libSBML C++ API
5.18.0
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libSBML NEWS -- History of user-visible changes ==================================================================== 5.18.0 (2019-04-18) ==================================================================== STABLE RELEASE * New features - LibSBML now defines a DefinitionURLRegistry to allow a user to log their own values of the 'definitionURL' attribute on a math <csymbol> element. Once logged these definitionURL values will not trigger the unknown csymbol error when reading a model that uses them. - LibSBML now defines a CallbackRegistry which allows a user to register a callback to interrupt a long running read operation. Examples for C++ and Python are included. In future it would be anticipated that would have callbacks to interrupt long running validation or conversion processes. * Bug fixes - Validation was incorrectly stating that the id of a <localParameter> that mirrorred the id of a <species> should be listed as a <modifierSpeciesReference> in the enclosing <reaction>. It no longer issue an incorrect error. - The string to MathML parser was failing to identify known constants as arguments to a lambda function. lambda(pi, pi*2) should treat 'pi' as an unknown argument not the constant pi. This has been fixed. - The MathML parser adds logbase and degree to log and root elements respectively. These are dimensionless integers and but unit validation was failing. This has been corrected. Note this means that for L3 models libSBML will write out the dimensionless units on the relevant <cn> element explicitly. This may cause an apparent difference in models if reading and then writing. - In MathML a <bvar> element within a <lambda> can only contain a <ci> child element. Validation was failing to spot when this was not the case. This has been corrected. - MathML within a <semantics> element was not being properly validated. This has been improved. - 'layout' package-specific bug fixes: - Code was failing to roundtrip glyphs that contained both a <curve> and a <boundingBox> element. This has been fixed. * Configuration/build system changes - The cmake files that enable using the check library on a Linux OS have been updated to make this easier. - Python 3.7 is now supported. * Miscellaneous - Several obscure memory leaks have been plugged. EXPERIMENTAL RELEASE * New features - 'distrib' package-specific updates: - The code has been updated to reflect the specification agreed during HARMONY 2019 version 0.24. - 'spatial' package-specific updates: - The code has been updated to reflect the specification version 0.93. - Attributes 'id' and 'name' have been added to the SpatialPoints class in anticipation of these being added to the specification. - Plugin code has changed so that child element class members are initialised to NULL. This saves memory but may cause existing code to hit an issue when using a getAbc function; which may now return a NULL object when previously it did not. ==================================================================== 5.17.2-experimental (2018-12-06) ==================================================================== *** Experimental only release *** This is an experimental only release, that is, a release of those files provided in the experimental folder of a full release. This includes updates to all the SBML L3 packages that are not yet accepted and undergoing development. NOTE: An experimental release is not as rigorously tested as a full release. Any changes/fixes listed as either referring to stable or experimental code may change before the next full release. STABLE RELEASE * New features - The math code has been refactored to use the more efficient math-legacy code in combination with a math plugin system. This code has been optimized and we welcome feedback on any performance issues. This means there is no longer a math-legacy build option. - The new math constructs introduced in SBML L3V2 have been refactored as a math extension; which facilitates the use of these math functions in an SBML L3V1 document. - 'comp' package-specific updates: - The 'comp' specification states that an external model must be an L3V1 document. Since this specification predates SBML L3V2 we have relaxed the restriction to allow an L3V2 model using Model Composition to use an L3V2 external model. - The converter that 'flattens' a comp model has been optimized for speed with significant improvement for larger models. - Python interface specific updates: - In libSBML the set/add/unset methods return a code to indicate success or failure of the operation. The Python interface has been improved to produce a warning when a function fails. This behaviour can be enabled by setting a CMAKE configure option or an environment variable. - Sourceforge Tracker item #456: The Python interface has been changed to return an empty List of CVTerms rather than a None object. - Users have raised issued about Model objects retrieved from within an SBMLDocument object going out of scope when the document object is removed from scope. We have adjusted the code to allow a Model to remain in scope without it's parent document. Feedback would be apprceiated about whether this is sufficient or whether all child objects should be available regardless of whether their parent is still available. - Sourceforge Tracker item #468: Functions deprecated in Python 3.6 have been replaced to avoid deprecation warning messages. * Bug fixes - The function SBMLTypeCode_toString was not retuning the correct string for a ListOf element originating in a package. This has been corrected. - Using an SBML L3 package in an L2 document could cause a crash. This has been fixed. Thanks to Thomas Hamm for reporting it. - The code that checked for use of an L3V2 package with an L3V1 document could cause a crash. This has been fixed. - Writing out a document without a model and no level and version was using level = version = 0; which is not valid. This has been changed to write a L3V2 document with no model. - There was an issue with newer architectures when casting a NaN to an integer - this has been now been avoided. - MATLAB interface specific bug fixes: - The matlab binding was failing to distinguish between a functionDefinition where the id ended with a logical operator, e.g. 'myor' and the actual logical function. This has been corrected. - 'comp' package-specific bug fixes: - There was an issue with flattening 'comp' models using conversion factors. This has been tracked down and fixed. Thanks to Matthias Konig for reporting it and providing examples. - 'render' package-specific bug fixes: - Historical render code did not create a NULL BoundingBox. Current code has been brought in line with this. * Configuration/build system changes - Python 3.7 is now supported and included in the builds. - The USE_LEGACY_MATH option has been removed as code has been reverted to use this math implementation (see above). EXPERIMENTAL RELEASE * New features - 'distrib' package-specific updates: - The distrib package code has been updated to include the use of csymbols to reference distributions. This is in line with the latest distrib specification. ==================================================================== 5.17.0 (2018-05-21) ==================================================================== STABLE RELEASE * Addition of support for the SBML Render package - Now that the first official version of the specification for the SBML Level 3 Rendering package is available, the libSBML API for 'render' is now included in the stable release of libSBML. This means that all prebuilt binaries for the stable release will include the 'render' package code. The src archive containing libSBML core code will continue to be available, with additional src archives available in the stable branch: one containing libSBML core plus all stable packages and additional archives of the individual package code. NOTE: The libSBML GNU make-based build system has not been updated for packages. Thus, to build from src, it is necessary to use the CMake build system. * New features - The MATLAB language interface function TranslateSBML has been optimized for speed. - The MATLAB interface function OutputSBML can now be called with an output argument and no inputs; doing so will return information about the libSBML version and enabled packages used to build the binary files. - A new function getDefaultSBMLStruct has been added to the MATLAB interface. This function takes a string name of the element with level and version information and returns the relevant MATLAB-SBML structure for the element. Many thanks go to Thomas Pfau for supplying this function. - On occasion, the function getDerivedUnitDefinition that returns calculated units would report incorrect units without flagging any issues. This has been made less ambiguous and a derived UnitDefinition will not contain any units if it cannot be correctly determined. - Unit validation has been optimized and significantly speeded up for larger models. - 'comp' package-specific updates: - The C API for comp has been completed. - 'fbc' package-specific updates: - SourceForge Tracker item #455: Error messages have been improved. - 'multi' package-specific updates: - The C API for multi has been completed. - 'qual' package-specific updates: - SourceForge Tracker item #455: Error messages have been improved. - 'render' package-specific updates: - A full C API for the render package has been added. * Bug fixes - SourceForge Tracker item #459: An error in the function that converts libSBML infix notation to MATLAB infix notation failed when log functions failed. This is fixed. Thanks to Sven Thiele for reporting the issue. - The validation check for duplicate values of the 'metaid' attribute was not being extended to all packages. This has been fixed. - Python examples have been updated to work with Python v3. - 'qual' package-specific bug fixes: - SourceForge Tracker item #457: Validation of rule qual-20311 was producing an error when it should have been a warning. Thanks to Justin McManus for reporting the problem. EXPERIMENTAL RELEASE * New features - 'distrib' package-specific updates: - The 'distrib' package has undergone significant changes. The code has been fully updated to match this. We have also used a Distrib prefix on all classes to prevent clashes with other packages or even other libraries. We welcome feedback on this approach. ==================================================================== 5.16.0 (2017-12-07) ==================================================================== STABLE RELEASE * Note The L3 Render Package has been approved by the SBML Editors, but approval came too late in the libSBML release cycle to include it in this stable release of libSBML. There are now two implementations of support for SBML Level 3 Version 2 Core. The libSBML code for L3V2 can now be considered stable and will only change for bug fixes. * New features - The MATLAB interface now supports both the 'qual' and 'groups' packages, in addition to 'fbc'. - Unit checking has been expanded to include checking the <math> of <trigger>, <constraint> and <stoichiometryMath> to at least allow detection of values with undeclared units. - Writing out an XMLNode that represented XHTML with multiple nested text elements could distrupt indentation (see bug fixes). A new function XMLNode::writeToStream(XMLOutputStream&) checks the indentation is correctly recovered after writing out the XMLNode. - 'comp' package-specific updates: - There has been some improvements made to the reporting of line numbers for errors and warnings. * Bug fixes - SF Tracker #450: Code validating the shadowing of localParameter was checking both 'id' and 'species' attributes. This rule should only check the species attribute. - SBML validation failed to distinguish between LocalParameters and Parameters in L3V1 when reporting errors. This is fixed. - libSBML had incorrectly reported that the 'fast' attribute was a required attribute of L3V2 <reaction> elements. This is fixed. - The libSBML C API does not work with default arguments. There were previously a few stray ones left in the API code. These have been removed. - The SBMLTransforms::evaluateASTNode function previously failed to check that model values had been evaluated prior to trying to evaluate an ASTNode. The relevant function now checks whether the map of values is present and populates it, if necessary. - Code that checked the syntax for attributes of type ID and IDREF did not always use the appropriate function. These cases have been fixed. - The use of an invalid syntax as the sbml:units attribute on a math <cn> element was not being detected. This has been fixed. Thanks to Nicolas Rodriguez for the report. - The SBMLTransforms::evaluateASTNode function missed the fact that in SBML Level 2, stoichiometry defaulted to '1'. This has been corrected. - The use of certain combinations of text elements in a <notes> element could derail the entire indentation of the document. This has been reported by several people. Hopefully this time we have fixed the situation for all cases where it may occur. - The interactive help text stored with the functions and classes in the Python bindings had many formatting problems and outright omissions due to bugs in our "rewrite_pydoc.py" code. Many of these problems should be fixed now. - 'fbc' package-specific bug fixes: - Validation incorrectly reported an empty <listOfFluxObjectives> even when a model was being created and did in fact have a <fluxObjective> element. This has been fixed. Thanks to Arthur Goldberg for reporting it. - An empty <geneProductAssociation> caused the reading of model files to crash libSBML. This no longer happens. - 'layout' package-specific bug fixes: - Conversion between Level 2 annotations using both layout and render and Level 3 packages has been corrected. - 'qual' package-specific bug fixes: - Functions to get math on a <functionTerm> element were missing from the C API. They have been added. * Configuration/build system changes - SourceForge Tracker item #447: Configuration no longer defines HAVE_IEEEFP_H when using MSVC compilers as it is not needed and not always present. Thanks to Alan Garny for spotting this. - SourceForge Tracker item #443 & separate unreported problems: Build failures with Java 9 should be fixed now. Thanks to Chris West for reporting the issue related to building the docs. * Miscellaneous - SWIG only supports Javascript node 6x. Thus we cannot currently support later versions of node. - Documentation for the C API has been extensively improved. - Support has been added for Python 2 unicode input. - Currently we supply lib files built with MSVC2010 as part of the windows installers. These will be removed from future releases. Please let us know if this is an issue for you. EXPERIMENTAL RELEASE * New features - 'render' package-specific updates: - At the request of the SBMLEditors the attribute 'name' has been added to render elements. * Bug fixes - 'render' package-specific bug fixes: - Conversion between Level 2 annotations using both layout and render and Level 3 packages has been corrected. - 'spatial' package-specific bug fixes: - There was a mismatch in the SetOperation enumeration in the specification. This has been agreed as 'union', 'intersection' and 'difference' and libSBML code has changed to reflect this. - Corrected the output of a <csGeometry> element to correctly use an upper case G. ==================================================================== 5.15.2 (2017-07-27) ==================================================================== *** Experimental only release *** This is an experimental only release, that is, a release of those files provided in the experimental folder of a full release. This includes updates to all the SBML L3 packages that are not yet accepted and undergoing development. NOTE: An experimental release is not as rigorously tested as a full release. Any changes/fixes listed as either referring to stable or experimental code may change before the next full release. STABLE RELEASE * New features There are no features in the stable branch; although there has been some optimization of code. We have also included testing of examples code in our test protocol. * Bug fixes - Infix parsing of lambda functions was failing to consider variable names as variables, when they might overlap with other names for MathML constructs or csymbols e.g. 