Andreas Tille · Andreas Tille · Andreas Tille · Andreas Tille · Andreas Tille · Andreas Tille
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -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 "")

--- a/LICENSE.html
+++ b/LICENSE.html
@@ -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>

--- a/LICENSE.txt
+++ b/LICENSE.txt
@@ -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

--- a/Makefile.in
+++ b/Makefile.in
@@ -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)                      \

--- a/NEWS.txt
+++ b/NEWS.txt
-           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'

--- a/README.txt
+++ b/README.txt
@@ -322,7 +322,7 @@ software included in and used by the libSBML distribution.

 The majority of the libSBML source code 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

--- a/VERSION.txt
+++ b/VERSION.txt
-5.17.0
+5.17.2
--- a/config/makefile-common-vars.mk.in
+++ b/config/makefile-common-vars.mk.in
@@ -176,6 +176,7 @@ USE_QUAL          = @USE_QUAL@
 USE_GROUPS        = @USE_GROUPS@
 USE_MULTI         = @USE_MULTI@
 USE_RENDER        = @USE_RENDER@
+USE_L3V2EXTENDEDMATH        = @USE_L3V2EXTENDEDMATH@

 USE_SWIG          = @USE_SWIG@
 SWIG              = @SWIG@
@@ -258,7 +259,6 @@ LIBSBML_VERSION   = @PACKAGE_VERSION@
 LIBSBML_VERSION_NUMERIC = @LIBSBML_VERSION_NUMERIC@

 LIBSBML_SHARED_VERSION = @LIBSBML_SHARED_VERSION@
-LIBSBML_USE_LEGACY_MATH = @LIBSBML_USE_LEGACY_MATH@
 LIBSBML_USE_STRICT_INCLUDES = @LIBSBML_USE_STRICT_INCLUDES@

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

--- a/configure
+++ b/configure
 #! /bin/sh
-# From configure.ac Revision: 25196 .
+# From configure.ac Revision: 25690 .
 # Guess values for system-dependent variables and create Makefiles.
-# Generated by GNU Autoconf 2.69 for libSBML 5.17.0.
+# Generated by GNU Autoconf 2.69 for libSBML 5.17.2.
 #
 # Report bugs to <libsbml-team@googlegroups.com>.
 #
@@ -735,8 +735,8 @@ MAKEFLAGS=
 # Identity of this package.
 PACKAGE_NAME='libSBML'
 PACKAGE_TARNAME='libsbml'
-PACKAGE_VERSION='5.17.0'
-PACKAGE_STRING='libSBML 5.17.0'
+PACKAGE_VERSION='5.17.2'
+PACKAGE_STRING='libSBML 5.17.2'
 PACKAGE_BUGREPORT='libsbml-team@googlegroups.com'
 PACKAGE_URL='http://sbml.org/Software/libSBML'
  
@@ -921,7 +921,6 @@ build_vendor
 build_cpu
 build
 LIBSBML_USE_STRICT_INCLUDES
-LIBSBML_USE_LEGACY_MATH
 LIBSBML_SHARED_VERSION
 USE_COMPRESSION
 PACKAGE_QUAL_ERRATA_URL
@@ -956,6 +955,8 @@ PACKAGE_COMP_ERRATA_URL
 PACKAGE_COMP_SPEC_URL
 PACKAGE_COMP_RELEASE
 PACKAGE_COMP_VERSION
+LIBSBML_HAS_PACKAGE_L3V2EXTENDEDMATH
+USE_L3V2EXTENDEDMATH
 LIBSBML_HAS_PACKAGE_MULTI
 USE_MULTI
 LIBSBML_HAS_PACKAGE_GROUPS
@@ -1024,9 +1025,9 @@ enable_fbc
 enable_qual
 enable_groups
 enable_multi
+enable_l3v2extendedmath
 enable_compression
 enable_shared_version
-enable_legacy_math
 enable_strict_includes
 enable_m32
 enable_m64
@@ -1617,7 +1618,7 @@ if test "$ac_init_help" = "long"; then
  # Omit some internal or obsolete options to make the list less imposing.
  # This message is too long to be a string in the A/UX 3.1 sh.
  cat <<_ACEOF
-\`configure' configures libSBML 5.17.0 to adapt to many kinds of systems.
+\`configure' configures libSBML 5.17.2 to adapt to many kinds of systems.
  
 Usage: $0 [OPTION]... [VAR=VALUE]...
  
