Apply JuliaFormatter to fix code formatting

lib/DDEProblemLibrary/src/qs.jl

@@ -11,9 +11,8 @@ Cultures of Pseudomonas Putida IsoF By Use of ELISA and UHPLC/qTOF-MS-derived Me
 and Mathematical Models, Analytical and Bioanalytical Chemistry.
 """
 const prob_dde_qs = let S₀ = 1, τ = 2, D = 0.1, γₛ = 1.3e-12, Kₘ = 0.38, nₛ = 1.3, a = 0.66,
-    αₐ = 2.3e-19,
-    βₐ = 2.3e-18, C₁ = 70e-9, n₁ = 2.3, γₐ = 0.05, αC = 4e4, R = 5e-7, γ₃ = 0.08,
-    Kₑ = 1.5e-4, αₗ = 1.1e-8, C₂ = 70e-9, n₂ = 2.5, γₗ = 0.005
+    αₐ = 2.3e-19, βₐ = 2.3e-18, C₁ = 70e-9, n₁ = 2.3, γₐ = 0.05, αC = 4e4, R = 5e-7,
+    γ₃ = 0.08, Kₑ = 1.5e-4, αₗ = 1.1e-8, C₂ = 70e-9, n₂ = 2.5, γₗ = 0.005
 
     function hill_growth(x, K, n)
         if x > K

lib/JumpProblemLibrary/src/JumpProblemLibrary.jl

@@ -141,8 +141,13 @@ rs = @reaction_network begin
     kAdp, S8 --> S5
     kAdp, S9 --> S3
 end
-rates = [:kon, :kAon, :koff, :kAoff, :kAp, :kAdp] .=>
-    params[[rsi[:kon], rsi[:kAon], rsi[:koff], rsi[:kAoff], rsi[:kAp], rsi[:kAdp]]]
+rates = [:kon,
+    :kAon,
+    :koff,
+    :kAoff,
+    :kAp,
+    :kAdp] .=> params[[
+    rsi[:kon], rsi[:kAon], rsi[:koff], rsi[:kAoff], rsi[:kAp], rsi[:kAdp]]]
 u0 = [:S1 => params[1], :S2 => params[2], :S3 => params[3], :S4 => 0, :S5 => 0,
     :S6 => 0, :S7 => 0, :S8 => 0, :S9 => 0]
 tf = 100.0

lib/NonlinearProblemLibrary/src/NonlinearProblemLibrary.jl

@@ -264,7 +264,7 @@ p12_dict = Dict("n" => n, "start" => x_start, "sol" => x_sol,
 
 @inbounds function p13_f!(out, x, p = nothing)
     n = length(x)
-    out[1] = broyden_tridiag_kernel(x[1]) -2.0 * x[2]
+    out[1] = broyden_tridiag_kernel(x[1]) - 2.0 * x[2]
     for k in 2:(n - 1)
         out[k] = broyden_tridiag_kernel(x[k]) - x[k - 1] - 2.0 * x[k + 1]
     end

lib/ODEProblemLibrary/src/ODEProblemLibrary.jl

@@ -37,7 +37,6 @@ export prob_ode_linear, prob_ode_bigfloatlinear, prob_ode_2Dlinear,
     end
 end
 
-
 include("ode_linear_prob.jl")
 include("ode_simple_nonlinear_prob.jl")
 include("brusselator_prob.jl")