'time' or 'pi'. This has been corrected so that a lambda function will correctly produce the necessary <bvar> elements. - Conversion of interchangeable booleans and numbers was not reporting consistent information. This has been improved. - Conversion between SBML levels and versions was failing to correctly identify a speciesReference identifier. This is now sorted. - Sourceforge Tracker #8: The MATLAB bindings were failing to correctly convert logical functions. This has been fixed. Thanks to Fabian Froehlich for the report. - The check that reports <localParameters> shadowing other identifiers was not noticing when it shadowed a speciesReference. This has been corrected. - The evaluateAST function was not correctly dealing with a missing math element. - 'comp' package-specific bug fixes: - Reading in externally referenced documents during 'comp' validation and/or flattening was consuming large amounts of memory. This has now been optimized. - There were some slight discrepancies with writing out the id attribute in an L3V2 document using 'comp' L3V1V1. These have been sorted out. - There was a very obscure endless loop in validation that Chris Myers managed to find. This is now closed. Thanks Chris. - 'groups' package-specific bug fixes: - Sourceforge libSBML Tracker #438: The C API for the plugin objects was missing. This has been corrected. Thanks to CJF for the report. EXPERIMENTAL RELEASE * New features - 'arrays' package-specific updates: - A basic ArraysFlatteningConverter has been added. As yet, this does not deal with arrays of submodels from the 'comp' package. - 'distrib' package-specific updates: - NOTE: the code has not been updated to the latest proposed version of the 'distrib' specification as this is currently under major review. * Bug fixes - 'arrays' package-specific bug fixes: - The 'arrays' code was not always correctly reading and writing the namespace. This has been fixed. ==================================================================== 5.15.0 (2017-04-06) ==================================================================== NOTE: This release includes support for the SBML L3V2(RC1) Release Candidate specifications. This specification is not yet official and thus it, and the supporting code, may change. STABLE RELEASE * Multistate and Multicomponent Species - The first official version of the specification of the Multistate and Multicomponent Species package is now available, and thus the libSBML code for 'multi' is now included in the stable release of libSBML. This means that all prebuilt binaries for the stable release will include the 'multi' package code. The src archive containing libSBML core code will continue to be available, with additional src archives available in the stable branch: one containing libSBML core plus all stable packages and additional archives of the individual package code. NOTE: The libSBML GNU make-based build system has not been updated for packages. Thus, to build from src, it is necessary to use the CMake build system. * New features - A new option has been added to the L3ParserSettings to allow users to turn off the parsing of the new L3 math elements. If enabled the parser will treat the new functions as generic user defined functions. - The L3Parser has been updated to parse '%' as rem. - The MATLAB binding has been updated to support SBML L3V2(RC 1). - Additional options are available for the TranslateSBML/OutputSBML functions for the MATLAB binding allowing users to add their own validation and customize the input/output of some fbc elements. (See documentation for more details.) - A new structure field 'cvterms' has been added to the MATLAB_SBML structure. This supports annotations as a set of fields relating to qualifiers and resources rather than relying on annotation in the string format. - A new function setCharacters has been added to the XMLToken class. - The SBMLDocument object resulting from an invalid read will now report level and version as '0'. This facilitates distinguishing between an invalid read and a Level 3 Version 2 document that does not contain a <model> element. * Bug fixes - Code was failing to recognize the math elements <pi/> and <exponentiale/> as returning numeric values. This has been corrected. - A <stoichiometryMath> element with no child <math> was causing code to crash. This has been sorted. - Validation of MathML was failing to report when a <math> element contained two top-level elements. This is now caught and correctly reported. - A speciesReference id which has been declared 'constant' cannot be changed by an event. Validation was failing to catch this situation. This is now fixed. - Several fixes have been made to the conversion of SBML documents to lower levels and versions. These include: loss of compartment size; evaluation of functionDefinitions and initialAssignments; conversion of fast reactions; evaluation of stoichiometry using initialAssignment and rules and expanding functionDefinitions with no bvar elements. - The export of the Avagadro constant as an exponential number was losing precision. This has been fixed. - Unit checking was failing to correctly associate the model 'timeUnits' with the use of the csymbol for time. This has been corrected. Thanks to Matthias König for reporting it. - 'comp' package-specific bug fixes: - Validation of a model that indirectly referenced a replacedBy element was causing a problem. This has been resolved. - The flattening routine was failing to correctly adjust the metaid referenced by annotation where necessary. This has been fixed. Thanks to Matthias König for reporting it. - 'fbc' package-specific bug fixes: - Validation was incorrectly reporting that a lower fluxBound could not have a value of -INF. This has been corrected. - The 'unsetActiveObjective' function now returns an OperationReturnValue in line with other set/unset functions. * Configuration/build system changes - The minizip library used for compression supported has been updated. There are no backwards compatability issues. - The CMake build has been extended to enable export of the configuration used in building. This will facilitate users who use libsbml and/or its dependencies as dependencies in other projects. * Miscellaneous - Beware that Doxygen 1.8.12 and later changed something in the HTML it creates, and as a result, the libSBML documentation-generation currently does not work for Doxygen versions after 1.8.11. This will be fixed in a later release. For the time being, use Doxygen 1.8.11. - We are aware that the released MATLAB binaries do not appear to work with MATLAB 2017a on Mac OSX. At present we are unable to address this issue but will resolve it and issue new binaries as soon as possible. - We are aware that the octave binding is not functioning as expected. We would be very interested to know of any users of the libsbml octave interface that are affected by this. EXPERIMENTAL RELEASE * New features - 'spatial' package-specific updates: - The spatial code has been adjusted for minor changes in the specification and now reflects rel0.91 of the specification. Some, but not all, validation has been added to the code. ==================================================================== 5.14.0 (2016-09-15) ==================================================================== *** Experimental only release *** This is an experimental only release, that is, a release of those files provided in the experimental folder of a full release. This includes updates to all the SBML L3 packages that are not yet accepted and undergoing development. NOTE: An experimental release is not as rigorously tested as a full release. Any changes/fixes listed as either referring to stable or experimental code may change before the next full release. This release includes support for the SBML L3V1R2(RC1) and L3V2(RC1) Release Candidate specifications. STABLE RELEASE * New features - An Iterator class has been added to the List utility. * Bug fixes - Validation was not being correctly invoked on <localParameter> objects. This has been fixed. - The functions for parsing a string to an ASTNode would cause a crash if passed a NULL pointer. This has been fixed. Thanks to Matthias König for reporting it. - The L3Parser has been improved to catch a case when a NULL input has been provided and return an error to the user. EXPERIMENTAL RELEASE * New features - 'multi' package-specific updates: - Code has been updated to reflect the latest v 1.0.7 specification. ==================================================================== 5.13.0 (2016-04-14) ==================================================================== STABLE RELEASE * Groups - The first official version of the specification of Groups is now available, and thus the libSBML code for 'groups' is now included in the stable release of libSBML. This means that all prebuilt binaries for the stable release will include the 'groups' package code. The src archive containing libSBML core code will continue to be available, but there will be additional src archives available in the stable branch: one containing libSBML core plus all stable packages and additional archives of the individual package code. NOTE: The libSBML GNU make-based build system has not been updated for packages. Thus, to build from src, it is necessary to use the CMake build system. * New features - New functions have been added to the XMLOutputStream to allow the optional XML comment to be further customized. - The Python binding now includes a __version__ field. - 'comp' package-specific updates: - The SBMLResolver interface has been exposed within language bindings. - 'fbc' package-specific updates: - The MATLAB interface has been expanded to include a dedicated FBC V2 structure. Thanks to the COBRA Toolbox team for their feedback and testing. - There was an issue with round-tripping geneProductAssociations between the expression and the infix representation. This has been sorted. - 'groups' package-specific updates: - A function named 'copyInformationToNestedLists' has been added to facilitate keeping information consistent when multiple <group> objects refer to the same thing. * Bug fixes - Validation was failing to catch when the <piece> element of a <piecewise> had an incorrect number of children. This has been fixed. Thanks to Jason Zwolak for the report. - Unit consistency checking was failing to interpret the units of <cn> elements when passed to a <functionDefinition>. This has been fixed. - The getListOfElements code was not being correctly ported to language bindings. This has been corrected. - Unit consistency checking was failing to correctly handle non-integer power expressions. This has been corrected. Thanks to Matthias König for reporting this. - The StrictUnitConsistencyValidator has been corrected to identify matching base SI units. Thus, 1000 litre will be correctly equated with 1 metre cubed. - Sourceforge libSBML Tracker #421: The MATLAB binding was failing to round-trip multi-byte characters used in strings. This has been fixed. Thanks to Will Matern for the report. - Validation was failing to report that a 'variable' attribute is not permitted on an AlgebraicRule. This has been corrected. - Sourceforge libSBML Tracker #418: Using the isnan() function can cause issues with some compilers. LibSBML has a util_isNaN() function which should be used when necessary. Thanks to Alan Garny for reporting this issue. - The functions that convert an enumeration value to a string had not been ported to language bindings. This has now been sorted. Thanks to Matthias König for letting us know. - The new ASTNode class instances were failing to deal correctly with semantic annotations. This has been fixed. - 'comp' package-specific bug fixes: - Failing to access an external model could cause an endless loop while attempting validation. This has been corrected. Thanks to Chris Myers for the report. - 'fbc' package-specific bug fixes: - Sourceforge libSBML Tracker #419: The converters provided for converting from COBRA style SBML models to SBML+fbc style models were losing a charge of '0' if explicitly set. This has been corrected. Thanks to Ali Ebrahim for reporting the problem. - 'layout' package-specific bug fixes: - In some cases the value of the 'id' attribute was being written out as the 'name'. This has been fixed. * Configuration/build system changes - The Python bindings can now be configured to install using setup.py. * Miscellaneous - The Python version of libSBML available via PyPi now includes binary wheels for Windows and Mac OSX operating systems. - The Python version of libSBML available via PyPi now includes all dependencies. - We conducted a review of the mathml-infix parsing code and compared inputs and outputs with those of JSBML. This has produced a more synchronized approach between the two APIs. - There is a known bug in GCC versions 5.1 and 5.2 which results in the problem that calling the copy constructor of a base class in the constructor of derived classes produces crashing code. The problem manifests itself in libSBML when using a language binding such as the Python interface. Workarounds have been added to the libSBML 'Known Issues' documentation. - Sourceforge libSBML Tracker #417: Documentation was failing to write using Python 3.5. This has been fixed. Thanks to Antonio Trande for reporting this. EXPERIMENTAL RELEASE * New features - 'multi' package-specific updates: - The code has been updated to reflect v 1.0.6 of the specification. ==================================================================== 5.12.0 (2015-11-12) ==================================================================== STABLE RELEASE * New features - In SBML Level 2, some units were defined by default and did not need to be explicitly included in a model. The SBMLLevelVersionConverter adds these units explicitly when converting to SBML Level 3. We have an added an option to disable this functionality and return Level 3 models without the units implied by Level 2. - Sourceforge libSBML Tracker #242: 'addProduct etc using a species' We have added functions addProduct/addReactant/addModifier that take a Species as argument, along with a number of other optional values to completely specify the SpeciesReference object being created. This is a slight divergence from the direction libSBML usually takes and we would be grateful for any feedback on these functions. - Validation speed has been dramatically improved for models that make use of FunctionDefinitions and in particular nested FunctionDefinitions. - 'comp' package-specific updates: - The 'flattening' routines have been expanded to correctly deal with FBC V2. - 'fbc' package-specific updates: - The FBC Version 2 package has been accepted by the SBML Editors. The code supporting this is now available as part of the stable release. * Bug fixes - There was a very subtle bug in unit checking that incorrectly applied a multiplication factor. Thanks to Mike Cooling for the detailed example and anaylysis that revealed this. It has now been fixed. - In the new math code using the children of an ASTNode could result in the math namespace declaration being unecessarily written out in many places. This has been sorted out. - Sourceforge libSBML Tracker #414: "A missing break statement" was added. * Configuration/build system changes - The CMake files have added an option to dynamically link to a python version on Mac OSX systems rather than automatically link. Thanks to Kyle Medley for supplying the initial patch for this. - The test code has been tweaked to build and run with MSVC 2015. Fortunately the main code base worked with no issues. * Miscellaneous - Further documentation improvements have been added, especially for the FBC package. EXPERIMENTAL RELEASE * New features - 'multi' package-specific updates: - Full validation has been added to the multi package code. Thanks to Fengkai Zhang for his continued efforts on this. ==================================================================== 5.11.6-experimental (2015-07-16) ==================================================================== *** Experimental only release *** This is an experimental only release, that is, a release of those files provided in the experimental folder of a full release. This includes updates to all the SBML L3 packages that are not yet accepted and undergoing development. NOTE: An experimental release is not as rigorously tested as a full release. Any changes/fixes listed as either referring to stable or experimental code may change before the next full release. STABLE RELEASE * New features - There is a new function on SBMLDocument, checkConsistencyWithStrictUnits(), which applies the same validation as the checkConsistency() function with one difference being that it will always apply unit validation using exact identity comparison between units and it logs all unit violations as Error regardless of the SBML Level and Version. - There is a new converter that will convert to SBML L1V1. The 'regular' SBMLLevelVersionConverter does not support this level and version as we generally discourage the use of it. However users have requested the facility and thus we have included a separate converter to meet that need. - 'const' versions of the getElementBySId() and getElementByMetaId() functions have been added. - 'fbc' package-specific updates: - Code has been updated to use support the FBC V2 format that is currently available as a Release Candidate document. Full validation for this format has been included. * Bug fixes - The static function UnitDefinition::reorder failed to correctly deal with situations where the same unit kind appeared multiple times. This has been fixed. Thanks to Matthias König for reporting the problem. - There were some discrepancies between math and math-legacy code reporting the incorrect use of the MathML <apply> tag. This has been standardized and more rigorously tested. * Miscellaneous - Several functions in libSBML checked for a NULL reference; something that it is considered a well-formed program should not be able to create. As more and more compilers are complaining about this code, on the grounds it should not be possible to create the NULL reference, we made the decision to remove this code. Please let us know if this is an issue for you. EXPERIMENTAL RELEASE * New features - L2V5 specific updates: - A new validation rule was identified during the review of the SBML Level 2 Version 5 specification. Support for this has been added. - 'arrays' package-specific updates: - The MathML elements included in the 'arrays' package has been reduced. The code now reflects this. - 'multi' package-specific updates: - The code has been updated to reflect v 1.0.4 of the specification. This includes full validation. Thanks to Fengkai Zhang for contributing the code. ==================================================================== 5.11.4 (2015-04-09) ==================================================================== STABLE RELEASE * New features - The ASTNode class has a new function double getValue() that returns the numerical value of the ASTNode as a double. This includes returning values for constants such as AST_CONSTANT_PI, AST_CONSTANT_E, and AST_NAME_AVOGADRO, or '1' for an ASTNode of type AST_CONSTANT_TRUE and '0' for AST_CONSTANT_FALSE. Note, it does not attempt to evaluate the node and thus will return NaN for a function or node representing a named variable, and AST_NAME_TIME. - There has been a complete review of validation messages. These have been unified in terms of spacing and line returns. In addition many have been enhanced with additional model specific information designed to assist in locating and fixing the issues. - There is now an interface to PHP. This has been tested on all platforms. - Historically libSBML did not provide unsetFoo functions where the attribute was a required attribute with a default value. At user request we have changed this so every attribute has a corresponding unset function. Note that where the attribute has a default value it is still considered 'set' but not considered to have been explicitly set and will therefore not appear in the written output. - The L3Parser will now correctly parse a unary plus. - The L3Parser will now parse chains of relational operators. Identical operators become ASTNodes with relational type and each argument as a direct child. Thus 'x < y < z' becomes an ASTNode of type AST_RELATIONAL_LT with three children representing x, y and z. Non identical operators use a logical 'and' function to combine the arguments. Thus 'x < y > z' becomes an ASTNode of type AST_LOGICAL_AND with two children each representing the relational operator; that is and(lt(x,y), gt(y,z)) - The ability to index lists in the python bindings has been improved. - A new value 'LIBSBML_MISSING_METAID' has been added to the OperationReturnValues_t enumeration. This value will be returned when a user attempts to set an annotation on an object that has no metaid attribute set. Note this is a change in behaviour as previously the value returned would have been 'LIBSBML_UNEXPECTED_ATTRIBUTE'. We hope this change makes the issue clearer to users. - The package extension mechanism has been expanded to allow the extension of individual ListOfFoo classes. * Bug fixes - Conversion from SBML Level 3 to Level 2 was losing some LocalParameters. This has been sorted. Thanks to Matthias König for spotting and reporting the