build: migrate to Symbolics 7, SymbolicUtils 4 and ModelingToolkitBase (#446)

Migrate to Symbolics 7 and SymbolicUtils 4, and replace the ModelingToolkit
weak dependency with ModelingToolkitBase 1. The extension is renamed from
ModelingToolkitExt to ModelingToolkitBaseExt accordingly.

Raise compat to HarmonicSteadyState 0.5, QuestBase 0.4.1 and
OrdinaryDiffEqTsit5 2, and set the minimum Julia version to 1.12. LTS support
will be restored in a following patch release.

Add regression tests for Krylov-Bogoliubov averaging of second order systems,
which Symbolics 7 broke via the new `order` field on `Differential`.

Update the documentation and benchmark environments for the new
QuantumCumulants and SciML APIs, and grant the benchmark workflow
`pull-requests: write` so alert comments can be posted on pull requests.

Author: oameye

.github/codecov.yml

@@ -0,0 +1,10 @@
+coverage:
+  status:
+    project:
+      default:
+        informational: true
+    patch:
+      default:
+        informational: true
+
+comment: false

.github/workflows/Benchmarks.yml

@@ -31,6 +31,7 @@ permissions:
     actions: write
     contents: write
     deployments: write
+    pull-requests: write
 
 jobs:
   benchmark:
@@ -40,7 +41,7 @@ jobs:
       - uses: actions/checkout@v7
       - uses: julia-actions/setup-julia@v3
         with:
-          version: '1'
+          version: '1.12'
           arch: x64
       - uses: julia-actions/cache@v3
       - name: Run benchmark

.github/workflows/Documentation.yml

@@ -35,7 +35,7 @@ jobs:
       - uses: actions/checkout@v7
       - uses: julia-actions/setup-julia@v3
         with:
-          version: 'lts'
+          version: '1.12'
       - uses: julia-actions/cache@v3
       - uses: julia-actions/julia-buildpkg@v1
       - uses: julia-actions/julia-docdeploy@v1

.github/workflows/Tests.yml

@@ -29,8 +29,7 @@ jobs:
       fail-fast: false
       matrix:
         version:
-          - 'lts'
-          - '1'
+          - '1.12'
         os:
           - ubuntu-latest
         arch:
@@ -60,4 +59,4 @@ jobs:
           files: lcov.info
           name: codecov-umbrella
           fail_ci_if_error: false
-        if: ${{ matrix.version == 'lts' }}
+        if: ${{ matrix.version == '1.12' }}

Project.toml

@@ -1,48 +1,46 @@
 name = "HarmonicBalance"
 uuid = "e13b9ff6-59c3-11ec-14b1-f3d2cc6c135e"
+version = "0.17.0"
 authors = ["Orjan Ameye <orjan.ameye@hotmail.com>", "Jan Kosata <kosataj@phys.ethz.ch>", "Javier del Pino <jdelpino@phys.ethz.ch>"]
-version = "0.16.0"
 
 [deps]
 DocStringExtensions = "ffbed154-4ef7-542d-bbb7-c09d3a79fcae"
 HarmonicSteadyState = "1158f75c-a779-4b85-8bfb-8fcf6bf02ced"
+ModelingToolkitBase = "7771a370-6774-4173-bd38-47e70ca0b839"
 PrecompileTools = "aea7be01-6a6a-4083-8856-8a6e6704d82a"
 QuestBase = "7e80f742-43d6-403d-a9ea-981410111d43"
 Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
 Reexport = "189a3867-3050-52da-a836-e630ba90ab69"
 SymbolicUtils = "d1185830-fcd6-423d-90d6-eec64667417b"
 Symbolics = "0c5d862f-8b57-4792-8d23-62f2024744c7"
 
-[weakdeps]
-ModelingToolkit = "961ee093-0014-501f-94e3-6117800e7a78"
-
 [extensions]
-ModelingToolkitExt = "ModelingToolkit"
+ModelingToolkitBaseExt = "ModelingToolkitBase"
 
 [compat]
 Aqua = "0.8.11"
 DocStringExtensions = "0.9.4"
 Documenter = "1.4"
 ExplicitImports = "1.6"
-HarmonicSteadyState = "0.4.0"
+HarmonicSteadyState = "0.5"
 JET = "0.9.18, 0.10"
-ModelingToolkit = "10.6.0"
-OrdinaryDiffEqTsit5 = "1.1"
+ModelingToolkitBase = "1"
+OrdinaryDiffEqTsit5 = "2"
 PrecompileTools = "1.2"
-QuestBase = "0.3.1"
+QuestBase = "0.4.1"
 Random = "1.10"
 Reexport = "1.2.2"
-SymbolicUtils = "3.25"
-Symbolics = "6.34.0"
+SymbolicUtils = "4"
+Symbolics = "7"
 Test = "1.10"
-julia = "1.10.10, 1.11.9, 1.12.5"
+julia = "1.12"
 
