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RELEASE_HISTORY.TXT
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######################################################################################
#- File: RELEASE_HISTORY.TXT
#-
#- This program comes with ABSOLUTELY NO WARRANTY.
#- This is free software, and you are welcome to redistribute it
#- under certain conditions. See file LICENSE.TXT for details.
#-
######################################################################################
Date Tag Preparer Notes
---- --- -------- -------
2013/09/25 RELEASE_0V53a ollivier Add support for Sundials/CVODE solver. Generate
associated C++ code and Octave wrapper.
New C++/CVODE solver combination.
Fix bug in factorization module.
Add support for ode_event_times when output
target is Octave.
2012/09/10 RELEASE_0V52 ollivier New config variables external_initial_values,
and external_parameters, both enabled by --extern.
More efficient dydt calculation through factoring
out common terms. Needs --fast_dydt switch to enable.
Fix numerical problem when extracting sub-intervals
out of TV vector based on event times.
2012/09/07 RELEASE_0V51 ollivier Added --extern switch, deprecated --noparams.
Added ability to detect which parameter expressions
are time dependent (dynamic) vs constant. Those that
are constant are calculated once in driver file. Only
dynamic parameters are re-calculated in dydt function
(Matlab/Octave only).
2012/09/05 RELEASE_0V50 ollivier Added partial support for Octave and SciPy.
Deprecated config variable matlab_odeset_options,
replaced by matlab_solver_options.
Improved plot commands issued in driver files.
In driver scripts, pass rate constants to dydt function
using a global variable instead of through function arg.
Added --run option.
2012/05/28 RELEASE_0V41 ollivier Better section headers in generated easystoch simulation.
Easystoch input file default name changed to xyz.seqn
(from xyz_simulation_input).
No functional changes.
2011/08/25 RELEASE_0V40 ollivier Command-line switch "--events" is deprecated, use "--ode_event_times"
instead. Likewise for CONFIG section variable "--event_times", use
"ode_event_times" instead.
New CONFIG variable "easystoch_sample_times" implements and extends
functionality formerly associated with "--events" switch for EasyStoch
export. New 'table' and 'vector' keywords, fixed some numerical issues
with square().
Much OOP refactoring of code. New Model and *List classes.
Fixed problem where some parameters are not exported to SBML.
Fixed problem with ode_event steady-state stopping condition
and added SS_AbsTol parameter.
2011/04/20 RELEASE_V30 ollivier Fixed help command and other patches for *nix shell independence.
Upgraded SBML.pm module to work with version 4 of libSBML.
Matlab script ode_event.m interface changes: new param SS_RelTol,
renamed param SS_timescale, param re-ordering, and re-worked
steady-state feature implementation and tests.
Eliminated wrapper script that calls solver function -- solver is
now called directly from driver script.
ODE function is now callable by other Matlab scripts.
2010/07/28 RELEASE_V26 ollivier Switch from CVS to Bazaar for version control.
Fixed major bug in easystoch output: rate expressions were not
being properly evaluated to numeric value, due to exponentiation
operator '^' not being translated to Perl's '**'. Also, substituted
values were not parenthesized.
Fix -P option so that probe expressions are still defined if not plotted.
2008/07/04 RELEASE_V25 ollivier Add support and testcases for steady-state events (Matlab only).
Fix minor bug whereby a time point was repeated 2x at an event point.
Fix minor bug when parsing CONFIG section.
2008/06/10 RELEASE_V24 ollivier Add support for --split option.
2008/05/?? RELEASE_V23 ollivier Moved *.pm files to modules directory.
Moved testcases to test directory.
Moved contents of various *.cmd files into Makefile.
Expressions no longer need to be quoted.
When a rate or variable is set to another variable (e.g. f1=f2),
the other variable's value is no longer substituted. Instead
the variable is treated like expression.
For EasyStoch output, expressions can now be a function of
other variables. E.g. f1=2*f3 is supported and will be evaluated.
For Mathematica output, replace exponentiation operator '**' with '^'.
When no value is given to a rate, plug in 0 and issue Warning
instead of an error and quitting.
? RELEASE_V22 ollivier Add support for PROBE section. Probes are output in Matlab files.
Implemented long-style (e.g. --matlab) options. Maintained short-style
abbreviations for backward compatibility. Simplified option processing.
Updated and improved help page.
Fix bug to allow whitespace in explicit variable expressions.
? RELEASE_V21 ollivier Check that we have Class::Std version 0.0.8 or better (otherwise Variable.pm reports
strange error).
? RELEASE_V20 ollivier Major upgrade from RELEASE_0V12. Object-oriented code.
Support for SBML, Maple, XPP, AUTO
system reduction was added. Numerous other improvements.
This version was used as basis for Bioinformatics journal paper.