lib/ODEProblemLibrary/src/brusselator_prob.jl

@@ -24,10 +24,12 @@ function brusselator_2d_loop(du, u, p, t)
             im1 = limit(i - 1, N)
             jp1 = limit(j + 1, N)
             jm1 = limit(j - 1, N)
-            du[i, j, 1] = α * (u[im1, j, 1] + u[ip1, j, 1] + u[i, jp1, 1] + u[i, jm1, 1] -
-                           4u[i, j, 1]) +
-                          B + u[i, j, 1]^2 * u[i, j, 2] - (A + 1) * u[i, j, 1] +
-                          brusselator_f(x, y, t)
+            du[i,
+                j,
+                1] = α * (u[im1, j, 1] + u[ip1, j, 1] + u[i, jp1, 1] + u[i, jm1, 1] -
+                      4u[i, j, 1]) +
+                     B + u[i, j, 1]^2 * u[i, j, 2] - (A + 1) * u[i, j, 1] +
+                     brusselator_f(x, y, t)
         end
         for I in CartesianIndices((N, N))
             i = I[1]
@@ -36,9 +38,11 @@ function brusselator_2d_loop(du, u, p, t)
             im1 = limit(i - 1, N)
             jp1 = limit(j + 1, N)
             jm1 = limit(j - 1, N)
-            du[i, j, 2] = α * (u[im1, j, 2] + u[ip1, j, 2] + u[i, jp1, 2] + u[i, jm1, 2] -
-                           4u[i, j, 2]) +
-                          A * u[i, j, 1] - u[i, j, 1]^2 * u[i, j, 2]
+            du[i,
+                j,
+                2] = α * (u[im1, j, 2] + u[ip1, j, 2] + u[i, jp1, 2] + u[i, jm1, 2] -
+                      4u[i, j, 2]) +
+                     A * u[i, j, 1] - u[i, j, 1]^2 * u[i, j, 2]
         end
     end
 end
@@ -104,10 +108,12 @@ function brusselator_1d_loop(du, u, p, t)
     @inbounds for i in 2:(N - 1)
         x = xyd_brusselator[i]
         ip1, im1 = i + 1, i - 1
-        du[i, 1] = alpha * (u[im1, 1] + u[ip1, 1] - 2u[i, 1]) +
-                   A + u[i, 1]^2 * u[i, 2] - (B + 1) * u[i, 1]
-        du[i, 2] = alpha * (u[im1, 2] + u[ip1, 2] - 2u[i, 2]) +
-                   B * u[i, 1] - u[i, 1]^2 * u[i, 2]
+        du[i,
+            1] = alpha * (u[im1, 1] + u[ip1, 1] - 2u[i, 1]) +
+                 A + u[i, 1]^2 * u[i, 2] - (B + 1) * u[i, 1]
+        du[i,
+            2] = alpha * (u[im1, 2] + u[ip1, 2] - 2u[i, 2]) +
+                 B * u[i, 1] - u[i, 1]^2 * u[i, 2]
     end
 end
 

lib/ODEProblemLibrary/src/ode_simple_nonlinear_prob.jl

@@ -70,7 +70,8 @@ with ``μ=1.0`` and ``u_0=[x => \\sqrt{3}, y => 0]``
 
 Non-stiff parameters.
 """
-prob_ode_vanderpol = ODEProblem(van, [y => 0, x => sqrt(3), μ => 1.0], (0.0, 1.0), jac=true, eval_module = @__MODULE__)
+prob_ode_vanderpol = ODEProblem(van, [y => 0, x => sqrt(3), μ => 1.0], (0.0, 1.0),
+    jac = true, eval_module = @__MODULE__)
 
 """
 Van der Pol Equations
@@ -86,7 +87,8 @@ with ``μ=10^6`` and ``u_0=[x => \\sqrt{3}, y => 0]``
 
 Stiff parameters.
 """
-prob_ode_vanderpol_stiff = ODEProblem(van, [y => 0, x => sqrt(3), μ => 1e6], (0.0, 1.0), jac=true, eval_module = @__MODULE__)
+prob_ode_vanderpol_stiff = ODEProblem(van, [y => 0, x => sqrt(3), μ => 1e6], (0.0, 1.0),
+    jac = true, eval_module = @__MODULE__)
 
 # ROBER
 @parameters k₁ k₂ k₃
@@ -116,13 +118,18 @@ Hairer Norsett Wanner Solving Ordinary Differential Equations I - Nonstiff Probl
 
 Usually solved on ``[0,1e11]``
 """
-prob_ode_rober = ODEProblem(rober, [[y₁, y₂, y₃] .=> [1.0; 0.0; 0.0]; [k₁, k₂, k₃] .=> (0.04, 3e7, 1e4)], (0.0, 1e11), jac = true, eval_module = @__MODULE__)
+prob_ode_rober = ODEProblem(
+    rober, [[y₁, y₂, y₃] .=> [1.0; 0.0; 0.0]; [k₁, k₂, k₃] .=> (0.04, 3e7, 1e4)],
+    (0.0, 1e11), jac = true, eval_module = @__MODULE__)
 
 # Three Body
 const threebody_μ = big(0.012277471);
 const threebody_μ′ = 1 - threebody_μ;
 
-threebody = (du, u, p, t) -> begin
+threebody = (du,
+    u,
+    p,
+    t) -> begin
     # 1 = y₁
     # 2 = y₂
     # 3 = y₁'
@@ -200,8 +207,10 @@ or Hairer Norsett Wanner Solving Ordinary Differential Equations I - Nonstiff Pr
 
