Update SciMLTesting QA compat to 2.1 (#66)

* Update SciMLTesting QA compat to 2.1

Co-Authored-By: Chris Rackauckas <accounts@chrisrackauckas.com>

* Keep SciMLTesting QA setup on 2.1

Co-Authored-By: Chris Rackauckas <accounts@chrisrackauckas.com>

* Fix FiniteStateProjection ModelingToolkit integration

Co-Authored-By: Chris Rackauckas <accounts@chrisrackauckas.com>

* Make telegraph core test deterministic

Seed the telegraph model test before drawing random parameters so tight analytic comparisons do not depend on CI RNG draws.

Co-Authored-By: Chris Rackauckas <accounts@chrisrackauckas.com>

* Add Random to test dependencies

Co-Authored-By: Chris Rackauckas <accounts@chrisrackauckas.com>

---------

Co-authored-by: ChrisRackauckas-Claude <accounts@chrisrackauckas.com>

Author: ChrisRackauckas-Claude

Project.toml

@@ -7,6 +7,7 @@ version = "0.3.5"
 Catalyst = "479239e8-5488-4da2-87a7-35f2df7eef83"
 DiffEqBase = "2b5f629d-d688-5b77-993f-72d75c75574e"
 MacroTools = "1914dd2f-81c6-5fcd-8719-6d5c9610ff09"
+ModelingToolkit = "961ee093-0014-501f-94e3-6117800e7a78"
 Reexport = "189a3867-3050-52da-a836-e630ba90ab69"
 RuntimeGeneratedFunctions = "7e49a35a-f44a-4d26-94aa-eba1b4ca6b47"
 SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"
@@ -17,11 +18,13 @@ DiffEqBase = "6.165, 7"
 Distributions = "0.25"
 LinearAlgebra = "1"
 MacroTools = "^0.5.5"
+ModelingToolkit = "9, 10, 11"
 OrdinaryDiffEq = "6, 7"
+Random = "1"
 Reexport = "1.2.2"
 RuntimeGeneratedFunctions = "0.5"
 SafeTestsets = "0.1, 1"
-SciMLTesting = "1"
+SciMLTesting = "2.1"
 SparseArrays = "1"
 SteadyStateDiffEq = "2.5"
 Sundials = "4, 5, 6"
@@ -32,11 +35,12 @@ julia = "1.10"
 Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f"
 LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
 OrdinaryDiffEq = "1dea7af3-3e70-54e6-95c3-0bf5283fa5ed"
+Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
 SafeTestsets = "1bc83da4-3b8d-516f-aca4-4fe02f6d838f"
 SciMLTesting = "09d9d899-5365-40a9-917a-5f67fddea283"
 SteadyStateDiffEq = "9672c7b4-1e72-59bd-8a11-6ac3964bc41f"
 Sundials = "c3572dad-4567-51f8-b174-8c6c989267f4"
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 
 [targets]
-test = ["Distributions", "LinearAlgebra", "OrdinaryDiffEq", "SafeTestsets", "SciMLTesting", "SteadyStateDiffEq", "Sundials", "Test"]
+test = ["Distributions", "LinearAlgebra", "OrdinaryDiffEq", "Random", "SafeTestsets", "SciMLTesting", "SteadyStateDiffEq", "Sundials", "Test"]

src/FiniteStateProjection.jl

@@ -4,6 +4,7 @@ using Reexport
 @reexport using Catalyst
 
 using MacroTools
+import ModelingToolkit
 using SparseArrays
 using DiffEqBase
 

src/build_rhs.jl

@@ -131,7 +131,7 @@ the work in the package happens; for best performance it is suggested to build a
 once for a given reaction system and reuse it instead of directly converting
 a reaction system to an `ODEProblem` (which implicitly calls this function).
 """
-Base.convert(::Type{ODEFunction}, sys::FSPSystem) = ODEFunction{true}(build_rhs(sys))
+Base.convert(::Type{ODEFunction}, sys::FSPSystem) = ODEFunction{true, SciMLBase.FullSpecialize}(build_rhs(sys))
 
 """
     DiffEqBase.ODEProblem(sys::FSPSystem, u0, tmax[, p])

src/build_rhs_ss.jl

@@ -82,7 +82,7 @@ Return an `ODEFunction` defining the right-hand side of the CME, for use
 with `SteadyStateProblem`s.
 """
 function Base.convert(::Type{ODEFunction}, sys::FSPSystem, ::SteadyState)
-    return ODEFunction{true}(build_rhs_ss(sys))
+    return ODEFunction{true, SciMLBase.FullSpecialize}(build_rhs_ss(sys))
 end
 
