaces-layout.cpp \

  src/bindings/r/local-downcast-namespaces-l3v2extendedmath.cpp \

  src/bindings/r/local-downcast-namespaces.cpp.in     \

  src/bindings/r/local-downcast-packages-layout.cpp   \

  src/bindings/r/local-downcast-packages-l3v2extendedmath.cpp   \

  src/bindings/r/local-downcast-converters.cpp.in     \

  src/bindings/r/local-downcast-converters-layout.cpp \

  src/bindings/r/local-downcast-plugins-layout.cpp    \

  src/bindings/r/local-downcast-plugins-l3v2extendedmath.cpp    \

  src/bindings/r/local-downcast-plugins.cpp.in        \

  src/bindings/r/local-downcast.cpp.in                \

  src/bindings/r/create-r-package.cmake               \

  src/bindings/r/cmake-r-install.cmake.in             \

  src/bindings/r/libsbml_rtype.swg                    \

  src/bindings/r/local-layout.i                       \

  src/bindings/r/local-l3v2extendedmath.i                       \

  src/bindings/r/local-packages.i.in                  \

  src/bindings/r/local.cpp                            \

  src/bindings/r/local.i                              \
@@ -424,19 +431,25 @@ jsbindings = \ 
  src/bindings/javascript/compile-native-files.cmake           \

  src/bindings/javascript/libsbml.i                            \

  src/bindings/javascript/local.cpp                            \

  src/bindings/javascript/local-downcast-astplugins-l3v2extendedmath.cpp     \

  src/bindings/javascript/local-downcast-astplugins.cpp.in     \

  src/bindings/javascript/local-downcast-converters.cpp.in     \

  src/bindings/javascript/local-downcast-converters-layout.cpp \

  src/bindings/javascript/local-downcast.cpp.in                \

  src/bindings/javascript/local-downcast-extension.cpp.in      \

  src/bindings/javascript/local-downcast-extension-layout.cpp  \

  src/bindings/javascript/local-downcast-extension-l3v2extendedmath.cpp  \

  src/bindings/javascript/local-downcast-namespaces.cpp.in     \

  src/bindings/javascript/local-downcast-namespaces-layout.cpp \

  src/bindings/javascript/local-downcast-namespaces-l3v2extendedmath.cpp \

  src/bindings/javascript/local-downcast-packages-layout.cpp   \

  src/bindings/javascript/local-downcast-packages-l3v2extendedmath.cpp   \

  src/bindings/javascript/local-downcast-plugins.cpp.in        \

  src/bindings/javascript/local-downcast-plugins-layout.cpp    \

  src/bindings/javascript/local-downcast-plugins-l3v2extendedmath.cpp    \

  src/bindings/javascript/local.i                              \

  src/bindings/javascript/local-layout.i                       \

  src/bindings/javascript/local-l3v2extendedmath.i                       \

  src/bindings/javascript/local-packages.i.in                  \
@@ -448,16 +461,22 @@ phpbindings = \ 
  src/bindings/php/libsbml.i                                   \

  src/bindings/php/local-downcast-converters-layout.cpp        \

  src/bindings/php/local-downcast-astplugins.cpp.in            \

  src/bindings/php/local-downcast-astplugins-l3v2extendedmath.cpp            \

  src/bindings/php/local-downcast-converters.cpp.in            \

  src/bindings/php/local-downcast-extension-layout.cpp         \

  src/bindings/php/local-downcast-extension-l3v2extendedmath.cpp         \

  src/bindings/php/local-downcast-extension.cpp.in             \

  src/bindings/php/local-downcast-namespaces-layout.cpp        \

  src/bindings/php/local-downcast-namespaces-l3v2extendedmath.cpp        \

  src/bindings/php/local-downcast-namespaces.cpp.in            \

  src/bindings/php/local-downcast-packages-layout.cpp          \

  src/bindings/php/local-downcast-packages-l3v2extendedmath.cpp          \

  src/bindings/php/local-downcast-plugins-layout.cpp           \

  src/bindings/php/local-downcast-plugins-l3v2extendedmath.cpp           \

  src/bindings/php/local-downcast-plugins.cpp.in               \

  src/bindings/php/local-downcast.cpp.in                       \

  src/bindings/php/local-layout.i                              \

  src/bindings/php/local-l3v2extendedmath.i                              \

  src/bindings/php/local-packages.i.in                         \

  src/bindings/php/local.cpp                                   \

  src/bindings/php/local.i                                     \
@@ -547,6 +566,7 @@ distfiles = \ 
  CMakeLists.txt                    \

  common.cmake                      \

  layout-package.cmake              \

  l3v2extendedmath-package.cmake    \

  $(examples)                       \

  $(jsbindings)                     \

  $(rbindings)                      \

NEWS.txt

+150 −28
Original line number Diff line number Diff line 
           libSBML NEWS -- History of user-visible changes

           libSBML NEWS -- History of user-visible changes



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

5.17.0 (2018-05-09)

5.17.2-experimental (2018-12-06)

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



***                 Experimental only release                    ***



This is an experimental only release, that is, a release of those

files provided in the experimental folder of a full release. 



