Release of libSBML-5.18.0

[Keating, Sarah M.]

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libSBML-5.18.0
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We are pleased to announce the release of libSBML-5.18.0,
which is available for download from

https://sourceforge.net/projects/sbml/files/libsbml/5.18.0/

and as python-libsbml-5.18.0 and python-libsbml-5.18.0-experimental

====================================================================
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 mirrored 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
initialized 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.

=====================================================

Please report any problems you encounter using libSBML either to the
mailing list libsbm...@googlegroups.com or using the issue tracker for
libSBML at

https://sourceforge.net/tracker/?group_id=71971&atid=942737

Thanks,

the LibSBMLTeam

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