Merge remote-tracking branch 'origin/master'

Author: ChrisRackauckas

Project.toml

@@ -1,7 +1,7 @@
 name = "JumpProcesses"
 uuid = "ccbc3e58-028d-4f4c-8cd5-9ae44345cda5"
 authors = ["Chris Rackauckas <[email protected]>"]
-version = "9.16.1"
+version = "9.17.0"
 
 [deps]
 ArrayInterface = "4fba245c-0d91-5ea0-9b3e-6abc04ee57a9"
@@ -32,28 +32,44 @@ KernelAbstractions = "63c18a36-062a-441e-b654-da1e3ab1ce7c"
 JumpProcessesKernelAbstractionsExt = ["Adapt", "KernelAbstractions"]
 
 [compat]
+ADTypes = "1"
 Adapt = "4"
+Aqua = "0.8"
 ArrayInterface = "7.9"
 DataStructures = "0.18, 0.19"
 DiffEqBase = "6.180"
 DiffEqCallbacks = "4.3.0"
 DocStringExtensions = "0.9"
+ExplicitImports = "1"
 FastBroadcast = "0.3"
 FunctionWrappers = "1.1"
 Graphs = "1.9"
 KernelAbstractions = "0.9"
+LinearAlgebra = "1"
+LinearSolve = "2, 3"
+Markdown = "1"
+OrdinaryDiffEq = "6"
+Pkg = "1"
 PoissonRandom = "0.4"
+Random = "1"
 RecursiveArrayTools = "3.12"
 Reexport = "1.0"
+SafeTestsets = "0.1"
 SciMLBase = "2.59"
 Setfield = "1"
+StableRNGs = "1"
 StaticArrays = "1.9"
+Statistics = "1"
+StochasticDiffEq = "6"
 SymbolicIndexingInterface = "0.3.13"
+Test = "1"
 UnPack = "1.0.2"
 julia = "1.10"
 
 [extras]
 ADTypes = "47edcb42-4c32-4615-8424-f2b9edc5f35b"
+Aqua = "4c88cf16-eb10-579e-8560-4a9242c79595"
+ExplicitImports = "7d51a73a-1435-4ff3-83d9-f097790105c7"
 FastBroadcast = "7034ab61-46d4-4ed7-9d0f-46aef9175898"
 LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
 LinearSolve = "7ed4a6bd-45f5-4d41-b270-4a48e9bafcae"
@@ -66,4 +82,4 @@ StochasticDiffEq = "789caeaf-c7a9-5a7d-9973-96adeb23e2a0"
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 
 [targets]
-test = ["ADTypes", "LinearAlgebra", "LinearSolve", "OrdinaryDiffEq", "Pkg", "SafeTestsets", "StableRNGs", "Statistics", "StochasticDiffEq", "Test", "FastBroadcast"]
+test = ["ADTypes", "Aqua", "ExplicitImports", "LinearAlgebra", "LinearSolve", "OrdinaryDiffEq", "Pkg", "SafeTestsets", "StableRNGs", "Statistics", "StochasticDiffEq", "Test", "FastBroadcast"]

analyze_imports.jl

@@ -0,0 +1,16 @@
+using Pkg
+Pkg.activate(".")
+Pkg.instantiate()
+
+using ExplicitImports
+using JumpProcesses
+
+# Analyze what's being imported
+println("=== Analyzing JumpProcesses module ===\n")
+
+# Check for implicit imports
+println("Checking for implicit imports that should be explicit:")
+print_explicit_imports(JumpProcesses)
+
+println("\n=== Check for unnecessary explicit imports ===")
+print_explicit_imports_nonrecursive(JumpProcesses)

src/JumpProcesses.jl

@@ -1,37 +1,52 @@
 module JumpProcesses
 
-using Reexport
+using Reexport: Reexport, @reexport
 @reexport using DiffEqBase
 
-using LinearAlgebra, Markdown, DocStringExtensions
-using DataStructures, PoissonRandom, Random, ArrayInterface
-using FunctionWrappers, UnPack
-using Graphs
-using SciMLBase: SciMLBase, isdenseplot
+# Explicit imports from standard libraries
+using LinearAlgebra: LinearAlgebra, I, mul!
+using Markdown: Markdown
+using Random: Random, randexp, randexp!
+
+# Explicit imports from external packages
+using DocStringExtensions: DocStringExtensions, FIELDS, TYPEDEF
+using DataStructures: DataStructures, MutableBinaryMinHeap, sizehint!, top_with_handle
+using PoissonRandom: PoissonRandom, pois_rand
+using ArrayInterface: ArrayInterface
+using FunctionWrappers: FunctionWrappers
+using UnPack: UnPack, @unpack
+using Graphs: Graphs, AbstractGraph, dst, grid, src
+using StaticArrays: StaticArrays, SA, SVector, @SVector, setindex
+using Base.Threads: Threads, @threads
 using Base.FastMath: add_fast
 using Setfield: @set, @set!
 