This includes updates to all the SBML L3 packages that are not yet

accepted and undergoing development.



NOTE: An experimental release is not as rigorously tested as a 

full release.  Any changes/fixes listed as either referring to

stable or experimental code may change before the next full release.





STABLE RELEASE



* Render

* New features



  - 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.

  - The math code has been refactored to use the more efficient 

    math-legacy code in combination with a math plugin system. 

    This code has been optimized and we welcome feedback on any 

    performance issues.  This means there is no longer a math-legacy 

    build option.



  - The new math constructs introduced in SBML L3V2 have been refactored 

    as a math extension; which facilitates the use of these math functions

    in an SBML L3V1 document.



  

  - 'comp' package-specific updates:



    - The 'comp' specification states that an external model must be

      an L3V1 document. Since this specification predates SBML L3V2

      we have relaxed the restriction to allow an L3V2 model using 

      Model Composition to use an L3V2 external model.



    - The converter that 'flattens' a comp model has been optimized

      for speed with significant improvement for larger models.



  - Python interface specific updates:



    - In libSBML the set/add/unset methods return a code to indicate

      success or failure of the operation. The Python interface has

      been improved to produce a warning when a function fails. This 

      behaviour can be enabled by setting a CMAKE configure option

      or an environment variable.



    - Sourceforge Tracker item #456: The Python interface has

      been changed to return an empty List of CVTerms rather

      than a None object.



    - Users have raised issued about Model objects retrieved from within an

      SBMLDocument object going out of scope when the document object

      is removed from scope. We have adjusted the code to allow a Model

      to remain in scope without it's parent document. Feedback would

      be apprceiated about whether this is sufficient or whether all child

      objects should be available regardless of whether their parent is

      still available. 



    - Sourceforge Tracker item #468:  Functions deprecated in Python 3.6

      have been replaced to avoid deprecation warning messages. 

    



* Bug fixes



  - The function SBMLTypeCode_toString was not retuning the correct 

    string for a ListOf element originating in a package. This

    has been corrected.



  - Using an SBML L3 package in an L2 document could cause a crash.

    This has been fixed. Thanks to Thomas Hamm for reporting it.



  - The code that checked for use of an L3V2 package with an L3V1

    document could cause a crash. This has been fixed. 



  - Writing out a document without a model and no level and version

    was using level = version = 0; which is not valid. This has been

    changed to write a L3V2 document with no model.



  - There was an issue with newer architectures when casting a

    NaN to an integer - this has been now been avoided.



  - MATLAB interface specific bug fixes:



    - The matlab binding was failing to distinguish between a

      functionDefinition where the id ended with a logical operator,

      e.g. 'myor' and the actual logical function. This has been corrected.





  - 'comp' package-specific bug fixes:



    - There was an issue with flattening 'comp' models using conversion 

      factors. This has been tracked down and fixed. Thanks to Matthias 

      Konig for reporting it and providing examples.



  - 'render' package-specific bug fixes:



    - Historical render code did not create a NULL BoundingBox. 

      Current code has been brought in line with this.



* Configuration/build system changes



  - Python 3.7 is now supported and included in the builds.



  - The USE_LEGACY_MATH option has been removed as code has been

    reverted to use this math implementation (see above).





EXPERIMENTAL RELEASE



* New features



  - 'distrib' package-specific updates:



    - The distrib package code has been updated to include the use

      of csymbols to reference distributions. This is in line with 

      the latest distrib specification.





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

5.17.0 (2018-05-21)

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



STABLE RELEASE



* Addition of support for the SBML Render package



  - Now that the first official version of the specification for the

    SBML Level 3 Rendering package is available, the libSBML API 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
@@ -25,25 +147,25 @@ STABLE RELEASE 


* New features



  - The libSBML-matlab interface function TranslateSBML has been

  - The MATLAB language 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 

  - The MATLAB interface function OutputSBML can now be called with an

    output argument and no inputs; doing so will 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.

  - A new function getDefaultSBMLStruct has been added to the 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.

  - On occasion, the function getDerivedUnitDefinition that returns

    calculated units would report 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.
@@ -71,8 +193,8 @@ STABLE RELEASE 
* 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

    converts libSBML infix notation to MATLAB infix notation failed

    when log functions failed. This is fixed. Thanks to Sven Thiele

    for reporting the issue.



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