problem. - Fixed a bug where using the expat parser failed to correctly report the presence of invalid XML namespaces. - Sourceforge libSBML Tracker #393: LibSBML was failing when built on an ARM processor running Fedora. This has been sorted out. Thanks to Zbigniew Jedrzejewski-Szmek for reporting the issue and testing solutions. - The formulaParser was incorrectly parsing particular syntax involving exponential, plus/minus signs and no spacing i.e. '2e3-3' was failing to parse. This has been corrected. Thanks to Kieran Smallbone for reporting this and apologies for the length of time it took to fix. - Sourceforge libSBML Tracker #402: The functions that deal with user data on both ASTNode and SBase objects have been made to work with const versions of objects where appropriate. Thanks to Takeshi Abe for the request and the patch. - 'comp' package-specific bug fixes: - The code for determining whether an external file is available has been further tightened up. - 'fbc' package-specific bug fixes: - A bug in the code that reads GeneAssociations as an annotation meant information was being lost. This has been corrected. Thanks to Matthias König for reporting the problem. - 'layout' package-specific bug fixes: - The names of some functions meant they were failing to correctly port to the Python bindings. The binding mechanism has been fixed to correct this. Thanks to Kieran Smallbone for reporting this. - The SpeciesReferenceGlyph attribute 'role' can take the value 'undefined' but this was not written out. This has been changed. * Configuration/build system changes - This release includes pre-built binaries for the MATLAB bindings that should work for many Linux and MacOSX platforms. Please advise us it you find a combination of platform and MATLAB version for which these fail. * Miscellaneous - The names of some arguments to functions have been modified to convey the fact that the object is not owned by the collection object to which it has been added. EXPERIMENTAL RELEASE * New features - 'distrib' package-specific updates: - There are new example programs that will create the examples given in the current specification. - 'multi' package-specific updates: - The multi code has been updated in line with the specification Release 1.0.2 dated November 2014. This code has been contributed by Fengkai Zhang. Many thanks, Fengkai. - 'spatial' package-specific updates: - The spatial code has been updated in line with the specification Release 0.90 dated March 2015. * Bug fixes - 'multi' package-specific bug fixes: - The multi attributes that can be added to a math <ci> element where being lost when written out. This has been fixed. ==================================================================== 5.11.2-experimental (2015-01-15) ==================================================================== ******************************************************************** *** Experimental only release *** This is an experimental only release, that is, a release of those files provided in the experimental folder of a full release. This includes updates to all the SBML L3 packages that are not yet accepted and undergoing development. NOTE: An experimental release is not as rigorously tested as a full release. Any changes/fixes listed as either referring to stable or experimental code may change before the next full release. ******************************************************************** STABLE RELEASE * New features - Functions have been added to allow users to determine the number of SBML L3 packages within a document that the build of libSBML does not support. - The StripPackageConverter has a new option 'stripAllUnrecognized' which if set to true will strip all SBML L3 packages that are not supported by the build of libSBML being used. - The XMLErrorLog::remove(unsigned int errorId) function only removes the first instance of the error with the matching identifier. A new function removeAll(unsigned int errorId) has been added that will remove all instances of the error with the given id. * Bug fixes - A stack overflow could occur when libSBML was built with certain compilers on certain platforms. We have eliminated this problem from the situations in which we can replicate it. The issue occurred when performing intensive validation. - The math-legacy code was being caught in an endless loop when trying to read a nested piecewise function. This has been fixed. - Validation was failing to recognize some cases when the conditional part of a piecewise function returned a boolean and incorrectly indicated that such a model was incorrect. We have fixed this as robustly as possible but encourage reports of situations where we have missed something. - 'layout' package-specific bug fixes: - Validation of layout was not correctly reporting line and column numbers. This has been corrected. * Configuration/build system changes - The CMake configuration has been improved to clearly report failure to find files necessary to work with particular language bindings. - Sourceforge libSBML Tracker #394: The '\n' symbol was not being correctly expanded on some systems. This has been made more robust. Thanks to Antonio Trande for reporting this. EXPERIMENTAL RELEASE * New features - Support for the SBML Level 2 Version 5 Release 1 (Release Candidate) specification has been added. Additions to libSBML include: - new API for adding Nested Annotations used on the existing CVTerm object: int addNestedCVTerm(const CVTerm* term) CVTerm* removeNestedCVTerm(unsigned int n) unsigned int getNumNestedCVTerms() CVTerm* getNestedCVTerm(unsigned int n) List* getListNestdCVTerms() - new and changed validation rules as in the specification - the ability to convert core SBML to and from L2V5 - 'multi' package-specific updates: - The multi code has been updated in line with the specification Release 1.02 dated November 2014. - 'spatial' package-specific updates: - The spatial code has been updated in line with the specification Release 0.89 dated November 2014. * Bug fixes - 'spatial' package-specific bug fixes: - Sourceforge libsbml Tracker #387: The C# bindings for spatial were not working as expected. These have been fixed. Thanks to Harold Gómez for reporting this. ==================================================================== 5.11.0 (2014-11-27) ==================================================================== STABLE RELEASE * New features - There is now an interface for JavaScript. This has been tested on all platforms. Building requires SWIG version 3.0.2 or greater and depends on node-gyp. Feedback on this would be greatly appreciated. - We have made a source package for the libSBML R interface available for Linux and OSX users. - The facility of using the data members of objects as attributes in python has been extended to work with Python version 3. - The SBMLDocument class now has an 'isSetModel()' function. - There is a new writSBMLToStdString() function that returns a std::string rather than a char * that has to be freed by the caller. This facilitates cleaner memory management. Similarly there is a writeMathMLToStdString() function. - The errors reported by OutputSBML in the MATLAB binding have been extended to provide more information about the specific field causing a problem. Thanks to Thomas Pfau for providing a template for adding this information. - Support for the MIRIAM qualifiers hasTaxon, isInstanceOf and hasInstance has been added. - More information has been added to error messages. - There are new functions to allow users to retrieve and print errors from the ErrorLog based on the severity of the error. These are SBMLError* getErrorWithSeverity(unsigned int n, unsigned int severity) and printErrors(std::ostream& stream, unsigned int severity). - 'comp' package-specific updates: - A new flag has been added to the CompFlatteningConverter to allow a user to specify a comment separated list of packages that should be stripped before flattening is attempted. - The CompFlatteningConverter has been made more rigorous when it comes to specifying users options on models declared as ExternalModelDefinitions. * Bug fixes - There was an issue with using the libsbml namespace and the ReactionConverter. This has been fixed. Thanks to Andy Somogyi for reporting it. - The facility to use data members of objects as attributes was broken. This has now been fixed. - Code checking the values of units attributes was incorrectly allowing the default Level 2 units, such as substance, to be used in Level 3. This has been corrected. - Using unicode filenames with MATLAB on a Windows system proves to be very problematic. We have solved the problem but only for the case where filenames are entered directly via the dialogs that OutputSBML / TranslateSBML open up. There appears to be an issue with MATLAB using such filenames directly from the workspace. This has been added to the known issues documentation. - The C API function ConversionProperties_removeOption now returns a pointer to the option being removed. This is in line with other remove functions. - Validation failed to report an error when more than one model element was encountered and merely returned a document with the last model read. This has now been corrected. - The getDerivedUnitDefinition function returns a pointer to an existing unitDefinition object maintained by the model. However in the case of a Parameter a new unitDefinition object was being created, thus causing an inconsistency when it comes to freeing memory. This has now been corrected and Parameter::getDerivedUnitDefinition now returns an existing pointer. - 'comp' package-specific bug fixes: - Validation was failing to report when a portRef attribute had been used on a Port object and indeed this situation caused validation to crash in some cases. This has now been sorted. * Configuration/build system changes - When javac fails to compile a class no error was reported and a useless jar file was created. The build has been changed to highlight the issue. - Sourceforge libsbml Tracker #380: The use of #include Windows.h has been changed to lowercase to facilitate building using MinGW. Thanks to Takeshi Abi for reporting the problem. * Miscellaneous - We have continued our review of code and many more memory leaks have been plugged. Thanks to people, in particular Andy Somogyi, for reporting these. Stable code has been rigorously tested using both Valgrind (http://valgrind.org/) and Visual Leak Detector for Visual C++ (https://vld.codeplex.com/). Experimental code is currently being reviewed. - Sourceforge libsbml Tracker #372: Documentation has been corrected. Thanks to Gerard Weatherby for reporting the issues. - The sample Java programs and configuration/importing instructions for Java now use a shortened and simplified static loading block (i.e., the part that explains how to use System.loadLibrary() to load libSBML). - We've made efforts to simplify the instructions for downloading, configuring and accessing libSBML. Among the changes are that the API language manuals for Java, Python and C# now focus their instructions more on just those languages, rather than giving long generic instructions for all possible languages. - The SBML package extension mechanisms are now more thoroughly documented. EXPERIMENTAL RELEASE * New features Code for the Dynamic Structures ('dyn') package has been added. This reflects the draft specification Release 0.1 dated October 1 2014. - 'distrib' package-specific updates: - The UncertMLNode now uses a std::vector to save child members rather than the List class. - 'spatial' package-specific updates: - The spatial code has been updated in line with the specification Release 0.88 dated September 2014. * Bug fixes - 'distrib' package-specific bug fixes: - A number of memory leaks have been plugged. Thanks to Andy Somogyi for reporting them. - 'groups' package-specific bug fixes: - The values of the enumeration of SBMLGroupsTypeCode_t clashed with the values used by the comp enumeration. The ones in the groups package have been changed. - 'req' package-specific bug fixes: - Sourceforge libsbml Tracker #373: The code was not keeping proper track of parent-child relationships which could lead to incorrect namespaces being used. This is now sorted. Thanks to Gerard Weatherby for reporting it. ==================================================================== 5.10.2 (2014-07-17) ==================================================================== STABLE RELEASE * New features - The static functions implemented by the SBMLTransforms class that are used by the converters that in-line FunctionDefinitions or expand InitialAssignments has been made available to all language bindings. These are: replaceFD, expandInitialAssignments and evaluateASTNode. Examples of using these functions are also provided. - The L3ParserSettings object can now be configured to compare built-in functions and constants caselessly (as it did in the past; the default), or to only accept the lower-case forms. - 'layout' package-specific updates: - The C API has been improved and appropriate argument checking has been implemented. * Bug fixes - There was an issue with detecting NULL elements with the R bindings. This turns out to be a consequence of SWIG. A bug report has been filed with the SWIG development team, in the meantime, a revised SWIG file is included with the libSBML source and is used by the libSBML build when creating the R bindings. - The unit consistency checking code was ignoring numerical factors when checking the units of a KineticLaw matched the model wide units of extent per time (substance per time in SBML L1/L2). This has been changed. Thanks to Daniel Palm for the report that exposed this. - Unit checking code determines whether a math expression contains parameters or numbers with undefined units. However, depending on where these occurred within the expression, libSBML was not always correctly establishing this. This has been fixed. Thanks to Daniel Palm for reporting this. - The unit consistency checking code was losing numerical factors that were left after cancelling out units. This could affect the overall definition of the remaining unit and thus impact code that looked for exact identity between units. This has been fixed. Thanks to Daniel Palm for providing an example of a case where this was happening. - There was a bug in writing out MathML that manifested itself using the in-lining functionDefinition converter for a narrow set of functions. This has been fixed. - Validation has been improved so as to no longer warn a user that a variable has no initial value if there exists an initialAssignment or assignmentRule that would set the value. - The SBMLError reporting an over-determined model was being logged with the incorrect category of error. This has been changed. - LibSBML incorrectly reported the units of 'pi' as radians. This has been corrected to report 'dimensionless'. Thanks to Matthias König for reporting this. - The L3 parser did not recognize 'arcsinh' or 'asinh' as valid built-in functions. This has been fixed. - 'comp' package-specific bug fixes: - When libSBML detects an SBML L3 package that it does not support validation of 'comp' references can report that a reference may be to an identifier within the unknown package. However, the code was failing to check whether the reference could be located within the xml relating to supported packages before issuing this warning. This has been fixed. Thanks to Chris Myers for reporting it. * Configuration/build system changes - The CMake build system will now produce an uninstall target. * Miscellaneous - Continue our review of code a number of potential problems were highlighted during static analysis. These have been fixed. - Code review has also eliminated a number of compiler warnings raised by various different compilers on various different systems. - Various memory leaks have been plugged. Thanks to people, in particular Andy Somogyi, for reporting these. - The short error messages for the following error codes in SBMLErrorTable.h had trailing periods, which was inconsistent with most of the other messages; the periods have been removed: 20109, 99109, 99401, 99402, 99403, 99404, 99405, 99406. - In the API documentation, the instructions for setting PYTHONPATH was not correct for the installation produced by using CMake instead of GNU configure. Further, the PYTHONPATH instructions for Ubuntu were actually for other Linux/Unix variants and vice versa. This has been fixed by making the instructions use a single, more general approach that should work everywhere. - The API documentation lacked information about using PyPI for Python, and about how to install the R interface. Fixed. - Various issues in the Python documentation have been fixed. For example, in the table of member methods for each class in the API documentation for Python, the brief descriptions were missing -- all the short member descriptions had the same text, "Python method signature(s)". This was caused by a bug in our custom libSBML documentation generation tools. - The error code table in the documentation for SBMLError has been updated. EXPERIMENTAL RELEASE * New features - 'arrays' package-specific updates: - The arrays code has been updated in line with the specification dated June 19 2014. Changes include a change in attribute names and a revised set of supported math constructs. - Support for parsing from infix to ASTNodes and vice versa has been added for the majority of the math constructs currently listed within the arrays specification. - 'req' package-specific updates: - The req code has been updated in line with the specification Release 0.5 dated 30 May 2013. Users should be aware that this update represents a significant change in code to reflect the change in structure of the package. - 'spatial' package-specific updates: - The spatial code has been updated in line with the specification Release 0.87 dated June 2014. Users should be aware that this update represents a significant change in code to reflect the change in structure of the package. * Bug fixes - There was a potential stack-overflow issue with packages that extend SBase directly. This has been fixed where appropriate. Thanks to Chris Myers for reporting it. ==================================================================== 5.10.0 (2014-04-10) ==================================================================== STABLE RELEASE * New features - New ASTNode infrastructure The code underlying the ASTNode class has been refactored to facilitate the extension of MathML by SBML L3 packages. The API and behaviour has not changed except in places where invalid MathML was being incorrectly parsed or created. It is no longer possible to add a child to an ASTNode that represents a number, for example. Extensive testing has been done to ensure that the API and correct behaviour of the ASTNode class remains unchanged and unless you have derived your own classes