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NEWS.txt
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libSBML NEWS -- History of user-visible changes
====================================================================
5.19.1 (Current development branch)
====================================================================
STABLE RELEASE
* New features
- 'comp' package-specific updates:
- 'distrib' package-specific updates:
- 'fbc' package-specific updates:
- 'groups' package-specific updates:
- 'layout' package-specific updates:
- 'multi' package-specific updates:
- 'qual' package-specific updates:
- 'render' package-specific updates:
* Bug fixes
- A large number of code 'smells' have been cleaned up. Thanks to
Jamie Quinn for undertaking this laborious task.
- The python examples have been updated for Python 3.8 changes.
Thanks to Akira Funahashi for committing these fixes.
- The python code used for creating documentation has been
updated for Python 3.10 changes. Thanks to
Zbigniew Jędrzejewski-Szmek for submitting the changes.
- 'comp' package-specific bug fixes:
- 'distrib' package-specific bug fixes:
- 'fbc' package-specific bug fixes:
- 'groups' package-specific bug fixes:
- 'layout' package-specific bug fixes:
- 'multi' package-specific bug fixes:
- 'qual' package-specific bug fixes:
- 'render' package-specific bug fixes:
* Configuration/build system changes
- Extensive continuous integration testing has been added to
the GitHub repository.
* Miscellaneous
EXPERIMENTAL PACKAGES
* New features
- 'arrays' package-specific updates:
- 'dyn' package-specific updates:
- 'req' package-specific updates:
- 'spatial' package-specific updates:
* Bug fixes
- 'arrays' package-specific bug fixes:
- 'dyn' package-specific bug fixes:
- 'req' package-specific bug fixes:
- 'spatial' package-specific bug fixes:
====================================================================
5.19.0 (2020-11-27)
====================================================================
********************************************************************
The libSBML source code has moved to GitHub.
(https://github.com/sbmlteam/libsbml).
The stable branch reflects the latest released code. The development
branch is the main branch and we encourage users to create and
submit pull requests against this branch. We are no longer
maintaining a separate repository for experimental code for as yet
unfinished packages.
Please use the GitHub issue tracker to file any reports or submit a
fix and do a Pull Request.
We will gradually move away from SourceForge, but for this release
code will be available from both SourceForge and GitHub.
* Addition of support for the SBML Distributions package
- Now that the first official version of the specification for the
SBML Level 3 Distributions package is available, the libSBML API for
'distrib' is now included in the stable release of libSBML. This
means that all prebuilt binaries for the stable release will
include the 'distrib' package code. The src archive containing
libSBML core code will continue to be available, with 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
- Functions get/set/isSetMath have been added to the SBase class.
These do not allow interacting with a non-existant <math> element
but may facilitate using more generic functions.
* Bug fixes
- There was a memory leak introduced in the SWIG wrapper. Thanks to
Fabian Fröhlich for spotting and fixing this.
- The SBMLNamespaces class was being leaked in a number of places,
these have now been plugged.
- The MathML to infix parser was also leaking memory. Thanks to
Liam Keegan for spotting and fixing these.
- The validation code detecting assignment cycles was incorrectly
including local parameters within its search. These have now
been removed from the relevant code.
- Conversion code was failing to detect when a local parameter used
the 'id' of a speciesReference which is allowed in SBML Level 3.
These can be converted to SBML Level 2 and the code has now been
corrected so this conversion will take place.
- The L3 infix parser has been improved to recognize the use of a
name without parentheses as a misused function name or a csymbol,
if appropriate.
- There was an anomaly when using the addCVTerm() and
appendAnnotation() functions which meant that if used in a certain
order information could be lost. This has been corrected. Thanks
to Colin Halupczok for the detailed report.
- Converting a <localParameter> to a global <parameter> object was
failing if the metaid attribute was set. This has been changed to
produce the correct behavior.
* Configuration/build system changes
- Import of the python library has been sorted in line with recent Linux
changes to the location of the shared file.
- Code has been fixed to be MingGW compliant.
- The build configuration was updated to work with the latest version of R.
* Miscellaneous
- A number of memory leaks and possible access violations have been solved.
STABLE PACKAGES
- 'distrib' package-specific updates:
- A new converter, AnnotationToDistribConverter, has been added
to allow conversion from the existing annotation format used
with <functionDefinitions> to the new 'distrib' format. This
complements the existing DistribToAnnotationConverter that converts
'distrib' to annotations.
* Bug fixes
- 'comp' package-specific bug fixes:
- Comp flattening dropped conversion factors for particular
instances of assignment rules. This has been corrected.
Thanks to Matthias König for reporting this.
- 'distrib' package-specific bug fixes:
- There was unfortunately an infinite loop in the code using
the <uncertainty> element. This has been removed.
- 'render' package-specific bug fixes:
- Some render classes were not handled correctly by language
bindings. This has been fixed.
EXPERIMENTAL PACKAGES
* New features
- 'spatial' package-specific updates:
- Compression in the 'spatial' package is now based on strings.
The code has been changed to reflect this.
- Support for int and uint as DataKinds has been added to the
spatial code in line with changes in the specification.
- A range of validation tests have been added to the spatial
code. As this is an experimental passage package still in
development, we cannot guarantee that all validation has been
implemented.
* Bug fixes
- 'spatial' package-specific bug fixes:
- There were some memory leaks in the spatial code.
Thanks to Liam Keegan for spotting these and congratulations
for being our first GitHub user to address problems using a
Pull Request.
====================================================================
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