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@luciansmith luciansmith released this 27 Mar 00:19
· 18 commits to release since this release
v2.6.0
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Learn about vigilant mode.

Updates:

  • The seed for both the gillespie integrator and for 'distrib' constructs is now synchronized and settable from r.setSeed(val) and from the global configuration options (Config.setValue(Config.RANDOM_SEED, val)
  • The SBML L3v2 'rateOf' function is now implemented.
  • That seed value may be extremely large (larger than the previous erroneous 'int' cutoff; limit is now uint64).
  • The 'times' input vector for simulation runs has been upgraded:
    • It may now contain numpy ints.
    • It may contain repeated values (after the initial value) (useful when comparing output to collected data with replicates)
  • Piecewise functions are now much more robustly handled, with explicit root-finding for the moments when the function switches from one output to another.
  • The python 'setValues' command may now take a dictionary as input, instead of separate 'keys' and 'values' arguments.

Bugfixes:

  • The gillespie integrator is now initialized with a time-based random seed (in microseconds) instead of the same one every run.
  • Gillespie simulations no longer run on models with rate rules, instead of silently ignoring them.
  • Gillespie simulations warn for runs with 'time' in event triggers or with event delays.
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