[med-svn] [libsbml] branch master updated (e83d389 -> 3c0da35)
Andreas Tille
tille at debian.org
Mon Aug 7 16:23:45 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a change to branch master
in repository libsbml.
from e83d389 Upload to unstable
new a36c59c New upstream version 5.15.2+dfsg
new 1ee78da Updated version 5.15.2+dfsg from 'upstream/5.15.2+dfsg'
new b316bb1 New upstream version
new 3c0da35 Standards-Version: 4.0.0 (no changes needed)
The 4 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails. The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.
Summary of changes:
AUTHORS.txt | 2 +-
CMakeLists.txt | 159 +-
LICENSE.html | 2 +-
LICENSE.txt | 2 +-
Makefile.in | 9 +-
NEWS.txt | 387 +-
README.txt | 4 +-
VERSION.txt | 2 +-
VERSION_PACKAGES.ac | 13 +-
aclocal.m4 | 4 +-
arrays-package.cmake | 75 +-
cmake_uninstall.cmake.in | 2 +-
common.cmake | 2 +-
comp-package.cmake | 2 +-
config/bzip2.m4 | 4 +-
config/chk_swig_version.sh.in | 2 +-
config/csharp.m4 | 4 +-
config/doxygen.m4 | 13 +-
config/expat.m4 | 2 +-
config/java.m4 | 6 +-
config/libcheck.m4 | 2 +-
config/machine.m4 | 2 +-
config/makefile-common-actions.mk | 4 +-
config/makefile-common-vars.mk.in | 6 +-
config/matlab.m4 | 2 +-
config/octave.m4 | 2 +-
config/perl.m4 | 2 +-
config/platform.m4 | 2 +-
config/printJavaDataModel.java | 2 +-
config/python.m4 | 4 +-
config/ruby.m4 | 4 +-
config/runldpath.m4 | 2 +-
config/swig.m4 | 2 +-
config/xercesc.m4 | 2 +-
config/zlib.m4 | 4 +-
configure | 605 +-
configure.ac | 46 +-
debian/changelog | 7 +
debian/control | 2 +-
debian/patches/hardening.patch | 4 +-
debian/patches/mips-compile-with-O1.patch | 2 +-
debian/patches/perl-installdirs.patch | 2 +-
debian/patches/spelling.patch | 188 +-
debian/patches/swig-3.x.patch | 24 +-
distrib-package.cmake | 2 +-
docs/CMakeLists.txt | 2 +-
docs/Makefile.in | 4 +-
docs/src/Makefile.in | 18 +-
docs/src/common-text/astnode-types.html | 50 +-
docs/src/common-text/libsbml-blurb.html | 6 +-
docs/src/common-text/libsbml-communications.html | 2 +-
docs/src/common-text/libsbml-downloading.html.in | 272 +-
.../common-text/libsbml-group-comp-intro.html.in | 5 +-
.../common-text/libsbml-group-fbc-intro.html.in | 5 +-
.../common-text/libsbml-group-groups-intro.html.in | 4 +
.../common-text/libsbml-group-layout-intro.html.in | 6 +-
.../common-text/libsbml-group-multi-intro.html.in | 33 +
.../common-text/libsbml-group-qual-intro.html.in | 6 +-
docs/src/common-text/libsbml-installation.html.in | 2 +-
docs/src/common-text/pkg-marker-multi.html | 1 +
docs/src/common-text/pkg-marker-multi.txt | 1 +
.../common-text/sbml-specifications-table.html.in | 130 +-
docs/src/css/libsbml-base-stylesheet.css | 26 +-
docs/src/css/libsbml-doxygen-stylesheet.css | 54 +-
docs/src/doxygen-config-c.txt.cmake | 4 +
docs/src/doxygen-config-c.txt.in | 4 +
docs/src/doxygen-config-common.txt | 4 +
docs/src/doxygen-config-common.txt.cmake | 4 +
docs/src/doxygen-config-cpp.txt.cmake | 2 +-
docs/src/doxygen-config-cpp.txt.in | 2 +-
docs/src/doxygen-config-csharp.txt.cmake | 2 +-
docs/src/doxygen-config-csharp.txt.in | 2 +-
docs/src/doxygen-config-python.txt.cmake | 2 +-
docs/src/doxygen-config-python.txt.in | 2 +-
docs/src/doxygen-layout-c.xml | 1 +
docs/src/doxygen-layout-cpp.xml | 1 +
docs/src/doxygen-layout-csharp.xml | 1 +
docs/src/doxygen-layout-python.xml | 1 +
docs/src/filters/doc-filter-c.py | 2 +-
docs/src/filters/doc-filter-csharp.py | 2 +-
docs/src/filters/doc-filter-python.py | 2 +-
.../java-substitutions/libsbmlConstants.java.in | 488 +-
docs/src/libsbml-coding.txt | 4 +-
docs/src/libsbml-csharp-example-files.txt | 5 +
docs/src/libsbml-csharp-reading-files.txt | 2 +-
docs/src/libsbml-example-files.txt | 5 +
docs/src/libsbml-groups.txt | 6 +
docs/src/libsbml-java-example-footer.html | 2 +-
docs/src/libsbml-java-footer.html | 2 +-
docs/src/libsbml-java-overview.html | 4 +-
docs/src/libsbml-java-reading.html | 2 +-
docs/src/libsbml-matlab-reading-files.txt | 203 +-
docs/src/libsbml-python-reading-files.txt | 2 +-
docs/src/python-substitutions/CompPkgNamespaces.py | 2 +
docs/src/python-substitutions/FbcPkgNamespaces.py | 2 +
.../python-substitutions/GroupsPkgNamespaces.py | 1 +
.../python-substitutions/LayoutPkgNamespaces.py | 2 +
docs/src/python-substitutions/QualPkgNamespaces.py | 2 +
docs/src/python-substitutions/libsbml.py | 416 +
docs/src/utilities/compare-classes.py | 2 +-
docs/src/utilities/compare-constants.py | 3 +-
docs/src/utilities/generate-class-name-list.py | 2 +-
docs/src/utilities/generate-converters-list.py | 2 +-
.../utilities/generate-cplusplus-class-names.py | 2 +-
docs/src/utilities/generate-extensions-summary.py | 2 +-
docs/src/utilities/generate-pkg-stylesheet.py | 29 +-
dyn-package.cmake | 2 +-
examples/CMakeLists.txt | 2 +-
examples/README.txt | 2 +-
examples/c++/CMakeLists.txt | 277 +-
examples/c++/Makefile.in | 2 +-
examples/c++/addCVTerms.cpp | 2 +-
examples/c++/addCustomValidator.cpp | 2 +-
examples/c++/addModelHistory.cpp | 2 +-
examples/c++/addingEvidenceCodes_1.cpp | 2 +-
examples/c++/addingEvidenceCodes_2.cpp | 2 +-
examples/c++/appendAnnotation.cpp | 2 +-
examples/c++/arrays/CMakeLists.txt | 2 +-
examples/c++/callExternalValidator.cpp | 2 +-
examples/c++/comp/CMakeLists.txt | 2 +-
examples/c++/comp/Makefile.in | 6 +-
examples/c++/comp/SBMLHttpResolverExample.cpp | 2 +-
examples/c++/comp/flattenModel.cpp | 2 +-
examples/c++/comp/flattenModelAdvanced.cpp | 2 +-
examples/c++/comp/spec_example1.cpp | 2 +-
examples/c++/comp/spec_example2.cpp | 2 +-
examples/c++/comp/spec_example3.cpp | 2 +-
examples/c++/comp/spec_example4.cpp | 2 +-
examples/c++/convertReactions.cpp | 2 +-
examples/c++/convertSBML.cpp | 2 +-
examples/c++/convertToL1V1.cpp | 2 +-
examples/c++/createExampleSBML.cpp | 2 +-
examples/c++/dyn/CMakeLists.txt | 2 +-
examples/c++/dyn/dyn_example1.cpp | 2 +-
examples/c++/dyn/dyn_example2.cpp | 2 +-
examples/c++/echoSBML.cpp | 2 +-
examples/c++/fbc/CMakeLists.txt | 2 +-
examples/c++/fbc/Makefile.in | 6 +-
examples/c++/fbc/convertCobraToFbc.cpp | 2 +-
examples/c++/fbc/convertFbcToCobra.cpp | 2 +-
examples/c++/fbc/convertFbcV1ToV2.cpp | 2 +-
examples/c++/fbc/convertFbcV2ToV1.cpp | 2 +-
examples/c++/fbc/fbc_example1.cpp | 2 +-
examples/c++/getAllElementsWithNotes.cpp | 2 +-
examples/c++/inferUnits.cpp | 2 +-
examples/c++/inlineFunctionDefintions.cpp | 2 +-
examples/c++/layout/CMakeLists.txt | 2 +-
examples/c++/layout/Makefile.in | 6 +-
examples/c++/layout/addLayout.cpp | 2 +-
examples/c++/layout/convertLayout.cpp | 2 +-
examples/c++/printAnnotation.cpp | 2 +-
examples/c++/printMath.cpp | 2 +-
examples/c++/printNotes.cpp | 2 +-
examples/c++/printRegisteredPackages.cpp | 2 +-
examples/c++/printSBML.cpp | 2 +-
examples/c++/printSupported.cpp | 2 +-
examples/c++/printUnits.cpp | 2 +-
examples/c++/promoteParameters.cpp | 2 +-
examples/c++/qual/CMakeLists.txt | 2 +-
examples/c++/qual/Makefile.in | 6 +-
examples/c++/qual/qual_example1.cpp | 2 +-
examples/c++/readSBML.cpp | 2 +-
examples/c++/renameSId.cpp | 2 +-
examples/c++/rngvalidator.cpp | 4 +-
examples/c++/setIdFromNames.cpp | 2 +-
examples/c++/setNamesFromIds.cpp | 2 +-
examples/c++/stripPackage.cpp | 2 +-
examples/c++/translateL3Math.cpp | 4 +-
examples/c++/translateMath.cpp | 4 +-
examples/c++/unsetAnnotation.cpp | 2 +-
examples/c++/unsetNotes.cpp | 2 +-
examples/c++/util.c | 2 +-
examples/c++/util.h | 2 +-
examples/c++/validateSBML.cpp | 2 +-
examples/c/CMakeLists.txt | 131 +-
examples/c/FormulaGraphvizFormatter.h | 2 +-
examples/c/Makefile.in | 6 +-
examples/c/addCVTerms.c | 2 +-
examples/c/addModelHistory.c | 2 +-
examples/c/addingEvidenceCodes_1.c | 2 +-
examples/c/addingEvidenceCodes_2.c | 2 +-
examples/c/appendAnnotation.c | 2 +-
examples/c/comp/CMakeLists.txt | 2 +-
examples/c/comp/Makefile.in | 6 +-
examples/c/comp/flattenModel.c | 2 +-
examples/c/comp/spec_example1.c | 2 +-
examples/c/convertSBML.c | 2 +-
examples/c/createExampleSBML.c | 2 +-
examples/c/drawMath.c | 2 +-
examples/c/echoSBML.c | 2 +-
examples/c/printAnnotation.c | 2 +-
examples/c/printMath.c | 2 +-
examples/c/printNotes.c | 2 +-
examples/c/printRegisteredPackages.c | 2 +-
examples/c/printSBML.c | 2 +-
examples/c/printSupported.c | 2 +-
examples/c/printUnits.c | 2 +-
examples/c/promoteParameters.c | 2 +-
examples/c/readSBML.c | 2 +-
examples/c/stripPackage.c | 2 +-
examples/c/translateL3Math.c | 4 +-
examples/c/translateMath.c | 2 +-
examples/c/unsetAnnotation.c | 2 +-
examples/c/unsetNotes.c | 2 +-
examples/c/util.c | 6 +-
examples/c/util.h | 2 +-
examples/c/validateSBML.c | 2 +-
examples/comp-package.cmake | 2 +-
examples/csharp/CMakeLists.txt | 324 +-
examples/csharp/GetAllElementsWithNotes.cs | 2 +-
examples/csharp/Makefile.in | 2 +-
examples/csharp/SetIdFromNames.cs | 2 +-
examples/csharp/addCVTerms.cs | 2 +-
examples/csharp/addCustomValidator.cs | 2 +-