-import DiffEqCallbacks: gauss_points, gauss_weights
-import DiffEqBase: DiscreteCallback, init, solve, solve!, plot_indices, initialize!,
-                   get_tstops, get_tstops_array, get_tstops_max
+# Import functions we extend from Base
 import Base: size, getindex, setindex!, length, similar, show, merge!, merge
+
+# Import functions we extend from packages
+import DiffEqCallbacks: gauss_points, gauss_weights
+import DiffEqBase: DiscreteCallback, init, solve, solve!, initialize!
+import SciMLBase: plot_indices
 import DataStructures: update!
 import Graphs: neighbors, outdegree
-
 import RecursiveArrayTools: recursivecopy!
-using StaticArrays, Base.Threads
 import SymbolicIndexingInterface as SII
 
-import Random: AbstractRNG
+# Import additional types and functions from DiffEqBase and SciMLBase
+using DiffEqBase: DiffEqBase, CallbackSet, ContinuousCallback, DAEFunction,
+                  DDEFunction, DiscreteProblem, ODEFunction, ODEProblem,
+                  ODESolution, ReturnCode, SDEFunction, SDEProblem, add_tstop!,
+                  deleteat!, isinplace, remake, savevalues!, step!,
+                  u_modified!
+using SciMLBase: SciMLBase, DEIntegrator
 
 abstract type AbstractJump end
 abstract type AbstractMassActionJump <: AbstractJump end
 abstract type AbstractAggregatorAlgorithm end
 abstract type AbstractJumpAggregator end
 abstract type AbstractSSAIntegrator{Alg, IIP, U, T} <:
-              DiffEqBase.DEIntegrator{Alg, IIP, U, T} end
-
-import Base.Threads
+              DEIntegrator{Alg, IIP, U, T} end
 
 const DEFAULT_RNG = Random.default_rng()
 

src/aggregators/ssajump.jl

@@ -46,7 +46,7 @@ end
 end
 
 @inline function concretize_affects!(p::AbstractSSAJumpAggregator,
-        ::I) where {I <: DiffEqBase.DEIntegrator}
+        ::I) where {I <: SciMLBase.DEIntegrator}
     if (p.affects! isa Vector) &&
        !(p.affects! isa Vector{FunctionWrappers.FunctionWrapper{Nothing, Tuple{I}}})
         AffectWrapper = FunctionWrappers.FunctionWrapper{Nothing, Tuple{I}}
@@ -56,7 +56,7 @@ end
 end
 
 @inline function concretize_affects!(p::AbstractSSAJumpAggregator{T, S, F1, F2},
-        ::I) where {T, S, F1, F2 <: Tuple, I <: DiffEqBase.DEIntegrator}
+        ::I) where {T, S, F1, F2 <: Tuple, I <: SciMLBase.DEIntegrator}
     nothing
 end
 
@@ -75,7 +75,7 @@ end
 end
 
 # executing jump at the next jump time
-function (p::AbstractSSAJumpAggregator)(integrator::I) where {I <: DiffEqBase.DEIntegrator}
+function (p::AbstractSSAJumpAggregator)(integrator::I) where {I <: SciMLBase.DEIntegrator}
     affects! = p.affects!
     if affects! isa Vector{FunctionWrappers.FunctionWrapper{Nothing, Tuple{I}}}
         execute_jumps!(p, integrator, integrator.u, integrator.p, integrator.t, affects!)
@@ -88,7 +88,7 @@ function (p::AbstractSSAJumpAggregator)(integrator::I) where {I <: DiffEqBase.DE
 end
 
 function (p::AbstractSSAJumpAggregator{
-        T, S, F1, F2})(integrator::DiffEqBase.DEIntegrator) where
+        T, S, F1, F2})(integrator::SciMLBase.DEIntegrator) where
         {T, S, F1, F2 <: Union{Tuple, Nothing}}
     execute_jumps!(p, integrator, integrator.u, integrator.p, integrator.t, p.affects!)
     generate_jumps!(p, integrator, integrator.u, integrator.p, integrator.t)

src/variable_rate.jl

@@ -338,7 +338,7 @@ function initialize_vr_direct_cache!(cache::VR_DirectEventCache, u, t, integrato
 end
 