from the ASTNode class this change should not affect your implementation in any way. ** Please inform us if this turns out to be incorrect. We have tried to anticipate and test use cases but we are aware that it is possible that we have missed some. In order to allow people to continue to use the original AST code if they choose, the source code archives provide this code within a 'math-legacy' directory and the libSBML configuration system provides an option to build libSBML using this legacy code. - General maintenance: we have done a number of sweeps of code to identify and add such things as missing virtual functions. We have also investigated memory leaks reported by users and have done some extensive memory leak checking on the more intensive functionality such as validation/comp flattening etc. However, this remains an ongoing task. - There is a new converter, the SBMLReactionConverter, which will replace any Reactions within a Model with the equivalent RateRules. An example of the use of this converter can be found at examples/c++/convertReactions.cpp. - There are new functions available on the Model class: InitialAssignment* getInitialAssignmentBySymbol(const std::string& symbol); Rule* getRuleByVariable(const std::string& variable); AssignmentRule* getAssignmentRuleByVariable(const std::string& variable); RateRule* getRateRuleByVariable(const std::string& variable); These functions return the designated object using the 'symbol' or 'variable' attribute. This is duplicate functionality as the objects can be retrieved using getRule and getInitialAssignment. However the other similar functions on the Model class retrieve objects by the 'id' attribute. If future versions of SBML introduce the 'id' attribute on Rules and InitialAssignments we will need functions that act differently. - 'comp' package-specific updates: - The code that facilitates resolving files in relation to ExternalModelDefinitions has been reviewed and made as robust as possible. - The ability to customize the way SIds and SIdRefs are renamed during the flattening process has been added. A class of type PrefixTransformer can be created and assigned. This allows the user to add additional changes to the renaming process. An example that illustrates the use of this facility to also rename the 'name' attribute of objects originating in subModels has been included in the examples/c++/comp directory. - Unit tests have been added for the C API, and this exposed some missing functions. The missing functions have now been added. * Bug fixes - There were issues with propagating the package-enabling functionality through the children of an element. These issues have been resolved. - The converters that apply structural changes to the SBML document used a setDocument function that expected a const SBMLDocument object. Since the converters change the document, and in fact immediately re-cast the document object, this function was both confusing and inaccurate. There is now a setDocument function that does not expect a const SBMLDocument object. - There were some inconsistencies in the behaviour of LocalParameter objects from SBML Level 3 in relation to the 'constant' attribute. These have been fixed. - 'layout' package-specific bug fixes: - There were some discrepancies between the naming of arguments to some constructors and the actual values being set using these arguments. These have been corrected without changing the resulting behaviour. - Sometimes when an SBML Level 2 document with 'layout' and 'render' annotations was upgraded to SBML Level 3, the 'render' namespace went missed from the annotation in the Level 3 document. This has been fixed. - The 'render' package "objectRole" attribute was not being correctly handled by the 'layout' code when the 'render' package was disabled. This has been corrected. - 'qual' package-specific bug fixes: - Certain validation errors were not being correctly reported, with either missing information or bad line numbers. This problem has been fixed. Thanks to Nicolas Rodriguez for reporting the problem. * Configuration/build system changes - WARNING: There is a bug in the Microsoft Visual Studio 2013 compiler that can cause strange output when doing repetitive file reading and writing. We became aware of this when running our unit tests on the comp flattening routines. http://connect.microsoft.com/VisualStudio/feedback/details/ 808199/visual-c-2013-floating-point-broken-on-first-use We included a fix in our test files (libsbml/src/sbml/packages /comp/util/test/TestRunner.c) but users should be aware that this is an issue that may arise with this particular version of the MSVC compiler. - The CMake files have been updated to allow for the use when libSBML is merely being referenced within a CMake build, rather being specifically built. - Both the GNU make and CMake configuration systems generate certain header files that are specific to the libSBML build being requested. Previously, libSBML source code included project definition files for MSVC. These files were checked into SVN and included within the released src archive distribution. Their inclusion could potentially cause problems for people who wanted to create different build configurations from the same source code. Given that with CMake it is possible to generate MSVC project files directly, we no longer include them in the source archive distribution, and therefore, it is also not necessary to include the header files generated by the configuration process. Thus, these header files have been removed, and for CMake users they will be generated within the build directory to facilitate different builds using the same src tree. - There were issues with classes exported across the Windows dll interface. These have been fixed, and we have added additional tests to catch these issues. Thanks to Andy Somogyi for reporting the problem. * Miscellaneous - Python installers for various Linux distributions are now available from the Open Build Service and via pypi. Links to the relevant release can be found in the documentation on SourceForge download pages for libSBML. - The copyright statement for all example programs that we produced ourselves has been changed to use a less restrictive license, so that users can use the examples in their software without limitation. The new license is the MIT license. - The LICENSE.* files for libSBML now include a previously-missing 3rd party software acknowledgement for the Python argparse library by Steven J. Bethard. (The argparse.py module is included with libSBML distributions.) - A number of extraneous files have been removed from the documentation source directory (docs/src/); in addition, the directory has undergone some minor restructuring. - The Python API documentation lacked all the class constructors, due to a bug in the libSBML documentation production pipeline. This is now fixed. EXPERIMENTAL RELEASE * New features - Support for the 'arrays' package according to the specification dated September 11, 2013 (0.1 alpha) has been added to the experimental release files. Note the extended MathML is accessible via the ASTNode class; however, the current version version does not yet include support for parsing to and from infix notation. - 'multi' package-specific updates: - The ability to extend ASTNodes and hence use extended MathML has been added and thus it is now possible to use the attributes on the <ci> elements of math as specified by the 'multi' package. The example relating to this has been updated accordingly. * Bug fixes - 'render' package-specific bug fixes: - On occasion when an L2 document with layout and render annotations was being upgraded to L3 the render namespace was missed from the annotation in the L3 document. ==================================================================== 5.9.2-experimental (2014-01-31) ==================================================================== ******************************************************************** *** Experimental only release *** This is an experimental only release, that is, a release of those files provided in the experimental folder of a full release. This includes updates to all the SBML L3 packages that are not yet accepted and undergoing development. NOTE: An experimental release is not as rigorously tested as a full release. Any changes/fixes listed as either referring to stable or experimental code may change before the next full release. ******************************************************************** STABLE RELEASE * New features - The error messages relating to invalid SId syntax have been improved to report the attribute causing the problem. - The SBMLLevelVersionConverter has an option to ignore unrequired L3 packages. However there was no way to access this option when using the helper 'setLevelAndVersion' function. This function has no been given a default argument to allow users to specify the ignore packages option. - A new version of the SBMLTransforms::evaluateASTNode function is available; allowing the user to pass a map of ids and values to the function rather than needing a whole model. - Two new functions are available to allow users to determine the compiled dependencies for the given instance of libSBML. int isLibSBMLCompiledWith(const char* option) will take the name of a dependency library e.g. 'expat' as argument and return a positive integer this library was used to compile libSBML, 0 otherwise. const char* getLibSBMLDependencyVersionOf(const char* option) takes the name of the library and returns the version number of this library. * Bug fixes - Some of the perl examples had syntax errors - these have been fixed. Thanks to Joern Behre for reporting them. - Some subtle bugs in the ASTNode class have been fixed. These include returning 'bad allocation' as the name of a node; failing to replace the definitionURL of a csymbol node; not removing the units member when a node represents a function and incorrectly reporting failure when setting user data to NULL. Many additional tests have been added. - The Borland compiler does not handle implicit casts and unfortunately there was one such cast in the new code introduced for 5.9.0. This has now been fixed. Thanks to Totte Karlsson for reporting it. - A memory leak in SBasePluginCreator has been plugged. Thanks to Andy Somogyi for reporting it. - The instances of the extensions loaded into the ExtensionRegistry to facilitate plugins were not being correctly deleted. This has been corrected. - 'fbc' package-specific updates: - The CobraToFbcConverter was losing the charge and the capitalization of the formula when parsing the notes element. This has been fixed. * Configuration/build system changes - Any necessary fixes to facilitate the use of the new version of Mac OSX - Mac OSX 10.9 Mavericks - have been made. EXPERIMENTAL RELEASE * New features - 'req' package-specific updates: - The attributes in the req package are mandatory on all elements. This caused huge numbers of errors when reading files which used the req package but did not actually need to attributes on many elements. Thus the error has been suppressed. - 'spatial' package-specific updates: - The API for accessing compressed data has been improved to allow access to this data using language bindings. ImageData is now uncompressed during the first call to this and saved for subsequent access. Previously the data was uncompressed each time it was accessed. - Functions to determine whether an attribute has been set; i.e. the isSetFoo functions, have been provided where these were missing. Boolean attributes that have not been set are no longer written out. * Bug fixes - 'req' package-specific updates: - The csharp binding for this package was not complete. This has been corrected. - 'spatial' package-specific updates: - Errors relating to missing attributes have been sorted to correctly relate to attributes required by the specification. ==================================================================== Version 5.9.0 (2013-11-14) ==================================================================== STABLE RELEASE * Qualitative Models - The first official version of the specification of the Qualitative Models package is now available and thus the libSBML code for 'qual' is now included in the stable release of libSBML. This means that all prebuilt binaries for the stable release will include the 'qual' package code. The src archive containing libSBML core code will continue to be available but there will be additional src archives available in the stable branch: one containing libSBML core plus all stable packages and additional archives of the individual package code. NOTE: The libSBML GNU make-based build system has not been updated for packages. Thus, to build from src, it is necessary to use the CMake build system. * Layout - The layout specification for SBML Level 3 has been accepted and thus layout is now considered an official L3 package. Since layout code has been included with libSBML for many years, this has no impact on the code included within the stable release. * New features - There are two new function SBML_formulaToL3String(ASTNode_t*) and SBML_formulaToL3StringWithSettings(ASTNode_t* L3ParserSettings_t*) that provide reciprocal AST to infix functionality based on the previously released L3Parser code. - Within an SBML file it may be possible to infer units for parameters based on their use within mathematical expressions. A limited version of this functionality is now available using the SBMLInferUnitsConverter which will return a document with units attached to any parameters where it is possible to infer the units. - The SyntaxChecker class has a new function named isValidXMLanyURI(std::string) that can check whether a given string has the valid syntax for an XML anyURI datatype http://www.w3.org/TR/xmlschema-2/#anyURI. - There is a new base class ElementFilter that can be passed as an optional argument to the getAllElements function. When implemented this allows the elements to be filtered in whatever fashion before being added to the List returned by the getAllElements() function. The example getAllElementsWithNotes illustrates this functionality. - There is new functionality to facilitate replacing the id attribute and all references to that id within a model. There is a new base class IdentifierTransformer that when passed to the function renameAllIds on the Model object will perform the transformation specified by the IdentifierTransformer class on all id attributes within the model. Users should derive their own IdentifierTransformer class to perform the transformation they require. The example setIdFromName illustrates this functionality. - The class IdList which allows users to create and manipulate lists of 'id' strings has been made publically available. Previously this class has been used internally by validation and conversion code. It is now available in the sbml/util directory. - There is a new converter, the SBMLIdConverter, that will allow a user to replace several ids within a model. The converter requires a comma seperated list of existing ids and another of the replacement ids and will perform the necessary replacements. - There is a new converter, the SBMLLocalParameterConverter, that will allow a user to replace any localParameters with global parameters. The promoteParameters example illustrates the use of this converter. - Following the results of the user survey the L3Parser has changed the precedence of the '^' operator to be greater than a unary '-' operator and the precedence of the '!' operator to be higher than algebraic operators (and equal to the unary '-' operator). The precedence of '&&' remains the same as the precedence of '||'. - It is now possible to override the severity of errors logged or to disable error logging completely. Any override is applied to the errorLog until such time as the status is reset. This facilitates the use of functions, that may on occasion log errors, in a situiation were error logging is not required. - There is a new function XMLErrorLog::changeErrorSeverity (XMLErrorSeverity_t , XMLErrorSeverity_t, std::string package) that will change the severity of errors within the errorLog based on the package name supplied. - The XMLErrorLog and SBMLErrorLog classes now have explicit implementations for the copy and assignment constructors. - The SBase functions getURI() and getPrefix() that return information relating to the namespace of the object have been made public. Formerly these functions were protected. - The function removeTopLevelAnnotationElement(const std::string elementName, const std::string elementURI = "") allows users to remove a single top level element from the annotation node. If, having removed the specified annotation, the overall annotation node had no child elements the entire node was being deleted. There is now an additional optional argument to this function, bool removeEmpty, that allows the user to specify that they do not wish the annotation to be deleted. - There are two new function on the SBase class that allow an element to be read from and written to an XMLNode. The XMLNode is the underlying class used by the XML parsing layer of libSBML. The function XMLNode* SBase::toXMLNode() returns a pointer to an XMLNode that represents the SBase object; which will facilitate the ability to look up attributes of an object by name. The function void SBase::read(XMLNode& node, XMLErrorSeverityOverride_t) invokes the read functionality on a given XMLNode. This facilitates reading blocks of annotation that may represent SBML in some way. It should be noted that these functions are computational expensive in that they serialise to a string. This drawback will be addressed in future libSBML architecture but cannot be overcome with the current libSBML-5 implementation. - All set or add functions in libSBML return a value from the enumeration OperationReturnValue_t. There is now a function OperationReturnValue_toString that will return a string representation of the reason for the failure. - 'layout' package-specific updates: - The example code for layout has been moved to subdirectories named 'layout' beneath the appropriate language subdirectories in the examples directory. This reflects the structure used for example code from all packages. - The code reading and writing layout as an annotation has been adapted to use the new read/write to/from XMLNode functions. This greatly reduces the complexity and repetition of code previously needed to perform these functions. - 'comp' package-specific updates: - All the validation rules have been fully implemented, up through release 3 of the specification. - Validation is now incorporated into the flattening process. If there are no errors (or only warnings), the flattening process will proceed to produce a flattened version of the model. If there are errors, the flattening process will halt and return an unchanged version of the model, with