feat: Implement explicit Tau-Leaping Simulator with Mockito unit tests - #111
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dyrpsf wants to merge 2 commits into
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feat: Implement explicit Tau-Leaping Simulator with Mockito unit tests#111dyrpsf wants to merge 2 commits into
dyrpsf wants to merge 2 commits into
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draeger
approved these changes
Apr 24, 2026
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Overview
This PR introduces the Explicit Tau-Leaping Algorithm to the FERN simulation engine.
While the Exact Gillespie algorithm is highly accurate, it becomes computationally expensive for networks with massive molecule counts. This new$\tau$ ) and approximating the number of reaction firings using a Poisson distribution.
TauLeapingSimulatoraccelerates stochastic simulations by taking larger time steps (Changes Made
TauLeapingSimulator.javatofern.simulation.algorithm.AmountManagerto correctly process forward reaction firings (performReaction(i, 1)).mockito-coredependency (scope:test) to the rootpom.xmlto allow for clean, isolated testing of the FERN engine.TauLeapingSimulatorTest.javautilizing Mockito to successfully mock theNetworkand verify simulator initialization and abstract method inheritance.Validation
mvn clean compile).mvn clean test -Dtest=TauLeapingSimulatorTest).