 Usually solved from 0 to 20.
 """
-prob_ode_rigidbody = ODEProblem(rigid, [[y₁, y₂, y₃] .=> [1.0, 0.0, 0.9]; [I₁, I₂, I₃] .=> (-2.0, 1.25, -0.5)], (0.0, 20.0),
-                                jac = true, eval_module = @__MODULE__)
+prob_ode_rigidbody = ODEProblem(
+    rigid, [[y₁, y₂, y₃] .=> [1.0, 0.0, 0.9]; [I₁, I₂, I₃] .=> (-2.0, 1.25, -0.5)],
+    (0.0, 20.0),
+    jac = true, eval_module = @__MODULE__)
 
 # Pleiades Problem
 
@@ -216,6 +225,7 @@ pleiades = (du, u, p, t) -> begin
         du[i] = zero(eltype(u))
     end
     for i in 1:7, j in 1:7
+
         if i != j
             r = ((x[i] - x[j])^2 + (y[i] - y[j])^2)^(3 / 2)
             du[14 + i] += j * (x[j] - x[i]) / r
@@ -365,7 +375,8 @@ u0[1] = 1
 u0[8] = 0.0057
 
 u0 = [y1, y2, y3, y4, y5, y6, y7, y8] .=> u0
-p = [p1, p2, p3, p4, p5, p6, p7, p8, p9, p10, p11, p12] .=> (1.71, 0.43, 8.32, 0.0007, 8.75,
+p = [p1, p2, p3, p4, p5, p6, p7, p8, p9, p10, p11,
+    p12] .=> (1.71, 0.43, 8.32, 0.0007, 8.75,
     10.03, 0.035, 1.12, 1.745, 280.0, 0.69, 1.81)
 
 """
@@ -390,7 +401,8 @@ where ``f`` is defined by
 Reference: [demohires.pdf](http://www.radford.edu/~thompson/vodef90web/problems/demosnodislin/Demos_Pitagora/DemoHires/demohires.pdf)
 Notebook: [Hires.ipynb](http://nbviewer.jupyter.org/github/JuliaDiffEq/DiffEqBenchmarks.jl/blob/master/StiffODE/Hires.ipynb)
 """
-prob_ode_hires = ODEProblem(hires, [u0; p], (0.0, 321.8122), jac = true, eval_module = @__MODULE__)
+prob_ode_hires = ODEProblem(
+    hires, [u0; p], (0.0, 321.8122), jac = true, eval_module = @__MODULE__)
 
 @parameters p1 p2 p3
 @variables y1(t) y2(t) y3(t)
@@ -418,4 +430,6 @@ where ``s=77.27``, ``w=0.161`` and ``q=8.375⋅10^{-6}``.
 Reference: [demoorego.pdf](http://www.radford.edu/~thompson/vodef90web/problems/demosnodislin/Demos_Pitagora/DemoOrego/demoorego.pdf)
 Notebook: [Orego.ipynb](http://nbviewer.jupyter.org/github/JuliaDiffEq/DiffEqBenchmarks.jl/blob/master/StiffODE/Orego.ipynb)
 """
-prob_ode_orego = ODEProblem(orego, [[y1, y2, y3] .=> [1.0, 2.0, 3.0]; [p1, p2, p3] .=> [77.27, 8.375e-6, 0.161]], (0.0, 30.0), jac = true, eval_module = @__MODULE__)
+prob_ode_orego = ODEProblem(
+    orego, [[y1, y2, y3] .=> [1.0, 2.0, 3.0]; [p1, p2, p3] .=> [77.27, 8.375e-6, 0.161]],
+    (0.0, 30.0), jac = true, eval_module = @__MODULE__)

lib/ODEProblemLibrary/src/strange_attractors.jl

@@ -23,10 +23,10 @@ $(latexify(thomas))
 
 [Wikipedia](https://en.wikipedia.org/wiki/Thomas%27_cyclically_symmetric_attractor)
 """
-prob_ode_thomas = ODEProblem(thomas, [], (0.0, 1.0), jac=true, eval_module = @__MODULE__)
+prob_ode_thomas = ODEProblem(thomas, [], (0.0, 1.0), jac = true, eval_module = @__MODULE__)
 
 # Lorenz
-@parameters σ=10 ρ=28 β=8 / 3
+@parameters σ=10 ρ=28 β=8/3
 @variables x(t)=1 y(t)=0 z(t)=0
 
 eqs = [D(x) ~ σ * (y - x),
@@ -46,7 +46,7 @@ $(latexify(lorenz))
 