the errors noted in the model's error log. This provides the user with detailed information regarding why a document has failed to flatten as well as detailing any warnings related to the document returned on success. - There is an additional option for the CompFlatteningConverter to allow the users to request that the document not be validated before or after flattening. This allows the user to produce a flattened model irrespective of the validity of the original model. Errors produced during flattening will still stop the flattening process, as they make it impossible to flatten the model. - There is a further additional option for the CompFlatteningConverter to allow the users to specify how the required status of any unflattenable package should influence whether flattening is attempted or not. By default this option has a value of 'requiredOnly' which indicates that flattening will abort if it encounters an unflattenable package that has a 'required' attribute of 'true'. Other options are 'all' or 'none'. - The flattening routine has been extended to include all packages available within the stable release: layout, qual and fbc. NOTE: This means that the behavior of the flattening converter will be different than it used to be: in the past, the converter would either refuse to flatten a model with information from any of these packages, or would leave unmodified package information from the main model only. Now, all information from all submodels will be properly integrated into the flattened model. * Bug fixes - The converter that expanded functionDefinitions was failing to correctly deal with any csymbols it encountered in the math. This has been fixed. - Conversion between SBML Levels was not correctly handling the units attributes that appear on the Model object in an Level 3 model. This has been fixed. Thanks to Pratham Shah for the report. - The UnitDefinition::printUnits function had a mismatch between integer and double values for the exponent; causing incorrect values to be used on occasion. This has been fixed. Thanks to Pratham Shah for reporting this. - An annotation on a package element is permitted to use the SBML namespace. However, this situation was logging an error. This has been corrected. - A memory leak in the TranslateSBML function has been plugged. Thanks to Neil Swainston for reporting the issue and testing the fix. - 'comp' package-specific bug fixes: - It is possible to construct a model which tries to delete an object more than once. This was not being detected correctly. This has been addressed and flattening code will report this issue as an error. - Similarly replacing both an object and independently replacing a child of that object could also cause problems. These have been sorted. * Miscellaneous - The API manuals for Java, Python and C# now include information about the SBML Level 3 package extensions. In addition, many content errors have been fixed, many formatting errors have been resolved, new sections have been added, and finally, the overall look and feel of the documentation has been updated (and hopefully improved). - The copyrights and license statements in LICENSE.txt/LICENSE.html have been updated to reflect the inclusion of code from Ralph Gauges (EML, Heidelberg, Germany), a small program from Sun Microsystems used in generating documentation, and the PrettyTable and Google Code Prettify utilities mentioned below. - To help produce better documentation, the libSBML sources now use (and incorporate) two utilities, PrettyTable 0.7.2 (in src/bindings/python/doc-converter) and Google Code Prettify (in docs/src). Both are redistributable under terms compatible with the LGPL terms used for libSBML as a whole. Please see the file LICENSE.txt or LICENSE.html for specific information about the authors and license terms of these packages. - A new, simple tutorial example of creating a model using the Python language interface is now available in the Python documentation. The example was kindly provided by Martins Mednis (in 2012!). EXPERIMENTAL RELEASE * New features * Distributions - There is now a stabilized version of the specification for the Distributions package and the experimental release now includes code for this 'distrib' package. As is the case with all packages included in the Experimental Release the binaries are built with 'distrib' enabled and the libSBML source archive includes the source code. * Multistate, Multicomponent and Multicompartment Species - There is now a stabilized version of the specification for the Multistate, Multicomponent and Multicompartment Species Package and the experimental release now includes code for this 'multi' package. As is the case with all packages included in the Experimental Release the binaries are built with 'multi' enabled and the libSBML source archive includes the source code. It should be noted that it is not yet possible to extend the math <ci> element; which the 'multi' proposal does; however the definitionURL attribute can be used on the <ci> element to convey the necessary information until libSBML provides the ability to extend the math. * Groups - The 'groups' package code has been updated to include revisions made to the latest specification. ==================================================================== Version 5.8.0 (2013-02-28) ==================================================================== STABLE RELEASE * Flux Balance Constraints - The first official version of the specification of Flux Balance Constraints is now available and thus the libSBML code for 'fbc' is now included in the stable release of libSBML. This means that all prebuilt binaries for the stable release will include the 'fbc' package code. The src archive containing libSBML core code will continue to be available but there will be additional src archives available in the stable branch: one containing libSBML core plus all stable packages and additional archives of the individual package code. NOTE: The libSBML GNU make-based build system has not been updated for packages. Thus, to build from src, it is necessary to use the CMake build system. * New features - The converter that expands SBML FunctionDefinition constructs has been extended with an additional option that allows the user to specify particular <functionDefinition> objects that should not be expanded. - We have changed the behavior of the converter that converts between core Levels and Versions of SBML. This converter has a boolean option, 'strict', that determines whether an invalid model can be converted or produced. The code originally assumed that 'strict = false' refers to syntactic validity only, and so even when the flag was set to false, the converter could fail to convert a model if semantic validity was not preserved. This interpretation has been changed because people felt it was not useful; now, setting 'strict' to 'false' will always convert a model, and if there are errors related to altered semantics, the errors will be logged in the usual error log. - Documentation for the 'comp' and 'fbc' C++ API is now available. - 'comp' package updates: - The C API for comp is now available with an example of creating a model using this API. - The majority of 'comp' package validation rules have now been implemented and will be reported. Validation has also been expanded to apply validation from core and other packages (where appropriate) to any ModelDefinitions contained within a comp model. * Bug fixes - LibSBML was still writing out the deprecated, and in some cases removed, attribute 'charge' on a <species>. This is no longer the case. - Some files caused the SBML Level and Version converter to enter an endless loop. This has been fixed. Thanks to the good folks at Persistent Systems Ltd. for reporting this. - Reading an attribute with a value of type 'double' was failing to report when a different type was encountered for the value. This has now been sorted and will be correctly logged as an error by the readSBML functions. - The Level and Version converter was in some cases running unit validation even if the user had specified that they did not require strict unit validation. This was in fact done by libSBML to allow an error to be logged; however, it has become clear that the large computational overhead of running unit validation is unecessary to merely log an error. Thus, if the user has declared that they do not require unit validity, the checks will no longer be applied. - 'layout' package-specific bug fixes: - The extension namespaces were not being correctly set. This has been fixed. - 'comp' package-specific bug fixes: - The function 'renameSIdRefs' now functions properly for SBaseRef-derived classes. * Configuration/build system changes - 'fbc' package-specific build system changes: + The GNUMake build system has not been implemented for packages. Thus, to build from src, it is necessary to use CMake. * Miscellaneous - The structure of the API documentation has been slightly overhauled to provide clearer access to relevant information. EXPERIMENTAL RELEASE * New features - 'qual' package-specific new features: - New functions getInputBySpecies(std::string) and getOutputBySpecies(std::string) have been added to the Tranisition class. These will return the first Input/Output in the relevant list that matches the qualitativeSpecies attribute value supplied as argument. * Bug fixes - 'qual' package-specific bug fixes: - As validation of packages is starting to be introduced the situation whereby a ListOfFunctionTerms can contain no FunctionTerm elements but only a DefaultTerm caused issue with the code that reports an empty ListOf object. This has been fixed. - 'render' package-specific bug fixes: - Conversion between L3 and L2 annotation was not working as expected. This has been fixed. - The interaction between layout GraphicalObjects and the render 'objectRole' attribute was removing the attribute on occasion. This has been fixed and more fully tested. ==================================================================== Version 5.7.0 (2013-01-14) ==================================================================== STABLE RELEASE * Hierarchical Model Composition - The first official version of the specification of Hierarchical Model Composition is now available and thus the libSBML code for 'comp' is now included in the stable release of libSBML. This means that all prebuilt binaries for the stable release will include the 'comp' package code. The src archive containing libSBML core code will continue to be available but there will be additional src archives available in the stable branch: one containing libSBML core plus all stable packages and additional archives of the individual package code. NOTE: The libSBML GNU make-based build system has not been updated for packages. Thus, to build from src, it is necessary to use the CMake build system. Known limitations of the 'comp' code: + Documentation has not yet been integrated into the libSBML documentation. + Whilst the majority of validation rules have been implemented, some will report the schema error id rather than the specific comp validation rule id. The more involved rules involving circular dependencies and in-depth referencing have not been implemented. Validation of ModelDefinitions is implemented with respect to comp validation, but not with respect to core validation. + There is no C API for interacting directly with comp objects. However the C API for reading and validation will apply to the 'comp' package and flattening can be accessed via the converter C API to call the CompFlatteningConverter. * New features - Convenience functions have been added to the SBMLExtensionRegistry class to facilitate enabling/disabling packages using just the package name. For example: disablePackage(const std::string& package); enablePackage(const std::string& package); - Previously the setNotes function accepting a string as argument expected the string to contain the appropriate XHTML tags and would not set the value of the <notes> element to a string that did not meet this requirement. The functionality of the setNotes(const std::string&) function has been extended to allow a user to add an optional boolean argument addXHTMLMarkup. When the value of this argument is 'true' the function will accept a string; wrap it with the XHTML <p> tag and set the <notes> element to this. - A C API for use with the converters has been added. Examples of using the converter API are available in all supported languages. - 'comp' package - Access to the flattening routines has been restricted to the CompFlatteningConverter. This allows options to be specified by the user regarding ignoring other packages and whether to produce a document with no comp namespace or a document with the comp namespace but the required attribute set to 'false'. - Validation has been implemented (see note above). This is called via the checkConsistency function within core libSBML; which now accesses a checkConsistency function in the comp plugin. There are two categories of validation: LIBSBML_CAT_GENERAL_CONSISTENCY and LIBSBML_CAT_IDENTIFIER_CONSISTENCY which are enables or disable via the setConsistencyChecks() function on the SBMLDocument (in libSBML core). - The API for resolving external models has been updated to use a registry of resolvers. This facilitates the addition of user specific resolvers. * Bug fixes - The number of arguments expected by a piecewise function was incorrectly assumed to be two. However, a piecewise function can have a single argument. This has been corrected. - Validation of SBML Level 3 was issuing a general warning about missing required attributes but failing to identify which attribute had caused the error to be reported. This has been corrected. Thanks to Nicolas Rodriguez for pointing this out. - Validation was failing to report the incorrect use of a function call if the lambda function usesd expected no arguments. This has been fixed. - The L3Parser was not dealing with the sqrt function correctly. This has been sorted. - 'comp' package-specific bug fixes: + SBOTerms were not being correctly dealt with when they occured on a Port element. This has been corrected. Thanks to Chris Myers for reporting this. * Configuration/build system changes - Building the MATLAB binding for libSBML can be problematic due to the need to identify and use the MATLAB mex compiler. When MATLAB is being accessed over a network this can result in misleading error messages. The build system has been improved to halt compilation if the mex compiler is not available and to give a clearer error message as to how to proceed. - The build system has been updated to facilitate use with the Mac OS X 10.8 operating system (Mountain Lion). - 'comp' package-specific build system changes: + The GNUMake build system has not been implemented for packages. Thus, to build from src, it is necessary to use CMake. * Miscellaneous - It was reported that gcc 4.7 found the various definitions of isnan used within some parts of libSBML to be problematic. This problem has been addressed and there are now functions util_isNaN and util_isFinite in the util file that are used throughout libSBML. Thanks to Totte Karlsson for reporting this. - Where test files compare double values the comparisons have been unified to use the util_isEqual(double, double) function and thus avoid inaccurate results that can be machine dependent. - This NEWS.txt file has reduced in size with NEWS dating from prior to libSBML-5 now saved as an OLD_NEWS.txt file. EXPERIMENTAL RELEASE * New features - 'Qual' package: - The package specification redefined whether some attributes or elements were required; the code has been updated appropriately. - 'Fbc' package: - The package specification added some optional attributes and deprecated the use of strict less than or greater than; the code has been updated appropriately. * Bug fixes - 'Render' package: - In some cases the code was failing to add expected attributes to particular elements. This has been corrected. ==================================================================== Version 5.6.0 (2012-08-03) ==================================================================== A note on the use of SWIG: All aspects of libSBML-5.6.0 requiring SWIG are known to work with SWIG version 2.0.4. Issues with later versions have been found with respect to some areas of a libSBML build. These will be addressed in future releases but for libSBML-5.6.0 we recommend the use of SWIG 2.0.4. STABLE RELEASE * New features - LibSBML now includes a binding to R (The R Project for Statistical Computing). The binding is generated using SWIG and thus can be built by users. Alternatively, the libSBML-5.6.0 release provides R packages that can be installed directly into R. - During HARMONY 2012, people discussed the issue of providing support for Level 3 Layout in other SBML Level 3 packages. The conclusion was that additional GeneralGlyph elements should be added in order to support references to as-yet unknown types of objects to be defined in Level 3 packages. These additional elements have been included in the libSBML layout code. - Although libSBML GNU makefiles have technically supported Python 3 for some time, there had been no feedback regarding the use of Python 3 until recently. In response to the feedback, we have the updated the build system to facilitate the use of different versions of Python 3. On Windows, the libSBML release also includes prebuilt installers for Python 3.2. - The libSBML 'configure' command now accepts the additional option --with-python-interpreter, which allows you to specify the Python interpreter that should be used. This is useful when a system has multiple versions of Python installed in the same directories, and the version that should be used can be selected by explicitly invoking the desired version. The option takes a full path, as in "--with-python-interpreter=/usr/bin/python2.7". - In order to facilitate the use of identifiers.org URLs, we added an additional function, getSBOTermAsURL, to the SBase class. This function returns a string representation of the SBOTerm in its resolvable identifiers.org URL format; e.g., "http://identifiers.org/biomodels.sbo/SBO:NNNNNNN" - The use of libSBML get and set functions in Python; a by-product of the use of SWIG; is not particularly intuitive. LibSBML-5.6.0 applies a patch that allows the use of indexing in the python environment i.e. model->getSpecies(0)->getId() can be replaced with model.species[0].id. This patch is limited to Python 2 versions at present. It does not adversely effact existing functions for either Python 2 or Python 3. Many thanks to Gordon Ball (Computational Medicine, Karolinska Institute) for creating and sharing this patch. * Bug fixes - When using a copy of libSBML compiled with Level 3 package support, attributes from the "sbml" namespace were not given a namespace prefix when they should have been. This