v5.1 [Jun 22, 2014]
New features:
- The static functions implemented by the SBMLTransforms class that are used by the converters that in-line FunctionDefinitions or expand InitialAssignments has been made available to all language bindings. These are: replaceFD, expandInitialAssignments and evaluateASTNode. Examples of using these functions are also provided.
- The L3ParserSettings object can now be configured to compare built-in functions and constants caselessly (as it did in the past; the default), or to only accept the lower-case forms.
- The C API has been improved and appropriate argument checking has been implemented.
Bug fixes:
- There was an issue with detecting NULL elements with the R bindings. This turns out to be a consequence of SWIG. A bug report has been filed with the SWIG development team, in the meantime, a revised SWIG file is included with the libSBML source and is used by the libSBML build when creating the R bindings.
- The unit consistency checking code was ignoring numerical factors when checking the units of a KineticLaw matched the model wide units of extent per time (substance per time in SBML L1/L2). This has been changed. Thanks to Daniel Palm for the report that exposed this.
- Unit checking code determines whether a math expression contains parameters or numbers with undefined units. However, depending on where these occurred within the expression, libSBML was not always correctly establishing this. This has been fixed.
- The unit consistency checking code was losing numerical factors that were left after cancelling out units. This could affect the overall definition of the remaining unit and thus impact code that looked for exact identity between units. This has been fixed.
- There was a bug in writing out MathML that manifested itself using the in-lining functionDefinition converter for a narrow set of functions. This has been fixed.
- Validation has been improved so as to no longer warn a user that a variable has no initial value if there exists an initialAssignment or assignmentRule that would set the value.
- The SBMLError reporting an over-determined model was being logged with the incorrect category of error. This has been changed.
- LibSBML incorrectly reported the units of 'pi' as radians. This has been corrected to report 'dimensionless'.
- The L3 parser did not recognize 'arcsinh' or 'asinh' as valid built-in functions. This has been fixed.
- When libSBML detects an SBML L3 package that it does not support validation of 'comp' references can report that a reference may be to an identifier within the unknown package. However, the code was failing to check whether the reference could be located within the xml relating to supported packages before issuing this warning. This has been fixed.
Configuration/build system changes:
- The CMake build system will now produce an uninstall target.
Miscellaneous:
- Continue our review of code a number of potential problems were highlighted during static analysis. These have been fixed.
- Code review has also eliminated a number of compiler warnings raised by various different compilers on various different systems.
- Various memory leaks have been plugged.
- The short error messages for the following error codes in SBMLErrorTable.h had trailing periods, which was inconsistent with most of the other messages; the periods have been removed: 20109, 99109, 99401, 99402, 99403, 99404, 99405, 99406.
- In the API documentation, the instructions for setting PYTHONPATH was not correct for the installation produced by using CMake instead of GNU configure. Further, the PYTHONPATH instructions for Ubuntu were actually for other Linux/Unix variants and vice versa. This has been fixed by making the instructions use a single, more general approach that should work everywhere.
- The API documentation lacked information about using PyPI for Python, and about how to install the R interface. Fixed.
- Various issues in the Python documentation have been fixed. For example, in the table of member methods for each class in the API documentation for Python, the brief descriptions were missing -- all the short member descriptions had the same text, "Python method signature(s)". This was caused by a bug in our custom libSBML documentation generation tools.
- The error code table in the documentation for SBMLError has been updated.
