format

Author: oameye

src/CriticalTransitions.jl

@@ -20,11 +20,7 @@ using StochasticDiffEq:
     terminate!,
     u_modified!
 using DynamicalSystemsBase:
-    DynamicalSystemsBase,
-    CoupledSDEs,
-    dynamic_rule,
-    current_state,
-    set_state!
+    DynamicalSystemsBase, CoupledSDEs, dynamic_rule, current_state, set_state!
 
 #StochasticSystemsBase = Base.get_extension(DynamicalSystemsBase, :StochasticSystemsBase)
 #using DynamicalSystemsBase.StochasticSystemsBase: CoupledSDEs
@@ -68,10 +64,7 @@ include("../systems/CTLibrary.jl")
 using .CTLibrary
 
 # Core types
-export CoupledSDEs,
-    noise_process,
-    covariance_matrix,
-    diffusion_matrix
+export CoupledSDEs, noise_process, covariance_matrix, diffusion_matrix
 
 # Methods
 export equilib, basins, basinboundary, basboundary

src/largedeviations/action.jl

@@ -20,7 +20,7 @@ generalized norm ``||a||_Q^2 := \\langle a, Q^{-1} b \\rangle`` (see `anorm``).
 function fw_action(sys::CoupledSDEs, path, time)
     @assert all(diff(time) .≈ diff(time[1:2])) "Freidlin-Wentzell action is only defined for equispaced time"
     # Inverse of covariance matrix
-    A = inv(covariance_matrix(sys)) 
+    A = inv(covariance_matrix(sys))
 
     # Compute action integral
     integrand = fw_integrand(sys, path, time, A)

src/trajectories/equib.jl

@@ -12,7 +12,9 @@ Returns the equilibrium solution of the system `sys` for given initial condition
 * `dt = 0.01`: time step of the ODE solver.
 * `solver = Euler()`: ODE solver used for evolving the state.
 """
-function equilib(sys::CoupledSDEs, state=nothing; dt=0.01, tmax=1e5, abstol=1e-5, solver=Tsit5())
+function equilib(
+    sys::CoupledSDEs, state=nothing; dt=0.01, tmax=1e5, abstol=1e-5, solver=Tsit5()
+)
     condition(u, t, integrator) = norm(integrator.uprev - u) < abstol
     affect!(integrator) = terminate!(integrator)
     equilib_cond = DiscreteCallback(condition, affect!)

test/CoupledSDEs.jl

@@ -15,17 +15,15 @@
     u0 = zeros(2)
     sys = CoupledSDEs(fitzhugh_nagumo, u0, param; noise_strength=σ)
 
-    @testset "correlation" begin
-
-    end
+    @testset "correlation" begin end
 
     @testset "noise" begin
         diff = diffusion_matrix(sys)
         cov = covariance_matrix(sys)
         @test diff isa AbstractMatrix
         @test cov isa AbstractMatrix
         @test all(diag(diff) .== σ)
-        @test diff.^2 == cov
+        @test diff .^ 2 == cov
 
         W = noise_process(sys)
         int_cov = W.covariance
@@ -35,9 +33,8 @@
 
     @testset "drift" begin
         using CriticalTransitions: drift
-        drift_vector = drift(sys, [0,0])
-        drift_vector isa SVector{2, Float64}
-        @test drift_vector == [0,0]
+        drift_vector = drift(sys, [0, 0])
+        drift_vector isa SVector{2,Float64}
+        @test drift_vector == [0, 0]
     end
-
 end

test/basin/basin_boundary-N54XDK9GMK.jl renamed to test/basin/basin_boundary.jl

@@ -8,11 +8,11 @@
     box = intervals_to_box([-2.0, -2.0], [2.00, 2.0])
     step = 0.1
 
-    boas = basins(system, A, B, C, box; bstep = [step, step])
+    boas = basins(system, A, B, C, box; bstep=[step, step])
     X, Y, attractors, h = boas
     boundary = basinboundary(boas)
     @test length(attractors) == 2
     @test length(unique(h)) == 3
-    @test h[end÷2+1, end÷2+1] == -1
-    @test boundary[:,end÷2+1] == zeros(2)
+    @test h[end ÷ 2 + 1, end ÷ 2 + 1] == -1
+    @test boundary[:, end ÷ 2 + 1] == zeros(2)
 end

test/issue14.jl

@@ -2,21 +2,21 @@ using CriticalTransitions, StaticArrays, Test
 
 function meier_stein(u, p, t) # in-place
     x, y = u
-    dx = x-x^3 -10*x*y^2
-    dy = -(1+x^2)*y
-    SA[dx, dy]
+    dx = x - x^3 - 10 * x * y^2
+    dy = -(1 + x^2) * y
+    return SA[dx, dy]
 end
 σ = 0.25
 sys = StochSystem(meier_stein, [], zeros(2), σ, idfunc, nothing, I(2), "WhiteGauss")
 
