Make symbolics a Module (#270)

src/DifferentialEquation.jl

@@ -29,7 +29,7 @@ Return the dependent variables of `diff_eom`.
 Symbolics.get_variables(diff_eom::DifferentialEquation)::Vector{Num} =
     collect(keys(diff_eom.equations))
 
-is_harmonic(diff_eom::DifferentialEquation, t::Num)::Bool =
+ExprUtils.is_harmonic(diff_eom::DifferentialEquation, t::Num)::Bool =
     all([is_harmonic(eq, t) for eq in values(diff_eom.equations)])
 
 "Pretty printing of the newly defined types"

src/ExprUtils/ExprUtils.jl

@@ -0,0 +1,42 @@
+module ExprUtils
+
+using DocStringExtensions
+using OrderedCollections: OrderedDict
+
+using SymbolicUtils:
+    SymbolicUtils,
+    Postwalk,
+    Sym,
+    BasicSymbolic,
+    isterm,
+    ispow,
+    isadd,
+    isdiv,
+    ismul,
+    add_with_div,
+    frac_maketerm,
+    @compactified,
+    issym
+
+using Symbolics:
+    Symbolics,
+    Num,
+    unwrap,
+    wrap,
+    get_variables,
+    Equation,
+    Differential,
+    @variables,
+    arguments,
+    simplify_fractions,
+    substitute,
+    term,
+    expand,
+    operation
+
+include("Symbolics_utils.jl")
+include("exponentials.jl")
+include("fourier.jl")
+include("drop_powers.jl")
+
+end

src/modules/HC_wrapper.jl → src/HC_wrapper/HC_wrapper.jl

@@ -1,22 +1,17 @@
 module HC_wrapper
 
 using DocStringExtensions
-using Symbolics: Num, @variables
+using Symbolics: Num, @variables, expand_derivatives, get_variables
 using Symbolics.SymbolicUtils: isterm
 using LinearAlgebra: LinearAlgebra
 
 using HarmonicBalance:
-    HarmonicBalance,
-    HarmonicEquation,
-    _remove_brackets,
-    expand_derivatives,
-    var_name,
-    get_variables,
-    Problem
+    HarmonicBalance, HarmonicEquation, _remove_brackets, var_name, Problem
+
 using HomotopyContinuation
 using HomotopyContinuation: Variable, System
 
-include("HC_wrapper/homotopy_interface.jl")
+include("homotopy_interface.jl")
 
 export Problem
 

src/HarmonicBalance.jl

@@ -1,5 +1,11 @@
 module HarmonicBalance
 
+# default global settings
+IM_TOL::Float64 = 1E-6
+function set_imaginary_tolerance(x::Float64)
+    @eval(IM_TOL::Float64 = $x)
+end
+
 using DocStringExtensions
 using JLD2: JLD2
 using DelimitedFiles: DelimitedFiles, writedlm
@@ -16,54 +22,14 @@ const HC = HomotopyContinuation
 using Plots: Plots, plot, plot!, savefig, heatmap, Plot
 using Latexify: Latexify, latexify
 
-using PrecompileTools: @setup_workload, @compile_workload
-
-# default global settings
-IM_TOL::Float64 = 1E-6
-function set_imaginary_tolerance(x::Float64)
-    @eval(IM_TOL::Float64 = $x)
-end
+using Symbolics:
+    Symbolics, Num, Equation, @variables, expand_derivatives, get_variables, Differential
+using SymbolicUtils: SymbolicUtils
 
-using SymbolicUtils:
-    SymbolicUtils,
-    Postwalk,
-    Sym,
-    BasicSymbolic,
-    isterm,
-    ispow,
-    isadd,
-    isdiv,
-    ismul,
-    add_with_div,
-    frac_maketerm,
-    @compactified,
-    issym
+include("ExprUtils/ExprUtils.jl")
+using .ExprUtils: is_harmonic, substitute_all, drop_powers
 
-using Symbolics:
-    Symbolics,
-    Num,
-    unwrap,
-    wrap,
-    get_variables,
-    simplify,
-    expand_derivatives,
-    build_function,
-    Equation,
-    Differential,
-    @variables,
-    arguments,
-    simplify_fractions,
-    substitute,
-    term,
-    expand,
-    operation
-
-include("Symbolics/Symbolics_utils.jl")
-include("Symbolics/exponentials.jl")
-include("Symbolics/fourier.jl")
-include("Symbolics/drop_powers.jl")
-
-include("modules/extention_functions.jl")
+include("extention_functions.jl")
 include("utils.jl")
 include("types.jl")
 
@@ -90,34 +56,36 @@ export plot, plot!, plot_phase_diagram, savefig, plot_spaghetti
 export ParameterSweep, steady_state_sweep
 export plot_1D_solutions_branch, follow_branch
 
-include("modules/HC_wrapper.jl")
+include("HC_wrapper/HC_wrapper.jl")
 using .HC_wrapper
 
-include("modules/LinearResponse.jl")
+include("LinearResponse/LinearResponse.jl")
 using .LinearResponse
 export plot_linear_response, plot_rotframe_jacobian_response, get_Jacobian, plot_eigenvalues
 export transform_solutions
 
-include("modules/LimitCycles.jl")
+include("LimitCycles/LimitCycles.jl")
 using .LimitCycles
 export get_cycle_variables, get_limit_cycles, add_pairs!
 
