git: f98de8beb064 - main - biology/libsbml: Update to 5.20.0
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Date: Sat, 27 May 2023 04:25:36 UTC
The branch main has been updated by sunpoet:
URL: https://cgit.FreeBSD.org/ports/commit/?id=f98de8beb06429de26f80be627eb78e0044bc826
commit f98de8beb06429de26f80be627eb78e0044bc826
Author: Po-Chuan Hsieh <sunpoet@FreeBSD.org>
AuthorDate: 2023-05-27 04:07:11 +0000
Commit: Po-Chuan Hsieh <sunpoet@FreeBSD.org>
CommitDate: 2023-05-27 04:07:11 +0000
biology/libsbml: Update to 5.20.0
- Update MASTER_SITES
- Update WWW
- Sort PLIST
Changes: https://github.com/sbmlteam/libsbml/releases
---
biology/libsbml/Makefile | 44 ++-
biology/libsbml/distinfo | 6 +-
biology/libsbml/files/patch-CMakeLists.txt | 60 +++-
...-bindings-python-doc-converter-rewrite_pydoc.py | 279 ---------------
biology/libsbml/pkg-plist | 376 ++++++---------------
5 files changed, 199 insertions(+), 566 deletions(-)
diff --git a/biology/libsbml/Makefile b/biology/libsbml/Makefile
index 5d2aaca36803..791aaaac5e39 100644
--- a/biology/libsbml/Makefile
+++ b/biology/libsbml/Makefile
@@ -1,9 +1,7 @@
PORTNAME= libsbml
-PORTVERSION= 5.19.0
-PORTREVISION= 2
+PORTVERSION= 5.20.0
+DISTVERSIONPREFIX= v
CATEGORIES= biology devel
-MASTER_SITES= SF/sbml/libsbml/${PORTVERSION}/stable
-DISTNAME= libSBML-${PORTVERSION}-core-src
MAINTAINER= sunpoet@FreeBSD.org
COMMENT= API Library for Working with SBML File
@@ -14,22 +12,46 @@ WWW= https://sbml.org/software/libsbml/ \
LICENSE= LGPL21
LICENSE_FILE= ${WRKSRC}/COPYING.txt
-USES= cmake iconv:build pathfix
+USES= cmake:testing iconv:build pathfix
-CMAKE_OFF= EXIT_ON_ERROR LIBSBML_USE_STRICT_INCLUDES PYTHON_USE_API2_WARNINGS WITH_ALL_PACKAGES WITH_CHECK WITH_CPP_NAMESPACE WITH_CSHARP WITH_DOXYGEN WITH_JAVA WITH_JAVASCRIPT WITH_MATLAB WITH_OCTAVE WITH_PERL WITH_PHP WITH_R WITH_STABLE_PACKAGES WITH_WALL
-CMAKE_ON= LIBSBML_SHARED_VERSION WITH_BZIP2 WITH_SWIG WITH_ZLIB
+CMAKE_OFF= EXIT_ON_ERROR \
+ LIBSBML_USE_STRICT_INCLUDES \
+ PYTHON_USE_API2_WARNINGS \
+ WITH_ALL_PACKAGES \
+ WITH_CHECK \
+ WITH_CPP_NAMESPACE \
+ WITH_CSHARP \
+ WITH_DOXYGEN \
+ WITH_JAVA \
+ WITH_JAVASCRIPT \
+ WITH_MATLAB \
+ WITH_OCTAVE \
+ WITH_PERL \
+ WITH_PHP \
+ WITH_R \
+ WITH_STABLE_PACKAGES \
+ WITH_WALL
+CMAKE_ON= LIBSBML_SHARED_VERSION \
+ WITH_BZIP2 \
+ WITH_SWIG \
+ WITH_THREADSAFE_PARSER \
+ WITH_ZLIB
+CMAKE_TESTING_ON= WITH_CHECK
USE_CXXSTD= c++98
USE_LDCONFIG= yes
-WRKSRC= ${WRKDIR}/libsbml-${PORTVERSION}
PLIST_SUB= PORTVERSION=${PORTVERSION}
+USE_GITHUB= yes
+GH_ACCOUNT= sbmlteam
+
OPTIONS_DEFINE= EXAMPLES PYTHON RUBY
OPTIONS_SINGLE= XML
OPTIONS_SINGLE_XML= EXPAT LIBXML2 XERCES
OPTIONS_DEFAULT=LIBXML2 PYTHON
OPTIONS_SUB= yes
+EXAMPLES_CMAKE_BOOL= WITH_EXAMPLES
EXPAT_CMAKE_BOOL= WITH_EXPAT
EXPAT_LIB_DEPENDS= libexpat.so:textproc/expat2
LIBXML2_CMAKE_BOOL= WITH_LIBXML
@@ -37,7 +59,7 @@ LIBXML2_USE= GNOME=libxml2
LIBXML2_USES= gnome
PYTHON_BUILD_DEPENDS= swig:devel/swig
PYTHON_CMAKE_BOOL= WITH_PYTHON
-PYTHON_USES= python:3.6+
+PYTHON_USES= python:3.7+
PYTHON_CMAKE_ON= WITH_SWIG
RUBY_BUILD_DEPENDS= swig:devel/swig
RUBY_CMAKE_BOOL= WITH_RUBY
@@ -49,7 +71,7 @@ post-patch:
@${REINPLACE_CMD} -e 's|/usr/local|${LOCALBASE}|g' ${WRKSRC}/CMakeLists.txt
post-install-EXAMPLES-on:
- ${MKDIR} ${STAGEDIR}${EXAMPLESDIR}
- cd ${WRKSRC}/examples && ${COPYTREE_SHARE} . ${STAGEDIR}${EXAMPLESDIR} '! -name *Makefile*'
+ ${MV} ${STAGEDIR}${DATADIR}/examples ${STAGEDIR}${EXAMPLESDIR}
+ ${RMDIR} ${STAGEDIR}${DATADIR}
.include <bsd.port.mk>
diff --git a/biology/libsbml/distinfo b/biology/libsbml/distinfo
index 2610d16e3336..30a1bfe42dfa 100644
--- a/biology/libsbml/distinfo
+++ b/biology/libsbml/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1607539653