 [extras]
 Aqua = "4c88cf16-eb10-579e-8560-4a9242c79595"
 Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
 ExplicitImports = "7d51a73a-1435-4ff3-83d9-f097790105c7"
 JET = "c3a54625-cd67-489e-a8e7-0a5a0ff4e31b"
-ModelingToolkit = "961ee093-0014-501f-94e3-6117800e7a78"
+ModelingToolkitBase = "7771a370-6774-4173-bd38-47e70ca0b839"
 OrdinaryDiffEqTsit5 = "b1df2697-797e-41e3-8120-5422d3b24e4a"
 QuestBase = "7e80f742-43d6-403d-a9ea-981410111d43"
 Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
@@ -51,4 +49,4 @@ Symbolics = "0c5d862f-8b57-4792-8d23-62f2024744c7"
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 
 [targets]
-test = ["Aqua", "JET", "SymbolicUtils", "Symbolics", "ExplicitImports", "Test", "Random", "ModelingToolkit", "Documenter", "QuestBase", "OrdinaryDiffEqTsit5"]
+test = ["Aqua", "JET", "SymbolicUtils", "Symbolics", "ExplicitImports", "Test", "Random", "ModelingToolkitBase", "Documenter", "QuestBase", "OrdinaryDiffEqTsit5"]

benchmarks/Project.toml

@@ -9,8 +9,11 @@ OrdinaryDiffEqRosenbrock = "43230ef6-c299-4910-a778-202eb28ce4ce"
 OrdinaryDiffEqTsit5 = "b1df2697-797e-41e3-8120-5422d3b24e4a"
 Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80"
 QuantumCumulants = "35bcea6d-e19f-57db-af74-8011de6c7255"
+QuestBase = "7e80f742-43d6-403d-a9ea-981410111d43"
 SteadyStateDiffEq = "9672c7b4-1e72-59bd-8a11-6ac3964bc41f"
 
 [compat]
 Documenter = "1"
-julia = "1.10"
+HarmonicSteadyState = "0.5"
+QuestBase = "0.4.1"
+julia = "1.12"

docs/Project.toml

@@ -8,6 +8,7 @@ FunctionWrappers = "069b7b12-0de2-55c6-9aab-29f3d0a68a2e"
 HarmonicBalance = "e13b9ff6-59c3-11ec-14b1-f3d2cc6c135e"
 HarmonicSteadyState = "1158f75c-a779-4b85-8bfb-8fcf6bf02ced"
 HomotopyContinuation = "f213a82b-91d6-5c5d-acf7-10f1c761b327"
+Latexify = "23fbe1c1-3f47-55db-b15f-69d7ec21a316"
 LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
 Literate = "98b081ad-f1c9-55d3-8b20-4c87d4299306"
 ModelingToolkit = "961ee093-0014-501f-94e3-6117800e7a78"
@@ -26,5 +27,6 @@ Symbolics = "0c5d862f-8b57-4792-8d23-62f2024744c7"
 
 [compat]
 Documenter = "1"
-julia = "1.11"
-HarmonicSteadyState = "0.4.0"
+julia = "1.12"
+HarmonicSteadyState = "0.5"
+QuestBase = "0.4.1"

docs/make.jl

@@ -14,7 +14,7 @@ using OrdinaryDiffEqTsit5
 using SteadyStateDiffEq
 
 TimeEvolution = Base.get_extension(HarmonicSteadyState, :TimeEvolution)
-ModelingToolkitExt = Base.get_extension(HarmonicBalance, :ModelingToolkitExt)
+ModelingToolkitBaseExt = Base.get_extension(HarmonicBalance, :ModelingToolkitBaseExt)
 SteadyStateDiffEqExt = Base.get_extension(HarmonicSteadyState, :SteadyStateDiffEqExt)
 HarmonicBalanceExt = Base.get_extension(HarmonicSteadyState, :HarmonicBalanceExt)
 
@@ -23,7 +23,7 @@ bib = CitationBibliography(
     style=:numeric,  # default
 )
 
-using Plots
+using Plots, Latexify
 PlotsExt = Base.get_extension(HarmonicSteadyState, :PlotsExt)
 default(; fmt=:png)
 # Gotta set this environment variable when using the GR run-time on CI machines.
@@ -49,16 +49,18 @@ end
 makedocs(;
     sitename="HarmonicBalance.jl",
     authors="Quest group",
-    modules=[
-        HarmonicBalance,
-        QuestBase,
-        HarmonicSteadyState,
-        TimeEvolution,
-        ModelingToolkitExt,
-        SteadyStateDiffEqExt,
-        HarmonicSteadyState.LinearResponse,
-        PlotsExt,
-        HarmonicBalanceExt,
+    modules=Module[
+        m for m in [
+            HarmonicBalance,
+            QuestBase,
+            HarmonicSteadyState,
+            TimeEvolution,
+            ModelingToolkitBaseExt,
+            SteadyStateDiffEqExt,
+            HarmonicSteadyState.LinearResponse,
+            PlotsExt,
+            HarmonicBalanceExt,
+        ] if !isnothing(m)
     ],
     format=DocumenterVitepress.MarkdownVitepress(;
         repo="github.com/QuantumEngineeredSystems/HarmonicBalance.jl",

examples/ab_initio_noise.jl

@@ -68,8 +68,8 @@ 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′)
-output_func(sol, i) = (outputpsd(sol), false)
+prob_func(prob, ctx) = (prob′=remake(prob); setter!(prob′, ωrange[ctx.sim_id]); prob′)
+output_func(sol, ctx) = (outputpsd(sol), false)
 prob_ensemble = EnsembleProblem(sdeproblem; prob_func=prob_func, output_func=output_func)
 sol_ensemble = solve(
     prob_ensemble,

examples/forward_transmission.jl

@@ -10,7 +10,7 @@ h = hm ⊗ hc  # Hilbertspace
 
 @qnumbers m::Destroy(h, 1) c::Destroy(h, 2) # Operators
 
-@rnumbers Δ Vk Ωd γm γk # Parameters
+@variables Δ::Real Vk::Real Ωd::Real γm::Real γk::Real # Parameters
 param = [Δ, Vk, Ωd, γm, γk]
 
 H_RWA_sym = (