Merge pull request #35 from ChrisRackauckas/fix-formatting

Apply JuliaFormatter to fix code formatting

Author: ChrisRackauckas

docs/src/example.md

@@ -9,30 +9,30 @@ using OrdinaryDiffEqTsit5
 using LinearAlgebra
 
 mutable struct SubproblemParameters{P, Q, R}
-  p::P # tunable
-  q::Q
-  r::R
+    p::P # tunable
+    q::Q
+    r::R
 end
 
 mutable struct Parameters{P, C}
-  subparams::P
-  coeffs::C # tunable matrix
+    subparams::P
+    coeffs::C # tunable matrix
 end
 
 # the rhs is `du[i] = p[i] * u[i]^2 + q[i] * u[i] + r[i] * t` for i in 1:length(subparams)
 # and `du[length(subparams)+1:end] .= coeffs * u`
 function rhs!(du, u, p::Parameters, t)
-  for (i, subpars) in enumerate(p.subparams)
-    du[i] = subpars.p * u[i]^2 + subpars.q * u[i] + subpars.r * t
-  end
-  N = length(p.subparams)
-  mul!(view(du, (N+1):(length(du))), p.coeffs, u)
-  return nothing
+    for (i, subpars) in enumerate(p.subparams)
+        du[i] = subpars.p * u[i]^2 + subpars.q * u[i] + subpars.r * t
+    end
+    N = length(p.subparams)
+    mul!(view(du, (N + 1):(length(du))), p.coeffs, u)
+    return nothing
 end
 
 u = sin.(0.1:0.1:1.0)
 subparams = [SubproblemParameters(0.1i, 0.2i, 0.3i) for i in 1:5]
-p = Parameters(subparams, cos.([0.1i+0.33j for i in 1:5, j in 1:10]))
+p = Parameters(subparams, cos.([0.1i + 0.33j for i in 1:5, j in 1:10]))
 tspan = (0.0, 1.0)
 
 prob = ODEProblem(rhs!, u, tspan, p)
@@ -47,12 +47,13 @@ using SciMLSensitivity
 
 # 5 subparams[i].p, 50 elements in coeffs
 function simulate_with_tunables(tunables)
-  subpars = [SubproblemParameters(tunables[i], subpar.q, subpar.r) for (i, subpar) in enumerate(p.subparams)]
-  coeffs = reshape(tunables[6:end], size(p.coeffs))
-  newp = Parameters(subpars, coeffs)
-  newprob = remake(prob; p = newp)
-  sol = solve(newprob, Tsit5())
-  return sum(sol.u[end])
+    subpars = [SubproblemParameters(tunables[i], subpar.q, subpar.r)
+               for (i, subpar) in enumerate(p.subparams)]
+    coeffs = reshape(tunables[6:end], size(p.coeffs))
+    newp = Parameters(subpars, coeffs)
+    newprob = remake(prob; p = newp)
+    sol = solve(newprob, Tsit5())
+    return sum(sol.u[end])
 end
 ```
 
@@ -74,46 +75,49 @@ SS.ismutablescimlstructure(::Parameters) = true
 SS.hasportion(::SS.Tunable, ::Parameters) = true
 
 function SS.canonicalize(::SS.Tunable, p::Parameters)
-  # concatenate all tunable values into a single vector
-  buffer = vcat([subpar.p for subpar in p.subparams], vec(p.coeffs))
-
-  # repack takes a new vector of the same length as `buffer`, and constructs
-  # a new `Parameters` object using the values from the new vector for tunables
-  # and retaining old values for other parameters. This is exactly what replace does,
-  # so we can use that instead.
-  repack = let p = p
-    function repack(newbuffer)
-      SS.replace(SS.Tunable(), p, newbuffer)
+    # concatenate all tunable values into a single vector
+    buffer = vcat([subpar.p for subpar in p.subparams], vec(p.coeffs))
+
+    # repack takes a new vector of the same length as `buffer`, and constructs
+    # a new `Parameters` object using the values from the new vector for tunables
+    # and retaining old values for other parameters. This is exactly what replace does,
+    # so we can use that instead.
+    repack = let p = p
+        function repack(newbuffer)
+            SS.replace(SS.Tunable(), p, newbuffer)
+        end
     end
-  end
-  # the canonicalized vector, the repack function, and a boolean indicating
-  # whether the buffer aliases values in the parameter object (here, it doesn't)
-  return buffer, repack, false
+    # the canonicalized vector, the repack function, and a boolean indicating
+    # whether the buffer aliases values in the parameter object (here, it doesn't)
+    return buffer, repack, false
 end
 
 function SS.replace(::SS.Tunable, p::Parameters, newbuffer)
-  N = length(p.subparams) + length(p.coeffs)
-  @assert length(newbuffer) == N
-  subparams = [SubproblemParameters(newbuffer[i], subpar.q, subpar.r) for (i, subpar) in enumerate(p.subparams)]
-  coeffs = reshape(view(newbuffer, (length(p.subparams)+1):length(newbuffer)), size(p.coeffs))
-  return Parameters(subparams, coeffs)
+    N = length(p.subparams) + length(p.coeffs)
+    @assert length(newbuffer) == N
+    subparams = [SubproblemParameters(newbuffer[i], subpar.q, subpar.r)
+                 for (i, subpar) in enumerate(p.subparams)]
+    coeffs = reshape(
+        view(newbuffer, (length(p.subparams) + 1):length(newbuffer)), size(p.coeffs))
+    return Parameters(subparams, coeffs)
 end
 
 function SS.replace!(::SS.Tunable, p::Parameters, newbuffer)
-  N = length(p.subparams) + length(p.coeffs)
-  @assert length(newbuffer) == N
-  for (subpar, val) in zip(p.subparams, newbuffer)
-    subpar.p = val
-  end
-  copyto!(coeffs, view(newbuffer, (length(p.subparams)+1):length(newbuffer)))
-  return p
+    N = length(p.subparams) + length(p.coeffs)
+    @assert length(newbuffer) == N
+    for (subpar, val) in zip(p.subparams, newbuffer)
+        subpar.p = val
+    end
+    copyto!(coeffs, view(newbuffer, (length(p.subparams) + 1):length(newbuffer)))
+    return p
 end
 ```
 
