Index: head/biology/libsbml/Makefile =================================================================== --- head/biology/libsbml/Makefile (revision 502096) +++ head/biology/libsbml/Makefile (revision 502097) @@ -1,55 +1,55 @@ # Created by: Wen Heping # $FreeBSD$ PORTNAME= libsbml -PORTVERSION= 5.17.0 +PORTVERSION= 5.18.0 CATEGORIES= biology devel MASTER_SITES= SF/sbml/${PORTNAME}/${PORTVERSION}/stable DISTNAME= libSBML-${PORTVERSION}-core-src MAINTAINER= ports@FreeBSD.org COMMENT= API Library for Working with SBML File LICENSE= LGPL21 LICENSE_FILE= ${WRKSRC}/COPYING.txt WRKSRC= ${WRKDIR}/${PORTNAME}-${PORTVERSION} USES= cmake iconv:build USE_CXXSTD= c++98 USE_GNOME= libxml2 USE_LDCONFIG= yes CFLAGS+= -I${ICONV_PREFIX}/include LDFLAGS+= -L${ICONV_PREFIX}/lib OPTIONS_DEFINE= EXAMPLES PYTHON RUBY OPTIONS_SUB= yes PLIST_SUB+= PORTVERSION=${PORTVERSION} PYTHON_BUILD_DEPENDS= swig3.0:devel/swig30 PYTHON_USES= python:2.7 PYTHON_CMAKE_ON= -DWITH_PYTHON:BOOL=ON \ -DPYTHON_INCLUDE_DIR:STRING="${PYTHON_INCLUDEDIR}" \ -DPYTHON_LIBRARY:STRING="${PYTHONBASE}/lib/lib${PYTHON_VERSION}.so" \ -DPYTHON_EXECUTABLE:STRING="${PYTHON_CMD}" PYTHON_BINARY_ALIAS= swig=swig3.0 RUBY_BUILD_DEPENDS= swig3.0:devel/swig30 RUBY_USE= ruby=yes RUBY_CMAKE_ON= -DWITH_RUBY:BOOL=ON RUBY_BINARY_ALIAS= swig=swig3.0 post-patch: @${REINPLACE_CMD} -e \ 's|/usr/local/include|${LOCALBASE}/include| ; \ s|/usr/local/lib|${LOCALBASE}/lib| ; \ s|$${CMAKE_INSTALL_LIBDIR}/pkgconfig|libdata/pkgconfig| ; \ /$${DOCUMENTATION_FILES}/s|^|#|' ${WRKSRC}/CMakeLists.txt post-install-EXAMPLES-on: ${MKDIR} ${STAGEDIR}${EXAMPLESDIR} cd ${WRKSRC}/examples && ${COPYTREE_SHARE} . \ ${STAGEDIR}${EXAMPLESDIR} '! -name *Makefile*' .include Index: head/biology/libsbml/distinfo =================================================================== --- head/biology/libsbml/distinfo (revision 502096) +++ head/biology/libsbml/distinfo (revision 502097) @@ -1,3 +1,3 @@ -TIMESTAMP = 1529913224 -SHA256 (libSBML-5.17.0-core-src.tar.gz) = ab2bd29720e8d5a92166eb3eacc8d77b34e3f94a83ac19924708e1b0e4317494 -SIZE (libSBML-5.17.0-core-src.tar.gz) = 14767045 +TIMESTAMP = 1558342307 +SHA256 (libSBML-5.18.0-core-src.tar.gz) = 900a8a41682c6fe69b162bce45e4221d7e23f30acb6c3d3516d1d931f353936a +SIZE (libSBML-5.18.0-core-src.tar.gz) = 14630152 Index: head/biology/libsbml/pkg-plist =================================================================== --- head/biology/libsbml/pkg-plist (revision 502096) +++ head/biology/libsbml/pkg-plist (revision 502097) @@ -1,541 +1,534 @@ include/sbml/AlgebraicRule.h include/sbml/AssignmentRule.h include/sbml/Compartment.h include/sbml/CompartmentType.h include/sbml/Constraint.h include/sbml/Delay.h include/sbml/Event.h include/sbml/EventAssignment.h include/sbml/ExpectedAttributes.h include/sbml/FunctionDefinition.h include/sbml/InitialAssignment.h include/sbml/KineticLaw.h include/sbml/ListOf.h include/sbml/LocalParameter.h include/sbml/Model.h include/sbml/ModifierSpeciesReference.h include/sbml/Parameter.h include/sbml/Priority.h include/sbml/RateRule.h include/sbml/Reaction.h include/sbml/Rule.h include/sbml/SBMLConstructorException.h include/sbml/SBMLDocument.h include/sbml/SBMLError.h include/sbml/SBMLErrorLog.h include/sbml/SBMLErrorTable.h include/sbml/SBMLNamespaces.h include/sbml/SBMLReader.h include/sbml/SBMLTransforms.h include/sbml/SBMLTypeCodes.h include/sbml/SBMLTypes.h include/sbml/SBMLVisitor.h include/sbml/SBMLWriter.h include/sbml/SBO.h include/sbml/SBase.h include/sbml/SimpleSpeciesReference.h include/sbml/Species.h include/sbml/SpeciesReference.h