Keating, Sarah M
Bergmann, Frank T
Olivier, Brett G
Smith, Lucian P
Hucka, Michael
2019-04-18
<p>====================================================================</p>
<p>5.18.0 (2019-04-18)</p>
<p>====================================================================</p>
<p> </p>
<p>STABLE RELEASE</p>
<p> </p>
<p>* New features</p>
<p> </p>
<p> - LibSBML now defines a DefinitionURLRegistry to allow a user to log</p>
<p> their own values of the 'definitionURL' attribute on a math <csymbol></p>
<p> element. Once logged these definitionURL values will not trigger the</p>
<p> unknown csymbol error when reading a model that uses them. </p>
<p> </p>
<p> - LibSBML now defines a CallbackRegistry which allows a user to register</p>
<p> a callback to interrupt a long running read operation. Examples for C++</p>
<p> and Python are included. In future it would be anticipated that would</p>
<p> have callbacks to interrupt long running validation or conversion </p>
<p> processes.</p>
<p> </p>
<p>* Bug fixes</p>
<p> </p>
<p> - Validation was incorrectly stating that the id of a <localParameter></p>
<p> that mirrorred the id of a <species> should be listed as a </p>
<p> <modifierSpeciesReference> in the enclosing <reaction>. It no longer</p>
<p> issue an incorrect error.</p>
<p> </p>
<p> - The string to MathML parser was failing to identify known constants</p>
<p> as arguments to a lambda function. lambda(pi, pi*2) should treat 'pi'</p>
<p> as an unknown argument not the constant pi. This has been fixed.</p>
<p> </p>
<p> - The MathML parser adds logbase and degree to log and root elements </p>
<p> respectively. These are dimensionless integers and but unit</p>
<p> validation was failing. This has been corrected. Note this means</p>
<p> that for L3 models libSBML will write out the dimensionless units </p>
<p> on the relevant <cn> element explicitly. This may cause an </p>
<p> apparent difference in models if reading and then writing. </p>
<p> </p>
<p> - In MathML a <bvar> element within a <lambda> can only contain a </p>
<p> <ci> child element. Validation was failing to spot when this was </p>
<p> not the case. This has been corrected.</p>
<p> </p>
<p> - MathML within a <semantics> element was not being properly validated.</p>
<p> This has been improved.</p>
<p> </p>
<p> - 'layout' package-specific bug fixes:</p>
<p> </p>
<p> - Code was failing to roundtrip glyphs that contained both a <curve></p>
<p> and a <boundingBox> element. This has been fixed.</p>
<p> </p>
<p> </p>
<p>* Configuration/build system changes</p>
<p> </p>
<p> - The cmake files that enable using the check library on </p>
<p> a Linux OS have been updated to make this easier.</p>
<p> </p>
<p> - Python 3.7 is now supported.</p>
<p> </p>
<p> </p>
<p>* Miscellaneous</p>
<p> </p>
<p> - Several obscure memory leaks have been plugged.</p>
<p> </p>
<p> </p>
<p>EXPERIMENTAL RELEASE</p>
<p> </p>
<p>* New features</p>
<p> </p>
<p> - 'distrib' package-specific updates:</p>
<p> </p>
<p> - The code has been updated to reflect the specification</p>
<p> agreed during HARMONY 2019 version 0.24.</p>
<p> </p>
<p> - 'spatial' package-specific updates:</p>
<p> </p>
<p> - The code has been updated to reflect the specification </p>
<p> version 0.93.</p>
<p> </p>
<p> - Attributes 'id' and 'name' have been added to the SpatialPoints</p>
<p> class in anticipation of these being added to the specification.</p>
<p> </p>
<p> - Plugin code has changed so that child element class members are</p>
<p> initialised to NULL. This saves memory but may cause existing</p>
<p> code to hit an issue when using a getAbc function; which may now</p>
<p> return a NULL object when previously it did not.</p>
https://doi.org/10.5281/zenodo.2645216
oai:zenodo.org:2645216
Zenodo
https://doi.org/10.5281/zenodo.2645215
info:eu-repo/semantics/openAccess
GNU Lesser General Public License v2.1 only
https://www.gnu.org/licenses/old-licenses/lgpl-2.1-standalone.html
SBML
Systems Biology
libSBML-5.18.0
info:eu-repo/semantics/other