Apply JuliaFormatter to fix code formatting

docs/make.jl

@@ -6,12 +6,12 @@ cp("./docs/Project.toml", "./docs/src/assets/Project.toml", force = true)
 include("pages.jl")
 
 makedocs(sitename = "ModelOrderReduction.jl",
-         authors = "Bowen S. Zhu",
-         modules = [ModelOrderReduction],
-         clean = true, doctest = false, linkcheck = true,
-         warnonly = [:missing_docs, :example_block],
-         format = Documenter.HTML(assets = ["assets/favicon.ico"],
-                                  canonical = "https://docs.sciml.ai/ModelOrderReduction/stable/"),
-         pages = pages)
+    authors = "Bowen S. Zhu",
+    modules = [ModelOrderReduction],
+    clean = true, doctest = false, linkcheck = true,
+    warnonly = [:missing_docs, :example_block],
+    format = Documenter.HTML(assets = ["assets/favicon.ico"],
+        canonical = "https://docs.sciml.ai/ModelOrderReduction/stable/"),
+    pages = pages)
 
 deploydocs(repo = "github.com/SciML/ModelOrderReduction.jl.git")

docs/pages.jl

@@ -1,5 +1,5 @@
 pages = [
     "Home" => "index.md",
     "Functions" => "functions.md",
-    "Tutorials" => Any["tutorials/deim_FitzHugh-Nagumo.md"],
+    "Tutorials" => Any["tutorials/deim_FitzHugh-Nagumo.md"]
 ]

docs/src/tutorials/deim_FitzHugh-Nagumo.md

@@ -107,7 +107,7 @@ svdval_w = svdvals(snapshot_w)
 svdval_fv = svdvals(snapshot_fv)
 using Plots, LaTeXStrings
 svd_plt = plot(yscale = :log10, xticks = eachindex(svdval_v), titlefont = 11,
-               legendfont = 10, title = "Singular values of the snapshots")
+    legendfont = 10, title = "Singular values of the snapshots")
 plot!(svd_plt, svdval_v, markershape = :circle, label = L"Singular Val of $v$")
 plot!(svd_plt, svdval_w, markershape = :circle, label = L"Singular Val of $w$")
 plot!(svd_plt, svdval_fv, markershape = :circle, label = L"Singular Val of $f(v)$")
@@ -118,9 +118,9 @@ points ``x`` from the full-order system.
 
 ```@example deim_FitzHugh_Nagumo
 full_plt = plot(xlabel = L"v(x,t)", ylabel = L"x", zlabel = L"w(x,t)", xlims = (-0.5, 2.0),
-                ylims = (0.0, L), zlims = (0.0, 0.25), legend = false, xflip = true,
-                camera = (50, 30), titlefont = 10,
-                title = "Phase−Space diagram of full $(nameof(pde_sys)) system")
+    ylims = (0.0, L), zlims = (0.0, 0.25), legend = false, xflip = true,
+    camera = (50, 30), titlefont = 10,
+    title = "Phase−Space diagram of full $(nameof(pde_sys)) system")
 @views for i in 1:nₓ
     plot!(full_plt, snapshot_v[i, :], _ -> sol_x[i], snapshot_w[i, :])
 end
@@ -149,9 +149,9 @@ And plot the result from the POD-DEIM reduced system.
 