include/sbml/SpeciesType.h include/sbml/StoichiometryMath.h include/sbml/SyntaxChecker.h include/sbml/Trigger.h include/sbml/Unit.h include/sbml/UnitDefinition.h include/sbml/UnitKind.h include/sbml/annotation/CVTerm.h include/sbml/annotation/Date.h include/sbml/annotation/ModelCreator.h include/sbml/annotation/ModelHistory.h include/sbml/annotation/RDFAnnotation.h include/sbml/annotation/RDFAnnotationParser.h include/sbml/common/common-documentation.h include/sbml/common/common-sbmlerror-codes.h include/sbml/common/common.h include/sbml/common/extern.h include/sbml/common/libsbml-config-common.h include/sbml/common/libsbml-config-packages.h include/sbml/common/libsbml-config.h include/sbml/common/libsbml-namespace.h include/sbml/common/libsbml-package.h include/sbml/common/libsbml-version.h include/sbml/common/operationReturnValues.h include/sbml/common/sbmlfwd.h include/sbml/compress/CompressCommon.h include/sbml/compress/InputDecompressor.h include/sbml/compress/OutputCompressor.h include/sbml/compress/bzfstream.h include/sbml/compress/crypt.h include/sbml/compress/ioapi.h include/sbml/compress/ioapi_mem.h include/sbml/compress/iowin32.h include/sbml/compress/unzip.h include/sbml/compress/zfstream.h include/sbml/compress/zip.h include/sbml/compress/zipfstream.h include/sbml/conversion/ConversionOption.h include/sbml/conversion/ConversionProperties.h include/sbml/conversion/SBMLConverter.h include/sbml/conversion/SBMLConverterRegister.h include/sbml/conversion/SBMLConverterRegistry.h include/sbml/conversion/SBMLConverterTypes.h include/sbml/conversion/SBMLFunctionDefinitionConverter.h include/sbml/conversion/SBMLIdConverter.h include/sbml/conversion/SBMLInferUnitsConverter.h include/sbml/conversion/SBMLInitialAssignmentConverter.h include/sbml/conversion/SBMLLevel1Version1Converter.h include/sbml/conversion/SBMLLevelVersionConverter.h include/sbml/conversion/SBMLLocalParameterConverter.h include/sbml/conversion/SBMLRateOfConverter.h include/sbml/conversion/SBMLReactionConverter.h include/sbml/conversion/SBMLRuleConverter.h include/sbml/conversion/SBMLStripPackageConverter.h include/sbml/conversion/SBMLUnitsConverter.h include/sbml/extension/ASTBasePlugin.h include/sbml/extension/ISBMLExtensionNamespaces.h include/sbml/extension/RegisterExtensions.h include/sbml/extension/SBMLDocumentPlugin.h include/sbml/extension/SBMLDocumentPluginNotRequired.h include/sbml/extension/SBMLExtension.h include/sbml/extension/SBMLExtensionException.h include/sbml/extension/SBMLExtensionNamespaces.h include/sbml/extension/SBMLExtensionRegister.h include/sbml/extension/SBMLExtensionRegistry.h include/sbml/extension/SBaseExtensionPoint.h include/sbml/extension/SBasePlugin.h include/sbml/extension/SBasePluginCreator.h include/sbml/extension/SBasePluginCreatorBase.h -include/sbml/math/ASTBase.h -include/sbml/math/ASTBinaryFunctionNode.h -include/sbml/math/ASTCSymbol.h -include/sbml/math/ASTCSymbolAvogadroNode.h -include/sbml/math/ASTCSymbolDelayNode.h -include/sbml/math/ASTCSymbolRateOfNode.h -include/sbml/math/ASTCSymbolTimeNode.h -include/sbml/math/ASTCiFunctionNode.h -include/sbml/math/ASTCiNumberNode.h -include/sbml/math/ASTCnBase.h -include/sbml/math/ASTCnExponentialNode.h -include/sbml/math/ASTCnIntegerNode.h -include/sbml/math/ASTCnRationalNode.h -include/sbml/math/ASTCnRealNode.h -include/sbml/math/ASTConstantNumberNode.h -include/sbml/math/ASTFunction.h -include/sbml/math/ASTFunctionBase.h -include/sbml/math/ASTLambdaFunctionNode.h -include/sbml/math/ASTNaryFunctionNode.h include/sbml/math/ASTNode.h -include/sbml/math/ASTNumber.h -include/sbml/math/ASTPiecewiseFunctionNode.h -include/sbml/math/ASTQualifierNode.h -include/sbml/math/ASTSemanticsNode.h -include/sbml/math/ASTTypes.h -include/sbml/math/ASTUnaryFunctionNode.h +include/sbml/math/ASTNodeType.h +include/sbml/math/DefinitionURLRegistry.h include/sbml/math/FormulaFormatter.h include/sbml/math/FormulaParser.h include/sbml/math/FormulaTokenizer.h include/sbml/math/L3FormulaFormatter.h include/sbml/math/L3Parser.h include/sbml/math/L3ParserSettings.h include/sbml/math/MathML.h +include/sbml/packages/l3v2extendedmath/common/L3v2extendedmathExtensionTypes.h +include/sbml/packages/l3v2extendedmath/common/l3v2extendedmathfwd.h +include/sbml/packages/l3v2extendedmath/extension/L3v2extendedmathASTPlugin.h +include/sbml/packages/l3v2extendedmath/extension/L3v2extendedmathExtension.h +include/sbml/packages/l3v2extendedmath/extension/L3v2extendedmathSBMLDocumentPlugin.h +include/sbml/packages/l3v2extendedmath/validator/L3v2extendedmathMathMLConsistencyValidator.h +include/sbml/packages/l3v2extendedmath/validator/L3v2extendedmathSBMLError.h +include/sbml/packages/l3v2extendedmath/validator/L3v2extendedmathSBMLErrorTable.h +include/sbml/packages/l3v2extendedmath/validator/L3v2extendedmathUnitConsistencyValidator.h +include/sbml/packages/l3v2extendedmath/validator/L3v2extendedmathValidator.h +include/sbml/packages/l3v2extendedmath/validator/constraints/L3v2EMArgumentsUnitsCheck.h +include/sbml/packages/l3v2extendedmath/validator/constraints/L3v2EMNumberArgsMathCheck.h include/sbml/units/FormulaUnitsData.h include/sbml/units/UnitFormulaFormatter.h include/sbml/units/UnitKindList.h +include/sbml/util/CallbackRegistry.h include/sbml/util/ElementFilter.h include/sbml/util/IdFilter.h include/sbml/util/IdList.h include/sbml/util/IdentifierTransformer.h include/sbml/util/List.h +include/sbml/util/MathFilter.h include/sbml/util/MetaIdFilter.h include/sbml/util/PrefixTransformer.h include/sbml/util/Stack.h include/sbml/util/StringBuffer.h include/sbml/util/memory.h include/sbml/util/util.h include/sbml/validator/ConsistencyValidator.h include/sbml/validator/ConstraintMacros.h include/sbml/validator/IdentifierConsistencyValidator.h include/sbml/validator/InternalConsistencyValidator.h include/sbml/validator/L1CompatibilityValidator.h include/sbml/validator/L2v1CompatibilityValidator.h include/sbml/validator/L2v2CompatibilityValidator.h include/sbml/validator/L2v3CompatibilityValidator.h include/sbml/validator/L2v4CompatibilityValidator.h include/sbml/validator/L3v1CompatibilityValidator.h include/sbml/validator/L3v2CompatibilityValidator.h include/sbml/validator/MathMLConsistencyValidator.h include/sbml/validator/ModelingPracticeValidator.h include/sbml/validator/OverdeterminedValidator.h include/sbml/validator/SBMLExternalValidator.h include/sbml/validator/SBMLInternalValidator.h include/sbml/validator/SBMLValidator.h include/sbml/validator/SBOConsistencyValidator.h include/sbml/validator/StrictUnitConsistencyValidator.h include/sbml/validator/UnitConsistencyValidator.h include/sbml/validator/VConstraint.h include/sbml/validator/Validator.h include/sbml/xml/ExpatAttributes.h include/sbml/xml/ExpatHandler.h include/sbml/xml/ExpatParser.h include/sbml/xml/LibXMLAttributes.h include/sbml/xml/LibXMLHandler.h include/sbml/xml/LibXMLNamespaces.h include/sbml/xml/LibXMLParser.h include/sbml/xml/LibXMLTranscode.h include/sbml/xml/XMLAttributes.h include/sbml/xml/XMLBuffer.h include/sbml/xml/XMLConstructorException.h include/sbml/xml/XMLError.h include/sbml/xml/XMLErrorLog.h include/sbml/xml/XMLExtern.h include/sbml/xml/XMLFileBuffer.h