-include("modules/KrylovBogoliubov.jl")
+include("KrylovBogoliubov/KrylovBogoliubov.jl")
 using .KrylovBogoliubov
 export first_order_transform!, is_rearranged_standard, rearrange_standard!, get_equations
 export get_krylov_equations
 
-include("modules/FFTWExt.jl")
+include("FFTWExt.jl")
 using .FFTWExt
 
-# @setup_workload begin
-#     # Putting some things in `@setup_workload` instead of `@compile_workload` can reduce the size of the
-#     # precompile file and potentially make loading faster.
-#     @compile_workload begin
-#         # all calls in this block will be precompiled, regardless of whether
-#         # they belong to your package or not (on Julia 1.8 and higher)
-#         include("precompilation.jl")
-#     end
-# end
+using PrecompileTools: @setup_workload, @compile_workload
+
+@setup_workload begin
+    # Putting some things in `@setup_workload` instead of `@compile_workload` can reduce the size of the
+    # precompile file and potentially make loading faster.
+    @compile_workload begin
+        # all calls in this block will be precompiled, regardless of whether
+        # they belong to your package or not (on Julia 1.8 and higher)
+        include("precompilation.jl")
+    end
+end
 
 end # module

src/HarmonicEquation.jl

@@ -82,7 +82,7 @@ function slow_flow(
 end
 
 #   Drop powers of `var` of degree >= `deg` from the equation set in `eom`.
-function drop_powers(eom::HarmonicEquation, terms::Vector{Num}, deg::Int)
+function ExprUtils.drop_powers(eom::HarmonicEquation, terms::Vector{Num}, deg::Int)
     new_eom = deepcopy(eom)
     new_eom.equations = drop_powers(eom.equations, terms, deg)
     return new_eom
@@ -157,7 +157,9 @@ end
 ###
 
 "Apply `rules` to both `equations` and `variables` field of `eom`"
-function substitute_all(eom::HarmonicEquation, rules::Union{Dict,Pair})::HarmonicEquation
+function ExprUtils.substitute_all(
+    eom::HarmonicEquation, rules::Union{Dict,Pair}
+)::HarmonicEquation
     new_eom = deepcopy(eom)
     new_eom.equations = expand_derivatives.(substitute_all(eom.equations, rules))
     return new_eom
@@ -205,11 +207,11 @@ function fourier_transform!(eom::HarmonicEquation, time::Num)
         eq = eom.equations[eq_idx]
         # "type" is usually "u" or "v" (harmonic) or ["a"] (zero-harmonic)
         if hvar.type == "u"
-            avg_eqs[i] = fourier_cos_term(eq, hvar.ω, time)
+            avg_eqs[i] = ExprUtils.fourier_cos_term(eq, hvar.ω, time)
         elseif hvar.type == "v"
-            avg_eqs[i] = fourier_sin_term(eq, hvar.ω, time)
+            avg_eqs[i] = ExprUtils.fourier_sin_term(eq, hvar.ω, time)
         elseif hvar.type == "a"
-            avg_eqs[i] = fourier_cos_term(eq, 0, time) # pick out the constants
+            avg_eqs[i] = ExprUtils.fourier_cos_term(eq, 0, time) # pick out the constants
         end
     end
     eom.equations = avg_eqs

src/HarmonicVariable.jl

@@ -24,11 +24,11 @@ end
 ###
 
 # when HV is used for substitute, substitute its symbol
-function substitute_all(eq::Union{Num,Equation}, rules::Dict{HarmonicVariable})
+function ExprUtils.substitute_all(eq::Union{Num,Equation}, rules::Dict{HarmonicVariable})
     return substitute(eq, Dict(zip(getfield.(keys(rules), :symbol), values(rules))))
 end
 
-function substitute_all(var::HarmonicVariable, rules)
+function ExprUtils.substitute_all(var::HarmonicVariable, rules)
     sym, freq = var.symbol, var.ω
     return HarmonicVariable(
         substitute_all(sym, rules),
@@ -39,7 +39,7 @@ function substitute_all(var::HarmonicVariable, rules)
     )
 end
 
-function substitute_all(vars::Vector{HarmonicVariable}, rules)
+function ExprUtils.substitute_all(vars::Vector{HarmonicVariable}, rules)
     return [substitute_all(var, rules) for var in vars]
 end
 