@@ -1682,7 +1683,7 @@ fi
  
 if test -n "$ac_init_help"; then
  case $ac_init_help in
-     short | recursive ) echo "Configuration of libSBML 5.17.0:";;
+     short | recursive ) echo "Configuration of libSBML 5.17.2:";;
   esac
  cat <<\_ACEOF
  
@@ -1699,13 +1700,14 @@ Optional Features:
  --enable-qual[=ARG]     build support for SBML 'qual' [default=no]
  --enable-groups[=ARG]   build support for SBML 'groups' [default=no]
  --enable-multi[=ARG]    build support for SBML 'multi' [default=no]
+  --enable-l3v2extendedmath[=ARG]
+                          build support for SBML 'l3v2extendedmath'
+                          [default=no]
  --enable-compression[=ARG]
                          enable file compression if possible [default=yes]
  --enable-shared-version[=ARG]
                          include version number into shared library
                          [default=yes]
-  --enable-legacy-math[=ARG]
-                          use legacy AST math implementation [default=no]
  --enable-strict-includes[=ARG]
                          use strict .h inclusion rules [default=no]
  --enable-m32            build 32-bit binaries [default=autodetect]
@@ -1837,7 +1839,7 @@ fi
 test -n "$ac_init_help" && exit $ac_status
 if $ac_init_version; then
  cat <<\_ACEOF
-libSBML configure 5.17.0
+libSBML configure 5.17.2
 generated by GNU Autoconf 2.69
  
 Copyright (C) 2012 Free Software Foundation, Inc.
@@ -2556,7 +2558,7 @@ cat >config.log <<_ACEOF
 This file contains any messages produced by compilers while
 running configure, to aid debugging if configure makes a mistake.
  
-It was created by libSBML $as_me 5.17.0, which was
+It was created by libSBML $as_me 5.17.2, which was
 generated by GNU Autoconf 2.69.  Invocation command line was
  
  $ $0 $@
@@ -2946,7 +2948,7 @@ ac_config_headers="$ac_config_headers src/sbml/common/libsbml-package.h"
 ac_config_headers="$ac_config_headers src/sbml/common/libsbml-namespace.h"
  
  
-LIBSBML_VERSION_NUMERIC=51700
+LIBSBML_VERSION_NUMERIC=51702
  
  
  
@@ -2958,7 +2960,7 @@ LIBSBML_MINOR_VERSION=17
  
  
  
-LIBSBML_REVISION_VERSION=0
+LIBSBML_REVISION_VERSION=2
  
  
  
@@ -3133,6 +3135,27 @@ $as_echo "#define LIBSBML_HAS_PACKAGE_MULTI 1" >>confdefs.h
  
 fi
  
+# Check whether --enable-l3v2extendedmath was given.
+if test "${enable_l3v2extendedmath+set}" = set; then :
+  enableval=$enable_l3v2extendedmath; enable_l3v2extendedmath=$enableval
+else
+  enable_l3v2extendedmath=no
+fi
+
+
+if test "$enable_l3v2extendedmath" != no; then
+
+$as_echo "#define USE_L3V2EXTENDEDMATH 1" >>confdefs.h
+
+
+$as_echo "#define LIBSBML_HAS_PACKAGE_L3V2EXTENDEDMATH 1" >>confdefs.h
+
+  USE_L3V2EXTENDEDMATH=1
+
+  LIBSBML_HAS_PACKAGE_L3V2EXTENDEDMATH=1
+
+fi
+
  
  
  
@@ -3281,23 +3304,6 @@ $as_echo "#define LIBSBML_SHARED_VERSION 1" >>confdefs.h
 fi
  
  
-# Check whether --enable-legacy-math was given.
-if test "${enable_legacy_math+set}" = set; then :
-  enableval=$enable_legacy_math; enable_use_legacy_math=$enableval
-else
-  enable_use_legacy_math=no
-fi
-
-
-if test "$enable_use_legacy_math" != no; then
-
-$as_echo "#define LIBSBML_USE_LEGACY_MATH 1" >>confdefs.h
-
-  LIBSBML_USE_LEGACY_MATH=1
-
-fi
-
-
 # Check whether --enable-strict-includes was given.
 if test "${enable_strict_includes+set}" = set; then :
  enableval=$enable_strict_includes; enable_use_strict_includes=$enableval
@@ -10055,7 +10061,7 @@ ia64-*-hpux*)
  ;;
 *-*-irix6*)
  # Find out which ABI we are using.
-  echo '#line 10058 "configure"' > conftest.$ac_ext
+  echo '#line 10064 "configure"' > conftest.$ac_ext
  if { { eval echo "\"\$as_me\":${as_lineno-$LINENO}: \"$ac_compile\""; } >&5
  (eval $ac_compile) 2>&5
  ac_status=$?
@@ -12273,11 +12279,11 @@ else
   -e 's:.*FLAGS}\{0,1\} :&$lt_compiler_flag :; t' \
   -e 's: [^ ]*conftest\.: $lt_compiler_flag&:; t' \
   -e 's:$: $lt_compiler_flag:'`
-   (eval echo "\"\$as_me:12276: $lt_compile\"" >&5)
+   (eval echo "\"\$as_me:12282: $lt_compile\"" >&5)
   (eval "$lt_compile" 2>conftest.err)
   ac_status=$?
   cat conftest.err >&5
-   echo "$as_me:12280: \$? = $ac_status" >&5
+   echo "$as_me:12286: \$? = $ac_status" >&5
   if (exit $ac_status) && test -s "$ac_outfile"; then
     # The compiler can only warn and ignore the option if not recognized
     # So say no if there are warnings other than the usual output.
@@ -12563,11 +12569,11 @@ else
   -e 's:.*FLAGS}\{0,1\} :&$lt_compiler_flag :; t' \
   -e 's: [^ ]*conftest\.: $lt_compiler_flag&:; t' \
   -e 's:$: $lt_compiler_flag:'`
-   (eval echo "\"\$as_me:12566: $lt_compile\"" >&5)
+   (eval echo "\"\$as_me:12572: $lt_compile\"" >&5)
   (eval "$lt_compile" 2>conftest.err)
   ac_status=$?
   cat conftest.err >&5
-   echo "$as_me:12570: \$? = $ac_status" >&5
+   echo "$as_me:12576: \$? = $ac_status" >&5
   if (exit $ac_status) && test -s "$ac_outfile"; then
     # The compiler can only warn and ignore the option if not recognized
     # So say no if there are warnings other than the usual output.
@@ -12667,11 +12673,11 @@ else
   -e 's:.*FLAGS}\{0,1\} :&$lt_compiler_flag :; t' \
   -e 's: [^ ]*conftest\.: $lt_compiler_flag&:; t' \
   -e 's:$: $lt_compiler_flag:'`
-   (eval echo "\"\$as_me:12670: $lt_compile\"" >&5)
+   (eval echo "\"\$as_me:12676: $lt_compile\"" >&5)
   (eval "$lt_compile" 2>out/conftest.err)
   ac_status=$?
   cat out/conftest.err >&5
-   echo "$as_me:12674: \$? = $ac_status" >&5
+   echo "$as_me:12680: \$? = $ac_status" >&5
   if (exit $ac_status) && test -s out/conftest2.$ac_objext
   then
     # The compiler can only warn and ignore the option if not recognized
@@ -14692,7 +14698,7 @@ else
  lt_dlunknown=0; lt_dlno_uscore=1; lt_dlneed_uscore=2
  lt_status=$lt_dlunknown
  cat > conftest.$ac_ext <<EOF
-#line 14695 "configure"
+#line 14701 "configure"
 #include "confdefs.h"
  