-SHA256 (libSBML-5.19.0-core-src.tar.gz) = 9d2837378e77a8732588d481327bb10c721ec06dd6cd72f8041d67d3b53d4e56
-SIZE (libSBML-5.19.0-core-src.tar.gz) = 14600103
+TIMESTAMP = 1684104306
+SHA256 (sbmlteam-libsbml-v5.20.0_GH0.tar.gz) = 400f1e1039ef0fc9addc99660a3a2559fefe9cb2c8315b1b488014b6101c438f
+SIZE (sbmlteam-libsbml-v5.20.0_GH0.tar.gz) = 28776286
diff --git a/biology/libsbml/files/patch-CMakeLists.txt b/biology/libsbml/files/patch-CMakeLists.txt
index 16351bdf126e..037277324c79 100644
--- a/biology/libsbml/files/patch-CMakeLists.txt
+++ b/biology/libsbml/files/patch-CMakeLists.txt
@@ -1,9 +1,56 @@
---- CMakeLists.txt.orig 2020-11-19 11:17:49 UTC
+--- CMakeLists.txt.orig 2023-04-03 10:48:28 UTC
+++ CMakeLists.txt
-@@ -1297,22 +1297,6 @@ endif()
+@@ -430,8 +430,6 @@ if(WITH_EXPAT)
+ set(LIBSBML_XML_LIBRARY_INCLUDE ${EXPAT_INCLUDE_DIR})
+ set(LIBSBML_XML_LIBRARY_LIBS ${EXPAT_LIBRARY})
+
+- list(APPEND LIBSBML_FIND_MODULES "${CMAKE_CURRENT_SOURCE_DIR}/CMakeModules/FindEXPAT.cmake")
+-
+ endif(WITH_EXPAT)
+
+
+@@ -452,8 +450,6 @@ if(WITH_LIBXML)
+ set(LIBSBML_XML_LIBRARY_INCLUDE ${LIBXML_INCLUDE_DIR})
+ set(LIBSBML_XML_LIBRARY_LIBS ${LIBXML_LIBRARY})
+
+- list(APPEND LIBSBML_FIND_MODULES "${CMAKE_CURRENT_SOURCE_DIR}/CMakeModules/FindLIBXML.cmake")
+-
+ endif(WITH_LIBXML)
+
+
+@@ -473,8 +469,6 @@ if(WITH_XERCES)
+ set(LIBSBML_XML_LIBRARY_INCLUDE ${XERCES_INCLUDE_DIR})
+ set(LIBSBML_XML_LIBRARY_LIBS ${XERCES_LIBRARY})
+
+- list(APPEND LIBSBML_FIND_MODULES "${CMAKE_CURRENT_SOURCE_DIR}/CMakeModules/FindXERCES.cmake")
+-
+ endif(WITH_XERCES)
###############################################################################
- #
+@@ -498,7 +492,6 @@ if(WITH_BZIP2)
+ set(USE_BZ2 ON)
+ add_definitions( -DUSE_BZ2 )
+ list(APPEND SWIG_EXTRA_ARGS -DUSE_BZ2)
+- list(APPEND LIBSBML_FIND_MODULES "${CMAKE_CURRENT_SOURCE_DIR}/CMakeModules/FindBZ2.cmake")
+ endif(WITH_BZIP2)
+
+
+@@ -608,8 +601,6 @@ valid. It should contain the file zlib.h, but it does
+ INTERFACE_INCLUDE_DIRECTORIES "${LIBZ_INCLUDE_DIR}")
+ endif()
+
+- list(APPEND LIBSBML_FIND_MODULES "${CMAKE_CURRENT_SOURCE_DIR}/CMakeModules/FindZLIB.cmake")
+-
+ endif(WITH_ZLIB)
+
+ # install find scripts only for used dependencies
+@@ -981,22 +972,6 @@ if(WITH_DOXYGEN)
+ add_subdirectory(docs)
+ endif()
+
+-
+-###############################################################################
+-#
-# Install documentation
-#
-
@@ -17,9 +64,6 @@
-)
-
-install(FILES ${DOCUMENTATION_FILES} DESTINATION ${MISC_PREFIX})
--
--###############################################################################
--#
- # Write libsbml.pc
- #
+ ###############################################################################
+ #
diff --git a/biology/libsbml/files/patch-src-bindings-python-doc-converter-rewrite_pydoc.py b/biology/libsbml/files/patch-src-bindings-python-doc-converter-rewrite_pydoc.py
deleted file mode 100644
index fb1a6b0be7d9..000000000000
--- a/biology/libsbml/files/patch-src-bindings-python-doc-converter-rewrite_pydoc.py
+++ /dev/null
@@ -1,279 +0,0 @@
-Obtained from: https://github.com/sbmlteam/libsbml/commit/4f01a15fde1d8afa9eaffb4c13dfc83a3404f183 (based on)
-
---- src/bindings/python/doc-converter/rewrite_pydoc.py.orig 2020-11-25 11:03:01 UTC
-+++ src/bindings/python/doc-converter/rewrite_pydoc.py
-@@ -118,7 +118,273 @@ import re
- import sys
- import os
- import textwrap
--from formatter import NullWriter, AbstractFormatter
-+try:
-+ from formatter import NullWriter, AbstractFormatter
-+except Exception:
-+ # issue 173 these classes have been removed in 3.10, so
-+ # as per the 3.10 release notes: Existing users should copy whatever
-+ # classes they use into their code. (Contributed by Dong-hee Na and
-+ # Terry J. Reedy in bpo-42299.)