 @inline function concretize_vr_direct_affects!(cache::VR_DirectEventCache,
-        ::I) where {I <: DiffEqBase.DEIntegrator}
+        ::I) where {I <: SciMLBase.DEIntegrator}
     if (cache.affect_funcs isa Vector) &&
        !(cache.affect_funcs isa Vector{FunctionWrappers.FunctionWrapper{Nothing, Tuple{I}}})
         AffectWrapper = FunctionWrappers.FunctionWrapper{Nothing, Tuple{I}}
@@ -349,7 +349,7 @@ end
 end
 
 @inline function concretize_vr_direct_affects!(cache::VR_DirectEventCache{T, RNG, F1, F2},
-        ::I) where {T, RNG, F1, F2 <: Tuple, I <: DiffEqBase.DEIntegrator}
+        ::I) where {T, RNG, F1, F2 <: Tuple, I <: SciMLBase.DEIntegrator}
     nothing
 end
 
@@ -458,15 +458,15 @@ function (cache::VR_DirectEventCache)(u, t, integrator)
 end
 
 @generated function execute_affect!(cache::VR_DirectEventCache{T, RNG, F1, F2},
-        integrator::I, idx) where {T, RNG, F1, F2 <: Tuple, I <: DiffEqBase.DEIntegrator}
+        integrator::I, idx) where {T, RNG, F1, F2 <: Tuple, I <: SciMLBase.DEIntegrator}
     quote
         @unpack affect_funcs = cache
         Base.Cartesian.@nif $(fieldcount(F2)) i -> (i == idx) i -> (@inbounds affect_funcs[i](integrator)) i -> (@inbounds affect_funcs[fieldcount(F2)](integrator))
     end
 end
 
 @inline function execute_affect!(cache::VR_DirectEventCache,
-        integrator::I, idx) where {I <: DiffEqBase.DEIntegrator}
+        integrator::I, idx) where {I <: SciMLBase.DEIntegrator}
     @unpack affect_funcs = cache
     if affect_funcs isa Vector{FunctionWrappers.FunctionWrapper{Nothing, Tuple{I}}}
         @inbounds affect_funcs[idx](integrator)

test/qa.jl

@@ -0,0 +1,30 @@
+using JumpProcesses
+using ExplicitImports
+using Aqua
+using Test
+
+@testset "QA Tests" begin
+    @testset "Aqua tests" begin
+        Aqua.test_all(JumpProcesses;
+                      ambiguities = false,  # TODO: fix ambiguities and enable
+                      deps_compat = true,
+                      piracies = false,  # We define default solvers for AbstractJumpProblem
+                      unbound_args = true,
+                      undefined_exports = true,
+                      project_extras = true,
+                      stale_deps = true,
+                      persistent_tasks = false)  # disabled due to false positives
+    end
+
+    @testset "ExplicitImports tests" begin
+        # Check that we're using explicit imports
+        @test check_no_implicit_imports(JumpProcesses) === nothing
+        
+        # Check for stale explicit imports (imports that are not used)
+        @test check_no_stale_explicit_imports(JumpProcesses) === nothing
+        
+        # Allow some flexibility for non-public imports during transition
+        # This can be made stricter once all non-public API usage is resolved
+        @test_nowarn check_all_explicit_imports_via_owners(JumpProcesses)
+    end
+end

test/runtests.jl

@@ -10,6 +10,10 @@ function activate_gpu_env()
 end
 
 @time begin
+    if GROUP == "All" || GROUP == "QA"
+        @time @safetestset "QA Tests" begin include("qa.jl") end
+    end
+    
     if GROUP == "All" || GROUP == "InterfaceI"
         @time @safetestset "Constant Rate Tests" begin include("constant_rate.jl") end
         @time @safetestset "Variable Rate Tests" begin include("variable_rate.jl") end