 #if HAVE_DLFCN_H
@@ -14792,7 +14798,7 @@ else
  lt_dlunknown=0; lt_dlno_uscore=1; lt_dlneed_uscore=2
  lt_status=$lt_dlunknown
  cat > conftest.$ac_ext <<EOF
-#line 14795 "configure"
+#line 14801 "configure"
 #include "confdefs.h"
  
 #if HAVE_DLFCN_H
@@ -17137,11 +17143,11 @@ else
   -e 's:.*FLAGS}\{0,1\} :&$lt_compiler_flag :; t' \
   -e 's: [^ ]*conftest\.: $lt_compiler_flag&:; t' \
   -e 's:$: $lt_compiler_flag:'`
-   (eval echo "\"\$as_me:17140: $lt_compile\"" >&5)
+   (eval echo "\"\$as_me:17146: $lt_compile\"" >&5)
   (eval "$lt_compile" 2>conftest.err)
   ac_status=$?
   cat conftest.err >&5
-   echo "$as_me:17144: \$? = $ac_status" >&5
+   echo "$as_me:17150: \$? = $ac_status" >&5
   if (exit $ac_status) && test -s "$ac_outfile"; then
     # The compiler can only warn and ignore the option if not recognized
     # So say no if there are warnings other than the usual output.
@@ -17241,11 +17247,11 @@ else
   -e 's:.*FLAGS}\{0,1\} :&$lt_compiler_flag :; t' \
   -e 's: [^ ]*conftest\.: $lt_compiler_flag&:; t' \
   -e 's:$: $lt_compiler_flag:'`
-   (eval echo "\"\$as_me:17244: $lt_compile\"" >&5)
+   (eval echo "\"\$as_me:17250: $lt_compile\"" >&5)
   (eval "$lt_compile" 2>out/conftest.err)
   ac_status=$?
   cat out/conftest.err >&5
-   echo "$as_me:17248: \$? = $ac_status" >&5
+   echo "$as_me:17254: \$? = $ac_status" >&5
   if (exit $ac_status) && test -s out/conftest2.$ac_objext
   then
     # The compiler can only warn and ignore the option if not recognized
@@ -18824,11 +18830,11 @@ else
   -e 's:.*FLAGS}\{0,1\} :&$lt_compiler_flag :; t' \
   -e 's: [^ ]*conftest\.: $lt_compiler_flag&:; t' \
   -e 's:$: $lt_compiler_flag:'`
-   (eval echo "\"\$as_me:18827: $lt_compile\"" >&5)
+   (eval echo "\"\$as_me:18833: $lt_compile\"" >&5)
   (eval "$lt_compile" 2>conftest.err)
   ac_status=$?
   cat conftest.err >&5
-   echo "$as_me:18831: \$? = $ac_status" >&5
+   echo "$as_me:18837: \$? = $ac_status" >&5
   if (exit $ac_status) && test -s "$ac_outfile"; then
     # The compiler can only warn and ignore the option if not recognized
     # So say no if there are warnings other than the usual output.
@@ -18928,11 +18934,11 @@ else
   -e 's:.*FLAGS}\{0,1\} :&$lt_compiler_flag :; t' \
   -e 's: [^ ]*conftest\.: $lt_compiler_flag&:; t' \
   -e 's:$: $lt_compiler_flag:'`
-   (eval echo "\"\$as_me:18931: $lt_compile\"" >&5)
+   (eval echo "\"\$as_me:18937: $lt_compile\"" >&5)
   (eval "$lt_compile" 2>out/conftest.err)
   ac_status=$?
   cat out/conftest.err >&5
-   echo "$as_me:18935: \$? = $ac_status" >&5
+   echo "$as_me:18941: \$? = $ac_status" >&5
   if (exit $ac_status) && test -s out/conftest2.$ac_objext
   then
     # The compiler can only warn and ignore the option if not recognized
@@ -21098,11 +21104,11 @@ else
   -e 's:.*FLAGS}\{0,1\} :&$lt_compiler_flag :; t' \
   -e 's: [^ ]*conftest\.: $lt_compiler_flag&:; t' \
   -e 's:$: $lt_compiler_flag:'`
-   (eval echo "\"\$as_me:21101: $lt_compile\"" >&5)
+   (eval echo "\"\$as_me:21107: $lt_compile\"" >&5)
   (eval "$lt_compile" 2>conftest.err)
   ac_status=$?
   cat conftest.err >&5
-   echo "$as_me:21105: \$? = $ac_status" >&5
+   echo "$as_me:21111: \$? = $ac_status" >&5
   if (exit $ac_status) && test -s "$ac_outfile"; then