examples/csharp/addModelHistory.cs | 2 +-
examples/csharp/addingEvidenceCodes_1.cs | 4 +-
examples/csharp/addingEvidenceCodes_2.cs | 2 +-
examples/csharp/appendAnnotation.cs | 2 +-
examples/csharp/callExternalValidator.cs | 2 +-
examples/csharp/comp/CMakeLists.txt | 2 +-
examples/csharp/comp/CompExample1.cs | 2 +-
examples/csharp/comp/CustomResolver.cs | 2 +-
examples/csharp/comp/FlattenModel.cs | 2 +-
examples/csharp/comp/SpecExample1.cs | 2 +-
examples/csharp/comp/SpecExample2.cs | 2 +-
examples/csharp/comp/SpecExample3.cs | 2 +-
examples/csharp/comp/SpecExample4.cs | 2 +-
examples/csharp/convertSBML.cs | 2 +-
examples/csharp/createExampleSBML.cs | 2 +-
examples/csharp/echoSBML.cs | 2 +-
examples/csharp/evaluateCustomMath.cs | 2 +-
examples/csharp/fbc/CMakeLists.txt | 2 +-
examples/csharp/fbc/convertCobraToFbc.cs | 2 +-
examples/csharp/fbc/convertFbcToCobra.cs | 2 +-
examples/csharp/fbc/fbc_example1.cs | 2 +-
examples/csharp/inlineInitialAssignments.cs | 2 +-
examples/csharp/layout/CMakeLists.txt | 2 +-
examples/csharp/multi/CMakeLists.txt | 60 +
examples/csharp/multi/multi_example1.cs | 139 +
examples/csharp/multi/multi_example2.cs | 107 +
examples/csharp/multi/multi_example3.cs | 147 +
examples/csharp/multi/printMulti.cs | 230 +
examples/csharp/printAnnotation.cs | 2 +-
examples/csharp/printMath.cs | 2 +-
examples/csharp/printNotes.cs | 2 +-
examples/csharp/printRegisteredPackages.cs | 2 +-
examples/csharp/printSBML.cs | 2 +-
examples/csharp/printUnits.cs | 2 +-
examples/csharp/printsupported.cs | 2 +-
examples/csharp/promoteParameters.cs | 2 +-
examples/csharp/qual/CMakeLists.txt | 2 +-
examples/csharp/qual/qual_example1.cs | 2 +-
examples/csharp/readSBML.cs | 2 +-
examples/csharp/replaceOneFD.cs | 2 +-
examples/csharp/stripPackage.cs | 2 +-
examples/csharp/translateMath.cs | 2 +-
examples/csharp/unsetAnnotation.cs | 2 +-
examples/csharp/unsetNotes.cs | 2 +-
examples/csharp/validateSBML.cs | 2 +-
examples/dyn-package.cmake | 2 +-
examples/fbc-package.cmake | 2 +-
examples/java/CMakeLists.txt | 329 +-
examples/java/Makefile.in | 2 +-
examples/java/addCVTerms.java | 2 +-
examples/java/addCustomValidator.java | 2 +-
examples/java/addModelHistory.java | 2 +-
examples/java/addingEvidenceCodes_1.java | 4 +-
examples/java/addingEvidenceCodes_2.java | 2 +-
examples/java/appendAnnotation.java | 2 +-
examples/java/callExternalValidator.java | 2 +-
examples/java/comp/CMakeLists.txt | 2 +-
examples/java/comp/customResolver.java | 2 +-
examples/java/comp/flattenModel.java | 2 +-
examples/java/convertSBML.java | 2 +-
examples/java/createExampleSBML.java | 2 +-
examples/java/echoSBML.java | 2 +-
examples/java/evaluateCustomMath.java | 2 +-
examples/java/evaluateMath.java | 2 +-
examples/java/fbc/CMakeLists.txt | 2 +-
examples/java/fbc/convertCobraToFbc.java | 2 +-
examples/java/fbc/convertFbcToCobra.java | 2 +-
examples/java/fbc/fbc_example1.java | 2 +-
examples/java/getAllElementsWithNotes.java | 2 +-
examples/java/inlineInitialAssignments.java | 2 +-
examples/java/layout/CMakeLists.txt | 2 +-
examples/java/multi/CMakeLists.txt | 73 +
examples/java/multi/multi_example1.java | 140 +
examples/java/multi/multi_example2.java | 106 +
examples/java/multi/multi_example3.java | 148 +
examples/java/printAnnotation.java | 2 +-
examples/java/printMath.java | 2 +-
examples/java/printNotes.java | 2 +-
examples/java/printRegisteredPackages.java | 2 +-
examples/java/printSBML.java | 2 +-
examples/java/printUnits.java | 2 +-
examples/java/printsupported.java | 2 +-
examples/java/promoteParameters.java | 2 +-
examples/java/qual/CMakeLists.txt | 2 +-
examples/java/qual/qual_example1.java | 2 +-
examples/java/readSBML.java | 2 +-
examples/java/replaceOneFD.java | 2 +-
examples/java/setIdFromNames.java | 2 +-
examples/java/spatial/CMakeLists.txt | 2 +-
examples/java/spatial/spatial_example1.java | 2 +-
examples/java/stripPackage.java | 2 +-
examples/java/translateMath.java | 2 +-
examples/java/unsetAnnotation.java | 2 +-
examples/java/unsetNotes.java | 2 +-
examples/java/validateSBML.java | 2 +-
examples/javascript/addCVTerms.js | 2 +-
examples/javascript/addModelHistory.js | 2 +-
examples/javascript/addingEvidenceCodes_1.js | 2 +-
examples/javascript/addingEvidenceCodes_2.js | 2 +-
examples/javascript/appendAnnotation.js | 2 +-
examples/javascript/callExternalValidator.js | 2 +-
examples/javascript/convertSBML.js | 2 +-
examples/javascript/createExampleSBML.js | 2 +-
examples/javascript/echoSBML.js | 2 +-
examples/javascript/printAnnotation.js | 2 +-
examples/javascript/printMath.js | 2 +-
examples/javascript/printNotes.js | 2 +-
examples/javascript/printRegisteredPackages.js | 2 +-
examples/javascript/printSBML.js | 2 +-
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examples/javascript/printsupported.js | 2 +-
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examples/javascript/readSBML.js | 2 +-
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examples/javascript/translateMath.js | 2 +-
examples/javascript/unsetAnnotation.js | 2 +-
examples/javascript/unsetNotes.js | 2 +-
examples/javascript/validateSBML.js | 2 +-
examples/layout-package.cmake | 2 +-
examples/multi-package.cmake | 4 +-
examples/perl/addCVTerms.pl | 2 +-
examples/perl/addCustomValidator.pl | 2 +-
examples/perl/addModelHistory.pl | 2 +-
examples/perl/addingEvidenceCodes_1.pl | 2 +-
examples/perl/addingEvidenceCodes_2.pl | 2 +-
examples/perl/appendAnnotation.pl | 2 +-
examples/perl/callExternalValidator.pl | 2 +-
examples/perl/comp/flattenModel.pl | 2 +-
examples/perl/createExampleSBML.pl | 2 +-
examples/perl/echoSBML.pl | 2 +-
examples/perl/fbc/convertCobraToFbc.pl | 2 +-
examples/perl/fbc/convertFbcToCobra.pl | 2 +-
examples/perl/fbc/example1.pl | 2 +-
examples/perl/printAnnotation.pl | 2 +-
examples/perl/printNotes.pl | 2 +-
examples/perl/printRegisteredPackages.pl | 2 +-
examples/perl/printUnits.pl | 2 +-
examples/perl/printsupported.pl | 2 +-
examples/perl/promoteParameters.pl | 2 +-
examples/perl/stripPackage.pl | 2 +-
examples/perl/unsetAnnotation.pl | 2 +-
examples/perl/unsetNotes.pl | 2 +-
examples/python/addCVTerms.py | 5 +-
examples/python/addCustomValidator.py | 119 +-
examples/python/addModelHistory.py | 2 +-
examples/python/addingEvidenceCodes_1.py | 2 +-
examples/python/addingEvidenceCodes_2.py | 2 +-
examples/python/appendAnnotation.py | 2 +-
examples/python/append_to_note.py | 98 +
examples/python/arrays/flattenArrays.py | 91 +
examples/python/callExternalValidator.py | 2 +-
examples/python/comp/flattenModel.py | 2 +-
examples/python/convertSBML.py | 2 +-
examples/python/createExampleSBML.py | 2 +-
examples/python/createSimpleModel.py | 2 +-
examples/python/dyn/dyn_example1.py | 2 +-
examples/python/dyn/dyn_example2.py | 2 +-
examples/python/echoSBML.py | 2 +-
examples/python/evaluateCustomMath.py | 2 +-
examples/python/fbc/convertCobraToFbc.py | 2 +-
examples/python/fbc/convertFbcToCobra.py | 2 +-
examples/python/fbc/fbc_example1.py | 2 +-
examples/python/getAllElementsWithNotes.py | 112 +-
examples/python/inlineInitialAssignments.py | 2 +-
examples/python/layout/convertLayout.py | 2 +-
examples/python/printAnnotation.py | 2 +-
examples/python/printMath.py | 2 +-
examples/python/printNotes.py | 2 +-
examples/python/printRegisteredPackages.py | 2 +-
examples/python/printSBML.py | 2 +-
examples/python/printUnits.py | 2 +-
examples/python/printsupported.py | 2 +-
examples/python/promoteParameters.py | 70 +-
examples/python/qual/qual_example1.py | 2 +-
examples/python/readSBML.py | 2 +-
examples/python/replaceOneFD.py | 2 +-
examples/python/setIdFromNames.py | 2 +-
examples/python/stripPackage.py | 2 +-
examples/python/translateMath.py | 2 +-
examples/python/unsetAnnotation.py | 2 +-
examples/python/unsetNotes.py | 2 +-
examples/python/validateSBML.py | 2 +-
examples/qual-package.cmake | 2 +-
examples/r/addCVTerms.R | 2 +-
examples/r/addModelHistory.R | 2 +-
examples/r/addingEvidenceCodes_1.R | 2 +-
examples/r/addingEvidenceCodes_2.R | 2 +-
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examples/r/comp/flattenModel.R | 2 +-
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examples/r/createExampleSBML.R | 2 +-
examples/r/echoSBML.R | 2 +-
examples/r/evaluateMath.R | 2 +-
examples/r/fbc/convertCobraToFbc.R | 2 +-
examples/r/fbc/convertFbcToCobra.R | 2 +-
examples/r/printAnnotation.R | 2 +-
examples/r/printMath.R | 2 +-
examples/r/printNotes.R | 2 +-
examples/r/printRegisteredPackages.R | 2 +-
examples/r/printSBML.R | 2 +-
examples/r/printSupported.R | 2 +-
examples/r/printUnits.R | 2 +-
examples/r/promoteParameters.R | 2 +-
examples/r/readSBML.R | 2 +-
examples/r/stripPackage.R | 2 +-
examples/r/translateMath.R | 2 +-
examples/r/unsetAnnotation.R | 2 +-
examples/r/unsetNotes.R | 2 +-
examples/r/validateSBML.R | 2 +-
examples/ruby/addCVTerms.rb | 2 +-
