LibSBML news
libSBML NEWS -- History of user-visible changes
====================================================================
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 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 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 element.
* Bug fixes
- Code was failing to recognize the math elements and
as returning numeric values. This has been
corrected.
- A element with no child