up

Author: TorkelE

test/extensions/homotopy_continuation.jl

@@ -25,12 +25,12 @@ let
     u0 = [:X1 => 2.0, :X2 => 2.0, :X3 => 2.0, :X2_2X3 => 2.0]
 
     # Computes the single steady state, checks that when given to the ODE rhs, all are evaluated to 0.
-    hc_ss = hc_steady_states(rs, ps; u0=u0, show_progress=false)
+    hc_ss = hc_steady_states(rs, ps; u0 = u0, show_progress = false, seed = 1234)
     hc_ss = Pair.(unknowns(rs), hc_ss[1])
-    @test maximum(abs.(f_eval(rs, hc_ss, ps, 0.0))) ≈ 0.0 atol=1e-12
+    @test maximum(abs.(f_eval(rs, hc_ss, ps, 0.0))) ≈ 0.0 atol = 1e-12
 
     # Checks that not giving a `u0` argument yields an error for systems with conservation laws.
-    @test_throws Exception hc_steady_states(rs, ps; show_progress=false)
+    @test_throws Exception hc_steady_states(rs, ps; show_progress = false)
 end
 
 # Tests for network with multiple steady state.
@@ -45,11 +45,11 @@ let
     end
     ps = [:k3 => 1.0, :k2 => 2.0, :k4 => 1.5, :k1=>8.0]
 
-    hc_ss_1 = hc_steady_states(wilhelm_2009_model, ps; seed=0x000004d1, show_progress=false)
-    @test sort(hc_ss_1, by=sol->sol[1]) ≈ [[0.0, 0.0], [0.5, 2.0], [4.5, 6.0]]
+    hc_ss_1 = hc_steady_states(wilhelm_2009_model, ps; seed = 1234, show_progress = false)
+    @test sort(hc_ss_1, by = sol->sol[1]) ≈ [[0.0, 0.0], [0.5, 2.0], [4.5, 6.0]]
 
-    hc_ss_2 = hc_steady_states(wilhelm_2009_model, ps; seed=0x000004d2, show_progress=false)
-    hc_ss_3 = hc_steady_states(wilhelm_2009_model, ps; seed=0x000004d2, show_progress=false)
+    hc_ss_2 = hc_steady_states(wilhelm_2009_model, ps; seed = 1234, show_progress = false)
+    hc_ss_3 = hc_steady_states(wilhelm_2009_model, ps; seed = 1234, show_progress = false)
     @test hc_ss_1 != hc_ss_2
     @test hc_ss_2 == hc_ss_3
 end
@@ -69,7 +69,7 @@ let
     ps = (:kY1 => 1.0, :kY2 => 3, :kZ1 => 1.0, :kZ2 => 4.0)
     u0_1 = (:Y1 => 1.0, :Y2 => 3, :Z1 => 10, :Z2 =>40.0)
 
-    ss_1 = sort(hc_steady_states(rs_1, ps; u0=u0_1, show_progress=false), by=sol->sol[1])
+    ss_1 = sort(hc_steady_states(rs_1, ps; u0 = u0_1, show_progress = false, seed = 1234), by = sol->sol[1])
     @test ss_1 ≈ [[0.2, 0.1, 3.0, 1.0, 40.0, 10.0]]
 
     rs_2 = @reaction_network begin
@@ -81,7 +81,7 @@ let
     end
     u0_2 = [:B2 => 1.0, :B1 => 3.0, :A2 => 10.0, :A1 =>40.0]
 
-    ss_2 = sort(hc_steady_states(rs_2, ps; u0=u0_2, show_progress=false), by=sol->sol[1])
+    ss_2 = sort(hc_steady_states(rs_2, ps; u0 = u0_2, show_progress = false, seed = 1234), by = sol->sol[1])
     @test ss_1 ≈ ss_2
 end
 
@@ -96,14 +96,15 @@ let
         d, X --> 0
     end
     ps = [:v => 5.0, :K => 2.5, :n => 3, :d => 1.0]
-    sss = hc_steady_states(rs, ps; filter_negative=false, show_progress=false)
+    sss = hc_steady_states(rs, ps; filter_negative = false, show_progress = false, seed = 1234)
 
     @test length(sss) == 4
     for ss in sss
-        @test f_eval(rs,sss[1], last.(ps), 0.0)[1] ≈ 0.0 atol=1e-12
+        @test f_eval(rs,sss[1], last.(ps), 0.0)[1] ≈ 0.0 atol = 1e-12
     end
 
-    @test_throws Exception hc_steady_states(rs, [:v => 5.0, :K => 2.5, :n => 2.7, :d => 1.0]; show_progress=false)
+    ps = [:v => 5.0, :K => 2.5, :n => 2.7, :d => 1.0]
+    @test_throws Exception hc_steady_states(rs, ps; show_progress = false, seed = 1234)
 end
 
 
@@ -124,7 +125,7 @@ let
 
     # Checks that homotopy continuation correctly find the system's single steady state.
     ps = [:p => 2.0, :d => 1.0, :k => 5.0]
-    hc_ss = hc_steady_states(rs, ps)
+    hc_ss = hc_steady_states(rs, ps; show_progress = false, seed = 1234)
     @test hc_ss ≈ [[2.0, 0.2, 10.0]]
 end
 
@@ -137,7 +138,7 @@ let
     p_start = [:p => 1.0, :d => 0.2]
 
     # Computes bifurcation diagram.
-    @test_throws Exception hc_steady_states(incomplete_network, p_start)
+    @test_throws Exception hc_steady_states(incomplete_network, p_start; show_progress = false, seed = 1234)
 end
 
 # Tests that non-autonomous system throws an error
@@ -146,5 +147,5 @@ let
         (k,t), 0 <--> X
     end
     ps = [:k => 1.0]
-    @test_throws Exception hc_steady_states(rs, ps)
+    @test_throws Exception hc_steady_states(rs, ps; show_progress = false, seed = 1234)
 end