 # initial path: parabola
-xx = range(-1.0,1.0, length=30)
-yy = 0.3 .* (- xx .^ 2 .+ 1)
+xx = range(-1.0, 1.0; length=30)
+yy = 0.3 .* (-xx .^ 2 .+ 1)
 init = Matrix([xx yy]')
 
-gm = geometric_min_action_method(sys, init, maxiter=1000)
-@test all(isapprox.(path[2,:][end-5:end], 0, atol=1e-3))
+gm = geometric_min_action_method(sys, init; maxiter=1000)
+@test all(isapprox.(path[2, :][(end - 5):end], 0, atol=1e-3))
 
 gm[2][end]
 
-isapprox(gm[2][end], 0.338, atol=1e-3)
+isapprox(gm[2][end], 0.338; atol=1e-3)

test/largedeviations/MAM.jl

@@ -9,7 +9,7 @@
         fhn, x_i, x_f, N, T; maxiter=100, verbose=false, save_info=false
     )
     S = fw_action(fhn, inst, range(0.0, T; length=N))
-    @test isapprox(S, 0.18, atol=0.01) broken=true
+    @test isapprox(S, 0.18, atol=0.01) broken = true
 end
 
 @testset "MAM Ornstein-Uhlenbeck" begin

test/largedeviations/action_fhn.jl

@@ -17,13 +17,13 @@ time = range(0.0, T; length=N)
 
 @testset "fw_action" begin
     S = fw_action(sys, path, time)
-    @test isapprox(S, 0.32, atol=0.01) broken=true
+    @test isapprox(S, 0.32, atol=0.01) broken = true
 end
 
 # Test om_action function
 @testset "om_action" begin
     S = om_action(sys, path, time, σ)
-    @test isapprox(S, 0.26, atol=0.01) broken=true
+    @test isapprox(S, 0.26, atol=0.01) broken = true
 end
 
 # Test action function
@@ -34,13 +34,13 @@ end
 # Test geometric_action function
 @testset "geometric_action" begin
     S = geometric_action(sys, path)
-    @test isapprox(S, 0.23, atol=0.01) broken=true
+    @test isapprox(S, 0.23, atol=0.01) broken = true
 end
 
 # Test fw_integrand function
 @testset "fw_integrand" begin
     integrand = CriticalTransitions.fw_integrand(sys, path, time, A)
-    @test minimum(integrand) > 0.18 skip=true
+    @test minimum(integrand) > 0.18 skip = true
     #^ This test is does not test something meaningful
 end
 

test/largedeviations/gMAM.jl

@@ -7,7 +7,7 @@
     N = 100
     res = geometric_min_action_method(fhn, x_i, x_f; N=75, maxiter=200, verbose=false)
     S = geometric_action(fhn, res[1][end])
-    @test isapprox(S, 0.18, atol=0.01) broken=true
+    @test isapprox(S, 0.18, atol=0.01) broken = true
 end
 
 @testset "gMAM Meier Stein" begin
@@ -36,7 +36,7 @@ end
         path = gm[1][end]
         action_val = gm[2][end]
         @test all(isapprox.(path[2, :][(end - 5):end], 0, atol=1e-3))
-        @test all(isapprox.(action_val, 0.3375, atol=1e-3)) broken=true
+        @test all(isapprox.(action_val, 0.3375, atol=1e-3)) broken = true
     end
 
     @testset "HeymannVandenEijnden" begin # broken

test/runtests.jl

@@ -45,7 +45,7 @@ end
 end
 
 @testset "CoupledSDEs" begin
-   include("CoupledSDEs.jl")
+    include("CoupledSDEs.jl")
 end
 
 @testset "ModelingToolkit" begin
@@ -59,7 +59,7 @@ end
 end
 
 @testset "utilities" begin
-   include("utils.jl")
+    include("utils.jl")
 end
 
 # @testset "Trajactories" begin

test/trajactories/transition.jl

@@ -22,7 +22,6 @@
     @test ensemble.t_trans ≈ 4.493941793363376 atol = 1e-2
     # SEED is different on github
     # SEED doesn;t work on github
-    @test length(ensemble.times) == 11 broken=true
-    @test ensemble.t_res ≈ 5299.98 broken=true
-
+    @test length(ensemble.times) == 11 broken = true
+    @test ensemble.t_res ≈ 5299.98 broken = true
 end