examples/ruby/addCustomValidator.rb | 2 +-
examples/ruby/addModelHistory.rb | 2 +-
examples/ruby/addingEvidenceCodes_1.rb | 2 +-
examples/ruby/addingEvidenceCodes_2.rb | 2 +-
examples/ruby/appendAnnotation.rb | 2 +-
examples/ruby/callExternalValidator.rb | 2 +-
examples/ruby/comp/flattenModel.rb | 2 +-
examples/ruby/convertSBML.rb | 2 +-
examples/ruby/createExampleSBML.rb | 2 +-
examples/ruby/echoSBML.rb | 2 +-
examples/ruby/fbc/convertCobraToFbc.rb | 2 +-
examples/ruby/fbc/convertFbcToCobra.rb | 2 +-
examples/ruby/fbc/example1.rb | 2 +-
examples/ruby/printAnnotation.rb | 2 +-
examples/ruby/printMath.rb | 2 +-
examples/ruby/printNotes.rb | 2 +-
examples/ruby/printRegisteredPackages.rb | 2 +-
examples/ruby/printSBML.rb | 2 +-
examples/ruby/printUnits.rb | 2 +-
examples/ruby/printsupported.rb | 2 +-
examples/ruby/promoteParameters.rb | 2 +-
examples/ruby/readSBML.rb | 2 +-
examples/ruby/stripPackage.rb | 2 +-
examples/ruby/translateMath.rb | 2 +-
examples/ruby/unsetAnnotation.rb | 2 +-
examples/ruby/unsetNotes.rb | 2 +-
examples/ruby/validateSBML.rb | 2 +-
examples/sample-models/README.txt | 2 +-
.../from-spec/level-3/enzymekineticext.xml | 96 +
fbc-package.cmake | 2 +-
groups-package.cmake | 2 +-
layout-package.cmake | 2 +-
libsbml-5.15.2/AUTHORS.txt | 16 +
libsbml-5.15.2/CMakeLists.txt | 1382 +
COPYING.html => libsbml-5.15.2/COPYING.html | 0
COPYING.txt => libsbml-5.15.2/COPYING.txt | 0
FUNDING.txt => libsbml-5.15.2/FUNDING.txt | 0
libsbml-5.15.2/LICENSE.html | 201 +
libsbml-5.15.2/LICENSE.txt | 167 +
libsbml-5.15.2/Makefile.in | 1021 +
libsbml-5.15.2/NEWS.txt | 3600 +
OLD_NEWS.txt => libsbml-5.15.2/OLD_NEWS.txt | 0
libsbml-5.15.2/README.txt | 415 +
libsbml-5.15.2/VERSION.txt | 1 +
libsbml-5.15.2/VERSION_PACKAGES.ac | 110 +
acinclude.m4 => libsbml-5.15.2/acinclude.m4 | 0
libsbml-5.15.2/aclocal.m4 | 15 +
libsbml-5.15.2/cmake_uninstall.cmake.in | 122 +
libsbml-5.15.2/common.cmake | 104 +
libsbml-5.15.2/config/bzip2.m4 | 157 +
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.../csharp-files-win/SimpleSpeciesReference.cs | 785 +
.../bindings/csharp/csharp-files-win/Species.cs | 2139 +
.../csharp/csharp-files-win/SpeciesReference.cs | 971 +
.../csharp/csharp-files-win/SpeciesType.cs | 786 +
.../csharp/csharp-files-win/StoichiometryMath.cs | 640 +
.../csharp/csharp-files-win/SyntaxChecker.cs | 520 +
.../bindings/csharp/csharp-files-win/Trigger.cs | 663 +
.../src/bindings/csharp/csharp-files-win/Unit.cs | 1508 +
.../csharp/csharp-files-win/UnitDefinition.cs | 1694 +
.../csharp/csharp-files-win/XMLAttributes.cs | 1345 +
.../csharp-files-win/XMLConstructorException.cs | 0
.../bindings/csharp/csharp-files-win/XMLError.cs | 1533 +
.../csharp/csharp-files-win/XMLErrorLog.cs | 490 +
.../csharp/csharp-files-win/XMLInputStream.cs | 0
.../csharp/csharp-files-win/XMLNamespaces.cs | 535 +
.../bindings/csharp/csharp-files-win/XMLNode.cs | 718 +
.../csharp/csharp-files-win/XMLOutputStream.cs | 1055 +
.../csharp-files-win/XMLOwningOutputFileStream.cs | 0
.../XMLOwningOutputStringStream.cs | 0
.../bindings/csharp/csharp-files-win/XMLToken.cs | 1913 +
.../bindings/csharp/csharp-files-win/XMLTriple.cs | 248 +
.../bindings/csharp/csharp-files-win/libsbml.cs | 3467 +
.../csharp/csharp-files-win/libsbmlPINVOKE.cs | 8937 +
.../src/bindings/csharp/csharp-files/ASTBase.cs | 633 +
.../bindings/csharp/csharp-files/ASTBasePlugin.cs | 460 +
.../src/bindings/csharp/csharp-files/ASTNode.cs | 2512 +
.../bindings/csharp/csharp-files/ASTNodeList.cs | 0
.../bindings/csharp/csharp-files/AlgebraicRule.cs | 404 +
.../bindings/csharp/csharp-files/AssignmentRule.cs | 507 +
.../src/bindings/csharp/csharp-files/CVTerm.cs | 1204 +
.../bindings/csharp/csharp-files/CVTermList.cs | 0
.../bindings/csharp/csharp-files/Compartment.cs | 2031 +
.../csharp/csharp-files/CompartmentType.cs | 798 +
.../src/bindings/csharp/csharp-files/Constraint.cs | 590 +
.../csharp/csharp-files/ConversionOption.cs | 588 +
.../csharp/csharp-files/ConversionProperties.cs | 773 +
.../src/bindings/csharp/csharp-files/Date.cs | 1242 +
.../src}/bindings/csharp/csharp-files/DateList.cs | 0
.../src/bindings/csharp/csharp-files/Delay.cs | 619 +
.../bindings/csharp/csharp-files/ElementFilter.cs | 0
.../src/bindings/csharp/csharp-files/Event.cs | 1817 +
.../csharp/csharp-files/EventAssignment.cs | 763 +
.../csharp/csharp-files/FunctionDefinition.cs | 993 +
.../csharp-files/ISBMLExtensionNamespaces.cs | 0
.../src}/bindings/csharp/csharp-files/IdList.cs | 0
.../csharp/csharp-files/IdentifierTransformer.cs | 0
.../csharp/csharp-files/InitialAssignment.cs | 750 +
.../src/bindings/csharp/csharp-files/KineticLaw.cs | 1212 +
.../csharp/csharp-files/L3ParserSettings.cs | 1334 +
.../src/bindings/csharp/csharp-files/ListOf.cs | 756 +
.../csharp/csharp-files/ListOfCompartmentTypes.cs | 354 +
.../csharp/csharp-files/ListOfCompartments.cs | 354 +
.../csharp/csharp-files/ListOfConstraints.cs | 311 +
.../csharp/csharp-files/ListOfEventAssignments.cs | 374 +
.../bindings/csharp/csharp-files/ListOfEvents.cs | 353 +
.../csharp-files/ListOfFunctionDefinitions.cs | 354 +
.../csharp-files/ListOfInitialAssignments.cs | 373 +
.../csharp/csharp-files/ListOfLocalParameters.cs | 376 +
.../csharp/csharp-files/ListOfParameters.cs | 354 +
.../csharp/csharp-files/ListOfReactions.cs | 346 +
.../bindings/csharp/csharp-files/ListOfRules.cs | 365 +
.../bindings/csharp/csharp-files/ListOfSpecies.cs | 353 +
.../csharp/csharp-files/ListOfSpeciesReferences.cs | 358 +
.../csharp/csharp-files/ListOfSpeciesTypes.cs | 354 +
.../csharp/csharp-files/ListOfUnitDefinitions.cs | 374 +
.../bindings/csharp/csharp-files/ListOfUnits.cs | 313 +
.../bindings/csharp/csharp-files/LocalParameter.cs | 417 +
.../src/bindings/csharp/csharp-files/MathFilter.cs | 76 +
.../src}/bindings/csharp/csharp-files/MathML.cs | 0
.../src/bindings/csharp/csharp-files/Model.cs | 4627 +
.../bindings/csharp/csharp-files/ModelCreator.cs | 617 +
.../csharp/csharp-files/ModelCreatorList.cs | 0
.../bindings/csharp/csharp-files/ModelHistory.cs | 469 +
.../csharp-files/ModifierSpeciesReference.cs | 256 +
.../src}/bindings/csharp/csharp-files/OFStream.cs | 0
.../src}/bindings/csharp/csharp-files/OStream.cs | 0
.../bindings/csharp/csharp-files/OStringStream.cs | 0
.../src/bindings/csharp/csharp-files/Parameter.cs | 1264 +
.../src/bindings/csharp/csharp-files/Priority.cs | 541 +
.../csharp/csharp-files/RDFAnnotationParser.cs | 643 +
.../src/bindings/csharp/csharp-files/RateRule.cs | 472 +
.../src/bindings/csharp/csharp-files/Reaction.cs | 2347 +
.../src/bindings/csharp/csharp-files/Rule.cs | 1076 +
.../csharp-files/SBMLConstructorException.cs | 0
.../bindings/csharp/csharp-files/SBMLConverter.cs | 554 +
.../csharp/csharp-files/SBMLConverterRegistry.cs | 0
.../bindings/csharp/csharp-files/SBMLDocument.cs | 2063 +
.../csharp/csharp-files/SBMLDocumentPlugin.cs | 517 +
.../src/bindings/csharp/csharp-files/SBMLError.cs | 11937 ++
.../bindings/csharp/csharp-files/SBMLErrorLog.cs | 374 +
.../bindings/csharp/csharp-files/SBMLExtension.cs | 0
.../csharp/csharp-files/SBMLExtensionException.cs | 97 +
.../csharp/csharp-files/SBMLExtensionRegistry.cs | 340 +
.../csharp/csharp-files/SBMLExternalValidator.cs | 160 +
.../SBMLFunctionDefinitionConverter.cs | 364 +
.../csharp/csharp-files/SBMLIdConverter.cs | 367 +
.../csharp/csharp-files/SBMLInferUnitsConverter.cs | 345 +
.../csharp-files/SBMLInitialAssignmentConverter.cs | 376 +
.../csharp-files/SBMLLevel1Version1Converter.cs | 374 +
.../csharp-files/SBMLLevelVersionConverter.cs | 415 +
.../csharp-files/SBMLLocalParameterConverter.cs | 352 +
.../bindings/csharp/csharp-files/SBMLNamespaces.cs | 842 +
.../csharp/csharp-files/SBMLNamespacesList.cs | 0
.../csharp/csharp-files/SBMLReactionConverter.cs | 365 +
.../src/bindings/csharp/csharp-files/SBMLReader.cs | 672 +
.../csharp/csharp-files/SBMLRuleConverter.cs | 374 +
.../csharp-files/SBMLStripPackageConverter.cs | 378 +
.../bindings/csharp/csharp-files/SBMLTransforms.cs | 142 +
.../csharp/csharp-files/SBMLUnitsConverter.cs | 360 +
.../bindings/csharp/csharp-files/SBMLValidator.cs | 378 +
.../src/bindings/csharp/csharp-files/SBMLWriter.cs | 386 +
.../src/bindings/csharp/csharp-files/SBO.cs | 943 +
.../src/bindings/csharp/csharp-files/SBase.cs | 4607 +
.../csharp/csharp-files/SBaseExtensionPoint.cs | 286 +
.../src}/bindings/csharp/csharp-files/SBaseList.cs | 0
.../bindings/csharp/csharp-files/SBasePlugin.cs | 728 +
.../csharp/csharp-files/SWIGTYPE_p_ASTFunction.cs | 0
.../csharp-files/SWIGTYPE_p_ExpectedAttributes.cs | 0
.../csharp-files/SWIGTYPE_p_FormulaUnitsData.cs | 0
.../csharp/csharp-files/SWIGTYPE_p_List.cs | 0
.../csharp-files/SWIGTYPE_p_StringBuffer_t.cs | 0
.../csharp/csharp-files/SWIGTYPE_p_std__ostream.cs | 0
.../SWIGTYPE_p_std__vectorT_XMLError_p_t.cs | 0
.../SWIGTYPE_p_std__vectorT_std__string_t.cs | 0
