Enforce strict SciMLTesting 2.4 QA (#98)

ChrisRackauckas-Claude · ChrisRackauckas · claude · web-flow · commit 3ea8c853dabc · 2026-07-29T01:32:05.000Z
* Enforce strict QA for PDEBase Co-Authored-By: Chris Rackauckas <accounts@chrisrackauckas.com> * Fix public API test on the Julia LTS `Base.ispublic` and the `public` keyword are Julia 1.11+, so the check errored on 1.10 (both the LTS and Downgrade jobs run on `lts`). Guard it and assert the name is defined on all versions. Also replace the docstring check: `Base.Docs.doc(mod, name)` reads `name` as a type signature and returns the module's own docstring, so it never detected a missing one. Query the binding in the module's doc metadata instead, and cover it with a negative case. Co-Authored-By: Chris Rackauckas <accounts@chrisrackauckas.com> Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_0117aJvytDT3y2jMi5Ng6Q5m --------- Co-authored-by: ChrisRackauckas-Claude <accounts@chrisrackauckas.com> Co-authored-by: Claude Opus 5 (1M context) <noreply@anthropic.com>
diff --git a/Project.toml b/Project.toml
@@ -1,37 +1,47 @@
 name = "PDEBase"
 uuid = "a7812802-0625-4b9e-961c-d332478797e5"
-version = "0.1.30"
+version = "0.2.0"
 authors = ["xtalax <alex.lemony@gmail.com>"]
 
 [deps]
 DomainSets = "5b8099bc-c8ec-5219-889f-1d9e522a28bf"
-ModelingToolkit = "961ee093-0014-501f-94e3-6117800e7a78"
+IntervalSets = "8197267c-284f-5f27-9208-e0e47529a953"
+ModelingToolkitBase = "7771a370-6774-4173-bd38-47e70ca0b839"
 PrecompileTools = "aea7be01-6a6a-4083-8856-8a6e6704d82a"
 SciMLBase = "0bca4576-84f4-4d90-8ffe-ffa030f20462"
+SciMLPublic = "431bcebd-1456-4ced-9d72-93c2757fff0b"
 SymbolicIndexingInterface = "2efcf032-c050-4f8e-a9bb-153293bab1f5"
 SymbolicUtils = "d1185830-fcd6-423d-90d6-eec64667417b"
 Symbolics = "0c5d862f-8b57-4792-8d23-62f2024744c7"
+TermInterface = "8ea1fca8-c5ef-4a55-8b96-4e9afe9c9a3c"
 
 [compat]
 AllocCheck = "0.2"
 BenchmarkTools = "1"
 DomainSets = "0.7, 0.8"
-ModelingToolkit = "11.26.7"
+IntervalSets = "0.7"
+ModelingToolkitBase = "1.57"
+ModelingToolkit = "11"
 PrecompileTools = "1.2.1"
 SciMLBase = "2.149.0, 3.1"
-SciMLTesting = "2.1"
+SciMLPublic = "1"
+SciMLTesting = "2.4"
+SafeTestsets = "0.0.1, 0.1, 1"
 SymbolicIndexingInterface = "0.3.43"
 SymbolicUtils = "4.31.0"
 Symbolics = "7.24.0"
+TermInterface = "2"
+Test = "1"
 julia = "1.10"
 
 [extras]
 AllocCheck = "9b6a8646-10ed-4001-bbdc-1d2f46dfbb1a"
 BenchmarkTools = "6e4b80f9-dd63-53aa-95a3-0cdb28fa8baf"
+ModelingToolkit = "961ee093-0014-501f-94e3-6117800e7a78"
 SafeTestsets = "1bc83da4-3b8d-516f-aca4-4fe02f6d838f"
 SciMLTesting = "09d9d899-5365-40a9-917a-5f67fddea283"
 SymbolicUtils = "d1185830-fcd6-423d-90d6-eec64667417b"
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 
 [targets]
-test = ["AllocCheck", "BenchmarkTools", "SafeTestsets", "SciMLTesting", "SymbolicUtils", "Test"]
+test = ["AllocCheck", "BenchmarkTools", "ModelingToolkit", "SafeTestsets", "SciMLTesting", "SymbolicUtils", "Test"]
diff --git a/docs/Project.toml b/docs/Project.toml
@@ -1,7 +1,9 @@
 [deps]
 Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
+ModelingToolkit = "961ee093-0014-501f-94e3-6117800e7a78"
 PDEBase = "a7812802-0625-4b9e-961c-d332478797e5"
 
 [compat]
 Documenter = "1"
-PDEBase = "0.1.19"
+ModelingToolkit = "11"
+PDEBase = "0.2"
diff --git a/docs/make.jl b/docs/make.jl
@@ -13,8 +13,8 @@ makedocs(
     sitename = "PDEBase.jl",
     authors = "Alex Jones, Chris Rackauckas et al.",
     clean = true,
-    doctest = false,
-    warnonly = [:missing_docs],
+    doctest = true,
+    checkdocs = :exports,
     modules = [PDEBase],
     format = Documenter.HTML(
         analytics = "UA-90474609-3",
diff --git a/docs/pages.jl b/docs/pages.jl
@@ -2,7 +2,7 @@ pages = [
     "Home" => "index.md",
     "Getting Started" => "getting_started.md",
     "Interface" => [
-        "PDESystem Interface" => "interface.md",
+        "Developer Extension API" => "interface.md",
         "Discretization Workflow" => "workflow.md",
     ],
     "Types" => [
diff --git a/docs/src/api.md b/docs/src/api.md
@@ -148,7 +148,7 @@ Tracks which variables have periodic boundary conditions.
 
 ## Interface Functions
 
-For detailed documentation of interface functions, see [PDESystem Interface](@ref).
+For detailed documentation of interface functions, see [Developer Extension API](@ref developer-extension-api).
 
 ### Summary
 
diff --git a/docs/src/boundaries.md b/docs/src/boundaries.md
@@ -266,6 +266,6 @@ This is used to determine when to wrap grid indices in finite difference stencil
 
 ## See Also
 
-- [PDESystem Interface](@ref) for how boundaries integrate with discretization
+- [Developer Extension API](@ref developer-extension-api) for how boundaries integrate with discretization
 - [Discretization Workflow](@ref workflow) for the complete processing pipeline
 - [VariableMap](@ref variablemap) for variable handling
diff --git a/docs/src/getting_started.md b/docs/src/getting_started.md
@@ -175,7 +175,7 @@ end
 
 ## Next Steps
 
-- Read the [PDESystem Interface](@ref) for detailed interface documentation
+- Read the [Developer Extension API](@ref developer-extension-api) for detailed interface documentation
 - Study [VariableMap](@ref variablemap) to understand variable handling
 - Review [Boundary Conditions](@ref boundaries) for BC types
 - See [Discretization Workflow](@ref workflow) for the complete pipeline
diff --git a/docs/src/index.md b/docs/src/index.md
@@ -34,7 +34,7 @@ PDEBase defines how a `ModelingToolkit.PDESystem` is converted into a discretize
 - Boundary conditions specified at domain boundaries
 - Initial conditions for time-dependent problems
 
-See [PDESystem Interface](@ref) for complete details.
+See [Developer Extension API](@ref developer-extension-api) for complete details.
 
 ### The Discretization Workflow
 
diff --git a/docs/src/interface.md b/docs/src/interface.md
@@ -1,6 +1,13 @@
-# PDESystem Interface
+# [Developer Extension API](@id developer-extension-api)
 
-PDEBase.jl provides a set of interface functions that discretization packages must implement to convert a `ModelingToolkit.PDESystem` into a discretized system (typically an `ODESystem` or `OptimizationSystem`).
+PDEBase.jl provides the versioned interface that discretization packages implement to convert a `ModelingToolkit.PDESystem` into a discretized system (typically an `ODESystem` or `OptimizationSystem`).
+
+!!! warning "Developer API, not ordinary user API"
+
+    These qualified hooks are for PDE discretizer authors. They are documented
+    and versioned so extension packages can depend on them, but applications
+    should use a discretizer such as MethodOfLines.jl rather than call or
+    extend this protocol directly.
 
 ## Key Assumptions about PDESystem
 
diff --git a/docs/src/variablemap.md b/docs/src/variablemap.md
@@ -199,5 +199,5 @@ Returns axis values at grid positions. Used internally during discretization.
 
 ## See Also
 
-- [PDESystem Interface](@ref) for how VariableMap is used in discretization
+- [Developer Extension API](@ref developer-extension-api) for how VariableMap is used in discretization
 - [Boundary Conditions](@ref boundaries) for how boundaries reference variables
diff --git a/docs/src/workflow.md b/docs/src/workflow.md
@@ -257,6 +257,6 @@ Implement these in your discretization to provide helpful error messages.
 
