build: fix compat Symbolics (#422)

oameye · web-flow · commit 9d3c25e52399 · 2025-04-11T14:24:23.000+01:00
* Update Project.toml

* format with formatter v2

* ne CI tests

* fix: update branch references from 'main' to 'master' in CI workflow

* bump SciMLBase compat

* bump ModelingToolkit

* up compat SteadyStateDiffEq
diff --git a/.github/workflows/Tests.yml b/.github/workflows/Tests.yml
@@ -1,4 +1,4 @@
-name: CI
+name: Tests
 on:
   push:
     tags:
@@ -13,6 +13,10 @@ concurrency:
   # Cancel intermediate builds: only if it is a pull request build.
   group: ${{ github.workflow }}-${{ github.ref }}
   cancel-in-progress: ${{ startsWith(github.ref, 'refs/pull/') }}
+
+env:
+  JULIA_NUM_THREADS: 11
+
 jobs:
   test:
     name: Julia ${{ matrix.version }} - ${{ matrix.os }} - ${{ matrix.arch }}
@@ -22,6 +26,7 @@ jobs:
       actions: write
       contents: read
     strategy:
+      fail-fast: false
       matrix:
         version:
           - 'pre'
@@ -44,11 +49,10 @@ jobs:
       - uses: julia-actions/julia-buildpkg@v1
       - uses: julia-actions/julia-runtest@v1
       # - uses: julia-actions/julia-processcoverage@v1
-      # - uses: codecov/codecov-action@v4
+      # - uses: codecov/codecov-action@v5
       #   with:
-      #     files: lcov.info
       #     token: ${{ secrets.CODECOV_TOKEN }}
+      #     file: lcov.info
+      #     name: codecov-umbrella
       #     fail_ci_if_error: false
-      # - uses: julia-actions/julia-uploadcoveralls@v1
-      #   env:
-      #     COVERALLS_TOKEN: ${{ secrets.COVERALLS_TOKEN }}
+      #   if: ${{ matrix.version == 'lts' }}
diff --git a/Project.toml b/Project.toml
@@ -42,16 +42,16 @@ DocStringExtensions = "0.9.3"
 FunctionWrappers = "1.1.3"
 HomotopyContinuation = "2.12"
 LinearSolve = "2.39.0, 3"
-ModelingToolkit = "9.60"
+ModelingToolkit = "9.70.0"
 NaNMath = "1.1"
 OrderedCollections = "1.6"
 OrdinaryDiffEqTsit5 = "1.1"
 Plots = "1.40.9"
 PrecompileTools = "1.2"
 ProgressMeter = "1.7.2"
 QuantumCumulants = "0.3.7"
-SciMLBase = "2.72.0"
-SteadyStateDiffEq = "2.4.1"
-SymbolicUtils = "3.11"
-Symbolics = "6.23"
+SciMLBase = "2.83.1"
+SteadyStateDiffEq = "2.5.0"
+SymbolicUtils = "3.25.1"
+Symbolics = "~6.34"
 julia = "1.10.0"
diff --git a/docs/make.jl b/docs/make.jl
@@ -52,7 +52,7 @@ makedocs(;
     pages=pages,
     source="src",
     build="build",
-    draft=!CI,
+    draft=(!CI),
     warnonly=if CI
         [:linkcheck, :cross_references]
     else
diff --git a/examples/ab_initio_noise.jl b/examples/ab_initio_noise.jl
@@ -68,9 +68,7 @@ plot(freqω, psd; yscale=:log10, xlabel="Frequency", ylabel="Power")
 
 # We will perform parameter sweep to generate noise spectra across the driving frequency $\omega$. For this we use the `EnsembleProblem` API from the SciML ecosystem.
 setter! = setp(sdesystem, ω)
-prob_func(prob, i, repeat) = (prob′ = remake(prob);
-setter!(prob′, ωrange[i]);
-prob′)
+prob_func(prob, i, repeat) = (prob′=remake(prob); setter!(prob′, ωrange[i]); prob′)
 output_func(sol, i) = (outputpsd(sol), false)
 prob_ensemble = EnsembleProblem(sdeproblem; prob_func=prob_func, output_func=output_func)
 sol_ensemble = solve(
diff --git a/examples/state_dependent_perturbation.jl b/examples/state_dependent_perturbation.jl
@@ -205,12 +205,9 @@ prob = HarmonicBalance.Problem(harmonic_tmp, varied, fixed)
 # We will sweep over the $\omega-\lambda$ plane and substitute the non-zero amplitude solution of the antisymmetric mode into the coupled equations of thesymmetric mode.
 