     # The compiler can only warn and ignore the option if not recognized
     # So say no if there are warnings other than the usual output.
@@ -21388,11 +21394,11 @@ else
   -e 's:.*FLAGS}\{0,1\} :&$lt_compiler_flag :; t' \
   -e 's: [^ ]*conftest\.: $lt_compiler_flag&:; t' \
   -e 's:$: $lt_compiler_flag:'`
-   (eval echo "\"\$as_me:21391: $lt_compile\"" >&5)
+   (eval echo "\"\$as_me:21397: $lt_compile\"" >&5)
   (eval "$lt_compile" 2>conftest.err)
   ac_status=$?
   cat conftest.err >&5
-   echo "$as_me:21395: \$? = $ac_status" >&5
+   echo "$as_me:21401: \$? = $ac_status" >&5
   if (exit $ac_status) && test -s "$ac_outfile"; then
     # The compiler can only warn and ignore the option if not recognized
     # So say no if there are warnings other than the usual output.
@@ -21492,11 +21498,11 @@ else
   -e 's:.*FLAGS}\{0,1\} :&$lt_compiler_flag :; t' \
   -e 's: [^ ]*conftest\.: $lt_compiler_flag&:; t' \
   -e 's:$: $lt_compiler_flag:'`
-   (eval echo "\"\$as_me:21495: $lt_compile\"" >&5)
+   (eval echo "\"\$as_me:21501: $lt_compile\"" >&5)
   (eval "$lt_compile" 2>out/conftest.err)
   ac_status=$?
   cat out/conftest.err >&5
-   echo "$as_me:21499: \$? = $ac_status" >&5
+   echo "$as_me:21505: \$? = $ac_status" >&5
   if (exit $ac_status) && test -s out/conftest2.$ac_objext
   then
     # The compiler can only warn and ignore the option if not recognized
@@ -26751,11 +26757,6 @@ ac_config_files="$ac_config_files src/sbml/math/Makefile"
 ac_config_files="$ac_config_files src/sbml/math/test/Makefile"
  
  
-ac_config_files="$ac_config_files src/sbml/math-legacy/Makefile"
-
-ac_config_files="$ac_config_files src/sbml/math-legacy/test/Makefile"
-
-
 ac_config_files="$ac_config_files src/sbml/units/Makefile"
  
 ac_config_files="$ac_config_files src/sbml/units/test/Makefile"
@@ -26888,6 +26889,23 @@ ac_config_files="$ac_config_files src/sbml/packages/layout/validator/test/Makefi
 ac_config_files="$ac_config_files src/sbml/packages/layout/validator/test/test-data/Makefile"
  
  
+ac_config_files="$ac_config_files src/sbml/packages/l3v2extendedmath/Makefile"
+
+ac_config_files="$ac_config_files src/sbml/packages/l3v2extendedmath/common/Makefile"
+
+ac_config_files="$ac_config_files src/sbml/packages/l3v2extendedmath/extension/Makefile"
+
+ac_config_files="$ac_config_files src/sbml/packages/l3v2extendedmath/extension/test/Makefile"
+
+ac_config_files="$ac_config_files src/sbml/packages/l3v2extendedmath/validator/Makefile"
+
+ac_config_files="$ac_config_files src/sbml/packages/l3v2extendedmath/validator/constraints/Makefile"
+
+ac_config_files="$ac_config_files src/sbml/packages/l3v2extendedmath/validator/test/Makefile"
+
+ac_config_files="$ac_config_files src/sbml/packages/l3v2extendedmath/validator/test/test-data/Makefile"
+
+
 if test -d src/sbml/packages/qual; then
 if test "$enable_qual" != "no" ; then
  ac_config_files="$ac_config_files src/sbml/packages/qual/Makefile"
@@ -27724,7 +27742,7 @@ cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
 # report actual input values of CONFIG_FILES etc. instead of their
 # values after options handling.
 ac_log="
-This file was extended by libSBML $as_me 5.17.0, which was
+This file was extended by libSBML $as_me 5.17.2, which was
 generated by GNU Autoconf 2.69.  Invocation command line was
  
