Releases: harfel/stocal
Releases · harfel/stocal
1.2
Added
- Added Gibson & Bruck's NextReactionMethod
- Added Cao et al's tau leaping method in stocal.experimental.tauleap
- Added statistical validation suite in stocal.examples.validation and stocal.samples.dsmts
- Added modular trajectory sampling interface stocal.experimental.samplers
- Added flattening of rule-based processes into static processes
- StochasticSimulationAlgorithm instances accept an optional random seed
Deprecated
- Deprecated AndersonNRM in favour of AndersonMethod
- Deprecated TrajectorySampler in favour of StochasticSimulationAlgorithm
- Deprecated ReactionRule in favour of TransitionRule
- Deprecated Process.trajectory in favour of Process.sample
Changed
- TrajectorySampler instances now use an internal random number generator (sampler.rng) rather than python's global one.
- Improved performance of DirectMethod and AndersonMethod
- Improved performance of transition inference in TransitionRule
1.1.2
Fixed
- Fixed issue #1 in Event.next_occurrence
- Fixed issue #2 in ReactionRule.infer_transitions
- Fixed issue with printing transitions with non-string reactants
- Fixed issue #3 in AndersonNRM
- Fixed issue #4 in FirstReactionMethod
Added
- Added type support of reaction rules via ReactionRule.signature
- Added support for time dependent reaction rates
Changed
- ReactionRule.Transition can alternatively be specified through return type annotation in python3
- MassAction.__repr__ now also prints rate constant
- stocal.examples.type_rules now does what it claims to do
- Events that occurr at tmax are now explicitly included in a trajectory
1.0.2
Fixed
- Fixed error in tutorial
Added
- Added python3 compatibility
Deprecated
- Deprecated dict support of several functions in favor of multisets
- Deprecated some method parameter names
Removed
- Removed requirement for ReactionRule.order
Changed
- Changed package organization