.../csharp/csharp-files/SimpleSpeciesReference.cs | 792 +
.../src/bindings/csharp/csharp-files/Species.cs | 2152 +
.../csharp/csharp-files/SpeciesReference.cs | 976 +
.../bindings/csharp/csharp-files/SpeciesType.cs | 791 +
.../csharp/csharp-files/StoichiometryMath.cs | 646 +
.../bindings/csharp/csharp-files/SyntaxChecker.cs | 529 +
.../src/bindings/csharp/csharp-files/Trigger.cs | 669 +
.../src/bindings/csharp/csharp-files/Unit.cs | 1513 +
.../bindings/csharp/csharp-files/UnitDefinition.cs | 1702 +
.../bindings/csharp/csharp-files/XMLAttributes.cs | 1359 +
.../csharp/csharp-files/XMLConstructorException.cs | 0
.../src/bindings/csharp/csharp-files/XMLError.cs | 1536 +
.../bindings/csharp/csharp-files/XMLErrorLog.cs | 494 +
.../bindings/csharp/csharp-files/XMLInputStream.cs | 0
.../bindings/csharp/csharp-files/XMLNamespaces.cs | 549 +
.../src/bindings/csharp/csharp-files/XMLNode.cs | 726 +
.../csharp/csharp-files/XMLOutputStream.cs | 1077 +
.../csharp-files/XMLOwningOutputFileStream.cs | 0
.../csharp-files/XMLOwningOutputStringStream.cs | 0
.../src/bindings/csharp/csharp-files/XMLToken.cs | 1939 +
.../src/bindings/csharp/csharp-files/XMLTriple.cs | 254 +
.../src/bindings/csharp/csharp-files/libsbml.cs | 3473 +
.../bindings/csharp/csharp-files/libsbmlPINVOKE.cs | 8698 +
libsbml-5.15.2/src/bindings/csharp/libsbml.i | 34 +
.../src/bindings/csharp/libsbml_wrap-win.cpp | 45681 +++++
.../src/bindings/csharp/libsbml_wrap.cpp | 42250 +++++
.../src}/bindings/csharp/libsbml_wrap.h | 0
.../bindings/csharp/local-downcast-astplugins.i.in | 7 +
.../csharp/local-downcast-converters-layout.i | 0
.../bindings/csharp/local-downcast-converters.i.in | 0
.../csharp/local-downcast-extension-layout.i | 0
.../bindings/csharp/local-downcast-extension.i.in | 0
.../csharp/local-downcast-namespaces-layout.i | 0
.../bindings/csharp/local-downcast-namespaces.i.in | 17 +
.../src/bindings/csharp/local-packages-layout.i | 241 +
.../src/bindings/csharp/local-packages.i.in | 20 +
libsbml-5.15.2/src/bindings/csharp/local.cpp | 296 +
libsbml-5.15.2/src/bindings/csharp/local.i | 1487 +
.../src/bindings/csharp/swig-binding.cmake.in | 91 +
.../bindings/csharp/test/annotation/TestCVTerms.cs | 0
.../test/annotation/TestCVTerms_newSetters.cs | 0
.../csharp/test/annotation/TestCopyAndClone.cs | 0
.../csharp/test/annotation/TestDate_newSetters.cs | 0
.../csharp/test/annotation/TestL3ModelHistory.cs | 433 +
.../test/annotation/TestModelCreator_newSetters.cs | 0
.../csharp/test/annotation/TestModelHistory.cs | 0
.../test/annotation/TestModelHistory_newSetters.cs | 0
.../csharp/test/annotation/TestRDFAnnotation.cs | 680 +
.../csharp/test/annotation/TestRDFAnnotation2.cs | 0
.../csharp/test/annotation/TestRDFAnnotationC.cs | 319 +
.../csharp/test/annotation/TestValidation.cs | 0
.../src}/bindings/csharp/test/math/TestASTNode.cs | 0
.../csharp/test/math/TestL3FormulaParserC.cs | 0
.../bindings/csharp/test/math/TestReadFromFile1.cs | 0
.../bindings/csharp/test/math/TestReadFromFile2.cs | 0
.../bindings/csharp/test/math/TestReadMathML.cs | 1118 +
.../bindings/csharp/test/math/TestValidASTNode.cs | 0
.../bindings/csharp/test/math/TestWriteMathML.cs | 711 +
.../bindings/csharp/test/sbml/TestAlgebraicRule.cs | 0
.../src}/bindings/csharp/test/sbml/TestAncestor.cs | 0
.../csharp/test/sbml/TestAssignmentRule.cs | 0
.../bindings/csharp/test/sbml/TestCompartment.cs | 0
.../csharp/test/sbml/TestCompartmentType.cs | 0
.../test/sbml/TestCompartmentType_newSetters.cs | 0
.../csharp/test/sbml/TestCompartmentVolumeRule.cs | 0
.../csharp/test/sbml/TestCompartment_newSetters.cs | 0
.../csharp/test/sbml/TestConsistencyChecks.cs | 0
.../bindings/csharp/test/sbml/TestConstraint.cs | 0
.../csharp/test/sbml/TestConstraint_newSetters.cs | 0
.../bindings/csharp/test/sbml/TestCopyAndClone.cs | 0
.../src}/bindings/csharp/test/sbml/TestDelay.cs | 0
.../src}/bindings/csharp/test/sbml/TestEvent.cs | 0
.../csharp/test/sbml/TestEventAssignment.cs | 0
.../test/sbml/TestEventAssignment_newSetters.cs | 0
.../csharp/test/sbml/TestEvent_newSetters.cs | 0
.../csharp/test/sbml/TestFunctionDefinition.cs | 0
.../test/sbml/TestFunctionDefinition_newSetters.cs | 0
.../csharp/test/sbml/TestGetMultipleObjects.cs | 0
.../csharp/test/sbml/TestInitialAssignment.cs | 0
.../test/sbml/TestInitialAssignment_newSetters.cs | 0
.../test/sbml/TestInternalConsistencyChecks.cs | 0
.../bindings/csharp/test/sbml/TestKineticLaw.cs | 0
.../csharp/test/sbml/TestKineticLaw_newSetters.cs | 0
.../bindings/csharp/test/sbml/TestL3Compartment.cs | 0
.../src}/bindings/csharp/test/sbml/TestL3Event.cs | 0
.../bindings/csharp/test/sbml/TestL3KineticLaw.cs | 0
.../csharp/test/sbml/TestL3LocalParameter.cs | 0
.../src}/bindings/csharp/test/sbml/TestL3Model.cs | 0
.../bindings/csharp/test/sbml/TestL3Parameter.cs | 0
.../bindings/csharp/test/sbml/TestL3Reaction.cs | 0
.../bindings/csharp/test/sbml/TestL3Species.cs | 0
.../csharp/test/sbml/TestL3SpeciesReference.cs | 0
.../bindings/csharp/test/sbml/TestL3Trigger.cs | 0
.../src}/bindings/csharp/test/sbml/TestL3Unit.cs | 0
.../src}/bindings/csharp/test/sbml/TestListOf.cs | 0
.../src}/bindings/csharp/test/sbml/TestModel.cs | 0
.../csharp/test/sbml/TestModel_newSetters.cs | 0
.../test/sbml/TestModifierSpeciesReference.cs | 0
.../bindings/csharp/test/sbml/TestParameter.cs | 0
.../bindings/csharp/test/sbml/TestParameterRule.cs | 0
.../csharp/test/sbml/TestParameter_newSetters.cs | 0
.../src}/bindings/csharp/test/sbml/TestPriority.cs | 0
.../src}/bindings/csharp/test/sbml/TestRateRule.cs | 0
.../src}/bindings/csharp/test/sbml/TestReaction.cs | 0
.../csharp/test/sbml/TestReaction_newSetters.cs | 0
.../bindings/csharp/test/sbml/TestReadFromFile1.cs | 0
.../bindings/csharp/test/sbml/TestReadFromFile2.cs | 0
.../bindings/csharp/test/sbml/TestReadFromFile3.cs | 0
.../bindings/csharp/test/sbml/TestReadFromFile4.cs | 0
.../bindings/csharp/test/sbml/TestReadFromFile5.cs | 0
.../bindings/csharp/test/sbml/TestReadFromFile6.cs | 0
.../bindings/csharp/test/sbml/TestReadFromFile7.cs | 0
.../bindings/csharp/test/sbml/TestReadFromFile8.cs | 0
.../bindings/csharp/test/sbml/TestReadFromFile9.cs | 0
.../src}/bindings/csharp/test/sbml/TestReadSBML.cs | 0
.../csharp/test/sbml/TestRequiredAttributes.cs | 0
.../csharp/test/sbml/TestRequiredElements.cs | 0
.../src}/bindings/csharp/test/sbml/TestRule.cs | 0
.../csharp/test/sbml/TestRule_newSetters.cs | 0
.../test/sbml/TestSBMLConstructorException.cs | 0
.../bindings/csharp/test/sbml/TestSBMLConvert.cs | 0
.../csharp/test/sbml/TestSBMLConvertStrict.cs | 0
.../bindings/csharp/test/sbml/TestSBMLDocument.cs | 281 +
.../src/bindings/csharp/test/sbml/TestSBMLError.cs | 186 +
.../csharp/test/sbml/TestSBMLNamespaces.cs | 0
.../csharp/test/sbml/TestSBMLParentObject.cs | 0
.../csharp/test/sbml/TestSBMLTransforms.cs | 0
.../src}/bindings/csharp/test/sbml/TestSBase.cs | 0
.../csharp/test/sbml/TestSBase_newSetters.cs | 0
.../src}/bindings/csharp/test/sbml/TestSpecies.cs | 0
.../test/sbml/TestSpeciesConcentrationRule.cs | 0
.../csharp/test/sbml/TestSpeciesReference.cs | 0
.../test/sbml/TestSpeciesReference_newSetters.cs | 0
.../bindings/csharp/test/sbml/TestSpeciesType.cs | 0
.../csharp/test/sbml/TestSpeciesType_newSetters.cs | 0
.../csharp/test/sbml/TestSpecies_newSetters.cs | 0
.../csharp/test/sbml/TestStoichiometryMath.cs | 0
.../bindings/csharp/test/sbml/TestSyntaxChecker.cs | 0
.../src}/bindings/csharp/test/sbml/TestTrigger.cs | 0
.../src}/bindings/csharp/test/sbml/TestUnit.cs | 0
.../csharp/test/sbml/TestUnitDefinition.cs | 0
.../test/sbml/TestUnitDefinition_newSetters.cs | 0
.../src}/bindings/csharp/test/sbml/TestUnitKind.cs | 0
.../csharp/test/sbml/TestUnit_newSetters.cs | 0
.../bindings/csharp/test/sbml/TestWriteL3SBML.cs | 0
.../bindings/csharp/test/sbml/TestWriteSBML.cs | 0
.../bindings/csharp/test/xml/TestCopyAndClone.cs | 0
.../bindings/csharp/test/xml/TestXMLAttributes.cs | 0
.../bindings/csharp/test/xml/TestXMLAttributesC.cs | 0
.../src}/bindings/csharp/test/xml/TestXMLError.cs | 0
.../src}/bindings/csharp/test/xml/TestXMLErrorC.cs | 0
.../bindings/csharp/test/xml/TestXMLNamespaces.cs | 0
.../src}/bindings/csharp/test/xml/TestXMLNode.cs | 0
.../csharp/test/xml/TestXMLNode_newSetters.cs | 0
.../csharp/test/xml/TestXMLOutputStream.cs | 0
.../src}/bindings/csharp/test/xml/TestXMLToken.cs | 0
.../csharp/test/xml/TestXMLToken_newSetters.cs | 0
.../src}/bindings/csharp/test/xml/TestXMLTriple.cs | 0
.../src/bindings/java/AutoTestRunner.java | 270 +
libsbml-5.15.2/src/bindings/java/CMakeLists.txt | 359 +
libsbml-5.15.2/src/bindings/java/Makefile.in | 569 +
.../src}/bindings/java/Manifest.txt.in | 0
.../src/bindings/java/compile-native-files.cmake | 129 +
.../java/java-files/org/sbml/libsbml/ASTBase.java | 530 +
.../java-files/org/sbml/libsbml/ASTBasePlugin.java | 402 +