  CONFIG_FILES    = $CONFIG_FILES
@@ -27787,7 +27805,7 @@ _ACEOF
 cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
 ac_cs_config="`$as_echo "$ac_configure_args" | sed 's/^ //; s/[\\""\`\$]/\\\\&/g'`"
 ac_cs_version="\\
-libSBML config.status 5.17.0
+libSBML config.status 5.17.2
 configured by $0, generated by GNU Autoconf 2.69,
  with options \\"\$ac_cs_config\\"
  
@@ -27938,8 +27956,6 @@ do
    "src/sbml/annotation/test/Makefile") CONFIG_FILES="$CONFIG_FILES src/sbml/annotation/test/Makefile" ;;
    "src/sbml/math/Makefile") CONFIG_FILES="$CONFIG_FILES src/sbml/math/Makefile" ;;
    "src/sbml/math/test/Makefile") CONFIG_FILES="$CONFIG_FILES src/sbml/math/test/Makefile" ;;
-    "src/sbml/math-legacy/Makefile") CONFIG_FILES="$CONFIG_FILES src/sbml/math-legacy/Makefile" ;;
-    "src/sbml/math-legacy/test/Makefile") CONFIG_FILES="$CONFIG_FILES src/sbml/math-legacy/test/Makefile" ;;
    "src/sbml/units/Makefile") CONFIG_FILES="$CONFIG_FILES src/sbml/units/Makefile" ;;
    "src/sbml/units/test/Makefile") CONFIG_FILES="$CONFIG_FILES src/sbml/units/test/Makefile" ;;
    "src/sbml/Makefile") CONFIG_FILES="$CONFIG_FILES src/sbml/Makefile" ;;
@@ -27996,6 +28012,14 @@ do
    "src/sbml/packages/layout/validator/constraints/Makefile") CONFIG_FILES="$CONFIG_FILES src/sbml/packages/layout/validator/constraints/Makefile" ;;
    "src/sbml/packages/layout/validator/test/Makefile") CONFIG_FILES="$CONFIG_FILES src/sbml/packages/layout/validator/test/Makefile" ;;
    "src/sbml/packages/layout/validator/test/test-data/Makefile") CONFIG_FILES="$CONFIG_FILES src/sbml/packages/layout/validator/test/test-data/Makefile" ;;
+    "src/sbml/packages/l3v2extendedmath/Makefile") CONFIG_FILES="$CONFIG_FILES src/sbml/packages/l3v2extendedmath/Makefile" ;;
+    "src/sbml/packages/l3v2extendedmath/common/Makefile") CONFIG_FILES="$CONFIG_FILES src/sbml/packages/l3v2extendedmath/common/Makefile" ;;
+    "src/sbml/packages/l3v2extendedmath/extension/Makefile") CONFIG_FILES="$CONFIG_FILES src/sbml/packages/l3v2extendedmath/extension/Makefile" ;;
+    "src/sbml/packages/l3v2extendedmath/extension/test/Makefile") CONFIG_FILES="$CONFIG_FILES src/sbml/packages/l3v2extendedmath/extension/test/Makefile" ;;
+    "src/sbml/packages/l3v2extendedmath/validator/Makefile") CONFIG_FILES="$CONFIG_FILES src/sbml/packages/l3v2extendedmath/validator/Makefile" ;;
+    "src/sbml/packages/l3v2extendedmath/validator/constraints/Makefile") CONFIG_FILES="$CONFIG_FILES src/sbml/packages/l3v2extendedmath/validator/constraints/Makefile" ;;
+    "src/sbml/packages/l3v2extendedmath/validator/test/Makefile") CONFIG_FILES="$CONFIG_FILES src/sbml/packages/l3v2extendedmath/validator/test/Makefile" ;;
+    "src/sbml/packages/l3v2extendedmath/validator/test/test-data/Makefile") CONFIG_FILES="$CONFIG_FILES src/sbml/packages/l3v2extendedmath/validator/test/test-data/Makefile" ;;
    "src/sbml/packages/qual/Makefile") CONFIG_FILES="$CONFIG_FILES src/sbml/packages/qual/Makefile" ;;
    "src/sbml/packages/qual/common/Makefile") CONFIG_FILES="$CONFIG_FILES src/sbml/packages/qual/common/Makefile" ;;
    "src/sbml/packages/qual/extension/Makefile") CONFIG_FILES="$CONFIG_FILES src/sbml/packages/qual/extension/Makefile" ;;
@@ -28878,6 +28902,10 @@ fi
 if test "$enable_qual" != "no" ; then
  echo "  SBML 'qual'                   = $enable_qual"
 fi
+if test "$enable_l3v2extendedmath" != "no" ; then
+  echo "  SBML 'l3v2extendedmath'                 = $enable_l3v2extendedmath"
+fi
+
  
 echo ""
 echo "Other potentially important settings:"