-+ #
-+ # So here they are:
-+
-+
-+ class NullWriter:
-+ """Minimal writer interface to use in testing & inheritance.
-+
-+ A writer which only provides the interface definition; no actions are
-+ taken on any methods. This should be the base class for all writers
-+ which do not need to inherit any implementation methods.
-+
-+ """
-+ def __init__(self): pass
-+ def flush(self): pass
-+ def new_alignment(self, align): pass
-+ def new_font(self, font): pass
-+ def new_margin(self, margin, level): pass
-+ def new_spacing(self, spacing): pass
-+ def new_styles(self, styles): pass
-+ def send_paragraph(self, blankline): pass
-+ def send_line_break(self): pass
-+ def send_hor_rule(self, *args, **kw): pass
-+ def send_label_data(self, data): pass
-+ def send_flowing_data(self, data): pass
-+ def send_literal_data(self, data): pass
-+
-+ class AbstractFormatter:
-+ """The standard formatter.
-+
-+ This implementation has demonstrated wide applicability to many writers,
-+ and may be used directly in most circumstances. It has been used to
-+ implement a full-featured World Wide Web browser.
-+
-+ """
-+
-+ # Space handling policy: blank spaces at the boundary between elements
-+ # are handled by the outermost context. "Literal" data is not checked
-+ # to determine context, so spaces in literal data are handled directly
-+ # in all circumstances.
-+
-+ def __init__(self, writer):
-+ self.writer = writer # Output device
-+ self.align = None # Current alignment
-+ self.align_stack = [] # Alignment stack
-+ self.font_stack = [] # Font state
-+ self.margin_stack = [] # Margin state
-+ self.spacing = None # Vertical spacing state
-+ self.style_stack = [] # Other state, e.g. color
-+ self.nospace = 1 # Should leading space be suppressed
-+ self.softspace = 0 # Should a space be inserted
-+ self.para_end = 1 # Just ended a paragraph
-+ self.parskip = 0 # Skipped space between paragraphs?
-+ self.hard_break = 1 # Have a hard break
-+ self.have_label = 0
-+
-+ def end_paragraph(self, blankline):
-+ if not self.hard_break:
-+ self.writer.send_line_break()
-+ self.have_label = 0
-+ if self.parskip < blankline and not self.have_label:
-+ self.writer.send_paragraph(blankline - self.parskip)
-+ self.parskip = blankline
-+ self.have_label = 0
-+ self.hard_break = self.nospace = self.para_end = 1
-+ self.softspace = 0
-+
-+ def add_line_break(self):
-+ if not (self.hard_break or self.para_end):
-+ self.writer.send_line_break()
-+ self.have_label = self.parskip = 0
-+ self.hard_break = self.nospace = 1
-+ self.softspace = 0
-+
-+ def add_hor_rule(self, *args, **kw):
-+ if not self.hard_break:
-+ self.writer.send_line_break()
-+ self.writer.send_hor_rule(*args, **kw)
-+ self.hard_break = self.nospace = 1
-+ self.have_label = self.para_end = self.softspace = self.parskip = 0
-+
-+ def add_label_data(self, format, counter, blankline = None):
-+ if self.have_label or not self.hard_break:
-+ self.writer.send_line_break()
-+ if not self.para_end:
-+ self.writer.send_paragraph((blankline and 1) or 0)
-+ if isinstance(format, str):
-+ self.writer.send_label_data(self.format_counter(format, counter))
-+ else:
-+ self.writer.send_label_data(format)
-+ self.nospace = self.have_label = self.hard_break = self.para_end = 1
-+ self.softspace = self.parskip = 0
-+
-+ def format_counter(self, format, counter):
-+ label = ''
-+ for c in format:
-+ if c == '1':
-+ label = label + ('%d' % counter)
-+ elif c in 'aA':
-+ if counter > 0:
-+ label = label + self.format_letter(c, counter)
-+ elif c in 'iI':
-+ if counter > 0:
-+ label = label + self.format_roman(c, counter)
-+ else:
-+ label = label + c
-+ return label
-+
-+ def format_letter(self, case, counter):
-+ label = ''
-+ while counter > 0:
-+ counter, x = divmod(counter-1, 26)
-+ # This makes a strong assumption that lowercase letters
-+ # and uppercase letters form two contiguous blocks, with
-+ # letters in order!