.../java/java-files/org/sbml/libsbml/ASTNode.java | 2540 +
.../java-files/org/sbml/libsbml/ASTNodeList.java | 0
.../java-files/org/sbml/libsbml/AlgebraicRule.java | 379 +
.../org/sbml/libsbml/AssignmentRule.java | 475 +
.../java/java-files/org/sbml/libsbml/CVTerm.java | 1211 +
.../java-files/org/sbml/libsbml/CVTermList.java | 0
.../java-files/org/sbml/libsbml/Compartment.java | 1896 +
.../org/sbml/libsbml/CompartmentType.java | 717 +
.../java-files/org/sbml/libsbml/Constraint.java | 526 +
.../org/sbml/libsbml/ConversionOption.java | 717 +
.../org/sbml/libsbml/ConversionProperties.java | 844 +
.../java/java-files/org/sbml/libsbml/Date.java | 1409 +
.../java/java-files/org/sbml/libsbml/DateList.java | 0
.../java/java-files/org/sbml/libsbml/Delay.java | 552 +
.../java-files/org/sbml/libsbml/ElementFilter.java | 0
.../java/java-files/org/sbml/libsbml/Event.java | 1691 +
.../org/sbml/libsbml/EventAssignment.java | 689 +
.../org/sbml/libsbml/FunctionDefinition.java | 904 +
.../org/sbml/libsbml/ISBMLExtensionNamespaces.java | 0
.../java/java-files/org/sbml/libsbml/IdList.java | 0
.../org/sbml/libsbml/IdentifierTransformer.java | 0
.../org/sbml/libsbml/InitialAssignment.java | 678 +
.../java-files/org/sbml/libsbml/KineticLaw.java | 1133 +
.../org/sbml/libsbml/L3ParserSettings.java | 1356 +
.../java/java-files/org/sbml/libsbml/ListOf.java | 756 +
.../org/sbml/libsbml/ListOfCompartmentTypes.java | 302 +
.../org/sbml/libsbml/ListOfCompartments.java | 302 +
.../org/sbml/libsbml/ListOfConstraints.java | 263 +
.../org/sbml/libsbml/ListOfEventAssignments.java | 320 +
.../java-files/org/sbml/libsbml/ListOfEvents.java | 301 +
.../sbml/libsbml/ListOfFunctionDefinitions.java | 302 +
.../org/sbml/libsbml/ListOfInitialAssignments.java | 319 +
.../org/sbml/libsbml/ListOfLocalParameters.java | 322 +
.../org/sbml/libsbml/ListOfParameters.java | 302 +
.../org/sbml/libsbml/ListOfReactions.java | 294 +
.../java-files/org/sbml/libsbml/ListOfRules.java | 311 +
.../java-files/org/sbml/libsbml/ListOfSpecies.java | 301 +
.../org/sbml/libsbml/ListOfSpeciesReferences.java | 304 +
.../org/sbml/libsbml/ListOfSpeciesTypes.java | 302 +
.../org/sbml/libsbml/ListOfUnitDefinitions.java | 320 +
.../java-files/org/sbml/libsbml/ListOfUnits.java | 265 +
.../org/sbml/libsbml/LocalParameter.java | 367 +
.../java-files/org/sbml/libsbml/MathFilter.java | 65 +
.../java/java-files/org/sbml/libsbml/MathML.java | 0
.../java/java-files/org/sbml/libsbml/Model.java | 4233 +
.../java-files/org/sbml/libsbml/ModelCreator.java | 602 +
.../org/sbml/libsbml/ModelCreatorList.java | 0
.../java-files/org/sbml/libsbml/ModelHistory.java | 474 +
.../org/sbml/libsbml/ModifierSpeciesReference.java | 216 +
.../java/java-files/org/sbml/libsbml/OFStream.java | 0
.../java/java-files/org/sbml/libsbml/OStream.java | 0
.../java-files/org/sbml/libsbml/OStringStream.java | 0
.../java-files/org/sbml/libsbml/Parameter.java | 1167 +
.../java/java-files/org/sbml/libsbml/Priority.java | 482 +
.../org/sbml/libsbml/RDFAnnotationParser.java | 480 +
.../java/java-files/org/sbml/libsbml/RateRule.java | 440 +
.../java/java-files/org/sbml/libsbml/Reaction.java | 2177 +
.../java/java-files/org/sbml/libsbml/Rule.java | 994 +
.../org/sbml/libsbml/SBMLConstructorException.java | 0
.../java-files/org/sbml/libsbml/SBMLConverter.java | 375 +
.../org/sbml/libsbml/SBMLConverterRegistry.java | 0
.../java-files/org/sbml/libsbml/SBMLDocument.java | 2060 +
.../org/sbml/libsbml/SBMLDocumentPlugin.java | 317 +
.../java-files/org/sbml/libsbml/SBMLError.java | 11545 ++
.../java-files/org/sbml/libsbml/SBMLErrorLog.java | 346 +
.../java-files/org/sbml/libsbml/SBMLExtension.java | 0
.../org/sbml/libsbml/SBMLExtensionException.java | 87 +
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libsbml-5.15.2/src/bindings/javascript/local.cpp | 327 +
libsbml-5.15.2/src/bindings/javascript/local.i | 412 +
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libsbml-5.15.2/src/bindings/matlab/Makefile.in | 392 +
libsbml-5.15.2/src/bindings/matlab/OutputSBML.cpp | 3367 +
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libsbml-5.15.2/src/bindings/matlab/getValueType.m | 3294 +
libsbml-5.15.2/src/bindings/matlab/installSBML.m | 410 +
libsbml-5.15.2/src/bindings/matlab/isEnabled.m | 90 +
libsbml-5.15.2/src/bindings/matlab/isFbcEnabled.m | 76 +
libsbml-5.15.2/src/bindings/matlab/isSBML_Model.m | 343 +
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libsbml-5.15.2/src/bindings/octave/CMakeLists.txt | 145 +
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libsbml-5.15.2/src/bindings/octave/Makefile.in | 223 +
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libsbml-5.15.2/src/bindings/perl/CMakeLists.txt | 334 +
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libsbml-5.15.2/src/bindings/perl/LibSBML.pm | 44218 +++++
libsbml-5.15.2/src/bindings/perl/LibSBML.pod | 37019 ++++
.../src}/bindings/perl/LibSBML.txt | 0
libsbml-5.15.2/src/bindings/perl/LibSBML_wrap.cxx | 153190 ++++++++++++++++
{src => libsbml-5.15.2/src}/bindings/perl/MANIFEST | 0
libsbml-5.15.2/src/bindings/perl/Makefile.PL.in | 152 +
libsbml-5.15.2/src/bindings/perl/Makefile.in | 310 +
libsbml-5.15.2/src/bindings/perl/README.txt | 46 +
.../src}/bindings/perl/list_get_fix.i | 0
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.../bindings/perl/local-downcast-astplugins.cpp.in | 7 +
.../perl}/local-downcast-converters-layout.cpp | 0
.../perl}/local-downcast-converters.cpp.in | 0
.../perl}/local-downcast-extension-layout.cpp | 0
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libsbml-5.15.2/src/bindings/perl/local.cpp | 333 +
libsbml-5.15.2/src/bindings/perl/local.i | 279 +
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.../src/bindings/perl/t/05__AssignmentRuleL3.t | 118 +
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libsbml-5.15.2/src/bindings/perl/t/05__ModelL3.t | 682 +
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libsbml-5.15.2/src/bindings/php/CMakeLists.txt | 281 +
libsbml-5.15.2/src/bindings/php/libsbml.i | 38 +
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.../php}/local-downcast-packages-layout.cpp | 0
.../bindings/php/local-downcast-plugins-layout.cpp | 19 +
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.../src}/bindings/php/local-layout.i | 0
.../src/bindings/php}/local-packages.i.in | 0
libsbml-5.15.2/src/bindings/php/local.cpp | 326 +
libsbml-5.15.2/src/bindings/php/local.i | 267 +
libsbml-5.15.2/src/bindings/python/CMakeLists.txt | 623 +
libsbml-5.15.2/src/bindings/python/Makefile.in | 603 +
.../src/bindings/python/add_version.cmake | 43 +
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.../bindings/python/doc-converter/rewrite_pydoc.py | 820 +
.../src/bindings/python/libsbml-doxygen.py | 82488 +++++++++
libsbml-5.15.2/src/bindings/python/libsbml.i | 34 +
libsbml-5.15.2/src/bindings/python/libsbml.py | 67942 +++++++
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libsbml-5.15.2/src/bindings/python/local-contrib.i | 267 +
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.../python/local-downcast-plugins-layout.cpp | 19 +
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libsbml-5.15.2/src/bindings/python/local.cpp | 325 +
libsbml-5.15.2/src/bindings/python/local.i | 1097 +
libsbml-5.15.2/src/bindings/python/pydoc-doxygen.i | 72496 ++++++++
libsbml-5.15.2/src/bindings/python/pydoc-normal.i | 56360 ++++++
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libsbml-5.15.2/src/bindings/python/setup.py.in | 76 +
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.../python/test/annotation/TestRDFAnnotation.py | 757 +
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libsbml-5.15.2/src/bindings/r/CMakeLists.txt | 491 +
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libsbml-5.15.2/src/bindings/r/Makevars.in | 44 +
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libsbml-5.15.2/src/bindings/r/create_package.cmake | 287 +
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libsbml-5.15.2/src/bindings/r/local.cpp | 329 +
libsbml-5.15.2/src/bindings/r/local.i | 418 +
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libsbml-5.15.2/src/bindings/r/swig-binding.cmake | 73 +
libsbml-5.15.2/src/bindings/ruby/CMakeLists.txt | 225 +
libsbml-5.15.2/src/bindings/ruby/Makefile.in | 494 +
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libsbml-5.15.2/src/bindings/ruby/libsbml.i | 38 +
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.../bindings/ruby/test/sbml/TestReadFromFile9.rb | 0
.../src}/bindings/ruby/test/sbml/TestReadSBML.rb | 0
.../ruby/test/sbml/TestRequiredAttributes.rb | 0
.../ruby/test/sbml/TestRequiredElements.rb | 0
.../src}/bindings/ruby/test/sbml/TestRule.rb | 0
.../bindings/ruby/test/sbml/TestRule_newSetters.rb | 0
.../ruby/test/sbml/TestSBMLConstructorException.rb | 0
.../bindings/ruby/test/sbml/TestSBMLConvert.rb | 0