--- a/configure.ac
+++ b/configure.ac
@@ -50,7 +50,7 @@ AC_INIT([libSBML],

 AC_CONFIG_AUX_DIR(config)

-AC_REVISION($Revision: 25196 $)
+AC_REVISION($Revision: 25690 $)

 AC_CONFIG_SRCDIR(src/Makefile.in)

@@ -201,6 +201,19 @@ if test "$enable_multi" != no; then
  AC_SUBST(LIBSBML_HAS_PACKAGE_MULTI, 1)
 fi

+AC_ARG_ENABLE([l3v2extendedmath],
+  AS_HELP_STRING([--enable-l3v2extendedmath@<:@=ARG@:>@],
+                 [build support for SBML 'l3v2extendedmath' @<:@default=no@:>@]),
+  [enable_l3v2extendedmath=$enableval],
+  [enable_l3v2extendedmath=no])
+
+if test "$enable_l3v2extendedmath" != no; then
+  AC_DEFINE([USE_L3V2EXTENDEDMATH], 1, [Define to 1 to build support for SBML 'l3v2extendedmath'.])
+  AC_DEFINE([LIBSBML_HAS_PACKAGE_L3V2EXTENDEDMATH], 1, [Define to 1 to build support for SBML 'l3v2extendedmath'.])
+  AC_SUBST(USE_L3V2EXTENDEDMATH, 1)
+  AC_SUBST(LIBSBML_HAS_PACKAGE_L3V2EXTENDEDMATH, 1)
+fi
+
 dnl -------------------------------------------------------
 dnl Other SBML L3 package variables
 dnl -------------------------------------------------------
@@ -237,21 +250,6 @@ if test "$enable_shared_version" != no; then
  AC_SUBST(LIBSBML_SHARED_VERSION, 1)
 fi

-dnl ---------------------------------------------------------------------------
-dnl LIBSBML_USE_LEGACY_MATH
-dnl ---------------------------------------------------------------------------
-
-AC_ARG_ENABLE([legacy-math],
-  AS_HELP_STRING([--enable-legacy-math@<:@=ARG@:>@],
-                 [use legacy AST math implementation @<:@default=no@:>@]),
-  [enable_use_legacy_math=$enableval],
-  [enable_use_legacy_math=no])
-
-if test "$enable_use_legacy_math" != no; then
-  AC_DEFINE([LIBSBML_USE_LEGACY_MATH], 1, [Define to 1 to use the legacy math AST implementation.])
-  AC_SUBST(LIBSBML_USE_LEGACY_MATH, 1)
-fi
-
 dnl ---------------------------------------------------------------------------
 dnl LIBSBML_USE_STRICT_INCLUDES
 dnl ---------------------------------------------------------------------------
@@ -480,9 +478,6 @@ AC_CONFIG_FILES([src/sbml/annotation/test/Makefile])
 AC_CONFIG_FILES([src/sbml/math/Makefile])
 AC_CONFIG_FILES([src/sbml/math/test/Makefile])

-AC_CONFIG_FILES([src/sbml/math-legacy/Makefile])
-AC_CONFIG_FILES([src/sbml/math-legacy/test/Makefile])
-
 AC_CONFIG_FILES([src/sbml/units/Makefile])
 AC_CONFIG_FILES([src/sbml/units/test/Makefile])

@@ -559,6 +554,15 @@ AC_CONFIG_FILES([src/sbml/packages/layout/validator/constraints/Makefile])
 AC_CONFIG_FILES([src/sbml/packages/layout/validator/test/Makefile])
 AC_CONFIG_FILES([src/sbml/packages/layout/validator/test/test-data/Makefile])

+AC_CONFIG_FILES([src/sbml/packages/l3v2extendedmath/Makefile])
+AC_CONFIG_FILES([src/sbml/packages/l3v2extendedmath/common/Makefile])
+AC_CONFIG_FILES([src/sbml/packages/l3v2extendedmath/extension/Makefile])
+AC_CONFIG_FILES([src/sbml/packages/l3v2extendedmath/extension/test/Makefile])
+AC_CONFIG_FILES([src/sbml/packages/l3v2extendedmath/validator/Makefile])
+AC_CONFIG_FILES([src/sbml/packages/l3v2extendedmath/validator/constraints/Makefile])
+AC_CONFIG_FILES([src/sbml/packages/l3v2extendedmath/validator/test/Makefile])
+AC_CONFIG_FILES([src/sbml/packages/l3v2extendedmath/validator/test/test-data/Makefile])
+
 if test -d src/sbml/packages/qual; then
 if test "$enable_qual" != "no" ; then
  AC_CONFIG_FILES([src/sbml/packages/qual/Makefile])
@@ -895,6 +899,10 @@ fi
 if test "$enable_qual" != "no" ; then
  echo "  SBML 'qual'                   = $enable_qual"
 fi
+if test "$enable_l3v2extendedmath" != "no" ; then
+  echo "  SBML 'l3v2extendedmath'                 = $enable_l3v2extendedmath"
+fi
+

 echo ""
 echo "Other potentially important settings:"

