use affect! as ABM property (#69)

src/api.jl

@@ -1,6 +1,5 @@
 export position, direction, speed, velocity, motilepattern,
     turnrate, rotational_diffusivity, radius, state,
-    tumblebias,
     distance, distancevector
 
 Base.position(m::AbstractMicrobe) = m.pos

src/chemotaxis/brown-berg.jl

@@ -1,4 +1,4 @@
-export BrownBerg, chemotaxis!
+export BrownBerg
 
 """
     BrownBerg{D} <: AbstractMicrobe{D}
@@ -41,10 +41,6 @@ function chemotaxis!(microbe::BrownBerg, model)
     return nothing
 end # function
 
-function affect!(microbe::BrownBerg, model)
-    chemotaxis!(microbe, model)
-end
-
 function tumblebias(microbe::BrownBerg)
     g = microbe.gain
     S = microbe.state

src/chemotaxis/brumley.jl

@@ -1,4 +1,4 @@
-export Brumley, chemotaxis!
+export Brumley
 
 """
     Brumley{D} <: AbstractMicrobe{D}
@@ -51,10 +51,6 @@ function chemotaxis!(microbe::Brumley, model)
     return nothing
 end # function
 
-function affect!(microbe::Brumley, model)
-    chemotaxis!(microbe, model)
-end
-
 function tumblebias(microbe::Brumley)
     Γ = microbe.gain
     S = microbe.state

src/chemotaxis/celani.jl

@@ -1,4 +1,4 @@
-export Celani, chemotaxis!
+export Celani
 
 """
     Celani{D} <: AbstractMicrobe{D}
@@ -49,10 +49,6 @@ function chemotaxis!(microbe::Celani, model)
     return nothing
 end # function
 
-function affect!(microbe::Celani, model)
-    chemotaxis!(microbe, model)
-end
-
 function tumblebias(microbe::Celani)
     β = microbe.gain
     S = microbe.state

src/chemotaxis/xie.jl

@@ -1,4 +1,4 @@
-export Xie, chemotaxis!
+export Xie
 
 """
     Xie{D} <: AbstractMicrobe{D}
@@ -80,10 +80,6 @@ function chemotaxis!(microbe::Xie, model; ε=1e-16)
     return nothing
 end
 
-function affect!(microbe::Xie, model)
-    chemotaxis!(microbe, model)
-end
-
 function tumblebias(microbe::Xie)
     S = state(microbe)
     if state(motilepattern(microbe)) == Forward

src/microbe_step.jl

@@ -1,4 +1,4 @@
-export microbe_step!, microbe_pathfinder_step!, turnrate, affect!
+export microbe_step!, microbe_pathfinder_step!
 
 """
     microbe_step!(microbe, model)
@@ -16,7 +16,7 @@ function microbe_step!(microbe::AbstractMicrobe, model)
     # reorient through rotational diffusion
     rotational_diffusion!(microbe, model)
     # update microbe state
-    affect!(microbe, model)
+    model.affect!(microbe, model)
     # evaluate instantaneous turn rate
     ω = turnrate(microbe) * tumblebias(microbe)
     if rand(abmrng(model)) < ω * dt # if true reorient microbe
@@ -37,19 +37,11 @@ function microbe_pathfinder_step!(microbe::AbstractMicrobe, model)
     # reorient through rotational diffusion
     rotational_diffusion!(microbe, model)
     # update microbe state
-    affect!(microbe, model)
+    model.affect!(microbe, model)
     # evaluate instantaneous turn rate
     ω = turnrate(microbe) * tumblebias(microbe)
     if rand(abmrng(model)) < ω * dt # if true reorient microbe
         turn!(microbe, model)
     end
     nothing
 end
-
-# no bias for generic non-chemotactic microbe
-tumblebias(microbe::AbstractMicrobe) = 1.0
-"""
-    affect!(microbe, model)
-Can be used to arbitrarily update `microbe` state.
-"""
-affect!(microbe::AbstractMicrobe, model) = nothing

src/microbes.jl

@@ -1,4 +1,4 @@
-export Microbe
+export Microbe, chemotaxis!, tumblebias
 
 """
     Microbe{D} <: AbstractMicrobe{D}
@@ -26,6 +26,11 @@ and the default parameters
     state::Float64 = 0.0
 end
 
+# fallback functions for default random behavior
+chemotaxis!(microbe::AbstractMicrobe, model) = nothing
+tumblebias(microbe::AbstractMicrobe) = 1.0
+
+
 r2dig(x) = round(x, digits=2)
 function Base.show(io::IO, ::MIME"text/plain", m::AbstractMicrobe{D}) where D
     println(io, "$(typeof(m)) with $(typeof(motilepattern(m)))")

src/model.jl

@@ -28,6 +28,7 @@ DEFAULT_ABM_PROPERTIES = Dict(
     :concentration_time_derivative => (pos,model) -> 0.0, # scalar
     # required by models of chemotaxis, default value is glutamate diffusivity
     :compound_diffusivity => 608.0,
+    :affect! => chemotaxis!
 )
 ```
 By including these default properties, we make sure that all the chemotaxis models
@@ -97,4 +98,5 @@ DEFAULT_ABM_PROPERTIES = Dict(
     :concentration_time_derivative => (pos,model) -> 0.0,
     # required by models of chemotaxis, default value is glutamate diffusivity
     :compound_diffusivity => 608.0,
+    :affect! => chemotaxis!
 )

test/model-creation.jl

@@ -13,6 +13,7 @@ using LinearAlgebra: norm
             :concentration_gradient,
             :concentration_time_derivative,
             :compound_diffusivity,
+            :affect!
         ))
     end
 

test/model-stepping.jl

@@ -29,16 +29,12 @@ using LinearAlgebra: norm
 
         # customize microbe affect! function
         # decreases microbe state value by D at each step
-        MicrobeAgents.affect!(microbe::Microbe{D}, model) = (microbe.state -= D)
-        model = StandardABM(Microbe{D}, space, dt; container)
+        affect!(microbe::Microbe{D}, model) where D = (microbe.state -= D)
+        properties = Dict(:affect! => affect!)
+        model = StandardABM(Microbe{D}, space, dt; container, properties)
         add_agent!(model)
         run!(model, 1)
         @test model[1].state == -D
-        # restore default affect! function
-        MicrobeAgents.affect!(microbe::Microbe{D}, model) = nothing
-        run!(model, 1)
-        # now the state has not changed from previous step
-        @test model[1].state == -D
 
         # customize model_step! function
         properties = Dict(:square_t => 0)