has been fixed. - The L3Parser had some subtle bugs on some operating systems when dealing with very long numbers or exponentials. These have been tracked down and fixed. - Although libSBML explicitly prevented History or CVTerm objects from being added to the annotation of an object when that object had no metaid attribute value, it was still possible to add History and CVTerm directly to the annotation. This could lead to invalid MIRIAM annotations because they lacked a metaid attribute value. LibSBML now checks that an object to which any MIRIAM compliant annotation is being added has a metaid. - When returning a MIRIAM-compliant annotation, all CVTerms were lost if just one had an invalid qualifier. This has been fixed. - The decompression code uses a macro OF that is not defined for all versions of linux. A definition has been added to avoid problems. Thanks to Kai Wohlfahrt for reporting this. - There was a potential memory leak issue while registering SBMLConverters. Thanks to Akira Funahashi and his team for spotting the problem and supplying a fix. * Configuration/build system changes - As SBML Level 3 packages and their code become available, there is a increasing number of possibilities in the matrix of what a particular instance of libSBML has included. In order to facilitate code that may rely on the presence of one or more packages, the CMake configuration process has been improved to include a set of flags that identify the packages included in a particular build. The file convertLayout.cpp in the examples/c++ directory illustrates the use of these #define's. - The MATLAB bindings failed to build on Mac OS X whenever an Xcode version was used that did not include the Mac OS 10.6 SDK. This has been fixed. - The CMake build system has been made more resilient to finding include files from previous libSBML installations. EXPERIMENTAL RELEASE * New features - The Qualitative Modeling package "qual" is now supported. - The R binding is available for all packages. - 'Groups' package: - At HARMONY it was agreed that the 'group' element needed an additional attribute 'kind'. This has been added. - 'Spatial' package: - There was an issue with the encoding of image data for the spatial package. This has been solved by providing a function that will uncompress the data and return it to the user in a usable form. - 'Comp' package: - Instantiated Model objects in Submodels now are set to have that Submodel as their parent. The SBMLDocument is still set to the document of the original Model, so that its own Submodel references can be properly tracked down. ==================================================================== Version 5.5.0 (2012-05-11) ==================================================================== STABLE RELEASE * Revision of annotation and SBML MIRIAM RDF Following discussions on the libsbml-development mailing list we have adjusted the way functions affecting annotations interact with the SBML MIRIAM RDF classes for History and CVTerms. - Previously any annotation was assessed and if it contained MIRIAM RDF the corresponding classes were created and the original annotation XMLNodes relating to these objects was removed from the annotation. When the annotation was retrieved the xml was reconstructed from the History and CVTerm classes. This is no longer the case. In 5.5 we have changed the code so that the MIRIAM objects are created BUT the original annotation remains intact. It is only reconstructed if the code has directly altered the History or CVTerm classes via the class API, otherwise the original annotation is returned. - We reassessed the use of the appendAnnotation function. Previously any annotation was appended regardless of whether the existing annotation already contained a top level element with the same namespace. We considered this to be a bug, since it would result in invalid SBML. Thus, the appendAnnotation function now checks whether there is an existing top-level element with the same namespace of any it is to append and does not append if it encounters a duplicate. It returns an OperationReturnValue of LIBSBML_DUPLICATE_ANNOTATION_NS to indicate this to the user. - In our reassessment of appendAnnotation we came to the conclusion that it was virtually impossible to correctly determine the intent of the user in cases where both the existing and appending annotation contained RDF that complied with the SBML MIRIAM RDF History or CVTerms. Thus the appendAnnotation function no longer treats RDF as a "special" case. If there is existing RDF, no further RDF will be appended. Users wishing to alter existing History or CVTerms should use the API provided or construct their own annotation and use the setAnnotation function. - New functions removeTopLevelAnnotationElement(std::string name) and replaceTopLevelAnnotationElement(XMLNode* annotation) have been introduced to allow users to remove or replace a single top level annotation element whilst conserving any other annotation that may be present. * New features - There is now a version of the infix to MathML parser that is independent of L1 constructs. This parser is available as three functions: SBML_parseL3Formula(""), SBML_parseL3FormulaWithModel("", Model*) and SBML_parseL3FormulaWithSettings("", L3ParserSettings *). There is a new object L3ParserSettings that allows the user to tailor the results of the function, for example to parse "log" as natural log or log base 10; to allow users to enter units on numbers as "10m" or to disable this feature along with some other options. - The getLine() and getColumn() functions did on some occasions return a maximum int value when the correct lines and columns could not be determined. This produced inconsistent behaviour as some XML parsers return '0' as if they cannot determine location. This has been unified and libSBML's getLine()/getColumn() will now return '0' if the location is unknown. - There is a new class SBMLDocumentPluginNotRequired which allows a package code to derive from an object where the required attribute is considered 'false' until it has been set. Note this is not a "default" value it is just the value with which the boolean attribute is initialised. The existing SBMLDocumentPlugin class assumes a value of 'true'. This is in fact a change in behaviour but since users should set this value it should not cause a problem. * Bug fixes - Tracker issue#3509843 The annotation element in SBML should contain only elements. Schema validation reports this but libSBML was not. This has been corrected. Thanks to Camille Laibe for still running schema validation and reporting the issue. - There was a subtle bug involving accessing a NULL ModelHistory object. This has been fixed. - Area units were not being properly converted between SBML Levels. They are now. - An AST plus or times node that was created with more than two children was written out as only having two children; thus losing information. This behaviour has been corrected. - Functions used to add objects to other objects in libSBML check that the SBML Level/Version/Namespaces of the objects correspond. However these checks were imposing the condition that the number of namespaces on both objects be the same. This is not a necessary condition and the code has been relaxed. Thanks to Chris Myers for pointing it out. - In XML if the sbml element is not prefixed but the only declaration of the sbml namespace is, then technically the sbml element has not been placed into the sbml namespace. LibSBML was failing to report this. This has now been fixed. - There was a curious indentation issue that arose if notes used text as child elements of an element that also had another non-text child element. This could proliferate and cause models where the indentation ran into the thousands of spaces. This has been sorted out and no longer happens. * Miscellaneous - The uninstallation instructions were out of date. This is now updated, for example to mention that the Mac OS X installer does in fact provide an uninstall script. * Configuration/build system changes - Doxygen versions 1.7 and 1.8 are now supported, but due to differences in the new version, older versions of Doxygen are no longer supported. The 'configure' script will now only accept version 1.7 at minimum. - Some changes have been made to facilitate building libSBML with the Borland compiler. This included standardising the use of #ifdefined rather than using #if. Thanks to Totte Karlsson for the effort of getting this to work. - The CMake build has been updated to facilitate the use of the Intel compiler. EXPERIMENTAL RELEASE * New features - New macros provided so that SBMLNamespaces objects may easily be created to allow package elements to be extended by other packages (for example: a comp:modelDefinition to have a layout:listOfLayouts). These macros now used throughout package system when creating new package elements. - In 'comp': - ExternalModelDefinitions have a new function, 'getReferencedModel' that tries to find the referenced document and model, if the reference URI is a 'file' type. If the SBMLDocument has its fileURI set, this will use that to search for relative filenames. - With the above in place, automated flattening now works with ExternalModelDefinitions that point to local files. - May now use ModelDefinitions to create the main Model of an SBMLDocument. ====================================================================== Version 5.4.1 (2012-02-24) ====================================================================== STABLE RELEASE * Bug fixes - The MATLAB binding function isSBML_Model had a subtle bug that meant it could crash in certain circumstances. This has been addressed. Thanks to Ying Zhang for the report. - When determining units from rate rules unit checking failed to catch the case where time had been redefined as dimensionless. This is now fixed. Thanks to Kieran Smallbone for reporting it. - Documentation files for MATLAB were missing from the dmg installers for MacOS. This has been fixed. - 'getElementBySId' could potentially return initial assignments, event assignments, assignment rules, and rate rules that assigned *to* the SId in question, instead of returning the actual element with the SId. This has been fixed. EXPERIMENTAL RELEASE * Bug fixes - LibSBML will now automatically register any packages that are enabled in code. Previously libSBML could be built including package code but users needed to perform an additional step to actually use it. This was causing some confusion. ====================================================================== Version 5.4.0 (2012-02-16) ====================================================================== STABLE RELEASE * New features - Basic validation of MIRIAM compliant RDF annotations that are parsed into ModelHistory or CVTerm objects has been added to facilitate the use of annotations that are not yet quite complete. Warnings are now issued relating to whether or not the rdf:about attribute accurately points to the metaid of the containing object and whether the object that was created was consisdered a valid object in the attributes and subelements that are required. - It has been noted that unless the checkConsistency function is called immediately after reading an SBML document, it does not report all potential errors. Since users may wish to apply the function to a model being constructed this seems to be a disadvantage of the function. However, as this function has been in libSBML for many years it was decided not to alter the functionality but to add a new function 'validateSBML' which, when called from a document object, will force a write and read of the in memory object and report validation errors for the object as written. Thus, all errors will be reported with line numbers that would correspond to the document if written out. - Conversion of a model containing FunctionDefinitions to L1 is now supported. - Conversion of a model containing InitialAssignments to L2V1 and L1 is now supported. - There is a new isSetBody() function for the FunctionDefinition class that returns true if the body of the lambda function has been set. - The MATLAB/Octave binding function OutputSBML now takes an additional optional flag (extensions_allowed defaulting to true) that allows a user to specify whether the MATLAB_SBML structure should be considered valid if it contains any additional fields. - Multiple namespaces using the same prefix are not allowed in XML. The function that added XMLNamespaces in libSBML checks for an existing namespace with the prefix of the namespace being added and overwrites the original if a duplicate is found. This behaviour meant that it was possible to unintentionally remove the sbml namespace. The behaviour of the function has been altered such that if the namespace being added has a prefix that duplicates that of the existing sbml namepace then the function returns failure and the new namespace is not added. Should the sbml namespace need to be replaced it can be done by using the remove function before adding the new namespace. - SBase objects that occur in Level 3 package code need to keep track of the namespace of the package to which they belong. However, a conversion might alter the namespace; for example with layout where the level 2 layout annotation has its own namespace. The getURI function has been altered to adopt the approach used for tracking the core sbml namespace of any object i.e. the namespaces of the containing document take precedence and the namespace stored on an actual object is only considered if it does not belong to a document. An additional function getElementNamespace() can be used to obtain the namespace stored on the actual object. * Bug fixes - Tracker issue #3472034 Line numbers were not being reported as accurately for L2 models as for L3 models. We have overviewed all the code relating to line numbers and improved the accuracy and consistency of line numbers reported. Thanks to Raimund Rönn for the report. - Tracker issue #3471902 The documentation for the readSBMLFromString function claimed it prepend the xml encoding if it was not present. In fact, the function did not do this. This has been corrected. Thanks to Raimund Rönn for reporting it. - Tracker issue #3466104 Fixed inaccuracies in the documentation. Thanks to Raimund Rönn for his careful reading and taking the time to report the errors. - Validation failed to notice that csymbol avogadro was not valid in Level 2. This is fixed. - Exceptions were not being correctly wrapped for language bindings causing potential code crashes. This has been corrected. - A number of minor issues with regard to conversion between levels and versions have been fixed. These include conversion from L3 to L1 failing to include a compartment; stopping conversion of models with hasOnlySubstanceUnits = true to L1; correcting conversion of L3 models with localParameters and preventing conversion of L3 models where Events had Priorities or where the csymbol avogadro had been used. - The internalConsistency validator was incorrectly reporting that the an Event must have a listOfEventAssignments in a level 3 model. This restriction was actually removed in SBML Level 3. - The MathML subset used by SBML has plus/times/and/or/xor. In the MathML specification all these functions are nary functions i.e. they are permitted to have any number of arguments including zero. LibSBML had in fact restricted these functions to two or more arguments. This inconsistency has been corrected. - Validation was failing to apply constraints to L3 LocalParameters. This has been corrected. - Using a value for a units attribute that was not a builtin unit or the identifier of a UnitDefinition is invalid. However, the way in which this was reported varied according to which unit attribute caused the issue. This has been standardized to produce an id warning about a dangling UnitSIdRef and (if selected) unit warnings relating to the impact of the actual attribute. - In certain situations libSBML would write out both the stoichiometry attribute and a stoichiometryMath element. Since these are mutually exclusive this should not happen. It has been fixed. - The code that checked for consistent namespaces when adding one object to another was too restrictive. This has been sorted. Thanks to Chris Myers for reporting it. - Conversion between levels was inconsistent when it came to dealing with rational stoichiometry. This has been fixed. - The tests for the Perl bindings use of BigInt caused ActivePerl to crash on a Windows system. A workaround to prevent this has been put in place. - LibSBML class constructors currently throw exceptions rather than create objects with invalid SBML namespace/level/version information. This could potential result in code crashing when using one of the language bindings. These have now been rigorously tested and measures put in place to prevent such crashes from happening. - The SBMLTransforms class now correctly evaluates piecewise expressions. - The MathML infix converter now deals correctly with unary plus and times. - The help text for classes and methods in the Python library were previously unformatted, marked-up Doxygen input text, making the help text unhelpful. We wrote a new conversion program to process the marked-up text and produce plain-text documentation strings in the Python library. Users can now use the standard Python 'help' function to obtain help as expected. - The StripPackageConverter was not working as expected. This has been fixed. * Miscellaneous * Configuration/build system changes - As libSBML has evolved over the years the header files included by a given code file have expanded. This makes it necessary to recompile many files when only a single header file has been altered. In an attempt to eliminate unnecessary dependencies we have done an overview of the code. However, merely replacing existing include files with those that are actually required may cause build issues for other users. Thus we have introduced a LIBSBML_USE_STRICT_INCLUDES flag. This flag is not defined by default and thus no includes will change. Defining the flag means that code will only include the minimum number of necessary header files. We encourage people to consider using this flag as it may become the default behaviour in later versions of libSBML. The flag is available via the CMake build interface. EXPERIMENTAL RELEASE * New features - Code for the 'render' extension is now available. - All package code has been updated to use the new line/column number reporting mechanism. - Package language bindings have been updated to properly wrap exceptions and use covariant return types. - There is a new example with the 'layout' package that demonstrates conversion between the layout and render L3 package representation and the L2 annotation representation. ====================================================================== Version 5.3.0 (2011-12-23) ====================================================================== STABLE RELEASE * New features - Errors reported by the matlab binding function 'OutputSBML' have been improved to provide information about why the structure is invalid. - There is a new virtual function on an SBase object 'setElementText'. This enables a user to store text that the read functions encounter within an XML element. Previously such text was ignored as no such text existed as a part of an SBML Core element. Some L3 packages may use this XML feature and can thus utilize this function. - There is a new function on an ASTNode 'returnsBoolean' that returns a predicate indicating that the math of the ASTNode will return a boolean result or not. The function has an argument of type Model with a default value of NULL. Where necessary, that is, when the ASTNode involves a call to a user defined function, the check is done in the context of the supplied argument Model or the parent Model of the particular ASTNode if no argument is supplied. - There are new functions to facilitate the use of packages. The SBMLExtensionRegistry has a 'disableUnusedPackages' function which disables registered packages that are not being used by the target SBMLDocument. The base SBMLExtension class has a function 'isInUse' that will establish whether a package is being used by the target document. * Bug fixes - The conversion code incorrectly converted an L3 model where the stoichiometry was changed by a RateRule. This has been fixed. - Conversion from L3 to L2 was failing to write out the spatialDimensions attribute of a Compartment regardless of the value. It now correctly writes out a non default value. - The RegisterConverters class was not included in the LIBSBML_CPP_NAMESPACE. This has been corrected. Thanks to Christoph Flamm for letting us know. - There was a slight discrepancy in how the assignment operator for the SBMLExtensionNamespaces was behaving depending on OS. This has been sorted so that behaviour is the same for all. - Tracker issue #3438777 The XercesParser was failing to find the line and column number definitions with some compilers. This is now fixed. Thanks to David Fange for reporting it. - Tracker issue #3441615 There was an issue with SWIG, C# and MSVC compilers caused by conflict with MS MFC and GDI classes. This has been fixed by explicilty excluding these classes. Thanks to Totte Karlsson for reporting this. - Tracker issue #3461400 Writing out an L2 model with Layout annotation caused duplicate annotations to be written out. This has been fixed. Thanks to Raimund Rönn for reporting the problem. - Tracker issue #3462055 A couple of typos have been corrected. Thanks to Raimund Rönn for taking the time to report these. - The documentation for Python did not omit internal libSBML methods. This is now fixed, and the docs more properly reflect the public libSBML API. - We have fixed a number of errors in the Python API documentation, such as return values being reported as "char" when in fact they were strings, and have filled out more of the missing documentation. - We have fixed many other small documentation bugs and filled out more of the missing documentation. * Miscellaneous - The matlab binding contains a function 'isSBML_Model' that checks that the structure contains all the fields that are expected in an SBML model. This function is used by OutputSBML to determine if the model can be written out. Previously this function would only report that a model was valid if each of the substructures had the expected fields and no additional fields. This behaviour has changed to allow users to include extra information within the structure. Thus a model is considered invalid if it does not have all the expected fields; additional fields are ignored. - The libSBML examples code has been ported to all language bindings; so all examples exist in each language. - The API manuals for languages besides Java now feature a more modern and attractive appearance. * Configuration/build system changes - Using CMake to link against the static runtime libraries on windows when using libxml2 it was necessary to manually add links to other libraries. The build system now takes care of these. EXPERIMENTAL RELEASE * New features - There is now code to support the L3 render package. ====================================================================== Version 5.2.0 (2011-11-11) ====================================================================== * Download directory structure - Prior to this release we have provided stable libSBML source code and associated binary installers, but only provided the source code of the L3 packages that are in beta development. In response to requests to provide binaries including the package code, we have slightly reorganised the directory structure of the 5.2.0 release. The top level directory remains as expected https://sourceforge.net/projects/sbml/files/libsbml/5.2.0 This directory contains two sub-directories 'stable' and 'experimental'. 1) files/libsbml/5.2.0/stable This directory contains the source code and various binary installers arranged in a structure identical to that used in the 5.1.0-b0 and 5.0.0 releases. 2) files/libsbml/5.2.0/experimental This directory also contains two subdirectories. a) files/libsbml/5.2.0/experimental/src This directory contains the archives of the beta source code for the L3 packages; similar to those previously contained in the separate top level directory /5.1-packages-beta/. b) files/libsbml/5.2.0/experimental/binaries This directory contains binaries that include the stable source code plus the beta code for ALL of the packages. It should be noted that these binaries may be untested and are provided 'as-is' to facilitate experimentation with L3 packages. * New features - There is a new method 'removeFromParentAndDelete()' that enables the complete removal of child objects from any SBase object. - There is a new method 'getAllElements()' that returns a List containing all the children, both direct and indirect, of the object on which it is invoked. - There are new methods that will rename any references to SId and UnitSId throughout the model. - A new converter has been added that will convert the units of a model to base SI units. - A new converter has been added that will order AssignmentRules and InitialAssignments in such a way that forward references are avoided. - The validation API has been refactored to facilitate the use of third-party validators. The existing API has been maintained; in addition, it is now possible to call any external validator, regardless of programming language, using the new validator API. - There is a new UserData object on the SBase class. This facilitates storing additional application-specific information that may be useful to particular software. - A new function, appendFrom(ListOf *), on the ListOf class allows the contents of one ListOf object to be appended to another. - There are new functions getNumRegisteredPackages() and getRegisteredPackageName(index) that allow the user to establish which Level 3 packages have been enabled in the instance of the libSBML library being used. - The C API for interacting with the package plugin mechanism has been expanded. * Bug fixes - The functions that add SBase objects were only checking that the object being added had the correct Level and Version of SBML. It failed to check that any SBML namespaces used also matched. This has been corrected. - Error checking failed to catch SBML L3 models with an empty <listOfEventAssignments>. Fixed. - If the units of an object referred to a UnitDefinition that had no <lisOfUnits>, the warnings generated by the unit checking code were inconsistent. These have now been standardized. - The UnitDefinition::isVariantOfMass() function did not check that the exponent of any unit was '1'. This has been fixed. - The postal address for the Free Software Foundation was out of date in all files where it was mentioned. Fixed. - It was (erroneously) possible to allow the SBML namespace to be replaced and lead to the production of a document with no SBML namespace. Fixed. - Some of the older libSBML C code called the exit() function when a memory allocation error occurred. This is not an ideal way to handle a problem. Since the functionality has existed in libSBML for many years it has been removed from a standard build but can be reenabled using a configuration flag should any users wish to do so. - The point at which an MSVC call to the c_str() function tidies up its memory usage when running in debug mode is different to the point at which the memory is tidied up when running in release mode or with other C compilers. This means that a C function that returns a char * which is created using c_str() will return an invalid pointer. Unit testing does not highlight this issue as it only occurs in an MSVC Debug build. Duplicating the string before returning it solves the problem. LibSBML-5.1.0-b0 had three new functions where the string duplication was missing. This has now been fixed. - In the layout code, adding a <Point> to a <BoundingBox> produced an element with the wrong name. This has been fixed; a fix that revealed further issues with the constructors for packageNamespaces. This issue has also been fixed. Thanks to Chris Myers for reporting the original problem. * Miscellaneous - There were inconsistencies arising from the naming of functions related to packages; some being named doPkgFoobar and others doPackageFoobar. All of these functions now use the doPackageFoobar naming format. Existing functions using the Pkg format will still work but should be considered deprecated. - The text of many SBML validation and consistency-checking error messages have been edited to hopefully improve readability, clarity and consistency. - All example files have been overhauled and new ones added. - Users reported that some of the SBML files in the "test-data" directories were invalid, not realizing that this was actually intentional because the files are used for testing libSBML. In order to avoid confusion, the files containing invalid SBML have been renamed to append '-invalid' to their file names. - The files located in the validator/test-data directory, used for testing the SBML validation code, have been reorganised into smaller subdirectories. The new subdirectories group the files according to the type of validation being tested. * Configuration/build system changes ====================================================================== Version 5.1.0-b0 (2011-08-25) ====================================================================== This release includes a provisional implementation of support for an SBML Level 3 package for "layout" based on code from Ralph Gauges of the COPASI group. No other packages are included with this release; this applies to the "groups" package as well, which was in the beta release but is not in this release. However, the SVN repository on SourceForge has a branch for packages where ongoing development is proceeding, and as specifications and code for SBML Level 3 packages are settled, future libSBML releases will include stable versions of packages as they become available. Source code for beta versions of packages will also be made available from a separate download area, http://sf.net/projects/sbml/files/libsbml/5.1-packages-beta * New features - The inline formula code will now deal with a unary plus. - There is a new API for performing conversions between SBML Levels, Versions, and SBML Level 3 packages on an SBML Document. Existing functions such as setLevelAndVersion() have been reimplemented using the new API and so will continue to work as expected. The new API will facilitate the introduction of conversion routines that deal with Level 3 packages. - The MATLAB_SBML Structure produced using the MATLAB/Octave bindings now includes fields for the SBML Level and Version on all sub-structures. - There are new functions getElementBySId() and getElementByMetaId() that will traverse the entire document and return a pointer to an SBase object with the SId or MetaId supplied. - There are new functions on the SBO class to reflect the new top-level names introduced in the SBO ontology. * Bug fixes - There were a couple of places where the clone methods failed to create a proper copy. These have been fixed. Thanks to Nicolas Rodriguez for reporting this. - The introduction of the ability to place a units attribute from the SBML L3V1 core namespace into a <cn> MathML element meant that the code for reading and writing MathML needed to be fully aware of which SBML namespaces it was working with. This has been done. - Tracker issue #3296228 Importing a file with a large number of validation errors into MATLAB was causing memory issues within MATLAB. The handling of errors has been improved to avoid this situation. * Miscellaneous - Necessary updates to support the latest version of swig. * Configuration/build system changes - The introduction of Mac OS X 10.7 Lion produced issues with both XCode 4.0 and MATLAB. These have been addressed. ====================================================================== Version 5.0.0 (2011-04-14) ====================================================================== This is the first release of libSBML-5.0.0. There are three types of potential changes in this release compared to the beta 5.0.0 release: changes that relate to support for SBML Levels 1, 2 and Level 3 Core; changes that relate to support for L3 packages, and changes that were introduced in libSBML-4.3.1. These are listed separately below for convenience. This release includes a provisional implementation of support for an SBML Level 3 package for "layout" based on code from Ralph Gauges of the COPASI group. No other packages are included with this release; this applies to the "groups" package as well, which was in the beta release but is not in this release. However, the SVN repository on SourceForge has a branch for packages where ongoing development is proceeding, and as specifications and code for SBML Level 3 packages are settled, future libSBML releases will include stable versions of packages as they become available. Source code for beta versions of packages will also be made available from a separate download area, http://sf.net/projects/sbml/files/libsbml/5.0-packages-beta ------------------------- Known limitations ------------------------- At present, libSBML 5 will not attempt to convert a model between SBML Levels (e.g., from Level 3 to Level 2) if the model uses SBML Level 3 packages. This applies to SBML layout elements and annotations too. Our aim is to support conversion between L2 layout annotations and the L3 layout package, but this functionality will be introduced in a future release of libSBML. -------------------------------------- SBML Level 3 Package extension changes -------------------------------------- * New features - The extension mechanism for supporting SBML Level 3 packages now includes a full C API. - LibSBML now has greatly improved detection and error reporting of unimplemented/unknown SBML Level 3 packages. * Bug fixes - The "layout" extension now provides more seamless access to L2 layout annotations in L2 models. * Additional documentation - There is now more detailed and integrated documentation describing the use of CMake as an alternative to GNU make for building and installing libSBML. ------------------------------- General libsbml-core changes ------------------------------- * New features - There are now functions will set the Qualifier on a CVTerm from a string; in addition to the existing functions that use values from the enumeration of QualifierTypes. - SBML L2 contains an number of attributes that have default values. LibSBML does not write these values out. This behaviour has changed slightly for libSBML-5. If a user explicitly sets the value of an attribute to be the default value; then it will be written out. For example setting the spatialDimensions of an L2 <compartment> to be '3' will result in a document where this is explicitly written. - In SBML L3, it is possible to have a compartment with no spatialDimensions attribute declared. LibSBML-4 would not convert such a model to L2, since an L2 compartment has spatialDimensions '3' by default. This behaviour has been altered for libSBML-5 and if the user opts for nonstrict units when applying the conversion function, a compartment with no spatialDimensions declared will be converted. - There are additional functions XMLNamespaces::getNumNamespaces and XMLAttributes::getNumAttributes. These are aliases for the existing getLength functions but are more in keeping with the rest of the API. * Bug fixes - The conversion functions for converting an L2 model to L3 were failing to set the stoichiometry value. This has been fixed. - The internalConsistencyCheck was failing to report when required attributes or elements were missing from an object. This has been corrected. - The XMLConstructorException was not exposed. It is now. * Configuration/build system changes - The header files libsbml-config-win and libsbml-config-unix have been replaced with a single libsbml-config-common file. - The organization of the source directories has been radically changed, moving the previous directories src/annotation, src/math, etc., to become subdirectories of src/sbml. This allows us to entirely avoid a step that was previously to create a copy of all the header files into <libsbml>/include. That copy operation lead to a lot of wasted time when debugging code and accidentally making changes to the wrong file. - The 'win' directory that previously containing MSVC project files has been removed. The addition of packages made maintaining this directory problematic. The CMake build system provides an easy alternative for generating any project files required. ------------------------------- Libsbml-core changes from 4.3.x ------------------------------- Also available in Version 4.3.1 (Released 2011-03-29) * New features - There is now API documentation for the MATLAB and Octave bindings. * Bug fixes - Certain versions of the libxml2 parser fail to catch a prefix being assigned to an empty namespace. Additional code has been included to catch this error if the version of libxml2 has not reported it. - The improved build of the MATLAB interface proved unsuccessful in cases where the user had a startup.m file that changed directory. This has been corrected. - The SyntaxChecker::hasExpectedXHTMLSyntax(xhtml) function had not applied the relaxation on the XHTML restrictions for SBML Level 3. This has been sorted out. - The SyntaxChecker::isValidSBMLSId(string) function was incorrectly reporting that an empty string was a valid id. This has been corrected. * Miscellaneous changes - Choosing --enable-universal-binary on MacOS 10.5 now includes all three of the following architectures: i386, x86_64, ppc. It previously only selected i386 and ppc. Also