 ## See Also
 
-- [PDESystem Interface](@ref) for interface function details
+- [Developer Extension API](@ref developer-extension-api) for interface function details
 - [VariableMap](@ref variablemap) for variable handling
 - [Boundary Conditions](@ref boundaries) for boundary types
diff --git a/src/PDEBase.jl b/src/PDEBase.jl
@@ -1,20 +1,22 @@
 module PDEBase
-using SciMLBase
-using SciMLBase: AbstractDiscretization, AbstractDiscretizationMetadata
-
-using ModelingToolkit
-
-using ModelingToolkit: get_unknowns, ProblemTypeCtx, get_ps, get_bcs, get_dvs,
-    get_eqs, get_iv,
-    get_domain, get_ivs, get_systems, get_connector_type,
-    get_metadata, get_gui_metadata
-
-using Symbolics, SymbolicUtils
-using Symbolics: unwrap, setname, rename
-using SymbolicUtils: operation, arguments, Chain, Prewalk, maketerm, metadata,
-    iscall, getmetadata, unwrap_const, substitute
+import DomainSets
+using IntervalSets: var".."
+import ModelingToolkitBase
+import PrecompileTools
+import SciMLBase
+import Symbolics
+import SymbolicUtils
+using ModelingToolkitBase: PDESystem, System, get_bcs, get_connector_type, get_domain,
+    get_dvs, get_eqs, get_gui_metadata, get_iv, get_ivs, get_metadata, get_ps,
+    get_systems, get_unknowns, mtkcompile
+using PrecompileTools: @compile_workload, @setup_workload
+using SciMLBase: AbstractDiscretization, AbstractDiscretizationMetadata, NonlinearProblem,
+    ODEFunction, ODEProblem
+import SciMLPublic: @public
+using Symbolics: @variables, Differential, Equation, Num, unwrap
+using SymbolicUtils: arguments, getmetadata, iscall, operation, substitute, unwrap_const
 using SymbolicIndexingInterface: is_time_dependent
-using DomainSets
+using TermInterface: maketerm, metadata
 
 """
     AbstractEquationSystemDiscretization <: AbstractDiscretization
@@ -72,6 +74,8 @@ conditions are discretized.
 """
 abstract type AbstractDiscretizationState end
 
+struct PDEBaseMetadataCtx end
+
 include("symbolic_utils.jl")
 include("utils.jl")
 include("variable_map.jl")
@@ -101,4 +105,11 @@ export VariableMap
 export ivs, all_ivs, depvar, depvars, indvars, x2i
 export PeriodicMap
 
+# Versioned extension points for PDE discretization packages. These remain
+# qualified so that ordinary applications do not accidentally depend on them.
+@public interface_errors, check_boundarymap, should_transform, transform_pde_system!,
+    construct_disc_state, construct_discrete_space, construct_var_equation_mapping,
+    construct_differential_discretizer, discretize_equation!, generate_ic_defaults,
+    generate_metadata, generate_system, get_discvars, get_eqvar, add_metadata!
+
 end # module PDEBase
diff --git a/src/discretization_state.jl b/src/discretization_state.jl
@@ -126,7 +126,7 @@ function generate_system(
             eqs = map(_normalize_nonlinear_eq, alleqs)
             sys = System(
                 eqs, alldepvarsdisc, ps, initial_conditions = sys_defaults, name = name,
-                metadata = [ProblemTypeCtx => metadata], checks = checks
+                metadata = [PDEBaseMetadataCtx => metadata], checks = checks
             )
             return sys, nothing
         else
@@ -138,7 +138,7 @@ function generate_system(
                 initialization_eqs = init_eqs,
                 guesses = guesses,
                 name = name,
-                metadata = [ProblemTypeCtx => metadata], checks = checks
+                metadata = [PDEBaseMetadataCtx => metadata], checks = checks
             )
             return sys, tspan
         end
@@ -164,16 +164,16 @@ function SciMLBase.discretize(
     return try
         simpsys = mtkcompile(sys)
         if tspan === nothing
-            add_metadata!(getmetadata(sys, ProblemTypeCtx, nothing), sys)
+            add_metadata!(getmetadata(sys, PDEBaseMetadataCtx, nothing), sys)
             # MTK v11 requires symbolic map for initial guess
-            unknowns_list = ModelingToolkit.unknowns(simpsys)
+            unknowns_list = get_unknowns(simpsys)
             u0_guess = Dict(u => 1.0 for u in unknowns_list)
             return prob = NonlinearProblem(
                 simpsys, u0_guess;
                 discretization.kwargs..., kwargs...
             )
         else
-            mol_metadata = getmetadata(simpsys, ProblemTypeCtx, nothing)
+            mol_metadata = getmetadata(simpsys, PDEBaseMetadataCtx, nothing)
             add_metadata!(mol_metadata, sys)
             prob = ODEProblem(
                 simpsys, nothing, tspan;
@@ -206,31 +206,27 @@ function error_analysis(sys::System, e)
     t = get_iv(sys)
     println("The system of equations is:")
     println(eqs)
-    return if e isa ModelingToolkit.ExtraVariablesSystemException
-        rs = [Differential(t)(state) => state for state in unknowns]
-        extraunknowns = [state for state in unknowns]
-        extraeqs = [eq for eq in eqs]
-        numderivs = 0
-        for r in rs
-            for eq in extraeqs
-                if subsmatch(eq.lhs, r) | subsmatch(eq.rhs, r)
-                    extraunknowns = vec(setdiff(extraunknowns, [r.second]))
-                    extraeqs = vec(setdiff(extraeqs, [eq]))
-                    numderivs += 1
-                    break
-                end
+    rs = [Differential(t)(state) => state for state in unknowns]
+    extraunknowns = [state for state in unknowns]
+    extraeqs = [eq for eq in eqs]
+    numderivs = 0
+    for r in rs
+        for eq in extraeqs
+            if subsmatch(eq.lhs, r) | subsmatch(eq.rhs, r)
+                extraunknowns = vec(setdiff(extraunknowns, [r.second]))
+                extraeqs = vec(setdiff(extraeqs, [eq]))
+                numderivs += 1
+                break
             end
         end
-        println()
-        println("There are $(length(unknowns)) variables and $(length(eqs)) equations.\n")
-        println("There are $numderivs time derivatives.\n")
-        println("The variables without time derivatives are:")
-        println(extraunknowns)
-        println()
-        println("The equations without time derivatives are:")
-        println(extraeqs)
-        rethrow(e)
-    else
-        rethrow(e)
     end
+    println()
+    println("There are $(length(unknowns)) variables and $(length(eqs)) equations.\n")
+    println("There are $numderivs time derivatives.\n")
+    println("The variables without time derivatives are:")
+    println(extraunknowns)
+    println()
+    println("The equations without time derivatives are:")
+    println(extraeqs)
+    rethrow(e)
 end
diff --git a/src/make_pdesys_compatible.jl b/src/make_pdesys_compatible.jl
@@ -26,20 +26,36 @@ function _replace_ops(term, op_map)
     return term
 end
 