 [Wikipedia](https://en.wikipedia.org/wiki/Lorenz_system)
 """
-prob_ode_lorenz = ODEProblem(lorenz, [], (0.0, 1.0), jac=true, eval_module = @__MODULE__)
+prob_ode_lorenz = ODEProblem(lorenz, [], (0.0, 1.0), jac = true, eval_module = @__MODULE__)
 
 # Aizawa
 @parameters a=0.95 b=0.7 c=0.6 d=3.5 e=0.25 f=0.1
@@ -68,7 +68,7 @@ $(latexify(aizawa))
 [Reference](https://journals.ametsoc.org/view/journals/atsc/20/2/1520-0469_1963_020_0130_dnf_2_0_co_2.xml)
 
 """
-prob_ode_aizawa = ODEProblem(aizawa, [], (0.0, 1.0), jac=true, eval_module = @__MODULE__)
+prob_ode_aizawa = ODEProblem(aizawa, [], (0.0, 1.0), jac = true, eval_module = @__MODULE__)
 
 # Dadras
 @parameters a=3 b=2.7 c=1.7 d=2 e=9
@@ -90,7 +90,7 @@ $(latexify(dadras))
 [Reference](https://www.sciencedirect.com/science/article/abs/pii/S0375960109009591)
 
 """
-prob_ode_dadras = ODEProblem(dadras, [], (0.0, 1.0), jac=true, eval_module = @__MODULE__)
+prob_ode_dadras = ODEProblem(dadras, [], (0.0, 1.0), jac = true, eval_module = @__MODULE__)
 
 # chen
 @parameters a=35 b=3 c=28
@@ -112,7 +112,7 @@ $(latexify(chen))
 [Reference](https://www.worldscientific.com/doi/abs/10.1142/S0218127499001024)
 
 """
-prob_ode_chen = ODEProblem(chen, [], (0.0, 1.0), jac=true, eval_module = @__MODULE__)
+prob_ode_chen = ODEProblem(chen, [], (0.0, 1.0), jac = true, eval_module = @__MODULE__)
 
 # rossler
 @parameters a=0.2 b=0.2 c=5.7
@@ -135,7 +135,8 @@ $(latexify(rossler))
 [Wikipedia](https://en.wikipedia.org/wiki/R%C3%B6ssler_attractor)
 
 """
-prob_ode_rossler = ODEProblem(rossler, [], (0.0, 1.0), jac=true, eval_module = @__MODULE__)
+prob_ode_rossler = ODEProblem(
+    rossler, [], (0.0, 1.0), jac = true, eval_module = @__MODULE__)
 
 # rabinovich_fabrikant
 @parameters a=0.14 b=0.10
@@ -157,7 +158,8 @@ $(latexify(rabinovich_fabrikant))
 [Reference](https://en.wikipedia.org/wiki/Rabinovich%E2%80%93Fabrikant_equations)
 
 """
-prob_ode_rabinovich_fabrikant = ODEProblem(rabinovich_fabrikant, [], (0.0, 1.0), jac=true, eval_module = @__MODULE__)
+prob_ode_rabinovich_fabrikant = ODEProblem(
+    rabinovich_fabrikant, [], (0.0, 1.0), jac = true, eval_module = @__MODULE__)
 
 # sprott
 @parameters a=2.07 b=1.79
@@ -179,10 +181,10 @@ $(latexify(sprott))
 [Reference](https://sprott.physics.wisc.edu/pubs/paper423.pdf)
 
 """
-prob_ode_sprott = ODEProblem(sprott, [], (0.0, 1.0), jac=true, eval_module = @__MODULE__)
+prob_ode_sprott = ODEProblem(sprott, [], (0.0, 1.0), jac = true, eval_module = @__MODULE__)
 
 # hindmarsh_rose
-@parameters a=1 b=3 c=1 d=5 r=1e-2 s=4 xr=-8 / 5 i=5
+@parameters a=1 b=3 c=1 d=5 r=1e-2 s=4 xr=-8/5 i=5
 @variables x(t)=1 y(t)=0 z(t)=0
 
 eqs = [D(x) ~ y - a * x^3 + b * x^2 - z + i,
@@ -201,4 +203,5 @@ $(latexify(hindmarsh_rose))
 [Reference](https://en.wikipedia.org/wiki/Hindmarsh%E2%80%93Rose_model)
 
 """
-prob_ode_hindmarsh_rose = ODEProblem(hindmarsh_rose, [], (0.0, 1.0), jac=true, eval_module = @__MODULE__)
+prob_ode_hindmarsh_rose = ODEProblem(
+    hindmarsh_rose, [], (0.0, 1.0), jac = true, eval_module = @__MODULE__)