test: enable JET

src/HarmonicEquation.jl

@@ -167,7 +167,7 @@ end
 
 "Simplify the equations in HarmonicEquation."
 function simplify!(eom::HarmonicEquation)
-    return eom.equations = [simplify(eq) for eq in eom.equations]
+    return eom.equations = [Symbolics.simplify(eq) for eq in eom.equations]
 end
 
 """

src/HarmonicVariable.jl

@@ -25,7 +25,9 @@ end
 
 # when HV is used for substitute, substitute its symbol
 function ExprUtils.substitute_all(eq::Union{Num,Equation}, rules::Dict{HarmonicVariable})
-    return substitute(eq, Dict(zip(getfield.(keys(rules), :symbol), values(rules))))
+    return Symbolics.substitute(
+        eq, Dict(zip(getfield.(keys(rules), :symbol), values(rules)))
+    )
 end
 
 function ExprUtils.substitute_all(var::HarmonicVariable, rules)

src/KrylovBogoliubov/KrylovEquation.jl

@@ -116,7 +116,7 @@ function van_der_Pol(eom::DifferentialEquation, t::Num)
         D = Differential(t)
         nvar_t = diff2term(D(unwrap(nvar)))
         vdP_rules = Dict(D(hvar_u.symbol) => 0, D(hvar_v.symbol) => 0)
-        rules[nvar_t] = substitute(expand_derivatives(D(rule)), vdP_rules)
+        rules[nvar_t] = Symbolics.substitute(expand_derivatives(D(rule)), vdP_rules)
 
         uv_idx += 1
         push!(vars, hvar_u, hvar_v)

src/LinearResponse/LinearResponse.jl

@@ -8,7 +8,7 @@ using Plots: heatmap, theme_palette, scatter, RGB, cgrad
 using Latexify: Latexify, latexify, @L_str
 using Latexify.LaTeXStrings: LaTeXStrings
 
-using Symbolics: Num, Equation, substitute, unwrap
+using Symbolics: Symbolics, Num, Equation, unwrap
 using LinearAlgebra: norm, eigvals, eigen, eigvecs
 using OrderedCollections: OrderedDict
 

src/LinearResponse/Lorentzian_spectrum.jl

@@ -90,7 +90,8 @@ function JacobianSpectrum(res::Result; index::Int, branch::Int, force=false)
         for pair in _get_uv_pairs(hvars)
             u, v = hvars[pair]
             eigvec_2d = eigvec[pair] # fetch the relevant part of the Jacobian eigenvector
-            ωnum = real(unwrap(substitute(u.ω, solution_dict))) # the harmonic (numerical now) associated to this harmonic variable
+            ωnum = real(unwrap(Symbolics.substitute(u.ω, solution_dict)))
+            # ^ the harmonic (numerical now) associated to this harmonic variable
 
             # eigvec_2d is associated to a natural variable -> this variable gets Lorentzian peaks
             peaks = norm(eigvec_2d) * _pair_to_peaks(λ, eigvec_2d; ω=ωnum)

test/runtests.jl

@@ -5,10 +5,10 @@ using Random
 const SEED = 0xd8e5d8df
 Random.seed!(SEED)
 
-# @testset "Code linting" begin
-#     using JET
-#     JET.test_package(HarmonicBalance; target_defined_modules=true)
-# end
+@testset "Code linting" begin
+    using JET
+    JET.test_package(HarmonicBalance; target_defined_modules=true)
+end
 
 @testset "Code quality" begin
     using ExplicitImports, Aqua