include/sbml/xml/XMLHandler.h include/sbml/xml/XMLInputStream.h include/sbml/xml/XMLLogOverride.h include/sbml/xml/XMLMemoryBuffer.h include/sbml/xml/XMLNamespaces.h include/sbml/xml/XMLNode.h include/sbml/xml/XMLOutputStream.h include/sbml/xml/XMLParser.h include/sbml/xml/XMLToken.h include/sbml/xml/XMLTokenizer.h include/sbml/xml/XMLTriple.h include/sbml/xml/XercesAttributes.h 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 %%RUBY%%%%RUBY_SITEARCHLIBDIR%%/libSBML.so %%PORTEXAMPLES%%%%EXAMPLESDIR%%/CMakeLists.txt %%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 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/addingEvidenceCodes_1.cpp %%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/addingEvidenceCodes_2.cpp %%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/appendAnnotation.cpp %%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/callExternalValidator.cpp %%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/convertReactions.cpp %%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/convertSBML.cpp %%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/convertToL1V1.cpp %%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/createExampleSBML.cpp %%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/echoSBML.cpp %%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 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/printRegisteredPackages.cpp %%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/printSBML.cpp %%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/printSupported.cpp %%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/printUnits.cpp %%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/promoteParameters.cpp %%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/readSBML.cpp %%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/renameSId.cpp %%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/rngvalidator.cpp %%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/setIdFromNames.cpp %%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/setNamesFromIds.cpp %%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/stripPackage.cpp %%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/translateL3Math.cpp %%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/translateMath.cpp %%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/unsetAnnotation.cpp %%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/unsetNotes.cpp %%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 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%%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 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%%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 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%%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%%/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 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample-models/from-spec/level-2/delay.xml %%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample-models/from-spec/level-2/dimerization.xml %%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample-models/from-spec/level-2/enzymekinetics.xml %%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample-models/from-spec/level-2/events.xml %%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample-models/from-spec/level-2/functiondef.xml %%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample-models/from-spec/level-2/multicomp.xml %%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 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