ecell-devel Mailing List for E-Cell System

Version 3.1.92 (hek-noname)  has been released.

3.1.9x series is a countdown toward 3.2.   
Basically all the external specifications of the core to be appear in 3.2 are 
collected, and we are concentrating on fine tunes and debugs.

Major feature enhancements of this release include support for 
simulations using Gillespie-Gibson algorithm.   
(set the classnames of Stepper=NRStepper and Process=NRProcess.)


-sha



Changes of version 3.1.92 (from version 3.1.6)

In addition to many bugfixes,

libecs))

- Logger::getData performance tuning (gabor)
 
- A completely new DM syntax:  which is actually plain C++ code. 
  Use ecell3-dmc command to compile DMs in form of .cpp files (sha, tkitayama)

-  dm load path can be specified by ECELL3_DM_PATH env var., and
   ecell.ecs.set/getDmSearchPath() methods (sha)

-  changed envvar name: ECSTMPDIR to VVECTORTMPDIR (sha)

-  changed default vvector dir: /var/tmp to /tmp (sha)

-  implemented relative SystemPaths:  '..' and '.' can appear in SystemPath (sha)

-  In Logger::getData(s,e,i), checks if i is positive  (sha)


Standard DM library))

- Initial creation under ecell/dm. (sha)

- Imported SSystemProcess for S-System simulation (tkitayama)

- Ported all the 'standard reactors' from ecell1 (tkitayama)

- Renamings: differential Steppers are now: 
  ODE23Stepper (was Fehlberg23), ODE45Stepper (was DormandPrince547M),
  FixedODE1Stepper (was FixedEuler1), FixedODE4 (was FixedRungeKutta4).  (kaizu)

- Full support for multi-stepper simulations in ODE23 and ODE45 Steppers:
  ODE Steppers use Hermite Interpolation (kaizu)

- Eliminated ODE45Stepper::ErrorEstimate (kaizu)


- New NRStepper and NRProcess classes for Gillespie-Gibson simulations (sha)


libemc, pyecs))

- added ecell.ecs.getLibECSVersion() and getLibECSVersionInfo() methods (sha)

- Implemented Simulator.getDMInfo method (sha)


pyecell))

- New method: Session.saveModel() (taka-ken)

osogo))

- thoroughly reconstructed Entity- and PropertyWindows (osugi)

- And a long list of bugfixes by osugi and tkitayama


others))

- completely rewritten em2eml: ecell3-em2eml command using PLY.
  em2eml will be deprecated.   (taka-ken)

- eri2eml catchs up with recent versions (zak)





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