-+ s = chr(ord(case) + x)
-+ label = s + label
-+ return label
-+
-+ def format_roman(self, case, counter):
-+ ones = ['i', 'x', 'c', 'm']
-+ fives = ['v', 'l', 'd']
-+ label, index = '', 0
-+ # This will die of IndexError when counter is too big
-+ while counter > 0:
-+ counter, x = divmod(counter, 10)
-+ if x == 9:
-+ label = ones[index] + ones[index+1] + label
-+ elif x == 4:
-+ label = ones[index] + fives[index] + label
-+ else:
-+ if x >= 5:
-+ s = fives[index]
-+ x = x-5
-+ else:
-+ s = ''
-+ s = s + ones[index]*x
-+ label = s + label
-+ index = index + 1
-+ if case == 'I':
-+ return label.upper()
-+ return label
-+
-+ def add_flowing_data(self, data):
-+ if not data: return
-+ prespace = data[:1].isspace()
-+ postspace = data[-1:].isspace()
-+ data = " ".join(data.split())
-+ if self.nospace and not data:
-+ return
-+ elif prespace or self.softspace:
-+ if not data:
-+ if not self.nospace:
-+ self.softspace = 1
-+ self.parskip = 0
-+ return
-+ if not self.nospace:
-+ data = ' ' + data
-+ self.hard_break = self.nospace = self.para_end = \
-+ self.parskip = self.have_label = 0
-+ self.softspace = postspace
-+ self.writer.send_flowing_data(data)
-+
-+ def add_literal_data(self, data):
-+ if not data: return
-+ if self.softspace:
-+ self.writer.send_flowing_data(" ")
-+ self.hard_break = data[-1:] == '\n'
-+ self.nospace = self.para_end = self.softspace = \
-+ self.parskip = self.have_label = 0
-+ self.writer.send_literal_data(data)
-+
-+ def flush_softspace(self):
-+ if self.softspace:
-+ self.hard_break = self.para_end = self.parskip = \
-+ self.have_label = self.softspace = 0
-+ self.nospace = 1
-+ self.writer.send_flowing_data(' ')
-+
-+ def push_alignment(self, align):
-+ if align and align != self.align:
-+ self.writer.new_alignment(align)
-+ self.align = align
-+ self.align_stack.append(align)
-+ else:
-+ self.align_stack.append(self.align)
-+
-+ def pop_alignment(self):
-+ if self.align_stack:
-+ del self.align_stack[-1]
-+ if self.align_stack:
-+ self.align = align = self.align_stack[-1]
-+ self.writer.new_alignment(align)
-+ else:
-+ self.align = None
-+ self.writer.new_alignment(None)
-+
-+ def push_font(self, font):
-+ size, i, b, tt = font
-+ if self.softspace:
-+ self.hard_break = self.para_end = self.softspace = 0
-+ self.nospace = 1
-+ self.writer.send_flowing_data(' ')
-+ if self.font_stack:
-+ csize, ci, cb, ctt = self.font_stack[-1]
-+ if size is AS_IS: size = csize
-+ if i is AS_IS: i = ci
-+ if b is AS_IS: b = cb
-+ if tt is AS_IS: tt = ctt
-+ font = (size, i, b, tt)
-+ self.font_stack.append(font)
-+ self.writer.new_font(font)
-+
-+ def pop_font(self):
-+ if self.font_stack:
-+ del self.font_stack[-1]
-+ if self.font_stack:
-+ font = self.font_stack[-1]
-+ else:
-+ font = None
-+ self.writer.new_font(font)
-+
-+ def push_margin(self, margin):
-+ self.margin_stack.append(margin)
-+ fstack = filter(None, self.margin_stack)
-+ if not margin and fstack:
-+ margin = fstack[-1]
-+ self.writer.new_margin(margin, len(fstack))
-+
-+ def pop_margin(self):
-+ if self.margin_stack:
-+ del self.margin_stack[-1]
-+ fstack = filter(None, self.margin_stack)
-+ if fstack:
-+ margin = fstack[-1]
-+ else:
-+ margin = None
-+ self.writer.new_margin(margin, len(fstack))
-+
-+ def set_spacing(self, spacing):
-+ self.spacing = spacing
-+ self.writer.new_spacing(spacing)
-+
-+ def push_style(self, *styles):
-+ if self.softspace:
-+ self.hard_break = self.para_end = self.softspace = 0
-+ self.nospace = 1
-+ self.writer.send_flowing_data(' ')
-+ for style in styles:
-+ self.style_stack.append(style)
-+ self.writer.new_styles(tuple(self.style_stack))
-+
-+ def pop_style(self, n=1):
-+ del self.style_stack[-n:]
-+ self.writer.new_styles(tuple(self.style_stack))
-+
-+ def assert_line_data(self, flag=1):
-+ self.nospace = self.hard_break = not flag
-+ self.para_end = self.parskip = self.have_label = 0
-+
-+
- try:
- from htmllib import HTMLParser
- except Exception:
diff --git a/biology/libsbml/pkg-plist b/biology/libsbml/pkg-plist
index b357279ef9f7..7a382979c5e4 100644
--- a/biology/libsbml/pkg-plist
+++ b/biology/libsbml/pkg-plist
@@ -75,6 +75,7 @@ include/sbml/compress/zip.h
include/sbml/compress/zipfstream.h
include/sbml/conversion/ConversionOption.h
include/sbml/conversion/ConversionProperties.h
+include/sbml/conversion/ExpressionAnalyser.h
include/sbml/conversion/SBMLConverter.h
include/sbml/conversion/SBMLConverterRegister.h
include/sbml/conversion/SBMLConverterRegistry.h
@@ -87,6 +88,7 @@ include/sbml/conversion/SBMLLevel1Version1Converter.h
include/sbml/conversion/SBMLLevelVersionConverter.h
include/sbml/conversion/SBMLLocalParameterConverter.h
include/sbml/conversion/SBMLRateOfConverter.h
+include/sbml/conversion/SBMLRateRuleConverter.h
include/sbml/conversion/SBMLReactionConverter.h
include/sbml/conversion/SBMLRuleConverter.h
include/sbml/conversion/SBMLStripPackageConverter.h
@@ -196,53 +198,31 @@ include/sbml/xml/XercesHandler.h
include/sbml/xml/XercesNamespaces.h
include/sbml/xml/XercesParser.h
include/sbml/xml/XercesTranscode.h
-lib/libsbml-static.a
-lib/libsbml.so
-lib/libsbml.so.5
-lib/libsbml.so.%%PORTVERSION%%
-libdata/pkgconfig/libsbml.pc
-lib/cmake/sbml-config-release.cmake
lib/cmake/sbml-config-version.cmake
lib/cmake/sbml-config.cmake
-lib/cmake/sbml-static-config-release.cmake
lib/cmake/sbml-static-config-version.cmake
lib/cmake/sbml-static-config.cmake
-%%PYTHON%%%%PYTHON_SITELIBDIR%%/libsbml.pth
-%%PYTHON%%%%PYTHON_SITELIBDIR%%/libsbml/_libsbml.so
-%%PYTHON%%%%PYTHON_SITELIBDIR%%/libsbml/libsbml.py
+lib/cmake/sbml-static-targets-%%CMAKE_BUILD_TYPE%%.cmake
+lib/cmake/sbml-static-targets.cmake
+lib/cmake/sbml-targets-%%CMAKE_BUILD_TYPE%%.cmake
+lib/cmake/sbml-targets.cmake
+lib/libsbml-static.a
+lib/libsbml.so
+lib/libsbml.so.5
+lib/libsbml.so.%%PORTVERSION%%
+%%PYTHON_SITELIBDIR%%/libsbml.pth
+%%PYTHON_SITELIBDIR%%/libsbml/_libsbml.so
+%%PYTHON_SITELIBDIR%%/libsbml/libsbml.py
%%RUBY%%%%RUBY_SITEARCHLIBDIR%%/libSBML.so
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/CMakeLists.txt
+libdata/pkgconfig/libsbml.pc
+@comment share/cmake/Modules/FindBZ2.cmake
+@comment share/cmake/Modules/FindCHECK.cmake
+@comment share/cmake/Modules/FindEXPAT.cmake
+share/cmake/Modules/FindLIBSBML.cmake
+@comment share/cmake/Modules/FindLIBXML.cmake
+@comment share/cmake/Modules/FindXERCES.cmake
+@comment share/cmake/Modules/FindZLIB.cmake
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/README.txt
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/CMakeLists.txt
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/FormulaGraphvizFormatter.h
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/addCVTerms.c
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/addModelHistory.c
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/addingEvidenceCodes_1.c
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/addingEvidenceCodes_2.c
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/appendAnnotation.c
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/convertSBML.c