available in Version 4.3.0 (Released 2011-03-04) * New features - There was some disagreement about what libSBML when asked to write out a required attribute in Level 3 where the value of the attribute had not in fact been set. Following discussion within the libSBML team and subsequently the libsbml-development mailing list it was decided that the appropriate behaviour was to ignore the attribute when writing out the model and thus not inadvertently give the impression it has a value. - Conversion from Level 3 to Level 2 involving variable stoichiometry has now been implemented and this feature of L3 can now be converted to L2. - There is a getSupportedNamespaces function on the SBMLNamepaces class which returns a List of the SBMLNamespaces supported by this version of libSBML. - Tracker issue #2082682 The unit checking of math involving the root function has been fully addressed. Previously unit checking was only applied to the expression root(n, x) if n was an integer. It can now handle any value of n including an expression. - Checking of the units of measurement in math expressions has been further improved to provide checking to a deeper level with the overall math of the model. Thus, the units of the expression a^b can now be validated even if the value of b is assigned b = c and the model states elsewhere that c = 2. - SBML Level 3 has no default attribute values and thus a number of new isSetXYZ functions were introduced in libSBML-4.1.0. Users pointed out it was inconsistent that these functions returned 'false' for a Level 2 model in which the attribute concerned *did* have a default value. Thus, any newly introduced isSetXYZ function that deals with an attribute that had a default value in Level 2 will now return 'true' regardless of whether the user has explicitly set the function or not. - The MATLAB and Octave bindings now include the function OutputSBML() for writing the structure used in these environments back to SBML. This function has previously shipped as part of SBMLToolbox. - There is an additional constructor for an SBMLDocument object that takes an instance of SBMLNamespaces as its argument. This is similar to the constructors for all SBML objects. - There is now a custom manifest file included in the Java JAR file. It contains the version number of the libSBML release. An example program demonstrating how to access the information is included as the file examples/java/printLibSBMLVersion.java. - An API manual for the C# language bindings is now available. It is not as complete as the C++ and Java versions, but it is quite close. * Bug fixes - The InternalConsistency validator was failing to report the absence of required attributes or elements within an in-memory model. This has been sorted out with a large number of tests added. - Tracker issue #2960646 When writing out an SBML model containing the root function Octave was failing to convert the formula into the appropriate MathML. This has been fixed. - The code that checks for allowed functions in a Level 1 document was reporting an error if it encountered one of the predefined functions. This has been corrected. - Checking for NULL references has been greatly improved throughout. - The appendNotes function was not correctly checking for the xhtml namespaces declared at the top level. This has been fixed. - In some cases the facility to create new 'Bags' within CVTerms was not performing as expected. This has been sorted out. - Validation previously failed to report an error if a lambda function contained only <bvar> arguments and no actual function body. This has been fixed. - LibSBML checks that each element within a model being read has the correct default namespace. However, if the namespace had been 'declared' via a prefix this check was not being performed. This has been corrected. - The code that checked that the top-level elements of an annotation had unique namespaces was incorrectly comparing prefixes rather than actual XML namespaces. This has been fixed. Thanks to Waclaw Kusnierczyk for reporting this and supplying the fix. - The XML namespace for a <math> element may be declared on the <sbml> element. In this case, the XML namespace declaration must use a prefix. Code that checked that the MathML elements had a declared namespace failed to check whether a prefix was correctly used. This is now fixed. Thanks to the JSBML developers for spotting this. - The code that allows users to use LocalParameter and Parameter interchangeably had a small bug where it failed to spot a duplicate id for a Parameter but not a LocalParameter. This has been fixed. - If a <kineticLaw> element is present, it must contain a <math> element. Prior to SBML Level 3 Version 1 Core, this has never been explicitly stated as a validation rule but should have been reported as a schema error. In some case this was not happening. This is now fixed. - The printUnits.java example in examples/java incorrectly used getId() on SBML objects that aren't defined to have id's in SBML. Talk about setting a bad example! Fixed. * Configuration/build system changes - MATLAB 2010b introduced some inconsistencies in the build system on certain platforms. This has been fixed. In addition, the 'configure' script for Linux and MacOS no longer attempts to divine various properties of the MATLAB installation and run mex itself, and instead, invokes MATLAB to compile TranslateSBML and OutputSBML. This should lead to fewer problems building the bindings for MATLAB. - Beginning with this release, LibSBML requires SWIG version 2.0.0 or higher. This is to avoid a problem where the C# bindings will not work with .NET 4 with SWIG versions prior to 2.0.0. ====================================================================== Version 5.0.0-b1 (2010-12-31) ====================================================================== This is the first beta release of libSBML-5.0.0. There are two types of potential changes from the alpha release: those that relate to support for SBML L1, L2 and L3 core, and those that relate to support for L3 packages. These are listed separately for convenience. ------------------------- Package extension changes ------------------------- * New features - Language bindings can now be generated to include and use the package extension mechanisms. Given the slightly different nature of the MATLAB/Octave bindings, support for packages has not yet been extended to these languages. - Unit tests have been added for the code that implements the package extension mechanisms within libSBML core. - The appendAndOwn() function (used to add items to ListOf elements) has been updated to check that the item being added is appropriate for the ListOf to which it is being added. This makes use of the virtual function SBase::isValidTypeForList(). Package developers need to be aware that in cases where a ListOf element can contain items of different types, they will need to provide implementations for this function. ListOfRules provides an example; it can contain any of AlgebraicRule, AssignmentRule or RateRule. * API changes - Originally, information relating to packages, e.g. PackageName, PackageVersion, etc., was stored in static variables. This proved problematic with dynamic libraries on Windows, and therefore these variables have been replaced with static methods on the Extension classes. Example: getPackageName(). - The setEnable() and isEnable() functions have been renamed to setEnabled() and isEnabled(). - The getExtension() function now returns a clone of the required extension. This avoids a situation whereby a user could inadvertently delete an extension object. - The Check unit testing framework has been adapted to enable the tests to be run in a native Windows environment. This has lead to some slight changes in the signature of some methods in the annotation classes. C++ methods that previously return std::string now return a const std::string&. * Bug fixes - It is no longer possible to register the same extension on multiple occasions. * Configuration/build system changes - We anticipate moving from a GNU Make build system to a CMake system because this facilitates the inclusion of L3 packages. This libSBML release includes all the necessary files to use the CMake system in addition to the existing makefiles. The latter have been updated where necessary. Support for makefiles will be phased out in the near future as we move toward having package code developed by others outside of the libSBML Team. Documentation on using CMake has been included in the docs directory. * Additional documentation - README-Building_libsbml-5_with_CMake.pdf - README-Package_Integration.pdf Details how to create CMake files for package code that will enable one step integration with libsbml-5 source code or an existing libsbml-5 installation. ------------------------------- General libsbml-core changes ------------------------------- * New features - Checking of the units of measurement in math expressions has been further improved to provide checking to a deeper level with the overall math of the model. Thus, the units of the expression a^b can now be validated even if the value of b is assigned b = c and the model states elsewhere that c = 2. - SBML Level 3 has no default attribute values and thus a number of new isSetXYZ functions were introduced in libSBML-4.1.0. Users pointed out it was inconsistent that these functions returned 'false' for a Level 2 model in which the attribute concerned *did* have a default value. Thus, any newly introduced isSetXYZ function that deals with an attribute that had a default value in Level 2 will now return 'true' regardless of whever the user has explictily set the function or not. - The MATLAB and Octave bindings now include the function OutputSBML() for writing the structure used in these environments back to SBML. This function has previously shipped as part of SBMLToolbox. * Bug fixes - Checking for NULL references has been greatly improved throughtout. - Validation previously failed to report an error if a lambda function contained only <bvar> arguments and no actual function body. This has been fixed. - The documentation for a number of methods had fallen slightly out of date with respect to the possible operation return codes they could return. We've updated those documentation strings now. The methods affected are in the classes Compartment, KineticLaw, Model, Reaction, Rule, SBase, Species, Unit, UnitDefinition, and XMLToken. - A number of validation checks had an incorrect ErrorCategory labels; thus, though these were reported by the correct part of the libSBML validator, querying the category would produce an inconsistent value. These have been updated. - There were some character encoding issues in a number of error messages. These have been corrected. - The code that checked that the top-level elements of an annotation had unique namespaces was incorrectly comparing namespace prefixes, not the actual namespaces. This has been fixed. Thanks to Waclaw Kusnierczyk for reporting this and supplying the fix. - The XML namespace for a <math> element may be declared on the <sbml> element. In this case, the namespace must use a prefix. Code that checked that the MathML elements had a declared namespace failed to check whether any required prefix was correctly used. Thanks to the JSBML developers for spotting this. - The code that allows users to use LocalParameter and Parameter interchangeably had a small bug where it failed to spot a duplicate id for a Parameter but not a LocalParameter. This has been fixed. - If a <kineticLaw> element is present, it must contain a <math> element. Prior to SBML Level 3 Version 1 Core, this has never been explicitly stated as a validation rule but should have been reported as a schema error. In some case this was not happening. This is now fixed. - The 'configure' script help text incorrectly claimed that Xerces was the default XML parser; it now correctly states libxml2 is. * Configuration/build system changes - MATLAB 2010b introduced some inconsistencies in the build system on certain platforms. This has been fixed. - The organization of the source directories has been radically changed, moving the previous directories src/annotation, src/math, etc., to become subdirectories of src/sbml. This allows us to entirely avoid a step that was previously to create a copy of all the header files into <libsbml>/include. That copy operation lead to a lot of wasted time when debugging code and accidentally making changes to the wrong file. ====================================================================== Version 5.0.0-a1 (released 2010-10-05) ====================================================================== This is the next alpha release of libSBML-5. This includes full support for SBML Level 3 Core; as found in libSBML-4.2.0. It also includes mechanisms for support of a 'layout' and a 'groups' extension. This support extends to all language bindings with the exception of matlab/octave. Note these are dummy packages based on proposals for the layout and groups packages. They do not represent fully approved L3 packages. There have been no API changes from the pre-alpha release. It is anticipated that the next release (beta) will rearrange the directory structure for contributed package code and provide a new build system to facilitate the inclusion/exclusion of packages. * Changes to dependencies on 3rd-party libraries: - The language bindings now require SWIG 2.0.0 or later. * Known issues: - The C API is not yet implemented. ====================================================================== Version 5.0.0-a0 (released 2010-01-18) ====================================================================== This is a pre-alpha release of libSBML-5 which provides support for package extensions in SBML Level 3. Since libSBML-5 is currently in development stage the API may be changed in the future. Also, some features for package extensions (e.g. validation, language bindings and etc.) are not supported yet (please see "Known Issues" below). Currently, the code is based on the SVN trunk of Revision:10522 (i.e. based on 4.1.0-beta), and thus validating/converting SBML Level 3 core has not been supported yet. Please see the following bundled README files for details: (1) docs/00README-HowToUsePackageExtension.txt (For package developers) (2) docs/00README-ExtensionSupportClasses.txt (3) docs/00README-HowToImplementPackageExtension.txt (4) docs/00README-ChangesInSBase.txt * New Features: - Added new classes for supporting package extensions in 'src/extension'. - Added a new directory 'src/packages' in which additional package extensions will be located. - Added new functions for supporting package extensions in existing classes. Most of the new functions are implemented in SBase and SBMLNamespaces classes. - Added a package of layout extension as an example package in 'src/packages/layout'. The package is based on existing implementation of layout extension (implemented by Ralph Gauges) bundled with libSBML-4. "--enable-layout" option is required when running configure script to build the layout package. Example codes using the layout package are provided in "examples/layout/". Currently, the package is built as additional shared library files (e.g. libsbml-layout.a and libsbml-layout.so on Linux) that depend on the shared library of core libSBML (e.g. libsbml.a and libsbml.so on Linux) when built with make command. The package is built into existing libsbml.dll when built with MSVC on Windows. This build configuration may be changed in the future release. - Added a package of groups extension (based on the proposal on 2009-10) as another example package in 'src/packages/groups'. "--enable-groups" option is required when running configure script to build the groups package. Example codes using the groups package are provided in "examples/groups". Currently, the package is also built as additional shared library files (e.g. libsbml-groups.a and libsbml-groups.so on Linux) when built with make command whereas the package is built into libsbml.dll when built with MSVC on Windows. This build configuration may also be changed in the future release. * Changes: - Moved source files of layout extension from 'src/sbml/layout' to 'src/packages/layout'. - SBMLTypeCode_t (enum type) now contains only typecodes of SBase objects defined in the SBML core. Each package extension should define a similar enum type for typecodes of SBase objects defined in each package extension (e.g. SBMLLayoutTypeCode_t for "layout" extension (defined in LayoutExtension.h) , and SBMLGroupTypeCode_t for "groups" extension (defined in GroupExtension.h).) - Changed the type of return value of SBase::getTypeCode() and ListOf::getItemTypeCode() functions (SBMLTypeCode_t -> int). - Changed the usage of SBase::getTypeCode() and ListOf::getItemTypeCode() functions. Currently, the value of each typecode can be duplicated between those of different packages (this duplication problem doesn't happen with existing code which uses only SBase objects of the SBML core). To distinguish the typecodes of different packages, not only the return value of getTypeCode() but also that of getPackageName() should be checked as follows: void example (const SBase *sb) { const std::string pkgName = sb->getPackageName(); if (pkgName == "core") { switch (sb->getTypeCode()) { case SBML_MODEL: .... break; case SBML_REACTION: .... } } else if (pkgName == "layout") { switch (sb->getTypeCode()) { case SBML_LAYOUT_LAYOUT: .... break; case SBML_LAYOUT_REACTIONGLYPH: .... } } ... } - API changes: (- : libSBML-4 API, + : libSBML-5 API) - virtual SBMLTypeCode_t SBase::getTypeCode() const + virtual int SBase::getTypeCode() const - virtual SBMLTypeCode_t ListOf::getItemTypeCode() const + virtual int ListOf::getItemTypeCode() const - const char* SBMLTypeCode_toString (SBMLTypeCode_t typecode) + const char* SBMLTypeCode_toString (int typecode, const char* pkgName) - SBase* SBase::getAncestorOfType(SBMLTypeCode_t type) + SBase* SBase::getAncestorOfType(int type, const std::string pkgName="core") - virtual void SBase::readAttributes (const XMLAttributes& attributes) + virtual void SBase::readAttributes (const XMLAttributes& attributes, const ExpectedAttributes& expattr) * Known Issues: - Validating functions need to be extended for package extensions. - Converting functions need to be extended for package extensions. - Language bindings (SWIG configuration files and underlying support code such as local.cpp) need to be modified for supporting package extensions. Currently, language bindings of "layout" extension (Java, Python, Ruby, and C#) should work. - SBML Core and additional package extensions should be located in their own namespaces to avoid potential name conflictions. - C wrapper API needs to be added/updated. * Initial release, March 12, 2003. # The following is for [X]Emacs users. Please leave in place. # Local Variables: # fill-column: 70 # End: