[med-svn] [Git][med-team/libsbml][upstream] New upstream version 5.20.5+dfsg

Sat Dec 13 16:12:48 GMT 2025

Andreas Tille pushed to branch upstream at Debian Med / libsbml

Commits:
afbda43b by Andreas Tille at 2025-12-13T11:34:56+01:00
New upstream version 5.20.5+dfsg
- - - - -

181 changed files:

- .github/workflows/brief.yml
- .github/workflows/doxygen.yml
- .github/workflows/extensive.yml
- .github/workflows/matlab.yml
- .github/workflows/octave.yml
- .github/workflows/store-artefact.yml
- CMakeLists.txt
- CMakeModules/FindEXPAT.cmake
- CMakeModules/FindZLIB.cmake
- VERSION.txt
- artefacts.md
- config/java.m4
- configure
- configure.ac
- dev/utilities/sboTree/SBO.cpp.cmake
- dev/utilities/sboTree/updateSBO.cmake
- examples/c++/CMakeLists.txt
- + examples/c++/inferReactions.cpp
- src/CMakeLists.txt
- src/bindings/python/local.i
- src/bindings/swig/libsbml.h
- src/bindings/swig/libsbml.i
- src/bindings/swig/swigdoc.py
- src/sbml/Constraint.cpp
- src/sbml/Constraint.h
- src/sbml/SBMLDocument.cpp
- src/sbml/SBMLDocument.h
- src/sbml/SBMLError.cpp
- src/sbml/SBMLError.h
- src/sbml/SBMLErrorTable.h
- src/sbml/SBMLTransforms.cpp
- src/sbml/SBO.cpp
- src/sbml/SBase.cpp
- src/sbml/SBase.h
- src/sbml/common/libsbml-version.h
- src/sbml/conversion/SBMLRateRuleConverter.cpp
- src/sbml/conversion/test/TestSBMLRateRuleConverter.cpp
- src/sbml/extension/test/TestSBMLDocumentPlugin.cpp
- + src/sbml/extension/test/test-data/issue417.xml
- + src/sbml/html2md/COPYING
- + src/sbml/html2md/README.md
- + src/sbml/html2md/VERSION.txt
- + src/sbml/html2md/html2md.cpp
- + src/sbml/html2md/html2md.h
- + src/sbml/html2md/table.cpp
- + src/sbml/html2md/table.h
- + src/sbml/maddy/CMakeLists.txt
- + src/sbml/maddy/LICENSE
- + src/sbml/maddy/VERSION.txt
- + src/sbml/maddy/blockparser.h
- + src/sbml/maddy/breaklineparser.h
- + src/sbml/maddy/checklistparser.h
- + src/sbml/maddy/codeblockparser.h
- + src/sbml/maddy/emphasizedparser.h
- + src/sbml/maddy/headlineparser.h
- + src/sbml/maddy/horizontallineparser.h
- + src/sbml/maddy/htmlparser.h
- + src/sbml/maddy/imageparser.h
- + src/sbml/maddy/inlinecodeparser.h
- + src/sbml/maddy/italicparser.h
- + src/sbml/maddy/latexblockparser.h
- + src/sbml/maddy/lineparser.h
- + src/sbml/maddy/linkparser.h
- + src/sbml/maddy/orderedlistparser.h
- + src/sbml/maddy/paragraphparser.h
- + src/sbml/maddy/parser.h
- + src/sbml/maddy/parserconfig.h
- + src/sbml/maddy/quoteparser.h
- + src/sbml/maddy/strikethroughparser.h
- + src/sbml/maddy/strongparser.h
- + src/sbml/maddy/tableparser.h
- + src/sbml/maddy/unorderedlistparser.h
- src/sbml/packages/distrib/extension/DistribASTPlugin.cpp
- src/sbml/packages/distrib/extension/DistribSBMLDocumentPlugin.cpp
- src/sbml/packages/distrib/util/AnnotationToDistribConverter.cpp
- src/sbml/packages/distrib/util/DistribToAnnotationConverter.cpp
- src/sbml/packages/distrib/util/DistribToAnnotationConverter.h
- src/sbml/packages/distrib/util/test/TestDistribAnnotationConverter.cpp
- + src/sbml/packages/distrib/util/test/test-data/normal_l3v1_annot_uncertml.xml
- + src/sbml/packages/distrib/validator/DistribMathMLConsistencyValidator.cpp
- + src/sbml/packages/distrib/validator/DistribMathMLConsistencyValidator.h
- src/sbml/packages/distrib/validator/DistribSBMLError.h
- src/sbml/packages/distrib/validator/DistribSBMLErrorTable.h
- + src/sbml/packages/distrib/validator/DistribUnitConsistencyValidator.cpp
- + src/sbml/packages/distrib/validator/DistribUnitConsistencyValidator.h
- src/sbml/packages/distrib/validator/DistribValidator.cpp
- + src/sbml/packages/distrib/validator/constraints/DistribArgumentsUnitsCheck.cpp
- + src/sbml/packages/distrib/validator/constraints/DistribArgumentsUnitsCheck.h
- + src/sbml/packages/distrib/validator/constraints/DistribMathMLConsistencyConstraints.cpp
- + src/sbml/packages/distrib/validator/constraints/DistribMathMLConsistencyConstraintsDeclared.cxx
- + src/sbml/packages/distrib/validator/constraints/DistribNumberArgsMathCheck.cpp
- + src/sbml/packages/distrib/validator/constraints/DistribNumberArgsMathCheck.h
- + src/sbml/packages/distrib/validator/constraints/DistribUnitConsistencyConstraints.cpp
- + src/sbml/packages/distrib/validator/constraints/DistribUnitConsistencyConstraintsDeclared.cxx
- src/sbml/packages/distrib/validator/test/TestDistribConsistencyValidator.cpp
- src/sbml/packages/distrib/validator/test/TestFile.cpp
- src/sbml/packages/distrib/validator/test/TestValidator.cpp
- + src/sbml/packages/distrib/validator/test/test-data/distrib-unit-constraints/1510501-fail-01-01.xml
- + src/sbml/packages/distrib/validator/test/test-data/distrib-unit-constraints/1510501-fail-01-02.xml
- + src/sbml/packages/distrib/validator/test/test-data/distrib-unit-constraints/1510501-fail-01-03.xml
- + src/sbml/packages/distrib/validator/test/test-data/distrib-unit-constraints/1510501-pass-00-01.xml
- + src/sbml/packages/distrib/validator/test/test-data/math-constraints/1510210-fail-01-01.xml
- + src/sbml/packages/distrib/validator/test/test-data/math-constraints/1510210-fail-01-02.xml
- + src/sbml/packages/distrib/validator/test/test-data/math-constraints/1510210-fail-01-03.xml
- + src/sbml/packages/distrib/validator/test/test-data/math-constraints/1510210-fail-01-04.xml
- + src/sbml/packages/distrib/validator/test/test-data/math-constraints/1510210-fail-01-05.xml
- + src/sbml/packages/distrib/validator/test/test-data/math-constraints/1510210-fail-01-06.xml
- + src/sbml/packages/distrib/validator/test/test-data/math-constraints/1510210-fail-01-07.xml
- + src/sbml/packages/distrib/validator/test/test-data/math-constraints/1510210-fail-01-08.xml
- + src/sbml/packages/distrib/validator/test/test-data/math-constraints/1510210-fail-01-09.xml
- + src/sbml/packages/distrib/validator/test/test-data/math-constraints/1510210-fail-01-10.xml
- + src/sbml/packages/distrib/validator/test/test-data/math-constraints/1510210-fail-01-11.xml
- + src/sbml/packages/distrib/validator/test/test-data/math-constraints/1510210-fail-01-12.xml
- + src/sbml/packages/distrib/validator/test/test-data/math-constraints/1510210-fail-01-13.xml
- + src/sbml/packages/distrib/validator/test/test-data/math-constraints/1510210-fail-01-14.xml
- + src/sbml/packages/distrib/validator/test/test-data/math-constraints/1510210-fail-01-15.xml
- + src/sbml/packages/distrib/validator/test/test-data/math-constraints/1510210-fail-01-16.xml
- + src/sbml/packages/distrib/validator/test/test-data/math-constraints/1510210-pass-00-01.xml
- + src/sbml/packages/distrib/validator/test/test-data/math-constraints/1510210-pass-00-02.xml
- + src/sbml/packages/distrib/validator/test/test-data/math-constraints/1510210-pass-00-03.xml
- + src/sbml/packages/distrib/validator/test/test-data/math-constraints/1510210-pass-00-04.xml
- + src/sbml/packages/distrib/validator/test/test-data/math-constraints/1510210-pass-00-05.xml
- + src/sbml/packages/distrib/validator/test/test-data/math-constraints/1510210-pass-00-06.xml
- + src/sbml/packages/distrib/validator/test/test-data/math-constraints/1510210-pass-00-07.xml
- + src/sbml/packages/distrib/validator/test/test-data/math-constraints/1510210-pass-00-08.xml
- + src/sbml/packages/distrib/validator/test/test-data/math-constraints/1510210-pass-00-09.xml
- + src/sbml/packages/distrib/validator/test/test-data/math-constraints/1510210-pass-00-10.xml
- + src/sbml/packages/distrib/validator/test/test-data/math-constraints/1510210-pass-00-11.xml
- + src/sbml/packages/distrib/validator/test/test-data/math-constraints/1510210-pass-00-12.xml
- + src/sbml/packages/distrib/validator/test/test-data/math-constraints/1510210-pass-00-13.xml
- + src/sbml/packages/distrib/validator/test/test-data/math-constraints/1510210-pass-00-14.xml
- + src/sbml/packages/distrib/validator/test/test-data/math-constraints/1510210-pass-00-15.xml
- + src/sbml/packages/distrib/validator/test/test-data/math-constraints/1510210-pass-00-16.xml
- + src/sbml/packages/distrib/validator/test/test-data/math-constraints/1510210-pass-00-17.xml