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/createExampleSBML.c
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/drawMath.c
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/echoSBML.c
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/evaluateMath.c
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/printAnnotation.c
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/printMath.c
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/printNotes.c
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/printRegisteredPackages.c
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/printSBML.c
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/printSupported.c
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/printUnits.c
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/promoteParameters.c
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/readSBML.c
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/stripPackage.c
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/translateL3Math.c
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/translateMath.c
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/unsetAnnotation.c
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/unsetNotes.c
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/util.c
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/util.h
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/validateSBML.c
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/CMakeLists.txt
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/addCVTerms.cpp
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/addCustomValidator.cpp
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/addModelHistory.cpp
@@ -258,15 +238,6 @@ lib/cmake/sbml-static-config.cmake
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/getAllElementsWithNotes.cpp
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/inferUnits.cpp
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/inlineFunctionDefintions.cpp
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/layout/CMakeLists.txt
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/layout/addLayout.cpp
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/layout/convertLayout.cpp
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/layout/example1-L3.cpp
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/layout/example1.cpp
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/layout/example2-L3.cpp
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/layout/example2.cpp
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/layout/example3-L3.cpp
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/layout/example3.cpp
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/printAnnotation.cpp
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/printMath.cpp
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/printNotes.cpp
@@ -278,6 +249,7 @@ lib/cmake/sbml-static-config.cmake
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/readSBML.cpp
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/renameSId.cpp
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/rngvalidator.cpp
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/setAnnotation.cpp
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/setIdFromNames.cpp
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/setNamesFromIds.cpp
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/stripPackage.cpp
@@ -288,219 +260,95 @@ lib/cmake/sbml-static-config.cmake
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/util.c
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/util.h
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/validateSBML.cpp
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/csharp/CMakeLists.txt
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/csharp/GetAllElementsWithNotes.cs
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/csharp/SetIdFromNames.cs
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/csharp/addCVTerms.cs
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/csharp/addCustomValidator.cs
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/csharp/addModelHistory.cs
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/csharp/addingEvidenceCodes_1.cs
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/csharp/addingEvidenceCodes_2.cs
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/csharp/appendAnnotation.cs
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/csharp/callExternalValidator.cs
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/csharp/convertSBML.cs
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/csharp/createExampleSBML.cs
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/csharp/echoSBML.cs
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/csharp/evaluateCustomMath.cs
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/csharp/inlineInitialAssignments.cs
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/csharp/layout/CMakeLists.txt
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/csharp/layout/example1-L3.cs
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/csharp/printAnnotation.cs
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/csharp/printMath.cs
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/csharp/printNotes.cs
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/csharp/printRegisteredPackages.cs
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/csharp/printSBML.cs
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/csharp/printUnits.cs
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/csharp/printsupported.cs
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/csharp/promoteParameters.cs
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/csharp/readSBML.cs
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/csharp/replaceOneFD.cs
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/csharp/stripPackage.cs
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/csharp/translateMath.cs
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/csharp/unsetAnnotation.cs
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/csharp/unsetNotes.cs
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/csharp/validateSBML.cs
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/java/CMakeLists.txt
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/java/README.txt
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/java/addCVTerms.java
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/java/addCustomValidator.java
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/java/addModelHistory.java
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/java/addingEvidenceCodes_1.java
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/java/addingEvidenceCodes_2.java
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/java/appendAnnotation.java
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/java/callExternalValidator.java
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/java/convertSBML.java
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/java/createExampleSBML.java
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/java/echoSBML.java
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/java/evaluateCustomMath.java
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/java/evaluateMath.java
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/java/getAllElementsWithNotes.java
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/java/inlineInitialAssignments.java
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/java/layout/CMakeLists.txt
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/java/layout/SimpleLayoutConverter.java
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/java/layout/layout_example1.java
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/java/layout/layout_example1_L3.java
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/java/printAnnotation.java
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/java/printMath.java
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/java/printNotes.java
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/java/printRegisteredPackages.java
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/java/printSBML.java
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/java/printUnits.java
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/java/printsupported.java
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/java/promoteParameters.java
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/java/readSBML.java
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/java/replaceOneFD.java
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/java/setIdFromNames.java
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/java/stripPackage.java
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/java/translateMath.java
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/java/unsetAnnotation.java
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/java/unsetNotes.java
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/java/validateSBML.java
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/javascript/addCVTerms.js
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/javascript/addModelHistory.js
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/javascript/addingEvidenceCodes_1.js
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/javascript/addingEvidenceCodes_2.js
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/javascript/appendAnnotation.js
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/javascript/callExternalValidator.js
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/javascript/convertSBML.js
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/javascript/createExampleSBML.js
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/javascript/echoSBML.js
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/javascript/printAnnotation.js
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/javascript/printMath.js
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/javascript/printNotes.js
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/javascript/printRegisteredPackages.js
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/javascript/printSBML.js
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/javascript/printUnits.js
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/javascript/printsupported.js
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/javascript/promoteParameters.js
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/javascript/readSBML.js
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/javascript/stripPackage.js
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/javascript/translateMath.js
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/javascript/unsetAnnotation.js
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/javascript/unsetNotes.js
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/javascript/validateSBML.js
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/layout-package.cmake
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/layout/README.txt
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/perl/addCVTerms.pl
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/perl/addCustomValidator.pl
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/perl/addModelHistory.pl
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/perl/addingEvidenceCodes_1.pl
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/perl/addingEvidenceCodes_2.pl
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/perl/appendAnnotation.pl
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/perl/callExternalValidator.pl
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/perl/convertSBML.pl
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/perl/createExampleSBML.pl
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/perl/echoSBML.pl
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/perl/evaluateMath.pl
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/perl/extractReactionInfo.pl
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/perl/extractReactions.pl
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/perl/layout/example1-L3.pl
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/perl/printAnnotation.pl
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/perl/printMath.pl
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/perl/printNotes.pl
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/perl/printRegisteredPackages.pl
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/perl/printSBML.pl
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/perl/printUnits.pl
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/perl/printsupported.pl
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/perl/promoteParameters.pl
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/perl/readSBML.pl
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/perl/renameSId.pl
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/perl/stripPackage.pl
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/perl/translateMath.pl
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/perl/unsetAnnotation.pl
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/perl/unsetNotes.pl
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/perl/validateSBML.pl
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/php/createExampleSBML.php
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/php/echoSBML.php
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/php/validateSBML.php
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/python/addCVTerms.py
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/python/addCustomValidator.py
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/python/addModelHistory.py
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/python/addingEvidenceCodes_1.py