--- a/debian/changelog
+++ b/debian/changelog
-libsbml (5.17.0+dfsg-1) UNRELEASED; urgency=medium
+libsbml (5.17.2+dfsg-1) UNRELEASED; urgency=medium

  [ gregor herrmann ]
  * Fix Perl installdir
    Closes: #896531

  [ Andreas Tille ]
+  * New upstream version
  * Point Vcs fields to salsa.debian.org
-  * Standards-Version: 4.2.1
+  * Standards-Version: 4.3.0
+  * debhelper 12
  * Deal with issue in doclets by removing docs/src/SBMLDoclet.java
  * Remove libsbml-java-doc since doc does not build properly
  * Provide Python3 instead of Python2 bindings (SBML can only provide
@@ -21,10 +23,12 @@ libsbml (5.17.0+dfsg-1) UNRELEASED; urgency=medium
  * Build-Depends: libnewlib-dev, check
  * Remove Matlab related options from debian/cmake_opts (thanks for the
    hint to Nicolas Mora)
-  TODO: Issue when building with Python 3.7 reported here:
-     https://groups.google.com/forum/#!topic/libsbml-development/hiqhyd6-7s0
+  * WITH_R=off (we do not build an R package and something is wrong with
+    the R build)
+  * Do not provide Java doc since there are errors when creating it
+    and this solution was suggested by the Debian Java team

- -- Andreas Tille <tille@debian.org>  Mon, 03 Dec 2018 16:11:35 +0100
+ -- Andreas Tille <tille@debian.org>  Tue, 15 Jan 2019 18:10:07 +0100

 libsbml (5.16.0+dfsg-2) unstable; urgency=medium


--- a/debian/cmake_opts
+++ b/debian/cmake_opts
@@ -20,7 +20,7 @@
 -DWITH_PERL:BOOL=ON
 -DWITH_PYTHON:BOOL=ON
 -DWITH_PYTHON_INCLUDE:PATH=/usr/include/python2.7
-DWITH_R:BOOL=ON
+-DWITH_R:BOOL=OFF
 -DWITH_RUBY:BOOL=OFF
 -DWITH_SWIG:BOOL=ON
 -DWITH_WALL:BOOL=ON