 all_keys = cat(collect(keys(varied)), collect(keys(fixed)); dims=1)
-permutation =
-    first.(
-        filter(
-            !isempty, [findall(x -> isequal(x, par), all_keys) for par in prob.parameters]
-        )
-    )
+permutation = first.(
+    filter(!isempty, [findall(x -> isequal(x, par), all_keys) for par in prob.parameters])
+)
 
 param_ranges = collect(values(varied))
 input_array = collect(Iterators.product(param_ranges..., values(fixed)...))
diff --git a/examples/steady_state_sweep.jl b/examples/steady_state_sweep.jl
@@ -48,8 +48,9 @@ plot(time_soln.t, norm.(time_soln.u))
 # ## using follow_branch
 
 followed_branch, Ys = follow_branch(1, result_HB; y="√(u1^2+v1^2)")
-Y_followed_gr =
-    real.([Ys[param_idx][branch] for (param_idx, branch) in enumerate(followed_branch)]);
+Y_followed_gr = real.([
+    Ys[param_idx][branch] for (param_idx, branch) in enumerate(followed_branch)
+]);
 
 plot(result_HB, "sqrt(u1^2+v1^2)")
 plot!(ω_range, Y_followed_gr; c=:gray, ls=:dash)
@@ -64,8 +65,9 @@ plot!(ω_range, Y_followed_gr; c=:gray, ls=:dash)
 
 @btime begin
     followed_branch, Ys = follow_branch(1, result_HB; y="√(u1^2+v1^2)")
-    Y_followed_gr =
-        real.([Ys[param_idx][branch] for (param_idx, branch) in enumerate(followed_branch)])
+    Y_followed_gr = real.([
+        Ys[param_idx][branch] for (param_idx, branch) in enumerate(followed_branch)
+    ])
 end
 
 # Plotting them together gives:
diff --git a/ext/QuantumCumulantsExt.jl b/ext/QuantumCumulantsExt.jl
@@ -49,9 +49,9 @@ function replace_to_reals(eqs::Vector{String}, ops_av::Vector{String}, conjugate
         conj_replace = map(eachindex(pair)) do i
             op = ops_av[pair[i]] # ∨ f(i) contains "+" or "-"
             op => if is_real
-                "((" * op_r * ") / √(2))"       #=prefactor * " " *=#
+                "((" * op_r * ") / √(2))"
             else
-                "((" * op_r * " $(f(i)) im*" * op_i * ") / √(2))"                #=prefactor *=#
+                "((" * op_r * " $(f(i)) im*" * op_i * ") / √(2))"
             end
         end
         if isequal(pair...)
diff --git a/ext/TimeEvolution/ODEProblem.jl b/ext/TimeEvolution/ODEProblem.jl
@@ -37,7 +37,7 @@ function OrdinaryDiffEqTsit5.ODEProblem(
             unwrap.([
                 substitute(eq, Dict(zip(keys(sweep), [sweep[p](T) for p in keys(sweep)])))
                 for eq in eqs(v)
-            ])
+            ]),
         )
     end
 
diff --git a/src/DifferentialEquation.jl b/src/DifferentialEquation.jl
@@ -115,8 +115,9 @@ $(TYPEDSIGNATURES)
 
 Return the dependent variables of `diff_eom`.
 """
-Symbolics.get_variables(diff_eom::DifferentialEquation)::Vector{Num} =
-    collect(keys(diff_eom.equations))
+Symbolics.get_variables(diff_eom::DifferentialEquation)::Vector{Num} = collect(
+    keys(diff_eom.equations)
+)
 