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/python/addingEvidenceCodes_2.py
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/python/append_to_note.py
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/python/appendAnnotation.py
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/python/callExternalValidator.py
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/python/convertSBML.py
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/python/createExampleSBML.py
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/python/createSimpleModel.py
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/python/echoSBML.py
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/python/evaluateCustomMath.py
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/python/getAllElementsWithNotes.py
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/python/inlineFunctionDefinitions.py
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/python/inlineInitialAssignments.py
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/python/layout/convertLayout.py
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/python/layout/example1-L3.py
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/python/layout/example1.py
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/python/printAnnotation.py
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/python/printMath.py
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/python/printNotes.py
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/python/printRegisteredPackages.py
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/python/printSBML.py
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/python/printUnits.py
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/python/printsupported.py
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/python/promoteParameters.py
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/python/readSBML.py
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/python/renameSId.py
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/python/replaceOneFD.py
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/python/setIdFromNames.py
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/python/stringInput.py
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/python/stripPackage.py
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/python/translateMath.py
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/python/unsetAnnotation.py
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/python/unsetNotes.py
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/python/validateSBML.py
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/python/validateSBMLWithCallback.py
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/r/addCVTerms.R
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/r/addModelHistory.R
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/r/addingEvidenceCodes_1.R
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/r/addingEvidenceCodes_2.R
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/r/appendAnnotation.R
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/r/convertSBML.R
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/r/createExampleSBML.R
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/r/echoSBML.R
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/r/evaluateMath.R
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/r/printAnnotation.R
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/r/printMath.R
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/r/printNotes.R
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/r/printRegisteredPackages.R
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/r/printSBML.R
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/r/printSupported.R
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/r/printUnits.R
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/r/promoteParameters.R
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/r/readSBML.R
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/r/stripPackage.R
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/r/translateMath.R
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/r/unsetAnnotation.R
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/r/unsetNotes.R
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/r/validateSBML.R
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ruby/addCVTerms.rb
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ruby/addCustomValidator.rb
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ruby/addModelHistory.rb
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ruby/addingEvidenceCodes_1.rb
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ruby/addingEvidenceCodes_2.rb
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ruby/appendAnnotation.rb
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ruby/callExternalValidator.rb
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ruby/convertSBML.rb
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ruby/createExampleSBML.rb
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ruby/echoSBML.rb
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ruby/layout/example1-L3.rb
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ruby/printAnnotation.rb
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ruby/printMath.rb
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ruby/printNotes.rb
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ruby/printRegisteredPackages.rb
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ruby/printSBML.rb
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ruby/printUnits.rb
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ruby/printsupported.rb
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ruby/promoteParameters.rb
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ruby/readSBML.rb
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ruby/stripPackage.rb
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ruby/translateMath.rb
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ruby/unsetAnnotation.rb
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ruby/unsetNotes.rb
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ruby/validateSBML.rb
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample-models/README.txt
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample-models/from-spec/level-2/README.txt
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/FormulaGraphvizFormatter.h
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/addCVTerms.c
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/addModelHistory.c
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/addingEvidenceCodes_1.c
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/addingEvidenceCodes_2.c
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/appendAnnotation.c
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/convertSBML.c
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/createExampleSBML.c
