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[cellml-discussion] Announcing CellML API 1.12


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  • From: ak.miller at auckland.ac.nz (Andrew Miller)
  • Subject: [cellml-discussion] Announcing CellML API 1.12
  • Date: Thu, 01 Nov 2012 23:08:27 +1300
On 01/11/12 23:05, Andrew Miller wrote:
> Hi all,
>
> The CellML API release candidate version 1.11rc2 has been released with

Sorry, that should of course be 1.12rc2.

> a minor change to correct uncertainty solvers as CellML API version 1.12.
>
> The files making up this release candidate are available here:
> * http://cellml-api.sourceforge.net/download.html#1.12
>
> This release candidate has a number of significant improvements over the
> CellML API 1.12:

and that should be 'over the CellML API 1.11'.

> * Extra attributes are provided to make accessing a variable's
> initial value more convenient.
> * IVs on algebraic variables is supported with initial_value rather
> than RDF.
> * Documentation on using the CellML API from Java has been improved.
> * KINSOL, rather than LEVMAR, is used as the non-linear system
> solver. This avoids the global state used by LEVMAR, allowing multiple
> simulations to be working concurrently to return results more efficiently.
> * Error reporting for models underconstrained due to missing initial
> values has been added.
> * It is now possible to use the DOM to determine the order of
> elements in the CellML model and map from the DOM element to the CellML
> element.
> * An ambiguity in the TeLICeMS serialiser around the nesting of the
> equals operator has been fixed.
> * You can now create a CellML model from an existing DOM representation.
> * The C++ interface for performing query interfaces has been improved.
> * The generated binaries are smaller due to several changes,
> including not generating unnecessary Java bridges.
> * pcmpy has been completely removed from the source tree now that
> better Python bindings are provided by cgrspy.
> * More comprehensive tests have been written for (and passed by) the
> units validation part of the Validation Against CellML Specification
> Service.
> * The precedence rules in the MATLAB CeLEDS XML file have been
> corrected.
> * The error handling in TeLICeMS has been improved.
> * A number of minor issues with the Doxygen generated documentation
> has been cleaned up so it is now easier to use.
> * A number of problems that made the PCM -> Java bindings used for
> callbacks like the IntegrationProgressObserver unusable have been fixed.
> * Threading issues in the Java bindings have been fixed, preventing
> crashes when multiple threads are used.
> * The CellML API no longer automatically retrieves DTDs over the
> network, giving API users complete control over how models are loaded.
> * More sample code on how to use the RDF container APIs has been
> written.
> * The CellML API libraries now use versioning to avoid accidentally
> using the wrong version of the API; this allows multiple versions of the
> API to co-exist in the paths on the same system.
> * It is now possible to use a native libxml2 and SUNDIALS instead of
> the one shipped with the API by selecting an option at CMake configure
> time.
> * The order RDF triples are returned in is now more predictable.
> * Parallel builds now work correctly.
> * An RDF triple object can retrieved by subject, predicate, and
> object, allowing it to be unasserted straightforwardly.
> * A bug in CeVAS that meant it didn't look at nested encapsulation
> relationship_refs has been fixed.
> * New API operations have been added for retrieving annotations that
> don't throw exceptions (which are inefficient) when there is no
> annotation found.
> * A bug in the Java -> PCM bridge enumeration support (important for
> public / private interface retrieval) has been corrected.
>
> Best wishes,
> Andrew
> _______________________________________________
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> cellml-discussion at cellml.org
> http://lists.cellml.org/mailman/listinfo/cellml-discussion



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