 """
 $(TYPEDSIGNATURES)
@@ -125,8 +126,9 @@ Check if all equations in `diff_eom` are harmonic with respect to `t`. The funct
 differential equation system `diff_eom` and a variable `t`, and returns `true` if all equations
 are harmonic with respect to `t`, otherwise it returns `false`.
 """
-ExprUtils.is_harmonic(diff_eom::DifferentialEquation, t::Num)::Bool =
-    all([is_harmonic(eq, t) for eq in values(diff_eom.equations)])
+ExprUtils.is_harmonic(diff_eom::DifferentialEquation, t::Num)::Bool = all([
+    is_harmonic(eq, t) for eq in values(diff_eom.equations)
+])
 
 """
 $(TYPEDSIGNATURES)
diff --git a/src/HarmonicEquation.jl b/src/HarmonicEquation.jl
@@ -21,14 +21,14 @@ mutable struct HarmonicEquation
     # use a self-referential constructor with _parameters
     function HarmonicEquation(equations, variables, nat_eq)
         return (
-            x = new(
+            x=new(
                 equations,
                 variables,
                 Num[],
                 nat_eq,
                 dummy_symbolic_Jacobian(length(variables)),
             );
-            x.parameters = _parameters(x);
+            x.parameters=_parameters(x);
             x
         )
     end
diff --git a/src/HarmonicVariable.jl b/src/HarmonicVariable.jl
@@ -97,13 +97,15 @@ function ExprUtils.substitute_all(vars::Vector{HarmonicVariable}, rules)
 end
 
 "Returns the symbols of a `HarmonicVariable`."
-get_variables_nums(vars::Vector{Num}) =
+function get_variables_nums(vars::Vector{Num})
     unique(flatten([Num.(get_variables(x)) for x in vars]))
+end
 
 Symbolics.get_variables(var::HarmonicVariable)::Num = Num(first(get_variables(var.symbol)))
 
-Base.isequal(v1::HarmonicVariable, v2::HarmonicVariable)::Bool =
-    isequal(v1.symbol, v2.symbol)
+Base.isequal(v1::HarmonicVariable, v2::HarmonicVariable)::Bool = isequal(
+    v1.symbol, v2.symbol
+)
 
 "The derivative of f w.r.t. x of degree deg"
 function d(f::Num, x::Num, deg=1)::Num
diff --git a/src/modules/HC_wrapper.jl b/src/modules/HC_wrapper.jl
@@ -12,8 +12,9 @@ using HomotopyContinuation
 using HomotopyContinuation: Variable, System
 
 "Conversion from Symbolics.jl types to HomotopyContinuation types."
-HomotopyContinuation.Variable(var::Num) =
+function HomotopyContinuation.Variable(var::Num)
     isterm(var.val) ? Variable(string(var.val.f)) : Variable(string(var_name(var)))
+end
 
 "Converts a Num into Variable in the active namespace."
 function Num_to_Variable(x::Num)
@@ -23,8 +24,9 @@ function Num_to_Variable(x::Num)
 end
 
 "Converts a Num dictionary into a Variable dictionary."
-Num_to_Variable(dict::Dict{Num,T}) where {T<:Number} =
-    Dict{Variable,T}([[Variable(key), dict[key]] for key in keys(dict)]) # for the parameter assignments
+function Num_to_Variable(dict::Dict{Num,T}) where {T<:Number}
+    Dict{Variable,T}([[Variable(key), dict[key]] for key in keys(dict)])
+end # for the parameter assignments
 
 "Parse symbolic expressions as the Expression type in HomotopyContinuation."
 function parse_equations(eqs::Vector{Num})
diff --git a/src/modules/LinearResponse/Lorentzian_spectrum.jl b/src/modules/LinearResponse/Lorentzian_spectrum.jl
@@ -46,8 +46,9 @@ function add_peak(s1::JacobianSpectrum, s2::JacobianSpectrum)
 end
 
 "Gives the numerical value of a peak at ω."
-evaluate(peak::Lorentzian{T}, ω::T) where {T<:Real} =
+function evaluate(peak::Lorentzian{T}, ω::T) where {T<:Real}
     peak.A / sqrt(((peak.ω0 - ω)^2 + (peak.Γ)^2))
+end
 
