From 0daee903a822c1cc515fc7aad5a86366629b4e5e Mon Sep 17 00:00:00 2001
From: Riccardo Foffi <riccardo.foffi@protonmail.com>
Date: Thu, 28 Dec 2023 14:45:36 +0100
Subject: [PATCH] rename `cwbias` to `tumblebias` and only take `microbe` as
 input

---
 src/api.jl                   |  2 +-
 src/chemotaxis/brown-berg.jl |  2 +-
 src/chemotaxis/brumley.jl    |  2 +-
 src/chemotaxis/celani.jl     |  2 +-
 src/chemotaxis/xie.jl        |  4 ++--
 src/microbe_step.jl          | 13 ++++---------
 test/model-creation.jl       |  4 ++--
 7 files changed, 12 insertions(+), 17 deletions(-)

diff --git a/src/api.jl b/src/api.jl
index 42bf784..61d4fd7 100644
--- a/src/api.jl
+++ b/src/api.jl
@@ -1,6 +1,6 @@
 export position, direction, speed, velocity, motilepattern,
     turnrate, rotational_diffusivity, radius, state,
-    cwbias,
+    tumblebias,
     distance, distancevector
 
 Base.position(m::AbstractMicrobe) = m.pos
diff --git a/src/chemotaxis/brown-berg.jl b/src/chemotaxis/brown-berg.jl
index 04db08c..09f4beb 100644
--- a/src/chemotaxis/brown-berg.jl
+++ b/src/chemotaxis/brown-berg.jl
@@ -45,7 +45,7 @@ function affect!(microbe::BrownBerg, model)
     chemotaxis!(microbe, model)
 end
 
-function cwbias(microbe::BrownBerg, model)
+function tumblebias(microbe::BrownBerg)
     g = microbe.gain
     S = microbe.state
     return exp(-g*S)
diff --git a/src/chemotaxis/brumley.jl b/src/chemotaxis/brumley.jl
index 09310b0..4c7eb51 100644
--- a/src/chemotaxis/brumley.jl
+++ b/src/chemotaxis/brumley.jl
@@ -55,7 +55,7 @@ function affect!(microbe::Brumley, model)
     chemotaxis!(microbe, model)
 end
 
-function cwbias(microbe::Brumley, model)
+function tumblebias(microbe::Brumley)
     Γ = microbe.gain
     S = microbe.state
     return (1 + exp(-Γ*S))/2
diff --git a/src/chemotaxis/celani.jl b/src/chemotaxis/celani.jl
index 71b6162..a9e4f97 100644
--- a/src/chemotaxis/celani.jl
+++ b/src/chemotaxis/celani.jl
@@ -53,7 +53,7 @@ function affect!(microbe::Celani, model)
     chemotaxis!(microbe, model)
 end
 
-function cwbias(microbe::Celani, model)
+function tumblebias(microbe::Celani)
     β = microbe.gain
     S = microbe.state
     return (1 - β*S)
diff --git a/src/chemotaxis/xie.jl b/src/chemotaxis/xie.jl
index 7e817ea..8d418d0 100644
--- a/src/chemotaxis/xie.jl
+++ b/src/chemotaxis/xie.jl
@@ -84,7 +84,7 @@ function affect!(microbe::Xie, model)
     chemotaxis!(microbe, model)
 end
 
-function cwbias(microbe::Xie, model)
+function tumblebias(microbe::Xie)
     S = state(microbe)
     if state(motilepattern(microbe)) == Forward
         β = microbe.gain_forward
@@ -94,7 +94,7 @@ function cwbias(microbe::Xie, model)
     return (1 + β*S)
 end
 
-function turnrate(microbe::Xie, model)
+function turnrate(microbe::Xie)
     if state(motilepattern(microbe)) == Forward
         return microbe.turn_rate_forward
     else
diff --git a/src/microbe_step.jl b/src/microbe_step.jl
index 9849586..728e0c6 100644
--- a/src/microbe_step.jl
+++ b/src/microbe_step.jl
@@ -18,7 +18,7 @@ function microbe_step!(microbe::AbstractMicrobe, model)
     # update microbe state
     affect!(microbe, model)
     # evaluate instantaneous turn rate
-    ω = turnrate(microbe, model)
+    ω = turnrate(microbe) * tumblebias(microbe)
     if rand(abmrng(model)) < ω * dt # if true reorient microbe
         turn!(microbe, model)
     end
@@ -39,20 +39,15 @@ function microbe_pathfinder_step!(microbe::AbstractMicrobe, model)
     # update microbe state
     affect!(microbe, model)
     # evaluate instantaneous turn rate
-    ω = turnrate(microbe, model)
+    ω = turnrate(microbe) * tumblebias(microbe)
     if rand(abmrng(model)) < ω * dt # if true reorient microbe
         turn!(microbe, model)
     end
     nothing
 end
 
-"""
-    turnrate(microbe, model)
-Evaluate instantaneous turn rate of `microbe`.
-"""
-turnrate(microbe::AbstractMicrobe, model) = turnrate(microbe) * cwbias(microbe, model)
-# no CW bias for generic non-chemotactic microbe
-cwbias(microbe::AbstractMicrobe, model) = 1.0
+# no bias for generic non-chemotactic microbe
+tumblebias(microbe::AbstractMicrobe) = 1.0
 """
     affect!(microbe, model)
 Can be used to arbitrarily update `microbe` state.
diff --git a/test/model-creation.jl b/test/model-creation.jl
index 00c6a58..2afaa42 100644
--- a/test/model-creation.jl
+++ b/test/model-creation.jl
@@ -71,7 +71,7 @@ using LinearAlgebra: norm
                     fieldnames(T)
                 )
 
-                φ(microbe, model) = turnrate(microbe) * cwbias(microbe, model)
+                φ(microbe, model) = turnrate(microbe) * tumblebias(microbe)
                 if T == BrownBerg
                     @test φ(m, model) == m.turn_rate * exp(-m.gain*m.state)
                 elseif T == Brumley
@@ -96,7 +96,7 @@ using LinearAlgebra: norm
                     S = m.state
                     ω = m.turn_rate_forward
                     β = m.gain_forward
-                    @test turnrate(m, model) == ω * (1 + β*S)
+                    @test turnrate(m) == ω * (1 + β*S)
                 end
             end
         end