 ```@example deim_FitzHugh_Nagumo
 deim_plt = plot(xlabel = L"v(x,t)", ylabel = L"x", zlabel = L"w(x,t)", xlims = (-0.5, 2.0),
-                ylims = (0.0, L), zlims = (0.0, 0.25), legend = false, xflip = true,
-                camera = (50, 30), titlefont = 10,
-                title = "Phase−Space diagram of reduced $(nameof(pde_sys)) system")
+    ylims = (0.0, L), zlims = (0.0, 0.25), legend = false, xflip = true,
+    camera = (50, 30), titlefont = 10,
+    title = "Phase−Space diagram of reduced $(nameof(pde_sys)) system")
 @views for i in 1:nₓ
     plot!(deim_plt, sol_deim_v[i, :], _ -> sol_deim_x[i], sol_deim_w[i, :])
 end
@@ -178,12 +178,12 @@ function unconnected(v::AbstractVector, nₜ::Integer)
     vec(data)
 end
 plt_2 = plot(xlabel = L"v(x,t)", ylabel = L"x", zlabel = L"w(x,t)", xlims = (-0.5, 2.0),
-             ylims = (0.0, L), zlims = (0.0, 0.25), xflip = true, camera = (50, 30),
-             titlefont = 10, title = "Comparison of full and reduced systems")
+    ylims = (0.0, L), zlims = (0.0, 0.25), xflip = true, camera = (50, 30),
+    titlefont = 10, title = "Comparison of full and reduced systems")
 plot!(plt_2, unconnected(snapshot_v), unconnected(sol_x, nₜ), unconnected(snapshot_w),
-      label = "Full$(length(ode_sys.eqs))")
+    label = "Full$(length(ode_sys.eqs))")
 plot!(plt_2, unconnected(sol_deim_v), unconnected(sol_deim_x, nₜ_deim),
-      unconnected(sol_deim_w), label = "POD$(pod_dim)/DEIM$(deim_dim)")
+    unconnected(sol_deim_w), label = "POD$(pod_dim)/DEIM$(deim_dim)")
 ```
 
 As we can see, the reduced-order system captures the limit cycle of the original full-order

src/DataReduction/POD.jl

@@ -39,9 +39,9 @@ mutable struct POD <: AbstractDRProblem
     spectrum::Any
     # constructors
     function POD(snaps;
-                 min_renergy = 1.0,
-                 min_nmodes::Int = 1,
-                 max_nmodes::Int = length(snaps[1]))
+            min_renergy = 1.0,
+            min_nmodes::Int = 1,
+            max_nmodes::Int = length(snaps[1]))
         nmodes = min_nmodes
         errorhandle(snaps, nmodes, min_renergy, min_nmodes, max_nmodes)
         new(snaps, min_renergy, min_nmodes, max_nmodes, nmodes, missing, 1.0, missing)
@@ -66,7 +66,7 @@ end
 function reduce!(pod::POD, alg::SVD)
     u, s, v = _svd(pod.snapshots; alg.kwargs...)
     pod.nmodes, pod.renergy = determine_truncation(s, pod.min_nmodes, pod.max_nmodes,
-                                                   pod.min_renergy)
+        pod.min_renergy)
     pod.rbasis = u[:, 1:(pod.nmodes)]
     pod.spectrum = s
     nothing
@@ -94,6 +94,6 @@ function Base.show(io::IO, pod::POD)
     print(io, "POD \n")
     print(io, "Reduction Order = ", pod.nmodes, "\n")
     print(io, "Snapshot size = (", size(pod.snapshots, 1), ",", size(pod.snapshots[1], 2),
-          ")\n")
+        ")\n")
     print(io, "Relative Energy = ", pod.renergy, "\n")
 end

src/ErrorHandle.jl

@@ -7,7 +7,7 @@ function errorhandle(data::AbstractMatrix, nmodes::Int, max_energy, min_nmodes,
 end
 
 function errorhandle(data::AbstractVector{T}, nmodes::Int, max_energy, min_nmodes,
-                     max_nmodes) where {T <: AbstractVector}
+        max_nmodes) where {T <: AbstractVector}
     @assert size(data[1], 1)>1 "State vector is expected to be vector valued."
     s = min(size(data, 1), size(data[1], 1))
     @assert 0<nmodes<=s "Number of modes should be in {1,2,...,$s}."

src/deim.jl

@@ -65,9 +65,9 @@ the ``\\rho_i``-th column of the identity matrix ``I_n\\in\\mathbb R^{n\\times n
 - `linear_projection_eqs`: the linear projection mapping ``\\mathbf y=V\\hat{\\mathbf y}``.
 """
 function deim(full_vars::AbstractVector, linear_coeffs::AbstractMatrix,
-              constant_part::AbstractVector, nonlinear_part::AbstractVector,
-              reduced_vars::AbstractVector, linear_projection_matrix::AbstractMatrix,
-              nonlinear_projection_matrix::AbstractMatrix; kwargs...)
+        constant_part::AbstractVector, nonlinear_part::AbstractVector,
+        reduced_vars::AbstractVector, linear_projection_matrix::AbstractMatrix,
+        nonlinear_projection_matrix::AbstractMatrix; kwargs...)
     # rename variables for convenience
     y = full_vars
     A = linear_coeffs
@@ -119,8 +119,8 @@ nonlinear terms, which is computed by executing the runtime-generated function f
 nonlinear expressions.
 """
 function deim(sys::ODESystem, snapshot::AbstractMatrix, pod_dim::Integer;
-              deim_dim::Integer = pod_dim, name::Symbol = Symbol(nameof(sys), :_deim),
-              kwargs...)::ODESystem
+        deim_dim::Integer = pod_dim, name::Symbol = Symbol(nameof(sys), :_deim),
+        kwargs...)::ODESystem
     sys = deepcopy(sys)
     @set! sys.name = name
 
@@ -167,7 +167,7 @@ function deim(sys::ODESystem, snapshot::AbstractMatrix, pod_dim::Integer;
     fullstates = [map(eq -> eq.lhs, old_observed); dvs; ModelingToolkit.get_states(sys)]
     new_observed = [old_observed; linear_projection_eqs]
     new_sorted_observed = ModelingToolkit.topsort_equations(new_observed, fullstates;
-                                                            kwargs...)
+        kwargs...)
     @set! sys.observed = new_sorted_observed
 
     inv_dict = Dict(Symbolics.scalarize(ŷ .=> V' * dvs)) # reduced vars to original vars

test/runtests.jl

@@ -1,6 +1,14 @@
 using SafeTestsets
 
-@safetestset "Quality Assurance" begin include("qa.jl") end
-@safetestset "POD" begin include("DataReduction.jl") end
-@safetestset "utils" begin include("utils.jl") end
-@safetestset "DEIM" begin include("deim.jl") end
+@safetestset "Quality Assurance" begin
+    include("qa.jl")
+end
+@safetestset "POD" begin
+    include("DataReduction.jl")
+end
+@safetestset "utils" begin
+    include("utils.jl")
+end
+@safetestset "DEIM" begin
+    include("deim.jl")
+end