+function _replace_indexed_array_variables(term, replacements)
+    term = safe_unwrap(term)
+    iscall(term) || return term
+
+    op = operation(term)
+    args = arguments(term)
+    if op === getindex
+        array = first(args)
+        if iscall(array)
+            replacement = get(replacements, operation(array), nothing)
+            replacement === nothing || return replacement(arguments(array)...)
+        end
+    end
+
+    new_args = _replace_indexed_array_variables.(args, Ref(replacements))
+    return all(isequal.(args, new_args)) ? term : maketerm(typeof(term), op, new_args, metadata(term))
+end
+
 function chain_flatten_array_variables(dvs)
-    rs = []
+    replacements = Dict()
     for dv in dvs
         dv = safe_unwrap(dv)
         if isequal(operation(dv), getindex)
             name = operation(arguments(dv)[1])
-            args = arguments(arguments(dv)[1])
             idxs = arguments(dv)[2:end]
             fullname = Symbol(string(name) * "_" * string(idxs))
-            newop = (@variables $fullname(..))[1]
-            push!(rs, @rule getindex($(name)(~~a), idxs...) => newop(~a...))
+            replacements[name] = Symbolics.variable(fullname; T = SymbolicUtils.symtype(name))
         end
     end
-    return isempty(rs) ? identity : Prewalk(Chain(rs))
+    return isempty(replacements) ? identity : term -> _replace_indexed_array_variables(term, replacements)
 end
 
 function apply_lhs_rhs(f, eqs)
diff --git a/src/symbolic_discretize.jl b/src/symbolic_discretize.jl
@@ -6,7 +6,11 @@ function cardinalize_eqs!(pdesys)
     return
 end
 
-function SciMLBase.symbolic_discretize(pdesys::PDESystem, discretization::AbstractDiscretization; checks = true)
+function SciMLBase.symbolic_discretize(
+        pdesys::PDESystem,
+        discretization::Union{AbstractEquationSystemDiscretization, AbstractOptimizationSystemDiscretization};
+        checks = true
+    )
     t = get_time(discretization)
     pdesys, complexmap = handle_complex(pdesys)
     cardinalize_eqs!(pdesys)
diff --git a/src/symbolic_utils.jl b/src/symbolic_utils.jl
@@ -481,7 +481,8 @@ function ex2term(term, v)
     symdvs = filter(u -> all(x -> !(unwrap_const(safe_unwrap(x)) isa Number), arguments(u)), termdvs)
     exdv = last(sort(symdvs, by = u -> length(arguments(u))))
     name = Symbol("⟦" * string(term) * "⟧")
-    return setname(maketerm(typeof(exdv), rename(operation(exdv), name), arguments(exdv), metadata(exdv)), name)
+    newop = Symbolics.variable(name; T = SymbolicUtils.symtype(operation(exdv)))
+    return newop(arguments(exdv)...)
 end
 
 """
diff --git a/test/public_api.jl b/test/public_api.jl
diff --git a/test/qa/Project.toml b/test/qa/Project.toml
diff --git a/test/qa/qa.jl b/test/qa/qa.jl