.../ruby/test/sbml/TestSBMLConvertStrict.rb | 0
.../bindings/ruby/test/sbml/TestSBMLDocument.rb | 173 +
.../src/bindings/ruby/test/sbml/TestSBMLError.rb | 90 +
.../bindings/ruby/test/sbml/TestSBMLNamespaces.rb | 0
.../ruby/test/sbml/TestSBMLParentObject.rb | 0
.../bindings/ruby/test/sbml/TestSBMLTransforms.rb | 0
.../src}/bindings/ruby/test/sbml/TestSBase.rb | 0
.../ruby/test/sbml/TestSBase_newSetters.rb | 0
.../src}/bindings/ruby/test/sbml/TestSpecies.rb | 0
.../ruby/test/sbml/TestSpeciesConcentrationRule.rb | 0
.../ruby/test/sbml/TestSpeciesReference.rb | 0
.../test/sbml/TestSpeciesReference_newSetters.rb | 0
.../bindings/ruby/test/sbml/TestSpeciesType.rb | 0
.../ruby/test/sbml/TestSpeciesType_newSetters.rb | 0
.../ruby/test/sbml/TestSpecies_newSetters.rb | 0
.../ruby/test/sbml/TestStoichiometryMath.rb | 0
.../bindings/ruby/test/sbml/TestSyntaxChecker.rb | 0
.../src}/bindings/ruby/test/sbml/TestTrigger.rb | 0
.../src}/bindings/ruby/test/sbml/TestUnit.rb | 0
.../bindings/ruby/test/sbml/TestUnitDefinition.rb | 0
.../test/sbml/TestUnitDefinition_newSetters.rb | 0
.../src}/bindings/ruby/test/sbml/TestUnitKind.rb | 0
.../bindings/ruby/test/sbml/TestUnit_newSetters.rb | 0
.../bindings/ruby/test/sbml/TestWriteL3SBML.rb | 0
.../src}/bindings/ruby/test/sbml/TestWriteSBML.rb | 0
.../bindings/ruby/test/xml/TestXMLAttributes.rb | 0
.../bindings/ruby/test/xml/TestXMLAttributesC.rb | 0
.../bindings/ruby/test/xml/TestXMLCopyAndClone.rb | 0
.../src}/bindings/ruby/test/xml/TestXMLError.rb | 0
.../src}/bindings/ruby/test/xml/TestXMLErrorC.rb | 0
.../bindings/ruby/test/xml/TestXMLNamespaces.rb | 0
.../src}/bindings/ruby/test/xml/TestXMLNode.rb | 0
.../ruby/test/xml/TestXMLNode_newSetters.rb | 0
.../bindings/ruby/test/xml/TestXMLOutputStream.rb | 0
.../src}/bindings/ruby/test/xml/TestXMLToken.rb | 0
.../ruby/test/xml/TestXMLToken_newSetters.rb | 0
.../src}/bindings/ruby/test/xml/TestXMLTriple.rb | 0
libsbml-5.15.2/src/bindings/swig/ASTNodes.i | 119 +
libsbml-5.15.2/src/bindings/swig/ListWrapper.h | 161 +
libsbml-5.15.2/src/bindings/swig/OStream.cpp | 208 +
libsbml-5.15.2/src/bindings/swig/OStream.h | 232 +
.../src}/bindings/swig/README.txt | 0
.../src/bindings/swig}/argparse.py | 0
.../src}/bindings/swig/layout-package.h | 0
.../src}/bindings/swig/layout-package.i | 0
.../src/bindings/swig/libsbml-packages.h.in | 21 +
.../src/bindings/swig/libsbml-packages.i.in | 20 +
libsbml-5.15.2/src/bindings/swig/libsbml.h | 135 +
libsbml-5.15.2/src/bindings/swig/libsbml.i | 836 +
libsbml-5.15.2/src/bindings/swig/libsbmlutils.py | 153 +
.../src}/bindings/swig/std_set.i | 0
libsbml-5.15.2/src/bindings/swig/swigdoc.py | 1906 +
libsbml-5.15.2/src/layout-package.cmake | 88 +
libsbml-5.15.2/src/sbml/AlgebraicRule.cpp | 518 +
libsbml-5.15.2/src/sbml/AlgebraicRule.h | 741 +
libsbml-5.15.2/src/sbml/AssignmentRule.cpp | 678 +
libsbml-5.15.2/src/sbml/AssignmentRule.h | 876 +
libsbml-5.15.2/src/sbml/CMakeLists.txt | 57 +
libsbml-5.15.2/src/sbml/Compartment.cpp | 2561 +
libsbml-5.15.2/src/sbml/Compartment.h | 2852 +
libsbml-5.15.2/src/sbml/CompartmentType.cpp | 1026 +
libsbml-5.15.2/src/sbml/CompartmentType.h | 1107 +
libsbml-5.15.2/src/sbml/Constraint.cpp | 1259 +
libsbml-5.15.2/src/sbml/Constraint.h | 1122 +
libsbml-5.15.2/src/sbml/Delay.cpp | 974 +
libsbml-5.15.2/src/sbml/Delay.h | 1083 +
libsbml-5.15.2/src/sbml/Event.cpp | 2800 +
libsbml-5.15.2/src/sbml/Event.h | 2570 +
libsbml-5.15.2/src/sbml/EventAssignment.cpp | 1442 +
libsbml-5.15.2/src/sbml/EventAssignment.h | 1513 +
libsbml-5.15.2/src/sbml/ExpectedAttributes.cpp | 90 +
libsbml-5.15.2/src/sbml/ExpectedAttributes.h | 125 +
libsbml-5.15.2/src/sbml/FunctionDefinition.cpp | 1568 +
libsbml-5.15.2/src/sbml/FunctionDefinition.h | 1420 +
libsbml-5.15.2/src/sbml/InitialAssignment.cpp | 1423 +
libsbml-5.15.2/src/sbml/InitialAssignment.h | 1498 +
libsbml-5.15.2/src/sbml/KineticLaw.cpp | 2384 +
libsbml-5.15.2/src/sbml/KineticLaw.h | 2264 +
libsbml-5.15.2/src/sbml/ListOf.cpp | 814 +
libsbml-5.15.2/src/sbml/ListOf.h | 920 +
libsbml-5.15.2/src/sbml/LocalParameter.cpp | 1091 +
libsbml-5.15.2/src/sbml/LocalParameter.h | 1406 +
libsbml-5.15.2/src/sbml/Makefile.in | 328 +
libsbml-5.15.2/src/sbml/Model.cpp | 8714 +
libsbml-5.15.2/src/sbml/Model.h | 7191 +
.../src/sbml/ModifierSpeciesReference.cpp | 593 +
libsbml-5.15.2/src/sbml/ModifierSpeciesReference.h | 823 +
libsbml-5.15.2/src/sbml/Parameter.cpp | 2264 +
libsbml-5.15.2/src/sbml/Parameter.h | 1823 +
libsbml-5.15.2/src/sbml/Priority.cpp | 806 +
libsbml-5.15.2/src/sbml/Priority.h | 932 +
libsbml-5.15.2/src/sbml/RateRule.cpp | 678 +
libsbml-5.15.2/src/sbml/RateRule.h | 844 +
libsbml-5.15.2/src/sbml/Reaction.cpp | 3231 +
libsbml-5.15.2/src/sbml/Reaction.h | 2782 +
libsbml-5.15.2/src/sbml/Rule.cpp | 2263 +
libsbml-5.15.2/src/sbml/Rule.h | 1961 +
.../src/sbml/SBMLConstructorException.cpp | 82 +
libsbml-5.15.2/src/sbml/SBMLConstructorException.h | 92 +
libsbml-5.15.2/src/sbml/SBMLConvert.cpp | 2199 +
libsbml-5.15.2/src/sbml/SBMLDocument.cpp | 2694 +
libsbml-5.15.2/src/sbml/SBMLDocument.h | 2811 +
libsbml-5.15.2/src/sbml/SBMLError.cpp | 486 +
libsbml-5.15.2/src/sbml/SBMLError.h | 1260 +
libsbml-5.15.2/src/sbml/SBMLErrorLog.cpp | 392 +
libsbml-5.15.2/src/sbml/SBMLErrorLog.h | 346 +
libsbml-5.15.2/src/sbml/SBMLErrorTable.h | 12246 ++
libsbml-5.15.2/src/sbml/SBMLNamespaces.cpp | 890 +
libsbml-5.15.2/src/sbml/SBMLNamespaces.h | 776 +
libsbml-5.15.2/src/sbml/SBMLReader.cpp | 466 +
libsbml-5.15.2/src/sbml/SBMLReader.h | 632 +
libsbml-5.15.2/src/sbml/SBMLTransforms.cpp | 1405 +
libsbml-5.15.2/src/sbml/SBMLTransforms.h | 187 +
libsbml-5.15.2/src/sbml/SBMLTypeCodes.cpp | 109 +
libsbml-5.15.2/src/sbml/SBMLTypeCodes.h | 133 +
libsbml-5.15.2/src/sbml/SBMLTypes.h | 109 +
libsbml-5.15.2/src/sbml/SBMLVisitor.cpp | 291 +
libsbml-5.15.2/src/sbml/SBMLVisitor.h | 476 +
libsbml-5.15.2/src/sbml/SBMLWriter.cpp | 468 +
libsbml-5.15.2/src/sbml/SBMLWriter.h | 632 +
libsbml-5.15.2/src/sbml/SBO.cpp | 1409 +
libsbml-5.15.2/src/sbml/SBO.h | 625 +
libsbml-5.15.2/src/sbml/SBase.cpp | 7993 +
libsbml-5.15.2/src/sbml/SBase.h | 5337 +
libsbml-5.15.2/src/sbml/SimpleSpeciesReference.cpp | 936 +
libsbml-5.15.2/src/sbml/SimpleSpeciesReference.h | 657 +
libsbml-5.15.2/src/sbml/Species.cpp | 3283 +
libsbml-5.15.2/src/sbml/Species.h | 3170 +
libsbml-5.15.2/src/sbml/SpeciesReference.cpp | 2379 +
libsbml-5.15.2/src/sbml/SpeciesReference.h | 2319 +
libsbml-5.15.2/src/sbml/SpeciesType.cpp | 1009 +
libsbml-5.15.2/src/sbml/SpeciesType.h | 1101 +
libsbml-5.15.2/src/sbml/StoichiometryMath.cpp | 710 +
libsbml-5.15.2/src/sbml/StoichiometryMath.h | 824 +
libsbml-5.15.2/src/sbml/SyntaxChecker.cpp | 2093 +
libsbml-5.15.2/src/sbml/SyntaxChecker.h | 455 +
libsbml-5.15.2/src/sbml/Trigger.cpp | 1137 +
libsbml-5.15.2/src/sbml/Trigger.h | 1170 +
libsbml-5.15.2/src/sbml/Unit.cpp | 3255 +
libsbml-5.15.2/src/sbml/Unit.h | 2879 +
libsbml-5.15.2/src/sbml/UnitDefinition.cpp | 2738 +
libsbml-5.15.2/src/sbml/UnitDefinition.h | 2269 +
libsbml-5.15.2/src/sbml/UnitKind.c | 159 +
libsbml-5.15.2/src/sbml/UnitKind.h | 207 +
libsbml-5.15.2/src/sbml/annotation/CVTerm.cpp | 971 +
libsbml-5.15.2/src/sbml/annotation/CVTerm.h | 1800 +
libsbml-5.15.2/src/sbml/annotation/Date.cpp | 926 +
libsbml-5.15.2/src/sbml/annotation/Date.h | 1009 +
libsbml-5.15.2/src/sbml/annotation/Makefile.in | 176 +
.../src/sbml/annotation/ModelCreator.cpp | 792 +
libsbml-5.15.2/src/sbml/annotation/ModelCreator.h | 905 +
.../src/sbml/annotation/ModelHistory.cpp | 621 +
libsbml-5.15.2/src/sbml/annotation/ModelHistory.h | 685 +
libsbml-5.15.2/src/sbml/annotation/RDFAnnotation.h | 36 +
.../src/sbml/annotation/RDFAnnotationParser.cpp | 1573 +
.../src/sbml/annotation/RDFAnnotationParser.h | 656 +
.../src/sbml/annotation/test/CMakeLists.txt | 56 +
.../src/sbml/annotation/test/Makefile.in | 237 +
.../src/sbml/annotation/test/TestCVTerms.c | 535 +
.../sbml/annotation/test/TestCVTerms_newSetters.c | 211 +
.../src/sbml/annotation/test/TestCopyAndClone.cpp | 572 +
.../src/sbml/annotation/test/TestDate_newSetters.c | 415 +
.../sbml/annotation/test/TestL3ModelHistory.cpp | 688 +
.../annotation/test/TestModelCreator_newSetters.c | 223 +
.../src/sbml/annotation/test/TestModelHistory.c | 437 +
.../annotation/test/TestModelHistory_newSetters.c | 217 +
.../src/sbml/annotation/test/TestRDFAnnotation.cpp | 2178 +
.../sbml/annotation/test/TestRDFAnnotation2.cpp | 357 +
.../src/sbml/annotation/test/TestRDFAnnotationC.c | 345 +
.../annotation/test/TestRDFAnnotationMetaid.cpp | 281 +
.../test/TestRDFAnnotationNestedCVTerms.cpp | 1076 +
.../annotation/test/TestRDFAnnotationVCard4.cpp | 857 +
.../src/sbml/annotation/test/TestRunner.c | 152 +
.../sbml/annotation/test/TestSyncAnnotation.cpp | 1623 +
.../src/sbml/annotation/test/TestValidation.cpp | 311 +
.../sbml/annotation/test/test-data/annotation.xml | 0