 Now, we should be able to differentiate through the ODE solve.
 
 ```@example basic_tutorial
-Zygote.gradient(simulate_with_tunables, 0.1ones(length(SS.canonicalize(SS.Tunable(), p)[1])))
+Zygote.gradient(
+    simulate_with_tunables, 0.1ones(length(SS.canonicalize(SS.Tunable(), p)[1])))
 ```
 
 We can also implement a `Constants` portion to store the rest of the values:
@@ -122,29 +126,30 @@ We can also implement a `Constants` portion to store the rest of the values:
 SS.hasportion(::SS.Constants, ::Parameters) = true
 
 function SS.canonicalize(::SS.Constants, p::Parameters)
-  buffer = mapreduce(vcat, p.subparams) do subpar
-    [subpar.q, subpar.r]
-  end
-  repack = let p = p
-    function repack(newbuffer)
-      SS.replace(SS.Constants(), p, newbuffer)
+    buffer = mapreduce(vcat, p.subparams) do subpar
+        [subpar.q, subpar.r]
+    end
+    repack = let p = p
+        function repack(newbuffer)
+            SS.replace(SS.Constants(), p, newbuffer)
+        end
     end
-  end
 
-  return buffer, repack, false
+    return buffer, repack, false
 end
 
 function SS.replace(::SS.Constants, p::Parameters, newbuffer)
-  subpars = [SubproblemParameters(p.subparams[i].p, newbuffer[2i-1], newbuffer[2i]) for i in eachindex(p.subparams)]
-  return Parameters(subpars, p.coeffs)
+    subpars = [SubproblemParameters(p.subparams[i].p, newbuffer[2i - 1], newbuffer[2i])
+               for i in eachindex(p.subparams)]
+    return Parameters(subpars, p.coeffs)
 end
 
 function SS.replace!(::SS.Constants, p::Parameters, newbuffer)
-  for i in eachindex(p.subparams)
-    p.subparams[i].q = newbuffer[2i-1]
-    p.subparams[i].r = newbuffer[2i]
-  end
-  return p
+    for i in eachindex(p.subparams)
+        p.subparams[i].q = newbuffer[2i - 1]
+        p.subparams[i].r = newbuffer[2i]
+    end
+    return p
 end
 
 buf, repack, alias = SS.canonicalize(SS.Constants(), p)