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/drawMath.c
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/echoSBML.c
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/evaluateMath.c
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/printAnnotation.c
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/printMath.c
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/printNotes.c
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/printRegisteredPackages.c
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/printSBML.c
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/printSupported.c
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/printUnits.c
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/promoteParameters.c
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/readSBML.c
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/stripPackage.c
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/translateL3Math.c
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/translateMath.c
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/unsetAnnotation.c
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/unsetNotes.c
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/util.c
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/util.h
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/validateSBML.c
+%%PORTEXAMPLES%%%%PYTHON%%%%EXAMPLESDIR%%/python/addCVTerms.py
+%%PORTEXAMPLES%%%%PYTHON%%%%EXAMPLESDIR%%/python/addCustomValidator.py
+%%PORTEXAMPLES%%%%PYTHON%%%%EXAMPLESDIR%%/python/addModelHistory.py
+%%PORTEXAMPLES%%%%PYTHON%%%%EXAMPLESDIR%%/python/add_function_definition.py
+%%PORTEXAMPLES%%%%PYTHON%%%%EXAMPLESDIR%%/python/addingEvidenceCodes_1.py
+%%PORTEXAMPLES%%%%PYTHON%%%%EXAMPLESDIR%%/python/addingEvidenceCodes_2.py
+%%PORTEXAMPLES%%%%PYTHON%%%%EXAMPLESDIR%%/python/appendAnnotation.py
+%%PORTEXAMPLES%%%%PYTHON%%%%EXAMPLESDIR%%/python/append_to_note.py
+%%PORTEXAMPLES%%%%PYTHON%%%%EXAMPLESDIR%%/python/callExternalValidator.py
+%%PORTEXAMPLES%%%%PYTHON%%%%EXAMPLESDIR%%/python/convertSBML.py
+%%PORTEXAMPLES%%%%PYTHON%%%%EXAMPLESDIR%%/python/createExampleSBML.py
+%%PORTEXAMPLES%%%%PYTHON%%%%EXAMPLESDIR%%/python/createSimpleModel.py
+%%PORTEXAMPLES%%%%PYTHON%%%%EXAMPLESDIR%%/python/echoSBML.py
+%%PORTEXAMPLES%%%%PYTHON%%%%EXAMPLESDIR%%/python/evaluateCustomMath.py
+%%PORTEXAMPLES%%%%PYTHON%%%%EXAMPLESDIR%%/python/getAllElementsWithNotes.py
+%%PORTEXAMPLES%%%%PYTHON%%%%EXAMPLESDIR%%/python/inlineFunctionDefinitions.py
+%%PORTEXAMPLES%%%%PYTHON%%%%EXAMPLESDIR%%/python/inlineInitialAssignments.py
+%%PORTEXAMPLES%%%%PYTHON%%%%EXAMPLESDIR%%/python/printAnnotation.py
+%%PORTEXAMPLES%%%%PYTHON%%%%EXAMPLESDIR%%/python/printMath.py
+%%PORTEXAMPLES%%%%PYTHON%%%%EXAMPLESDIR%%/python/printNotes.py
+%%PORTEXAMPLES%%%%PYTHON%%%%EXAMPLESDIR%%/python/printRegisteredPackages.py
+%%PORTEXAMPLES%%%%PYTHON%%%%EXAMPLESDIR%%/python/printSBML.py
+%%PORTEXAMPLES%%%%PYTHON%%%%EXAMPLESDIR%%/python/printUnits.py
+%%PORTEXAMPLES%%%%PYTHON%%%%EXAMPLESDIR%%/python/printsupported.py
+%%PORTEXAMPLES%%%%PYTHON%%%%EXAMPLESDIR%%/python/promoteParameters.py
+%%PORTEXAMPLES%%%%PYTHON%%%%EXAMPLESDIR%%/python/readSBML.py
+%%PORTEXAMPLES%%%%PYTHON%%%%EXAMPLESDIR%%/python/renameSId.py
+%%PORTEXAMPLES%%%%PYTHON%%%%EXAMPLESDIR%%/python/replaceOneFD.py
+%%PORTEXAMPLES%%%%PYTHON%%%%EXAMPLESDIR%%/python/setIdFromNames.py
+%%PORTEXAMPLES%%%%PYTHON%%%%EXAMPLESDIR%%/python/setNamesFromIds.py
+%%PORTEXAMPLES%%%%PYTHON%%%%EXAMPLESDIR%%/python/stringInput.py
+%%PORTEXAMPLES%%%%PYTHON%%%%EXAMPLESDIR%%/python/stripPackage.py
+%%PORTEXAMPLES%%%%PYTHON%%%%EXAMPLESDIR%%/python/translateMath.py
+%%PORTEXAMPLES%%%%PYTHON%%%%EXAMPLESDIR%%/python/unsetAnnotation.py
+%%PORTEXAMPLES%%%%PYTHON%%%%EXAMPLESDIR%%/python/unsetNotes.py
+%%PORTEXAMPLES%%%%PYTHON%%%%EXAMPLESDIR%%/python/validateSBML.py
+%%PORTEXAMPLES%%%%PYTHON%%%%EXAMPLESDIR%%/python/validateSBMLWithCallback.py
+%%PORTEXAMPLES%%%%RUBY%%%%EXAMPLESDIR%%/ruby/addCVTerms.rb
+%%PORTEXAMPLES%%%%RUBY%%%%EXAMPLESDIR%%/ruby/addCustomValidator.rb
+%%PORTEXAMPLES%%%%RUBY%%%%EXAMPLESDIR%%/ruby/addModelHistory.rb
+%%PORTEXAMPLES%%%%RUBY%%%%EXAMPLESDIR%%/ruby/addingEvidenceCodes_1.rb
+%%PORTEXAMPLES%%%%RUBY%%%%EXAMPLESDIR%%/ruby/addingEvidenceCodes_2.rb
+%%PORTEXAMPLES%%%%RUBY%%%%EXAMPLESDIR%%/ruby/appendAnnotation.rb
+%%PORTEXAMPLES%%%%RUBY%%%%EXAMPLESDIR%%/ruby/callExternalValidator.rb
+%%PORTEXAMPLES%%%%RUBY%%%%EXAMPLESDIR%%/ruby/convertSBML.rb
+%%PORTEXAMPLES%%%%RUBY%%%%EXAMPLESDIR%%/ruby/createExampleSBML.rb
+%%PORTEXAMPLES%%%%RUBY%%%%EXAMPLESDIR%%/ruby/echoSBML.rb
+%%PORTEXAMPLES%%%%RUBY%%%%EXAMPLESDIR%%/ruby/printAnnotation.rb
+%%PORTEXAMPLES%%%%RUBY%%%%EXAMPLESDIR%%/ruby/printMath.rb
+%%PORTEXAMPLES%%%%RUBY%%%%EXAMPLESDIR%%/ruby/printNotes.rb
+%%PORTEXAMPLES%%%%RUBY%%%%EXAMPLESDIR%%/ruby/printRegisteredPackages.rb
+%%PORTEXAMPLES%%%%RUBY%%%%EXAMPLESDIR%%/ruby/printSBML.rb
+%%PORTEXAMPLES%%%%RUBY%%%%EXAMPLESDIR%%/ruby/printUnits.rb
+%%PORTEXAMPLES%%%%RUBY%%%%EXAMPLESDIR%%/ruby/printsupported.rb
+%%PORTEXAMPLES%%%%RUBY%%%%EXAMPLESDIR%%/ruby/promoteParameters.rb
+%%PORTEXAMPLES%%%%RUBY%%%%EXAMPLESDIR%%/ruby/readSBML.rb
+%%PORTEXAMPLES%%%%RUBY%%%%EXAMPLESDIR%%/ruby/stripPackage.rb
+%%PORTEXAMPLES%%%%RUBY%%%%EXAMPLESDIR%%/ruby/translateMath.rb
+%%PORTEXAMPLES%%%%RUBY%%%%EXAMPLESDIR%%/ruby/unsetAnnotation.rb
+%%PORTEXAMPLES%%%%RUBY%%%%EXAMPLESDIR%%/ruby/unsetNotes.rb
+%%PORTEXAMPLES%%%%RUBY%%%%EXAMPLESDIR%%/ruby/validateSBML.rb
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample-models/from-spec/level-2/algebraicrules.xml
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample-models/from-spec/level-2/assignmentrules.xml
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample-models/from-spec/level-2/boundarycondition.xml
@@ -513,7 +361,6 @@ lib/cmake/sbml-static-config.cmake
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample-models/from-spec/level-2/overdetermined.xml
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample-models/from-spec/level-2/twodimensional.xml
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample-models/from-spec/level-2/units.xml
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample-models/from-spec/level-3/README.txt
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample-models/from-spec/level-3/algebraicrules.xml
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample-models/from-spec/level-3/assignmentrules.xml
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample-models/from-spec/level-3/boundarycondition.xml
@@ -531,4 +378,3 @@ lib/cmake/sbml-static-config.cmake
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample-models/from-spec/level-3/overdetermined.xml
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample-models/from-spec/level-3/twoalgebraicrules.xml
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample-models/from-spec/level-3/twodimensional.xml
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/xslt/layout/layout2svg.xsl