.../sbml/annotation/test/test-data/annotation2.xml | 0
.../annotation/test/test-data/annotationL3.xml | 0
.../annotation/test/test-data/annotationL3_2.xml | 0
.../annotation/test/test-data/annotationL3_3.xml | 0
.../test/test-data/annotationNested-l2v5.xml | 85 +
.../test/test-data/annotationNested-l3v1.xml | 85 +
.../test/test-data/annotationNested-l3v2.xml | 85 +
.../test/test-data/annotationVcard4-l3v1.xml | 37 +
.../annotation/test/test-data/annotationVcard4.xml | 37 +
libsbml-5.15.2/src/sbml/common/Makefile.in | 173 +
.../src/sbml/common/common-documentation.h | 3659 +
.../src/sbml/common/common-sbmlerror-codes.h | 10208 ++
libsbml-5.15.2/src/sbml/common/common.h | 114 +
libsbml-5.15.2/src/sbml/common/extern.h | 110 +
.../src/sbml/common/libsbml-config-common.h | 130 +
.../src/sbml/common/libsbml-config-common.h.cmake | 109 +
.../src/sbml/common/libsbml-config-common.h.in | 129 +
libsbml-5.15.2/src/sbml/common/libsbml-config.h | 72 +
libsbml-5.15.2/src/sbml/common/libsbml-namespace.h | 69 +
.../src/sbml/common/libsbml-namespace.h.cmake | 68 +
.../src/sbml/common/libsbml-namespace.h.in | 68 +
libsbml-5.15.2/src/sbml/common/libsbml-package.h | 67 +
.../src/sbml/common/libsbml-package.h.cmake | 54 +
.../src/sbml/common/libsbml-package.h.in | 66 +
libsbml-5.15.2/src/sbml/common/libsbml-version.cpp | 210 +
libsbml-5.15.2/src/sbml/common/libsbml-version.h | 146 +
.../src/sbml/common/libsbml-version.h.cmake | 148 +
.../src/sbml/common/libsbml-version.h.in | 146 +
.../src/sbml/common/operationReturnValues.cpp | 296 +
.../src/sbml/common/operationReturnValues.h | 296 +
libsbml-5.15.2/src/sbml/common/sbmlfwd.h | 436 +
.../src}/sbml/compress/00README.txt | 0
.../src/sbml/compress/CompressCommon.cpp | 76 +
libsbml-5.15.2/src/sbml/compress/CompressCommon.h | 112 +
.../src/sbml/compress/InputDecompressor.cpp | 198 +
.../src/sbml/compress/InputDecompressor.h | 140 +
libsbml-5.15.2/src/sbml/compress/Makefile.in | 193 +
.../src/sbml/compress/OutputCompressor.cpp | 116 +
.../src/sbml/compress/OutputCompressor.h | 98 +
libsbml-5.15.2/src/sbml/compress/bzfstream.cpp | 507 +
libsbml-5.15.2/src/sbml/compress/bzfstream.h | 472 +
libsbml-5.15.2/src/sbml/compress/crypt.h | 130 +
libsbml-5.15.2/src/sbml/compress/ioapi.c | 369 +
libsbml-5.15.2/src/sbml/compress/ioapi.h | 175 +
libsbml-5.15.2/src/sbml/compress/ioapi_mem.c | 192 +
libsbml-5.15.2/src/sbml/compress/ioapi_mem.h | 55 +
libsbml-5.15.2/src/sbml/compress/iowin32.c | 588 +
libsbml-5.15.2/src/sbml/compress/iowin32.h | 33 +
libsbml-5.15.2/src/sbml/compress/unzip.c | 1879 +
libsbml-5.15.2/src/sbml/compress/unzip.h | 316 +
.../src}/sbml/compress/zfstream.cpp | 0
.../src}/sbml/compress/zfstream.h | 0
libsbml-5.15.2/src/sbml/compress/zip.c | 2008 +
libsbml-5.15.2/src/sbml/compress/zip.h | 200 +
libsbml-5.15.2/src/sbml/compress/zipfstream.cpp | 682 +
libsbml-5.15.2/src/sbml/compress/zipfstream.h | 506 +
.../src/sbml/conversion/ConversionOption.cpp | 418 +
.../src/sbml/conversion/ConversionOption.h | 676 +
.../src/sbml/conversion/ConversionProperties.cpp | 567 +
.../src/sbml/conversion/ConversionProperties.h | 732 +
libsbml-5.15.2/src/sbml/conversion/Makefile.in | 195 +
.../src/sbml/conversion/RegisterConverters.cpp | 77 +
.../src/sbml/conversion/SBMLConverter.cpp | 224 +
libsbml-5.15.2/src/sbml/conversion/SBMLConverter.h | 319 +
.../src/sbml/conversion/SBMLConverterRegister.h | 113 +
.../src/sbml/conversion/SBMLConverterRegistry.cpp | 129 +
.../src/sbml/conversion/SBMLConverterRegistry.h | 181 +
.../src/sbml/conversion/SBMLConverterTypes.h | 57 +
.../conversion/SBMLFunctionDefinitionConverter.cpp | 331 +
.../conversion/SBMLFunctionDefinitionConverter.h | 207 +
.../src/sbml/conversion/SBMLIdConverter.cpp | 194 +
.../src/sbml/conversion/SBMLIdConverter.h | 202 +
.../sbml/conversion/SBMLInferUnitsConverter.cpp | 275 +
.../src/sbml/conversion/SBMLInferUnitsConverter.h | 207 +
.../conversion/SBMLInitialAssignmentConverter.cpp | 162 +
.../conversion/SBMLInitialAssignmentConverter.h | 211 +
.../conversion/SBMLLevel1Version1Converter.cpp | 304 +
.../sbml/conversion/SBMLLevel1Version1Converter.h | 235 +
.../sbml/conversion/SBMLLevelVersionConverter.cpp | 1398 +
.../sbml/conversion/SBMLLevelVersionConverter.h | 320 +
.../conversion/SBMLLocalParameterConverter.cpp | 206 +
.../sbml/conversion/SBMLLocalParameterConverter.h | 187 +
.../src/sbml/conversion/SBMLRateOfConverter.cpp | 660 +
.../src/sbml/conversion/SBMLRateOfConverter.h | 256 +
.../src/sbml/conversion/SBMLReactionConverter.cpp | 512 +
.../src/sbml/conversion/SBMLReactionConverter.h | 242 +
.../src/sbml/conversion/SBMLRuleConverter.cpp | 405 +
.../src/sbml/conversion/SBMLRuleConverter.h | 214 +
.../sbml/conversion/SBMLStripPackageConverter.cpp | 246 +
.../sbml/conversion/SBMLStripPackageConverter.h | 230 +
.../src/sbml/conversion/SBMLUnitsConverter.cpp | 1872 +
.../src/sbml/conversion/SBMLUnitsConverter.h | 258 +
.../src/sbml/conversion/test/CMakeLists.txt | 59 +
.../src/sbml/conversion/test/Makefile.in | 225 +
.../sbml/conversion/test/TestConversionOption.cpp | 198 +
.../conversion/test/TestConversionProperties.cpp | 168 +
.../conversion/test/TestInferUnitsConverter.cpp | 411 +
.../conversion/test/TestLevelVersionConverter.cpp | 354 +
.../sbml/conversion/test/TestRateOfConverter.cpp | 525 +
.../src/sbml/conversion/test/TestRunner.c | 140 +
.../conversion/test/TestSBMLConverterRegistry.cpp | 190 +
.../sbml/conversion/test/TestSBMLRuleConverter.cpp | 390 +
.../conversion/test/TestStripPackageConverter.cpp | 167 +
.../sbml/conversion/test/TestUnitsConverter.cpp | 2351 +
.../sbml/conversion/test/TestUnitsConverter2.cpp | 2052 +
.../sbml/conversion/test/TestUnitsConverterL2.cpp | 1340 +
.../conversion/test/test-data/00856-sbml-l3v1.xml | 0
.../src}/sbml/conversion/test/test-data/README.txt | 0
.../sbml/conversion/test/test-data/extend_l3.xml | 0
.../conversion/test/test-data/ia-ternary-lt.xml | 0
.../conversion/test/test-data/inferUnits-2.xml | 0
.../conversion/test/test-data/inferUnits-3.xml | 0
.../sbml/conversion/test/test-data/inferUnits.xml | 0
.../test/test-data/inline_bug_minimal.xml | 0
.../conversion/test/test-data/l2v5-components.xml | 0
.../conversion/test/test-data/l3v1-components.xml | 44 +
.../conversion/test/test-data/multiple_rateOf.xml | 91 +
.../test/test-data/multiple_rateOf_FD.xml | 106 +
.../conversion/test/test-data/nested_rateOf.xml | 27 +
.../conversion/test/test-data/nested_rateOf_FD.xml | 42 +
.../test/test-data/package1-comp_stripped.xml | 0
.../test/test-data/package1-stripped.xml | 0
.../test-data/package1-unknownreq_stripped.xml | 0
.../sbml/conversion/test/test-data/package1.xml | 0
.../sbml/conversion/test/test-data/test_rateOf.xml | 24 +
.../conversion/test/test-data/test_rateOf_FD.xml | 39 +
.../src}/sbml/conversion/test/test-data/units1.xml | 0
.../src}/sbml/conversion/test/test-data/units2.xml | 0
.../src}/sbml/conversion/test/test-data/units3.xml | 0
.../test/test-data/wrongl3v1-invalid.xml | 0
.../src/sbml/extension/ASTBasePlugin.cpp | 1306 +
libsbml-5.15.2/src/sbml/extension/ASTBasePlugin.h | 938 +
.../sbml/extension/ISBMLExtensionNamespaces.cpp | 75 +
.../src/sbml/extension/ISBMLExtensionNamespaces.h | 82 +
libsbml-5.15.2/src/sbml/extension/Makefile.in | 184 +
.../src}/sbml/extension/RegisterExtensions.cxx.in | 0
.../src}/sbml/extension/RegisterExtensions.h.in | 0
.../src/sbml/extension/SBMLDocumentPlugin.cpp | 347 +
.../src/sbml/extension/SBMLDocumentPlugin.h | 456 +
.../extension/SBMLDocumentPluginNotRequired.cpp | 137 +
.../sbml/extension/SBMLDocumentPluginNotRequired.h | 156 +
.../src/sbml/extension/SBMLExtension.cpp | 741 +
libsbml-5.15.2/src/sbml/extension/SBMLExtension.h | 961 +
.../src/sbml/extension/SBMLExtensionException.cpp | 48 +
.../src/sbml/extension/SBMLExtensionException.h | 80 +
.../src/sbml/extension/SBMLExtensionNamespaces.cpp | 106 +
.../src/sbml/extension/SBMLExtensionNamespaces.h | 343 +
.../src/sbml/extension/SBMLExtensionRegister.h | 86 +
.../src/sbml/extension/SBMLExtensionRegistry.cpp | 731 +
.../src/sbml/extension/SBMLExtensionRegistry.h | 610 +
.../src/sbml/extension/SBaseExtensionPoint.cpp | 206 +
.../src/sbml/extension/SBaseExtensionPoint.h | 277 +
libsbml-5.15.2/src/sbml/extension/SBasePlugin.cpp | 1141 +
libsbml-5.15.2/src/sbml/extension/SBasePlugin.h | 1355 +
.../src/sbml/extension/SBasePluginCreator.h | 140 +
.../src/sbml/extension/SBasePluginCreatorBase.cpp | 238 +
.../src/sbml/extension/SBasePluginCreatorBase.h | 337 +
.../src/sbml/extension/test/CMakeLists.txt | 49 +
libsbml-5.15.2/src/sbml/extension/test/Makefile.in | 230 +
.../src/sbml/extension/test/TestPackage.cpp | 448 +
.../src/sbml/extension/test/TestPackage.h | 148 +
.../src/sbml/extension/test/TestRunner.c | 130 +
.../sbml/extension/test/TestSBMLDocumentPlugin.cpp | 153 +
.../src/sbml/extension/test/TestSBMLExtension.cpp | 274 +
