Re: [cellml-discussion] Announcing CellML API 1.12
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 ___ cellml-discussion mailing list cellml-discussion@cellml.org http://lists.cellml.org/mailman/listinfo/cellml-discussion ___ cellml-discussion mailing list cellml-discussion@cellml.org http://lists.cellml.org/mailman/listinfo/cellml-discussion
[cellml-discussion] Announcing CellML API 1.12 release candidate 2
Hi all, The second release candidate for the CellML API 1.12 (1.12-rc2) has been released. This release candidate will become the CellML API 1.12 if no-one reports any problems with it by next Tuesday (New Zealand time). Please try out the the API and report any problems on the Physiome Tracker at https://tracker.physiomeproject.org/, by e-mailing cellml-tools-develop...@cellml.org (you will need to subscribe to the list first using this page: http://lists.cellml.org/mailman/listinfo/cellml-tools-developers), or by e-mailing ak.mil...@auckland.ac.nz. The files making up this release candidate are available here: * http://cellml-api.sourceforge.net/download.html#1.12rc2 This release candidate has a number of significant improvements over the CellML API 1.12rc1: * Don't load DTDs when loading a document from text, as well as when loading from the network. * Increment the restart counter when trying to solve for initial conditions so we eventually fail after too many random re-starts. * Minor changes to the packaging scripts. Best wishes, Andrew ___ cellml-discussion mailing list cellml-discussion@cellml.org http://lists.cellml.org/mailman/listinfo/cellml-discussion
[cellml-discussion] Announcing CellML API 1.12 release candidate 1
Hi all, The first release candidate for the CellML API 1.12 (1.12-rc1) has been released. This release candidate will become the CellML API 1.12 if no-one reports any problems with it by next Wednesday (New Zealand time). Please try out the the API and report any problems on the Physiome Tracker at https://tracker.physiomeproject.org/, by e-mailing cellml-tools-develop...@cellml.org (you will need to subscribe to the list first using this page: http://lists.cellml.org/mailman/listinfo/cellml-tools-developers), or by e-mailing ak.mil...@auckland.ac.nz. The files making up this release candidate are available here: * http://cellml-api.sourceforge.net/download.html#1.12rc1 This release candidate has a number of significant improvements 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 ___ cellml-discussion mailing list cellml-discussion@cellml.org http://lists.cellml.org/mailman/listinfo/cellml-discussion