 """

src/fspsystem.jl

@@ -65,8 +65,11 @@ function compile_ratefunc(ex_rf, params)
     return @RuntimeGeneratedFunction(ex)
 end
 
+_parameter_symbol(key::Symbol) = key
+_parameter_symbol(key) = Symbol(ModelingToolkit.value(key))
+
 function pmap_to_p(sys::FSPSystem, pmap)
-    pmap_conv = eltype(pmap) <: Pair{Symbol} ? Catalyst.symmap_to_varmap(sys.rs, pmap) :
-        pmap
-    return ModelingToolkit.varmap_to_vars(pmap_conv, Catalyst.parameters(sys.rs))
+    pmap isa SciMLBase.NullParameters && return pmap
+    values_by_parameter = Dict(_parameter_symbol(k) => v for (k, v) in pmap)
+    return [values_by_parameter[p] for p in Symbol.(Catalyst.parameters(sys.rs))]
 end

test/qa/Project.toml

@@ -4,11 +4,8 @@ JET = "c3a54625-cd67-489e-a8e7-0a5a0ff4e31b"
 SciMLTesting = "09d9d899-5365-40a9-917a-5f67fddea283"
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 
-[sources]
-FiniteStateProjection = { path = "../.." }
-
 [compat]
 JET = "0.9,0.10,0.11"
-SciMLTesting = "1.7"
+SciMLTesting = "2.1"
 Test = "1"
 julia = "1.10"

test/qa/qa.jl

@@ -1,6 +1,17 @@
 using SciMLTesting, FiniteStateProjection, Test
 using JET
 
+const CATALYST_REEXPORTS = Tuple(intersect(names(FiniteStateProjection), names(FiniteStateProjection.Catalyst)))
+const API_DOCS_IGNORE = Tuple(
+    unique(
+        (
+            :SymbolicUtils,
+            :NaiveIndexHandler,
+            CATALYST_REEXPORTS...,
+        )
+    )
+)
+
 run_qa(
     FiniteStateProjection;
     explicit_imports = true,
@@ -24,13 +35,9 @@ run_qa(
                 :value,        # owner Symbolics, accessed via ModelingToolkit
             ),
         ),
-        # `Catalyst = "15"` pins the SciMLBase 2.x / ModelingToolkit 9.x / Symbolics 6.x
-        # ecosystem, so the public-API releases (SciMLBase 3.27 / MTK 11 / Symbolics 7)
-        # are NOT resolvable here. Verified on Julia 1.12 against the resolved stack
-        # (Catalyst 15.0.11, ModelingToolkit 9.84.0, Symbolics 6.58.0, SciMLBase 2.153.1):
-        # each of these names is still non-public in its owner at the resolvable version,
-        # and MacroTools/Catalyst have not declared theirs public. Drop each as its owner
-        # ships a public declaration that FiniteStateProjection can actually resolve.
+        # These names are still non-public in their resolvable owners, or are
+        # re-exported from a non-owner. Drop each ignore as its owner ships a public
+        # declaration that FiniteStateProjection can actually resolve.
         all_qualified_accesses_are_public = (;
             ignore = (
                 :_symbol_to_var,   # Catalyst (non-public)
@@ -42,11 +49,16 @@ run_qa(
                 :striplines,       # MacroTools (non-public)
                 :scalarize,        # ModelingToolkit (owner Symbolics; still non-public)
                 :value,            # ModelingToolkit (owner Symbolics; still non-public)
-                :varmap_to_vars,   # ModelingToolkit (non-public)
                 :NullParameters,   # SciMLBase (public in 3.30+, but Catalyst 15 pins 2.153.1 where it is not)
             ),
         ),
     ),
+    api_docs_kwargs = (;
+        # `@reexport using Catalyst` intentionally exposes Catalyst's symbolic
+        # stack. Require docstrings for FiniteStateProjection-owned public API
+        # here, and leave dependency API docs to their owner packages.
+        ignore = API_DOCS_IGNORE,
+    ),
     # Heavy `@reexport using Catalyst` plus the symbolic stack make ~23 names
     # implicit; making them all explicit is a risky mass refactor. Tracked in #60.
     ei_broken = (:no_implicit_imports,),

test/telegraph.jl

@@ -6,8 +6,10 @@ using FiniteStateProjection
 using SparseArrays
 using LinearAlgebra
 using Sundials
+using Random
 
 marg(vec; dims) = dropdims(sum(vec; dims); dims)
+Random.seed!(100)
 
 rs = @reaction_network begin
     σ_on * (1 - G), 0 --> G