.../extension/test/TestSBMLExtensionNamespaces.cpp | 102 +
.../extension/test/TestSBMLExtensionRegistry.cpp | 201 +
.../extension/test/TestSBaseExtensionPoint.cpp | 132 +
.../src/sbml/extension/test/TestSBasePlugin.cpp | 143 +
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create mode 100644 libsbml-5.15.2/src/sbml/validator/test/test-data/sbml-identifier-constraints/10309-pass-00-78.xml
copy {src => libsbml-5.15.2/src}/sbml/validator/test/test-data/sbml-identifier-constraints/10310-fail-01-01.xml (100%)
copy {src => libsbml-5.15.2/src}/sbml/validator/test/test-data/sbml-identifier-constraints/10310-fail-01-02.xml (100%)
copy {src => libsbml-5.15.2/src}/sbml/validator/test/test-data/sbml-identifier-constraints/10310-fail-01-03.xml (100%)
copy {src => libsbml-5.15.2/src}/sbml/validator/test/test-data/sbml-identifier-constraints/10310-fail-01-04.xml (100%)
copy {src => libsbml-5.15.2/src}/sbml/validator/test/test-data/sbml-identifier-constraints/10310-fail-01-05.xml (100%)
copy {src => libsbml-5.15.2/src}/sbml/validator/test/test-data/sbml-identifier-constraints/10310-fail-01-06.xml (100%)
copy {src => libsbml-5.15.2/src}/sbml/validator/test/test-data/sbml-identifier-constraints/10310-fail-01-07.xml (100%)
copy {src => libsbml-5.15.2/src}/sbml/validator/test/test-data/sbml-identifier-constraints/10310-fail-01-08.xml (100%)
copy {src => libsbml-5.15.2/src}/sbml/validator/test/test-data/sbml-identifier-constraints/10310-fail-01-09.xml (100%)
copy {src => libsbml-5.15.2/src}/sbml/validator/test/test-data/sbml-identifier-constraints/10310-fail-01-10.xml (100%)
copy {src => libsbml-5.15.2/src}/sbml/validator/test/test-data/sbml-identifier-constraints/10310-fail-01-11.xml (100%)
copy {src => libsbml-5.15.2/src}/sbml/validator/test/test-data/sbml-identifier-constraints/10310-fail-01-12.xml (100%)
copy {src => libsbml-5.15.2/src}/sbml/validator/test/test-data/sbml-identifier-constraints/10310-fail-01-13.xml (100%)
copy {src => libsbml-5.15.2/src}/sbml/validator/test/test-data/sbml-identifier-constraints/10310-fail-01-14.xml (100%)
copy {src => libsbml-5.15.2/src}/sbml/validator/test/test-data/sbml-identifier-constraints/10310-fail-01-15.xml (100%)
copy {src => libsbml-5.15.2/src}/sbml/validator/test/test-data/sbml-identifier-constraints/10310-fail-01-16.xml (100%)
create mode 100644 libsbml-5.15.2/src/sbml/validator/test/test-data/sbml-identifier-constraints/10310-fail-01-17.xml
create mode 100644 libsbml-5.15.2/src/sbml/validator/test/test-data/sbml-identifier-constraints/10310-fail-01-18.xml
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copy {src => libsbml-5.15.2/src}/sbml/validator/test/test-data/sbml-identifier-constraints/10310-pass-00-05.xml (100%)
copy {src => libsbml-5.15.2/src}/sbml/validator/test/test-data/sbml-identifier-constraints/10310-pass-00-06.xml (100%)
copy {src => libsbml-5.15.2/src}/sbml/validator/test/test-data/sbml-identifier-constraints/10310-pass-00-07.xml (100%)
copy {src => libsbml-5.15.2/src}/sbml/validator/test/test-data/sbml-identifier-constraints/10310-pass-00-08.xml (100%)
copy {src => libsbml-5.15.2/src}/sbml/validator/test/test-data/sbml-identifier-constraints/10310-pass-00-09.xml (100%)
copy {src => libsbml-5.15.2/src}/sbml/validator/test/test-data/sbml-identifier-constraints/10310-pass-00-10.xml (100%)
copy {src => libsbml-5.15.2/src}/sbml/validator/test/test-data/sbml-identifier-constraints/10310-pass-00-11.xml (100%)
copy {src => libsbml-5.15.2/src}/sbml/validator/test/test-data/sbml-identifier-constraints/10310-pass-00-12.xml (100%)
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create mode 100644 libsbml-5.15.2/src/sbml/validator/test/test-data/sbml-identifier-constraints/10310-pass-00-14.xml
create mode 100644 libsbml-5.15.2/src/sbml/validator/test/test-data/sbml-identifier-constraints/10310-pass-00-15.xml
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copy {src => libsbml-5.15.2/src}/sbml/validator/test/test-data/sbml-identifier-constraints/10311-fail-01-02.xml (100%)
copy {src => libsbml-5.15.2/src}/sbml/validator/test/test-data/sbml-identifier-constraints/10311-fail-01-03.xml (100%)
copy {src => libsbml-5.15.2/src}/sbml/validator/test/test-data/sbml-identifier-constraints/10311-fail-01-04.xml (100%)
copy {src => libsbml-5.15.2/src}/sbml/validator/test/test-data/sbml-identifier-constraints/10311-fail-01-05.xml (100%)
copy {src => libsbml-5.15.2/src}/sbml/validator/test/test-data/sbml-identifier-constraints/10311-fail-01-06.xml (100%)
copy {src => libsbml-5.15.2/src}/sbml/validator/test/test-data/sbml-identifier-constraints/10311-fail-01-07.xml (100%)
copy {src => libsbml-5.15.2/src}/sbml/validator/test/test-data/sbml-identifier-constraints/10311-fail-01-08.xml (100%)
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copy {src => libsbml-5.15.2/src}/sbml/validator/test/test-data/sbml-identifier-constraints/10311-fail-01-11.xml (100%)
copy {src => libsbml-5.15.2/src}/sbml/validator/test/test-data/sbml-identifier-constraints/10311-fail-01-12.xml (100%)
copy {src => libsbml-5.15.2/src}/sbml/validator/test/test-data/sbml-identifier-constraints/10311-fail-01-13.xml (100%)
copy {src => libsbml-5.15.2/src}/sbml/validator/test/test-data/sbml-identifier-constraints/10311-fail-01-14.xml (100%)
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copy {src => libsbml-5.15.2/src}/sbml/validator/test/test-data/sbml-identifier-constraints/10311-fail-01-16.xml (100%)
copy {src => libsbml-5.15.2/src}/sbml/validator/test/test-data/sbml-identifier-constraints/10311-fail-01-17.xml (100%)
copy {src => libsbml-5.15.2/src}/sbml/validator/test/test-data/sbml-identifier-constraints/10311-fail-01-18.xml (100%)
copy src/sbml/validator/test/test-data/sbml-identifier-constraints/10311-fail-01-19.xml => libsbml-5.15.2/src/sbml/validator/test/test-data/sbml-identifier-constraints/10311-fail-01-19-10313.xml (100%)
copy src/sbml/validator/test/test-data/sbml-identifier-constraints/10311-fail-01-20.xml => libsbml-5.15.2/src/sbml/validator/test/test-data/sbml-identifier-constraints/10311-fail-01-20-10313.xml (100%)
copy src/sbml/validator/test/test-data/sbml-identifier-constraints/10311-fail-01-21.xml => libsbml-5.15.2/src/sbml/validator/test/test-data/sbml-identifier-constraints/10311-fail-01-21-10313.xml (100%)
copy src/sbml/validator/test/test-data/sbml-identifier-constraints/10311-fail-01-22.xml => libsbml-5.15.2/src/sbml/validator/test/test-data/sbml-identifier-constraints/10311-fail-01-22-10313.xml (100%)
copy {src => libsbml-5.15.2/src}/sbml/validator/test/test-data/sbml-identifier-constraints/10311-fail-01-23-10313.xml (100%)
copy {src => libsbml-5.15.2/src}/sbml/validator/test/test-data/sbml-identifier-constraints/10311-fail-01-24-10313.xml (100%)
copy {src => libsbml-5.15.2/src}/sbml/validator/test/test-data/sbml-identifier-constraints/10311-fail-01-25-10313.xml (100%)
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create mode 100644 libsbml-5.15.2/src/sbml/validator/test/test-data/sbml-identifier-constraints/10311-fail-01-27-10313.xml
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create mode 100644 libsbml-5.15.2/src/sbml/validator/test/test-data/sbml-identifier-constraints/10311-fail-01-30-10313.xml
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create mode 100644 libsbml-5.15.2/src/sbml/validator/test/test-data/sbml-identifier-constraints/10313-fail-01-19.xml
copy src/sbml/validator/test/test-data/sbml-identifier-constraints/99303-fail-01-05.xml => libsbml-5.15.2/src/sbml/validator/test/test-data/sbml-identifier-constraints/10313-fail-01-20.xml (100%)
copy src/sbml/validator/test/test-data/sbml-identifier-constraints/99303-fail-01-03.xml => libsbml-5.15.2/src/sbml/validator/test/test-data/sbml-identifier-constraints/10313-fail-01-21.xml (100%)
copy src/sbml/validator/test/test-data/sbml-identifier-constraints/99303-fail-01-06.xml => libsbml-5.15.2/src/sbml/validator/test/test-data/sbml-identifier-constraints/10313-fail-01-22.xml (100%)
copy src/sbml/validator/test/test-data/sbml-identifier-constraints/99303-fail-01-07.xml => libsbml-5.15.2/src/sbml/validator/test/test-data/sbml-identifier-constraints/10313-fail-01-23.xml (100%)
copy src/sbml/validator/test/test-data/sbml-identifier-constraints/99303-fail-01-08.xml => libsbml-5.15.2/src/sbml/validator/test/test-data/sbml-identifier-constraints/10313-fail-01-24.xml (100%)
rename src/sbml/validator/test/test-data/sbml-identifier-constraints/99303-fail-01-09.xml => libsbml-5.15.2/src/sbml/validator/test/test-data/sbml-identifier-constraints/10313-fail-01-25.xml (100%)
copy src/sbml/validator/test/test-data/sbml-identifier-constraints/99303-fail-01-10.xml => libsbml-5.15.2/src/sbml/validator/test/test-data/sbml-identifier-constraints/10313-fail-01-26.xml (100%)
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