 "Gives the numerical value of a JacobianSpectrum at ω"
 function evaluate(s::JacobianSpectrum{T}, ω::T) where {T<:Real}
diff --git a/src/modules/LinearResponse/utils.jl b/src/modules/LinearResponse/utils.jl
@@ -6,8 +6,8 @@ function _get_uv_pairs(hvars::Vector{HarmonicVariable})
         j = findall(
             x ->
                 isequal(x.ω, hvars[i].ω) &&
-                    x.type == "v" &&
-                    isequal(hvars[i].natural_variable, x.natural_variable),
+                x.type == "v" &&
+                isequal(hvars[i].natural_variable, x.natural_variable),
             hvars,
         )
         j = length(j) != 1 && error("no v coordinate found for ", hvars[i]) || j[1]
diff --git a/test/Project.toml b/test/Project.toml
@@ -28,7 +28,7 @@ Aqua = "0.8"
 Documenter = "1.4"
 ExplicitImports = "1.6"
 JET = "0.9.9"
-ModelingToolkit = "9.60"
+ModelingToolkit = "9.70.0"
 NonlinearSolve = "4.3"
 OrdinaryDiffEqRosenbrock = "1.4"
 OrdinaryDiffEqTsit5 = "1.1"
diff --git a/test/extensions/SteadyStateDiffEqExt.jl b/test/extensions/SteadyStateDiffEqExt.jl
@@ -39,23 +39,23 @@ using HarmonicBalance,
 
         eqs = [
             Differential(t)(u1) ~
-                (
-                    F * γ - u1 * γ * (ω^2) - u1 * γ * (ω0^2) - v1 * (γ^2) * ω -
-                    2 * v1 * (ω^3) + 2 * v1 * ω * (ω0^2) - (3//4) * (u1^3) * α * γ +
-                    (3//2) * (u1^2) * v1 * α * ω - (3//4) * u1 * (v1^2) * α * γ +
-                    (3//2) * (v1^3) * α * ω
-                ) / (γ^2 + (4) * (ω^2)),
+            (
+                F * γ - u1 * γ * (ω^2) - u1 * γ * (ω0^2) - v1 * (γ^2) * ω - 2 * v1 * (ω^3) +
+                2 * v1 * ω * (ω0^2) - (3//4) * (u1^3) * α * γ +
+                (3//2) * (u1^2) * v1 * α * ω - (3//4) * u1 * (v1^2) * α * γ +
+                (3//2) * (v1^3) * α * ω
+            ) / (γ^2 + (4) * (ω^2)),
             Differential(t)(v1) ~
-                (
-                    -2 * F * ω - u1 * (γ^2) * ω - (2) * u1 * (ω^3) +
-                    2 * u1 * ω * (ω0^2) +
-                    v1 * γ * (ω^2) +
-                    v1 * γ * (ω0^2) +
-                    (3//2) * (u1^3) * α * ω +
-                    (3//4) * (u1^2) * v1 * α * γ +
-                    (3//2) * u1 * (v1^2) * α * ω +
-                    (3//4) * (v1^3) * α * γ
-                ) / (-(γ^2) - (4) * (ω^2)),
+            (
+                -2 * F * ω - u1 * (γ^2) * ω - (2) * u1 * (ω^3) +
+                2 * u1 * ω * (ω0^2) +
+                v1 * γ * (ω^2) +
+                v1 * γ * (ω0^2) +
+                (3//2) * (u1^3) * α * ω +
+                (3//4) * (u1^2) * v1 * α * γ +
+                (3//2) * u1 * (v1^2) * α * ω +
+                (3//4) * (v1^3) * α * γ
+            ) / (-(γ^2) - (4) * (ω^2)),
         ]
 
         @named model = ODESystem(eqs, t, [u1, v1], [α, ω, ω0, F, γ])

Original file line number	Diff line number	Diff line change
`@@ -37,7 +37,7 @@ function OrdinaryDiffEqTsit5.ODEProblem(`
`37`	`37`	`unwrap.([`
`38`	`38`	`substitute(eq, Dict(zip(keys(sweep), [sweep[p](T) for p in keys(sweep)])))`
`39`	`39`	`for eq in eqs(v)`
`40`		`- ])`
	`40`	`+ ]),`
`41`	`41`	`)`
`42`	`42`	`end`
`43`	`43`