- + src/sbml/packages/distrib/validator/test/test-data/math-constraints/1510210-pass-00-18.xml
- + src/sbml/packages/distrib/validator/test/test-data/math-constraints/1510210-pass-00-19.xml
- + src/sbml/packages/distrib/validator/test/test-data/math-constraints/1510210-pass-00-20.xml
- + src/sbml/packages/distrib/validator/test/test-data/math-constraints/1510210-pass-00-21.xml
- + src/sbml/packages/distrib/validator/test/test-data/math-constraints/1510210-pass-00-22.xml
- + src/sbml/packages/distrib/validator/test/test-data/math-constraints/1510210-pass-00-23.xml
- + src/sbml/packages/distrib/validator/test/test-data/math-constraints/1510210-pass-00-24.xml
- + src/sbml/packages/distrib/validator/test/test-data/unit-constraints/1510523-fail-01-01.xml
- + src/sbml/packages/distrib/validator/test/test-data/unit-constraints/1510523-fail-01-02.xml
- + src/sbml/packages/distrib/validator/test/test-data/unit-constraints/1510523-pass-00-01.xml
- + src/sbml/packages/distrib/validator/validator/QualMathConsistencyValidator.cpp
- + src/sbml/packages/distrib/validator/validator/QualMathConsistencyValidator.h
- src/sbml/packages/fbc/extension/test/TestWriteFbcExtension.cpp
- src/sbml/packages/fbc/extension/test/test-data/fbc_example2_v3.xml
- src/sbml/packages/fbc/sbml/KeyValuePair.cpp
- src/sbml/packages/layout/extension/LayoutSBMLDocumentPlugin.cpp
- src/sbml/packages/layout/sbml/Layout.cpp
- src/sbml/packages/multi/validator/test/test-data/general-constraints/7020306-fail-01-01-10102.xml → src/sbml/packages/multi/validator/test/test-data/general-constraints/7020306-fail-01-01.xml
- src/sbml/packages/render/sbml/ListOfGlobalRenderInformation.cpp
- src/sbml/packages/render/sbml/ListOfLocalRenderInformation.cpp
- src/sbml/packages/render/sbml/RenderCurve.cpp
- src/sbml/packages/render/sbml/Style.cpp
- src/sbml/packages/render/sbml/Transformation2D.cpp
- + src/sbml/packages/render/validator/test/test-data/general-constraints/1322104-pass-00-01.xml
- src/sbml/test/TestConsistencyChecks.cpp
- src/sbml/test/TestConstraint.c
- src/sbml/test/TestSBase.cpp
- src/sbml/util/test/TestUtil.c
- src/sbml/util/util.cpp
- src/sbml/util/util.h
- src/sbml/validator/SBMLInternalValidator.cpp
- src/sbml/validator/Validator.cpp
- src/sbml/validator/constraints/MathMLBase.cpp
- src/sbml/validator/constraints/NumberArgsMathCheck.cpp
- src/sbml/validator/test/test-data/libsbml-constraints/99107-fail-01-04-10102.xml → src/sbml/validator/test/test-data/libsbml-constraints/99107-fail-01-06.xml
- src/sbml/validator/test/test-data/libsbml-constraints/99107-fail-01-06-10102.xml → src/sbml/validator/test/test-data/libsbml-constraints/99107-fail-01-07.xml
- src/sbml/validator/test/test-data/sbml-xml-constraints/10102-fail-01-27-20517.xml → src/sbml/validator/test/test-data/libsbml-constraints/99107-fail-01-08.xml
- src/sbml/validator/test/test-data/sbml-xml-constraints/10102-fail-01-29-20517.xml → src/sbml/validator/test/test-data/libsbml-constraints/99107-fail-01-09.xml
- src/sbml/validator/test/test-data/sbml-xml-constraints/10102-fail-01-28-20517.xml → src/sbml/validator/test/test-data/libsbml-constraints/99108-fail-01-06.xml
- src/sbml/validator/test/test-data/sbml-xml-constraints/10102-fail-01-30-20517.xml → src/sbml/validator/test/test-data/sbml-general-consistency-constraints/20517-fail-01-07.xml
- src/sbml/validator/test/test-data/sbml-xml-constraints/10102-fail-01-32-20517.xml → src/sbml/validator/test/test-data/sbml-general-consistency-constraints/20517-fail-01-08.xml
- src/sbml/validator/test/test-data/sbml-xml-constraints/10102-fail-01-31-20517.xml → src/sbml/validator/test/test-data/sbml-general-consistency-constraints/20517-fail-01-09.xml
- src/sbml/xml/XMLAttributes.cpp
- src/sbml/xml/XMLAttributes.h
- src/sbml/xml/XMLNode.cpp
- src/sbml/xml/XMLNode.h
- src/sbml/xml/test/TestXMLNode.cpp

The diff was not included because it is too large.

View it on GitLab: https://salsa.debian.org/med-team/libsbml/-/commit/afbda43b0c17fdcb183d17eeec25459fadf912b6

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