@@ -80,4 +80,4 @@ function var_name(x::Num)
     return var isa Expr ? String(var.args[1]) : String(var)
 end
 #  var_name(x::Term) = String(Symbolics._toexpr(x).args[1])
-var_name(x::Sym) = String(x.name)
+var_name(x::SymbolicUtils.Sym) = String(x.name)

src/modules/KrylovBogoliubov.jl → src/KrylovBogoliubov/KrylovBogoliubov.jl

@@ -11,20 +11,21 @@ using HarmonicBalance
 using HarmonicBalance:
     rearrange!,
     flatten,
-    is_harmonic,
     _create_harmonic_variable,
-    trig_reduce,
-    get_independent,
-    simplify_complex,
-    is_trig,
-    substitute_all,
     slow_flow,
     _remove_brackets,
-    get_all_terms,
     get_variables_nums
 
-include("KrylovBogoliubov/first_order_transform.jl")
-include("KrylovBogoliubov/KrylovEquation.jl")
+using HarmonicBalance.ExprUtils:
+    get_all_terms,
+    substitute_all,
+    trig_reduce,
+    get_independent,
+    simplify_complex,
+    is_trig,
+    is_harmonic
+include("first_order_transform.jl")
+include("KrylovEquation.jl")
 
 export first_order_transform!,
     is_rearranged_standard, rearrange_standard!, get_equations, get_krylov_equations

src/modules/LimitCycles.jl → src/LimitCycles/LimitCycles.jl

@@ -13,13 +13,13 @@ using HarmonicBalance:
     _free_symbols,
     _symidx,
     _is_physical,
-    get_all_terms,
     substitute_all,
     var_name
 using HarmonicBalance.LinearResponse: get_implicit_Jacobian
+using HarmonicBalance.ExprUtils: get_all_terms
 
-include("LimitCycles/gauge_fixing.jl")
-include("LimitCycles/analysis.jl")
+include("gauge_fixing.jl")
+include("analysis.jl")
 
 export get_cycle_variables, get_limit_cycles, add_pairs!
 

src/modules/LinearResponse.jl → 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, build_function, Equation, substitute, unwrap
+using Symbolics: Num, Equation, substitute, unwrap
 using LinearAlgebra: norm, eigvals, eigen, eigvecs
 using OrderedCollections: OrderedDict
 
@@ -32,12 +32,12 @@ using HarmonicBalance:
     is_rearranged
 using ..HC_wrapper
 
-include("LinearResponse/types.jl")
-include("LinearResponse/utils.jl")
-include("LinearResponse/jacobians.jl")
-include("LinearResponse/Lorentzian_spectrum.jl")
-include("LinearResponse/response.jl")
-include("LinearResponse/plotting.jl")
+include("types.jl")
+include("utils.jl")
+include("jacobians.jl")
+include("Lorentzian_spectrum.jl")
+include("response.jl")
+include("plotting.jl")
 
 export get_Jacobian, get_response, show
 export plot_linear_response, plot_rotframe_jacobian_response, plot_eigenvalues

src/modules/LinearResponse/response.jl → src/LinearResponse/response.jl

@@ -37,7 +37,7 @@ function ResponseMatrix(res::Result; rules=Dict())
     M = get_response_matrix(res.problem.eom.natural_equation, Δ; order=2)
     M = substitute_all(M, merge(res.fixed_parameters, rules))
     symbols = _free_symbols(res)
-    compiled_M = [build_function(el, cat(symbols, [Δ]; dims=1)) for el in M]
+    compiled_M = [Symbolics.build_function(el, cat(symbols, [Δ]; dims=1)) for el in M]
 
     return ResponseMatrix(eval.(compiled_M), symbols, res.problem.eom.variables)
 end

src/plotting_Plots.jl

@@ -136,7 +136,7 @@ function plot1D(
     branches=1:branch_count(res),
     add=false,
     kwargs...,
-)
+)::Plots.Plot
     if class == "default"
         args = [:x => x, :y => y, :branches => branches]
         if not_class == [] # plot stable full, unstable dashed
@@ -202,7 +202,7 @@ function plot2D(
     not_class=[],
     add=false,
     kwargs...,
-)
+)::Plots.Plot
     X, Y = values(res.swept_parameters)
     Z =
         getindex.(

src/solve_homotopy.jl

@@ -211,7 +211,7 @@ Substitute the values according to `fixed_parameters` and compile into a functio
 """
 function compile_matrix(mat, variables; rules=Dict(), postproc=x -> x)
     J = substitute_all.(mat, Ref(rules))
-    matrix = build_function(J, variables)
+    matrix = Symbolics.build_function(J, variables)
     matrix = eval(matrix[1]) # compiled allocating function, see Symbolics manual
     m(vals::Vector) = postproc(matrix(vals))
     m(s::OrderedDict) = m([s[var] for var in variables]) # for the UI