Biosimulators-libsbmlsim

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

* New features

- New memory management system was included to avoid memory leak.

* Bug fixes

- Several bug fixes on memory leak. Now, LibSBMLSim has small memory leak
on limited number of models (which include reversible fast reactions).

- Add support on CMake 3.x so that it can generate Java8 bindings.

- Fixed crash on python bindings which causes double free on gc.

libsbmlsim confirmed to pass SBML test cases from 00001 to 01185.

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

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

* New features

- Add wrapper script (wrapper.sh) for SBML Test Runner.

- Add -o option so that user can specify an output file. This will
enable SBML Test Runner to run wrapper.sh in parallel.

* Bug fixes

- Allocate including_species dynamically, so that the library can
handle more than 256 species.

- Fixed warnings (CMP0037 CMP0042) from cmake.

- Fixed alter_tree_structure to call ASTNode_setName() in the
proper order.

- Removed unused function (mySpecies_setLocatingCompartment()) from
mySpecies.

- Add -lm to linker option.

- Avoid a C preprocessor warning on Linux.

libsbmlsim confirmed to pass SBML test cases from 00001 to 01185.

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

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

* New features

- CMake uses C_INCLUDE_PATH, DYLD_LIBRARY_PATH and
LD_LIBRARY_PATH to find libSBML.

* Bug fixes

- Fixed to support fast and reversible reaction
(00986, 00987, 00988).

- Fixed crash when ASTNode only have 1 or 0 child under '+', '*',
'AND', 'OR', 'XOR' ASTNodes. (01112, 01113, 01114)

- Fixed crash when piecewise have odd number of children (which
means when piecewise doesn't have "otherwise" node)
(01115, 01116).

Now, libsbmlsim passed all the tests from 00001 to 01185.

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

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

* New features

- New integrators (5th order Runge-Kutta Fehlberg, 5th order Cash-Karp)
are included in this release. Both new integrators support variable
step size integration.
= 5th order Runge-Kutta Fehlberg : MTHD_RUNGE_KUTTA_FEHLBERG_5
= 5th order Cash-Karp : MTHD_NAME_CASH_KARP

- The C bindings functions are include in this release. Please see
examples/csharp/Test.cs for the sample code.

- Both 32bit(x86) and 64bit(x86_64) build for Windows are available.

- Binary Installer is available for Windows, MacOSX and Linux.

* Bug fixes

- Memory leaks in free_mySBML_objects() have been fixed.

* API changes

- myResult* simulateSBMLModel() now requires 3 additional parameters for
variable step integration.
myResult* simulateSBMLModel(Model_t *m, double sim_time, double dt,
int print_interval, int print_amount,
int method, int use_lazy_method,
double atol, double rtol, double facmax);
= double atol; Absolute error tolernace
= double rtol; Relative error tolerance
= double facmax; Maximum acceptable increasing factor
If you don't know the exact value for above 3 values, please just assign
"0.0" for all 3 values, then libsbmlsim will use the default values for
the integration.

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

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

* Initial release, 04 April 2012.