--- a/debian/compat
+++ b/debian/compat
-11
+12
--- a/debian/control
+++ b/debian/control
@@ -5,8 +5,9 @@ Uploaders: Ivo Maintz <ivo@maintz.de>,
 Section: science
 Testsuite: autopkgtest-pkg-python
 Priority: optional
-Build-Depends: debhelper (>= 11~),
+Build-Depends: debhelper (>= 12~),
               cmake,
+               dh-exec,
               doxygen,
               swig,
               libxml2-dev,
@@ -27,7 +28,7 @@ Build-Depends: debhelper (>= 11~),
               cli-common-dev,
               mono-runtime-common,
               texlive-latex-base
-Standards-Version: 4.2.1
+Standards-Version: 4.3.0
 Vcs-Browser: https://salsa.debian.org/med-team/libsbml
 Vcs-Git: https://salsa.debian.org/med-team/libsbml.git
 Homepage: http://www.sbml.org/
@@ -35,7 +36,6 @@ Homepage: http://www.sbml.org/
 Package: libsbml5-dev
 Architecture: any
 Section: libdevel
-Testsuite: autopkgtest-pkg-python
 Depends: libsbml5 (= ${binary:Version}),
         ${misc:Depends}
 Provides: libsbml-dev
@@ -50,7 +50,6 @@ Description: System Biology Markup Language library - development files
 Package: libsbml5
 Architecture: any
 Section: libs
-Testsuite: autopkgtest-pkg-python
 Depends: ${shlibs:Depends},
         ${misc:Depends}
 Pre-Depends: ${misc:Pre-Depends}
@@ -64,7 +63,6 @@ Description: System Biology Markup Language library
 Package: python3-libsbml5
 Architecture: any
 Section: python
-Testsuite: autopkgtest-pkg-python
 Depends: ${shlibs:Depends},
         ${misc:Depends},
         ${python3:Depends},
@@ -81,7 +79,6 @@ Description: System Biology Markup Language library - Python3 bindings
 Package: libsbml5-java
 Architecture: any
 Section: java
-Testsuite: autopkgtest-pkg-python
 Depends: ${shlibs:Depends},
         ${misc:Depends},
         jarwrapper
@@ -98,7 +95,6 @@ Description: System Biology Markup Language library - Java bindings
 Package: libsbml5-perl
 Architecture: any
 Section: perl
-Testsuite: autopkgtest-pkg-python
 Depends: ${shlibs:Depends},
         ${perl:Depends},
         ${misc:Depends}
@@ -114,7 +110,6 @@ Description: System Biology Markup Language library - Perl bindings
 Package: libsbml5-octave
 Architecture: any
 Section: math
-Testsuite: autopkgtest-pkg-python
 Depends: ${shlibs:Depends},
         ${misc:Depends},
         ${octave:Depends}
@@ -130,7 +125,6 @@ Description: System Biology Markup Language library - Octave bindings
 Package: libsbml5-cil
 Architecture: any
 Section: cli-mono
-Testsuite: autopkgtest-pkg-python
 Depends: ${shlibs:Depends},
         ${misc:Depends},
         ${cli:Depends},
@@ -147,7 +141,6 @@ Description: System Biology Markup Language library - CLI bindings
 Package: libsbml5-examples
 Architecture: all
 Section: doc
-Testsuite: autopkgtest-pkg-python
 Depends: ${misc:Depends}
 Suggests: libsbml5-dev (= ${binary:Version})
 Description: System Biology Markup Language library -- example files
@@ -161,7 +154,6 @@ Description: System Biology Markup Language library -- example files
 Package: libsbml5-doc
 Architecture: all
 Section: doc
-Testsuite: autopkgtest-pkg-python
 Depends: ${misc:Depends}
 Suggests: libsbml5-dev (= ${binary:Version})
 Description: System Biology Markup Language library -- documentation
@@ -175,7 +167,6 @@ Description: System Biology Markup Language library -- documentation
 Package: libsbml5-cil-doc
 Architecture: all
 Section: doc
-Testsuite: autopkgtest-pkg-python
 Depends: ${misc:Depends}
 Suggests: libsbml5-dev (= ${binary:Version})
 Description: System Biology Markup Language library -- CLI documentation
@@ -189,7 +180,6 @@ Description: System Biology Markup Language library -- CLI documentation
 Package: libsbml5-perl-doc
 Architecture: all
 Section: doc
-Testsuite: autopkgtest-pkg-python
 Depends: ${misc:Depends}
 Suggests: libsbml5-dev (= ${binary:Version})
 Description: System Biology Markup Language library -- Perl documentation
@@ -203,7 +193,6 @@ Description: System Biology Markup Language library -- Perl documentation
 Package: python3-libsbml5-doc
 Architecture: all
 Section: doc
-Testsuite: autopkgtest-pkg-python
 Depends: ${misc:Depends}
 Suggests: libsbml5-dev (= ${binary:Version})
 Description: System Biology Markup Language library - Python3 documentation

--- a/debian/libsbml5-cil.install
+++ b/debian/libsbml5-cil.install
-/usr/lib/mono
-debian/libsbmlcsP.dll.config	/usr/lib/mono/libsbmlcsP/
+#! /usr/bin/dh-exec
+/usr/lib/${DEB_HOST_MULTIARCH}/mono
+debian/libsbmlcsP.dll.config	/usr/lib/${DEB_HOST_MULTIARCH}/mono/libsbmlcsP/
--- a/debian/libsbml5-dev.install
+++ b/debian/libsbml5-dev.install
 usr/include/*
-usr/lib/libsbml-static.a
+usr/lib/*/libsbml-static.a
--- a/debian/libsbml5-java.install
+++ b/debian/libsbml5-java.install
-usr/lib/libsbmlj.so
+usr/lib/*/libsbmlj.so
 usr/share/java/libsbmlj.jar
--- a/debian/libsbml5-octave.install
+++ b/debian/libsbml5-octave.install
 #!/bin/sh

-echo "usr/lib/octave/site/oct/*/*.mex $(octave-config -p LOCALOCTFILEDIR)/libsbml5"
-echo "usr/lib/octave/site/oct/*/*.m $(octave-config -p LOCALFCNFILEDIR)/libsbml5"
+echo "usr/lib/*/octave/site/oct/*/*.mex $(octave-config -p LOCALOCTFILEDIR)/libsbml5"
+echo "usr/lib/*/octave/site/oct/*/*.m $(octave-config -p LOCALFCNFILEDIR)/libsbml5"
--- a/debian/libsbml5.install
+++ b/debian/libsbml5.install
-usr/lib/libsbml.so.*
+usr/lib/*/libsbml.so.*
--- a/debian/patches/fix_build_issue.patch
+++ b/debian/patches/fix_build_issue.patch
+Author: Andreas Tille <tille@debian.org>
+Last-Update: Tue, 15 Jan 2019 18:10:07 +0100
+Description: Avoid error
+   TypeError: '>=' not supported between instances of 'str' and 'int'
+
+--- a/src/bindings/swig/swigdoc.py
+++ b/src/bindings/swig/swigdoc.py
+@@ -467,7 +467,7 @@ class Method:
+     # this fixes a real problem in the Java documentation for libSBML.
+ 
+     if language == 'java' or language == 'csharp':
+-      if isConst and 'unsigned int' in args >= 0:
+      if isConst and 'unsigned int' in args : # >= 0:
+         self.args = ''
+       elif not args.strip() == '()':
+         if isConst: