new @agent syntax and ABM subtyping

src/chemotaxis/brown-berg.jl

@@ -14,7 +14,7 @@ Default parameters:
 - `receptor_binding_constant = 100` μM
 - `memory = 1` s
 """
-@agent BrownBerg{D} ContinuousAgent{D,Float64} where D AbstractMicrobe{D} begin
+@agent struct BrownBerg{D}(ContinuousAgent{D,Float64}) <: AbstractMicrobe{D}
     speed::Float64
     motility::AbstractMotility = RunTumble()
     turn_rate::Float64 = 1 / 0.67

src/chemotaxis/brumley.jl

@@ -17,7 +17,7 @@ Default parameters:
 - `chemotactic_precision = 6.0` → 'Π'
 - `radius = 0.5` μm → 'a'
 """
-@agent Brumley{D} ContinuousAgent{D,Float64} where D AbstractMicrobe{D} begin
+@agent struct Brumley{D}(ContinuousAgent{D,Float64}) <: AbstractMicrobe{D}
     speed::Float64
     motility::AbstractMotility = RunReverseFlick(speed_forward = [46.5])
     turn_rate::Float64 = 1 / 0.45

src/chemotaxis/celani.jl

@@ -19,7 +19,7 @@ Default parameters:
 - `memory = 1` s
 - `radius = 0.5` μm
 """
-@agent Celani{D} ContinuousAgent{D,Float64} where {D} AbstractMicrobe{D} begin
+@agent struct Celani{D}(ContinuousAgent{D,Float64}) <: AbstractMicrobe{D}
     speed::Float64
     motility::AbstractMotility = RunTumble(speed = [30.0])
     turn_rate::Float64 = 1 / 0.67

src/chemotaxis/xie.jl

@@ -29,7 +29,7 @@ Default parameters:
 - `chemotactic_precision = 0.0`
 - `radius = 0.5` μm
 """
-@agent Xie{D} ContinuousAgent{D,Float64} where D AbstractMicrobe{D} begin
+@agent struct Xie{D}(ContinuousAgent{D,Float64}) <: AbstractMicrobe{D}
     speed::Float64
     motility::AbstractMotility = RunReverseFlick(speed_forward = [46.5])
     turn_rate_forward::Float64 = 2.3

src/microbes.jl

@@ -17,7 +17,7 @@ Default parameters:
 - `vel::SVector{D,Float64}` unit velocity vector
 - `speed::Float64` magnitude of the velocity vector
 """
-@agent Microbe{D} ContinuousAgent{D,Float64} where D AbstractMicrobe{D} begin
+@agent struct Microbe{D}(ContinuousAgent{D,Float64}) <: AbstractMicrobe{D}
     speed::Float64
     motility::AbstractMotility = RunTumble()
     turn_rate::Float64 = 1.0

src/model.jl

@@ -171,15 +171,15 @@ in which case the simulations stops when `n` returns true.
 - `showprogress = false`
 See `Agents.run!` and `Agents.step!` for detailed information.
 """
-function Agents.run!(model::AgentBasedModel{S,A}, n = 1;
+function Agents.run!(model::AgentBasedModel{S}, n = 1;
     when = true,
     when_model = when,
     adata = nothing,
     mdata = nothing,
     obtainer = identity,
     agents_first = true,
     showprogress = false
-) where {S<:ContinuousSpace,A<:AbstractMicrobe}
+) where {S<:ContinuousSpace}
     run!(model, microbe_step!, model.update!, n;
         when, when_model,
         adata, mdata,

src/utils.jl

@@ -5,7 +5,7 @@ export random_velocity, random_speed, ChainedFunction, →, distance, distanceve
 Generate a random velocity vector with unit norm respecting the
 dimensionality of `model`.
 """
-function random_velocity(model::AgentBasedModel{S,A}) where {S,D,A<:AbstractMicrobe{D}}
+function random_velocity(model::AgentBasedModel{ContinuousSpace{D}}) where D
     random_velocity(abmrng(model), D)
 end
 function random_velocity(rng::AbstractRNG, D::Int)