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NonlinearOscillations · Jun 13, 2024 · 75c1241 · 75c1241
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Showing 6 changed files with 25 additions and 11 deletions.
diff --git a/Project.toml b/Project.toml
@@ -34,38 +34,40 @@ SteadyStateDiffEqExt = "SteadyStateDiffEq"
 TimeEvolution = "OrdinaryDiffEq"
 
 [compat]
+JET = "0.9"
+Aqua = "0.8"
 BijectiveHilbert = "0.3.0"
 DSP = "0.7.4"
 DelimitedFiles = "1"
 Distances = "0.10.7"
 DocStringExtensions = "0.9"
+ExplicitImports = "1.6"
 FFTW = "1.5.0"
 HomotopyContinuation = "2.6.4"
 JLD2 = "0.4.24"
 Latexify = "0.15.16, 0.16"
 ModelingToolkit = "9"
+NonlinearSolve = "3.12"
 OrderedCollections = "1.4.1"
 OrdinaryDiffEq = "v6.33.1"
-Peaks = "0.4.0, 0.5"
+Peaks = "0.4"
 Plots = "1.35.0"
 ProgressMeter = "1.7.2"
 SteadyStateDiffEq = "1, 2"
 SymbolicUtils = "2.0"
 Symbolics = "5.0.0"
 julia = "1.10.0"
-NonlinearSolve = "3.12"
-ExplicitImports = "1.6"
-Aqua = "0.8"
 
 [extras]
+JET = "c3a54625-cd67-489e-a8e7-0a5a0ff4e31b"
+Aqua = "4c88cf16-eb10-579e-8560-4a9242c79595"
 ExplicitImports = "7d51a73a-1435-4ff3-83d9-f097790105c7"
 ModelingToolkit = "961ee093-0014-501f-94e3-6117800e7a78"
 NonlinearSolve = "8913a72c-1f9b-4ce2-8d82-65094dcecaec"
 OrdinaryDiffEq = "1dea7af3-3e70-54e6-95c3-0bf5283fa5ed"
 Pkg = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f"
 SteadyStateDiffEq = "9672c7b4-1e72-59bd-8a11-6ac3964bc41f"
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
-Aqua = "4c88cf16-eb10-579e-8560-4a9242c79595"
 
 [targets]
 test = ["Pkg", "Test", "OrdinaryDiffEq", "ModelingToolkit", "SteadyStateDiffEq", "NonlinearSolve", "ExplicitImports", "Aqua"]
diff --git a/README.md b/README.md
@@ -4,6 +4,11 @@
 [![docs](https://img.shields.io/badge/docs-online-blue.svg)](https://nonlinearoscillations.github.io/HarmonicBalance.jl/stable/)
 [![Downloads](https://shields.io/endpoint?url=https://pkgs.genieframework.com/api/v1/badge/HarmonicBalance)](https://pkgs.genieframework.com?packages=HarmonicBalance)
 
+[![Code Style: Blue](https://img.shields.io/badge/code%20style-blue-4495d1.svg)](https://github.com/invenia/BlueStyle)
+[![Aqua QA](https://raw.githubusercontent.com/JuliaTesting/Aqua.jl/master/badge.svg)](https://github.com/JuliaTesting/Aqua.jl)
+[![JET](https://img.shields.io/badge/%E2%9C%88%EF%B8%8F%20tested%20with%20-%20JET.jl%20-%20red)](https://github.com/aviatesk/JET.jl)
+
+
 **HarmonicBalance.jl** is a Julia package for solving nonlinear differential equations using the method of harmonic balance.
 
 ## Installation

diff --git a/src/modules/FFTWExt.jl b/src/modules/FFTWExt.jl
@@ -34,7 +34,7 @@ function FFT_analyze(fft_u::Vector{ComplexF64}, fft_f)
     This correction works for a rectangular window."
 
     # retaining more sigdigits gives more ''spurious'' peaks
-    max_indices, mxval = Peaks.peakprom(round.(abs.(fft_u), sigdigits=3); minprom=1)
+    max_indices, mxval = Peaks.peakproms(round.(abs.(fft_u), sigdigits=3); minprom=1)
     Del = fft_f[2] - fft_f[1] # frequency spacing
     A1 = abs.(fft_u)[max_indices]
     df = zeros(length(max_indices))

diff --git a/src/solve_homotopy.jl b/src/solve_homotopy.jl
@@ -347,7 +347,7 @@ function _get_raw_solution(
         end
         for i in eachindex(parameter_values) # do NOT thread this
             p = parameter_values[i]
-            show_progress ? next!(bar) : nothing
+            show_progress ? ProgressMeter.next!(bar) : nothing
             result_full[i] = [
                 HC.solve(
                     problem.system;

diff --git a/src/sorting.jl b/src/sorting.jl
@@ -111,7 +111,7 @@ function sort_1D(solns::Vector{Vector{SteadyState}}; show_progress=true)
         )
     end
     for i in eachindex(solns[1:(end - 1)])
-        show_progress ? next!(bar) : nothing
+        show_progress ? ProgressMeter.next!(bar) : nothing
         matched_indices = align_pair(sorted_solns[i], solns[i + 1]) # pairs of matching indices
         next_indices = getindex.(matched_indices, 2) # indices of the next solution
         sorted_solns[i + 1] = (solns[i + 1])[next_indices]
@@ -185,7 +185,7 @@ function sort_2D(
         )
     end
     for i in 1:(length(idx_pairs) - 1)
-        show_progress ? next!(bar) : nothing
+        show_progress ? ProgressMeter.next!(bar) : nothing
         neighbors = get_nn_2D(idx_pairs[i + 1], size(solns, 1), size(solns, 2))
         reference = [sorted_solns[ind...] for ind in neighbors]
         matched_indices = align_pair(reference, solns[idx_pairs[i + 1]...]) # pairs of matching indices

diff --git a/test/runtests.jl b/test/runtests.jl
@@ -5,7 +5,7 @@ using Random
 const SEED = 0xd8e5d8df
 Random.seed!(SEED)
 
-@testset "Package health" begin
+@testset "Code quality" begin
     using ExplicitImports, Aqua
     ignore_deps = [:Random, :LinearAlgebra, :Printf, :Test, :Pkg]
 
@@ -21,10 +21,13 @@ Random.seed!(SEED)
         ),
         piracies=(treat_as_own=[HarmonicBalance.Num],),
         ambiguities=false,
-        persistent_tasks=false,
     )
 end
 
+@testset "Code linting" begin
+    JET.test_package(HarmonicBalance; target_defined_modules=true)
+end
+
 @testset "Symbolics customised" begin
     include("powers.jl")
     include("harmonics.jl")
@@ -65,3 +68,7 @@ end
     include("ModelingToolkitExt.jl")
     include("SteadyStateDiffEqExt.jl")
 end
+
+@testset "Doctests" begin
+    Documenter.doctest(HiddenMarkovModels)
+end