Remove unrelated formatting changes

Co-Authored-By: Chris Rackauckas <accounts@chrisrackauckas.com>

Author: ChrisRackauckas

src/JumpProcesses.jl

@@ -36,18 +36,18 @@ import SymbolicIndexingInterface as SII
 
 # Import additional types and functions from DiffEqBase and SciMLBase
 using DiffEqBase: DiffEqBase, CallbackSet, ContinuousCallback, DAEFunction,
-    DDEFunction, DiscreteProblem, ODEFunction, ODEProblem,
-    ODESolution, ReturnCode, SDEFunction, SDEProblem, add_tstop!,
-    deleteat!, isinplace, remake, savevalues!, step!,
-    derivative_discontinuity!
+                  DDEFunction, DiscreteProblem, ODEFunction, ODEProblem,
+                  ODESolution, ReturnCode, SDEFunction, SDEProblem, add_tstop!,
+                  deleteat!, isinplace, remake, savevalues!, step!,
+                  derivative_discontinuity!
 using SciMLBase: SciMLBase, DEIntegrator
 
 abstract type AbstractJump end
 abstract type AbstractMassActionJump <: AbstractJump end
 abstract type AbstractAggregatorAlgorithm end
 abstract type AbstractJumpAggregator end
 abstract type AbstractSSAIntegrator{Alg, IIP, U, T} <:
-DEIntegrator{Alg, IIP, U, T} end
+              DEIntegrator{Alg, IIP, U, T} end
 
 const DEFAULT_RNG = Random.default_rng()
 
@@ -156,7 +156,7 @@ export init, solve, solve!
 include("SSA_stepper.jl")
 export SSAStepper
 
-# leaping:
+# leaping: 
 include("simple_regular_solve.jl")
 export SimpleTauLeaping, SimpleExplicitTauLeaping, EnsembleGPUKernel
 

src/aggregators/aggregators.jl

@@ -172,10 +172,8 @@ algorithm with optimal binning,  Journal of Chemical Physics 143, 074108
 """
 struct DirectCRDirect <: AbstractAggregatorAlgorithm end
 
-const JUMP_AGGREGATORS = (
-    Direct(), DirectFW(), DirectCR(), SortingDirect(), RSSA(), FRM(),
-    FRMFW(), NRM(), RSSACR(), RDirect(), Coevolve(), CCNRM(),
-)
+const JUMP_AGGREGATORS = (Direct(), DirectFW(), DirectCR(), SortingDirect(), RSSA(), FRM(),
+    FRMFW(), NRM(), RSSACR(), RDirect(), Coevolve(), CCNRM())
 
 # For JumpProblem construction without an aggregator
 struct NullAggregator <: AbstractAggregatorAlgorithm end
@@ -257,11 +255,9 @@ is_spatial(aggregator::NSM) = true
 is_spatial(aggregator::DirectCRDirect) = true
 
 # return the fastest aggregator out of the available ones
-function select_aggregator(
-        jumps::JumpSet; vartojumps_map = nothing,
+function select_aggregator(jumps::JumpSet; vartojumps_map = nothing,
         jumptovars_map = nothing, dep_graph = nothing, spatial_system = nothing,
-        hopping_constants = nothing
-    )
+        hopping_constants = nothing)
 
     # detect if a spatial SSA should be used
     !isnothing(spatial_system) && !isnothing(hopping_constants) && return DirectCRDirect

src/aggregators/bracketing.jl

@@ -1,3 +1,8 @@
+# bracketing intervals for RSSA-based aggregators
+# see: "On the rejection-based algorithm for simulation and analysis of
+#       large-scale reaction networks", Thanh et al, J. Chem. Phys., 2015
+# note, expects the type of the bracketing variables [ulow,uhigh] to be the
+# same as the fluct_rate and ushift.
 """
     BracketData(fluctrate, threshold, Δu)
     BracketData{T1, T2}()
@@ -31,9 +36,9 @@ bd.fluctrate == 0.1
 ```
 """
 struct BracketData{T1, T2}
-    fluctrate::T1
-    threshold::T2
-    Δu::T2
+    fluctrate::T1         # interval should be [1-fluctrate,1+fluctrate] * u
+    threshold::T2         # for u below threshold interval is:
+    Δu::T2                #   [max(u-Δu,0),u+Δu]
 end
 
 # # suggested defaults
@@ -53,7 +58,7 @@ BracketData{T1, T2}() where {T1, T2} = BracketData(T1(0.1), T2(25), T2(4))
 @inline getΔu(bd::BracketData{T1, T2}, i) where {T1, T2 <: Number} = bd.Δu
 
 @inline function delta_bracket(u::Integer, δ)
-    return (trunc(typeof(u), (one(δ) - δ) * u), trunc(typeof(u), (one(δ) + δ) * u))
+    (trunc(typeof(u), (one(δ) - δ) * u), trunc(typeof(u), (one(δ) + δ) * u))
 end
 
 @inline delta_bracket(u, δ) = ((one(δ) - δ) * u), ((one(δ) + δ) * u)
@@ -75,7 +80,7 @@ end
 
 # Get propensity brackets of massaction jump k.
 @inline function get_majump_brackets(ulow, uhigh, k, majumps)
-    return evalrxrate(ulow, k, majumps), evalrxrate(uhigh, k, majumps)
+    evalrxrate(ulow, k, majumps), evalrxrate(uhigh, k, majumps)
 end
 
 # for constant rate jumps we must check the ordering of the bracket values
@@ -95,10 +100,8 @@ get brackets for the rate of reaction rx by first checking if the reaction is a
     if rx <= num_majumps
         return get_majump_brackets(p.ulow, p.uhigh, rx, ma_jumps)
     else
-        @inbounds return get_cjump_brackets(
-            p.ulow, p.uhigh, p.rates[rx - num_majumps],
-            params, t
-        )
+        @inbounds return get_cjump_brackets(p.ulow, p.uhigh, p.rates[rx - num_majumps],
+            params, t)
     end
 end
 
@@ -108,7 +111,7 @@ end
     @inbounds for (i, uval) in enumerate(u)
         ulow[i], uhigh[i] = get_spec_brackets(p.bracket_data, i, uval)
     end
-    return nothing
+    nothing
 end
 
 @inline function update_u_brackets!(p::AbstractSSAJumpAggregator, u::SVector)
@@ -117,12 +120,12 @@ end
         p.ulow = setindex(p.ulow, ulow, i)
         p.uhigh = setindex(p.uhigh, uhigh, i)
     end
-    return nothing
+    nothing
 end
 
 # For ExtendedJumpArray, only iterate over the species portion (u.u), not the jump tracking portion
 @inline function update_u_brackets!(p::AbstractSSAJumpAggregator, u::ExtendedJumpArray)
-    return update_u_brackets!(p, u.u)
+    update_u_brackets!(p, u.u)
 end
 
 # Set up bracketing. The aggregator must have fields
@@ -151,5 +154,5 @@ function set_bracketing!(p::AbstractSSAJumpAggregator, u, params, t)
     end
     p.sum_rate = sum_rate
 
-    return nothing
+    nothing
 end