Fix about types of transition arrays

core/common.jl

@@ -18,7 +18,7 @@ mutable struct ContinuousTimeModel <: Model
     map_var_idx::Dict{VariableModel,Int} # maps variable str to index in the state space
     _map_obs_var_idx::Dict{VariableModel,Int} # maps variable str to index in the observed state space
     map_param_idx::Dict{ParameterModel,Int} # maps parameter str to index in the parameter space
-    transitions::Vector{<:Transition}
+    transitions::Vector{Transition}
     p::Vector{Float64}
     x0::Vector{Int}
     t0::Float64
@@ -35,17 +35,17 @@ struct Trajectory <: AbstractTrajectory
     m::ContinuousTimeModel
     values::Vector{Vector{Int}}
     times::Vector{Float64}
-    transitions::Vector{<:Transition}
+    transitions::Vector{Transition}
 end
 
 struct Edge
-    transitions::Vector{<:Transition}
+    transitions::Vector{Transition}
     check_constraints::Function
     update_state!::Function
 end
 
 struct LHA
-    transitions::Vector{<:Transition}
+    transitions::Vector{Transition}
     locations::Vector{Location} 
     Λ::Dict{Location,Function}
     locations_init::Vector{Location}
@@ -74,7 +74,7 @@ struct SynchronizedTrajectory <: AbstractTrajectory
     sm::SynchronizedModel
     values::Vector{Vector{Int}}
     times::Vector{Float64}
-    transitions::Vector{<:Transition}
+    transitions::Vector{Transition}
 end
 
 struct ParametricModel
@@ -86,12 +86,13 @@ end
 
 # Constructors
 function ContinuousTimeModel(dim_state::Int, dim_params::Int, map_var_idx::Dict{VariableModel,Int}, 
-                             map_param_idx::Dict{ParameterModel,Int}, transitions::Vector{<:Transition}, 
+                             map_param_idx::Dict{ParameterModel,Int}, transitions::Vector{<:Transition},
                              p::Vector{Float64}, x0::Vector{Int}, t0::Float64, 
                              f!::Function, isabsorbing::Function; 
                              g::Vector{VariableModel} = keys(map_var_idx), time_bound::Float64 = Inf, 
                              buffer_size::Int = 10, estim_min_states::Int = 50, name::String = "Unnamed")
     dim_obs_state = length(g)
+    transitions = convert(Vector{Transition}, transitions)
     _map_obs_var_idx = Dict()
     _g_idx = Vector{Int}(undef, dim_obs_state)
     for i = 1:dim_obs_state

models/ER.jl

@@ -9,7 +9,7 @@ l_tr_ER = [:R1,:R2,:R3]
 p_ER = [1.0, 1.0, 1.0]
 x0_ER = [100, 100, 0, 0]
 t0_ER = 0.0
-function ER_f!(xnplus1::Vector{Int}, l_t::Vector{Float64}, l_tr::Vector{<:Transition},
+function ER_f!(xnplus1::Vector{Int}, l_t::Vector{Float64}, l_tr::Vector{Transition},
                xn::Vector{Int}, tn::Float64, p::Vector{Float64})
     @inbounds a1 = p[1] * xn[1] * xn[2]
     @inbounds a2 = p[2] * xn[3]

models/SIR.jl

@@ -9,7 +9,7 @@ l_tr_SIR = [:R1,:R2]
 p_SIR = [0.0012, 0.05]
 x0_SIR = [95, 5, 0]
 t0_SIR = 0.0
-function SIR_f!(xnplus1::Vector{Int}, l_t::Vector{Float64}, l_tr::Vector{<:Transition},
+function SIR_f!(xnplus1::Vector{Int}, l_t::Vector{Float64}, l_tr::Vector{Transition},
                 xn::Vector{Int}, tn::Float64, p::Vector{Float64})
     @inbounds a1 = p[1] * xn[1] * xn[2]
     @inbounds a2 = p[2] * xn[2]

models/SIR_tauleap.jl

@@ -10,7 +10,7 @@ l_tr_SIR_tauleap = [:U]
 p_SIR_tauleap = [0.0012, 0.05, 5.0]
 x0_SIR_tauleap = [95, 5, 0]
 t0_SIR_tauleap = 0.0
-function SIR_tauleap_f!(xnplus1::Vector{Int}, l_t::Vector{Float64}, l_tr::Vector{<:Transition},
+function SIR_tauleap_f!(xnplus1::Vector{Int}, l_t::Vector{Float64}, l_tr::Vector{Transition},
                 xn::Vector{Int}, tn::Float64, p::Vector{Float64})
     tau = p[3]
     a1 = p[1] * xn[1] * xn[2]

models/_bench_perf_test/ER_col.jl

@@ -10,7 +10,7 @@ p = [1.0, 1.0, 1.0]
 x0 = [100, 100, 0, 0]
 t0 = 0.0
 
-function ER_col_f!(xnplus1::Vector{Int}, tnplus1::Vector{Float64}, tr::Vector{<:Transition}, 
+function ER_col_f!(xnplus1::Vector{Int}, tnplus1::Vector{Float64}, tr::Vector{Transition}, 
            xn::AbstractVector{Int}, tn::Float64, p::Vector{Float64})
     a1 = p[1] * xn[1] * xn[2]
     a2 = p[2] * xn[3]

models/_bench_perf_test/ER_col_buffer.jl

@@ -9,7 +9,7 @@ l_tr = [:R1,:R2,:R3]
 p = [1.0, 1.0, 1.0]
 x0 = [100, 100, 0, 0]
 t0 = 0.0
-function ER_col_buffer_f!(mat_x::Matrix{Int}, l_t::Vector{Float64}, l_tr::Vector{<:Transition}, idx::Int,
+function ER_col_buffer_f!(mat_x::Matrix{Int}, l_t::Vector{Float64}, l_tr::Vector{Transition}, idx::Int,
            xn::AbstractVector{Int}, tn::Float64, p::Vector{Float64})
     a1 = p[1] * xn[1] * xn[2]
     a2 = p[2] * xn[3]

models/_bench_perf_test/ER_row_buffer.jl

@@ -9,7 +9,7 @@ l_tr = [:R1,:R2,:R3]
 p = [1.0, 1.0, 1.0]
 x0 = [100, 100, 0, 0]
 t0 = 0.0
-function ER_row_buffer_f!(mat_x::Matrix{Int}, l_t::Vector{Float64}, l_tr::Vector{<:Transition}, idx::Int,
+function ER_row_buffer_f!(mat_x::Matrix{Int}, l_t::Vector{Float64}, l_tr::Vector{Transition}, idx::Int,
            xn::AbstractVector{Int}, tn::Float64, p::Vector{Float64})
     a1 = p[1] * xn[1] * xn[2]
     a2 = p[2] * xn[3]

models/_bench_perf_test/SIR_col.jl

@@ -9,7 +9,7 @@ l_tr = [:R1,:R2]
 p = [0.0012, 0.05]
 x0 = [95, 5, 0]
 t0 = 0.0
-function SIR_col_f!(xnplus1::Vector{Int}, tnplus1::Vector{Float64}, tr::Vector{<:Transition}, 
+function SIR_col_f!(xnplus1::Vector{Int}, tnplus1::Vector{Float64}, tr::Vector{Transition}, 
                     xn::AbstractVector{Int}, tn::Float64, p::Vector{Float64})
     a1 = p[1] * xn[1] * xn[2]
     a2 = p[2] * xn[2]

models/_bench_perf_test/SIR_col_buffer.jl

@@ -9,7 +9,7 @@ l_tr = [:R1,:R2]
 p = [0.0012, 0.05]
 x0 = [95, 5, 0]
 t0 = 0.0
-function SIR_col_buffer_f!(mat_x::Matrix{Int}, l_t::Vector{Float64}, l_tr::Vector{<:Transition}, idx::Int,
+function SIR_col_buffer_f!(mat_x::Matrix{Int}, l_t::Vector{Float64}, l_tr::Vector{Transition}, idx::Int,
            xn::AbstractVector{Int}, tn::Float64, p::Vector{Float64})
     a1 = p[1] * xn[1] * xn[2]
     a2 = p[2] * xn[2]

models/_bench_perf_test/SIR_row_buffer.jl

@@ -9,7 +9,7 @@ l_tr = [:R1,:R2]
 p = [0.0012, 0.05]
 x0 = [95, 5, 0]
 t0 = 0.0
-function SIR_row_buffer_f!(mat_x::Matrix{Int}, l_t::Vector{Float64}, l_tr::Vector{<:Transition}, idx::Int,
+function SIR_row_buffer_f!(mat_x::Matrix{Int}, l_t::Vector{Float64}, l_tr::Vector{Transition}, idx::Int,
            xn::AbstractVector{Int}, tn::Float64, p::Vector{Float64})
     a1 = p[1] * xn[1] * xn[2]
     a2 = p[2] * xn[2]

models/poisson.jl

@@ -10,7 +10,7 @@ l_tr_poisson = [:R]
 p_poisson = [5.0]
 x0_poisson = [0]
 t0_poisson = 0.0
-function poisson_f!(xnplus1::Vector{Int}, l_t::Vector{Float64}, l_tr::Vector{<:Transition},
+function poisson_f!(xnplus1::Vector{Int}, l_t::Vector{Float64}, l_tr::Vector{Transition},
                     xn::Vector{Int}, tn::Float64, p::Vector{Float64})
     
     u1 = rand()