SciML · ChrisRackauckas-Claude · Jan 4, 2026
diff --git a/.JuliaFormatter.toml b/.JuliaFormatter.toml
diff --git a/.github/workflows/FormatCheck.yml b/.github/workflows/FormatCheck.yml
@@ -1,13 +1,19 @@
-name: "Format Check"
+name: format-check
 
 on:
   push:
     branches:
       - 'master'
+      - 'main'
+      - 'release-'
     tags: '*'
   pull_request:
 
 jobs:
-  format-check:
-    name: "Format Check"
-    uses: "SciML/.github/.github/workflows/format-check.yml@v1"
+  runic:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: fredrikekre/runic-action@v1
+        with:
+          version: '1'
diff --git a/benchmarks/extended_jump_array.jl b/benchmarks/extended_jump_array.jl
@@ -10,11 +10,11 @@ benchmark_out = ExtendedJumpArray(zeros(500000), zeros(500000))
 benchmark_in = ExtendedJumpArray(rand(rng, 500000), rand(rng, 500000))
 
 function test_single_dot(out, array)
-    @inbounds @. out = array + 1.23 * array
+    return @inbounds @. out = array + 1.23 * array
 end
 
 function test_double_dot(out, array)
-    @inbounds @.. out = array + 1.23 * array
+    return @inbounds @.. out = array + 1.23 * array
 end
 
 println("Base-case normal broadcasting")

diff --git a/docs/make.jl b/docs/make.jl
@@ -11,23 +11,33 @@ cp(joinpath(docpath, "Project.toml"), joinpath(assetpath, "Project.toml"), force
 
 include("pages.jl")
 
-mathengine = MathJax3(Dict(:loader => Dict("load" => ["[tex]/require", "[tex]/mathtools"]), :tex => Dict("inlineMath" => [["\$", "\$"], ["\\(", "\\)"]],
-        "packages" => [
-            "base",
-            "ams",
-            "autoload",
-            "mathtools",
-            "require"
-        ])))
+mathengine = MathJax3(
+    Dict(
+        :loader => Dict("load" => ["[tex]/require", "[tex]/mathtools"]), :tex => Dict(
+            "inlineMath" => [["\$", "\$"], ["\\(", "\\)"]],
+            "packages" => [
+                "base",
+                "ams",
+                "autoload",
+                "mathtools",
+                "require",
+            ]
+        )
+    )
+)
 
-makedocs(sitename = "JumpProcesses.jl", authors = "Chris Rackauckas", modules = [JumpProcesses],
+makedocs(
+    sitename = "JumpProcesses.jl", authors = "Chris Rackauckas", modules = [JumpProcesses],
     clean = true, doctest = false, linkcheck = true, warnonly = [:missing_docs],
-    format = Documenter.HTML(; assets = ["assets/favicon.ico"],
+    format = Documenter.HTML(;
+        assets = ["assets/favicon.ico"],
         canonical = "https://docs.sciml.ai/JumpProcesses/",
         prettyurls = (get(ENV, "CI", nothing) == "true"),
         mathengine,
         edit_link = "master",
-        repolink = "https://github.com/SciML/JumpProcesses.jl"),
-    pages = pages)
+        repolink = "https://github.com/SciML/JumpProcesses.jl"
+    ),
+    pages = pages
+)
 
 deploydocs(repo = "github.com/SciML/JumpProcesses.jl.git"; push_preview = true)
diff --git a/docs/pages.jl b/docs/pages.jl
@@ -1,14 +1,19 @@
 # Put in a separate page so it can be used by SciMLDocs.jl
 
-pages = ["index.md",
-    "Tutorials" => Any["tutorials/simple_poisson_process.md",
+pages = [
+    "index.md",
+    "Tutorials" => Any[
+        "tutorials/simple_poisson_process.md",
         "tutorials/discrete_stochastic_example.md",
         "tutorials/point_process_simulation.md",
         "tutorials/jump_diffusion.md",
-        "tutorials/spatial.md"],
+        "tutorials/spatial.md",
+    ],
     "Applications" => Any["applications/advanced_point_process.md"],
-    "Type Documentation" => Any["Jumps, JumpProblem, and Aggregators" => "jump_types.md",
-        "Jump solvers" => "jump_solve.md"],
+    "Type Documentation" => Any[
+        "Jumps, JumpProblem, and Aggregators" => "jump_types.md",
+        "Jump solvers" => "jump_solve.md",
+    ],
     "FAQ" => "faq.md",
-    "API" => "api.md"
+    "API" => "api.md",
 ]
diff --git a/ext/JumpProcessesKernelAbstractionsExt.jl b/ext/JumpProcessesKernelAbstractionsExt.jl
@@ -5,20 +5,24 @@ using KernelAbstractions, Adapt
 using StaticArrays
 using PoissonRandom, Random
 
-function SciMLBase.__solve(ensembleprob::SciMLBase.AbstractEnsembleProblem,
+function SciMLBase.__solve(
+        ensembleprob::SciMLBase.AbstractEnsembleProblem,
         alg::SimpleTauLeaping,
         ensemblealg::EnsembleGPUKernel;
         trajectories,
         seed = nothing,
         dt = error("dt is required for SimpleTauLeaping."),
-        kwargs...)
+        kwargs...
+    )
     if trajectories == 1
-        return SciMLBase.__solve(ensembleprob, alg, EnsembleSerial(); trajectories = 1,
-            seed, dt, kwargs...)
+        return SciMLBase.__solve(
+            ensembleprob, alg, EnsembleSerial(); trajectories = 1,
+            seed, dt, kwargs...
+        )
     end
 
     ensemblealg.backend === nothing ? backend = CPU() :
-    backend = ensemblealg.backend
+        backend = ensemblealg.backend
 
     jump_prob = ensembleprob.prob
 
@@ -31,36 +35,42 @@ function SciMLBase.__solve(ensembleprob::SciMLBase.AbstractEnsembleProblem,
 
     # Run vectorized solve
     ts,
-    us = vectorized_solve(
-        probs, jump_prob, SimpleTauLeaping(); backend, trajectories, seed, dt)
+        us = vectorized_solve(
+        probs, jump_prob, SimpleTauLeaping(); backend, trajectories, seed, dt
+    )
 
     # Convert to CPU for inspection
     _ts = Array(ts)
     _us = Array(us)
 
-    time = @elapsed sol = [begin
-                               ts = @view _ts[:, i]
-                               us = @view _us[:, :, i]
-                               sol_idx = findlast(x -> x != probs[i].prob.tspan[1], ts)
-                               if sol_idx === nothing
-                                   @error "No solution found" tspan=probs[i].tspan[1] ts
-                                   error("Batch solve failed")
-                               end
-                               @views ensembleprob.output_func(
-                                   SciMLBase.build_solution(probs[i].prob,
-                                       alg,
-                                       ts[1:sol_idx],
-                                       [us[j, :] for j in 1:sol_idx],
-                                       k = nothing,
-                                       stats = nothing,
-                                       calculate_error = false,
-                                       retcode = sol_idx !=
-                                                 length(ts) ?
-                                                 ReturnCode.Terminated :
-                                                 ReturnCode.Success),
-                                   i)[1]
-                           end
-                           for i in eachindex(probs)]
+    time = @elapsed sol = [
+        begin
+                ts = @view _ts[:, i]
+                us = @view _us[:, :, i]
+                sol_idx = findlast(x -> x != probs[i].prob.tspan[1], ts)
+                if sol_idx === nothing
+                    @error "No solution found" tspan = probs[i].tspan[1] ts
+                    error("Batch solve failed")
+            end
+                @views ensembleprob.output_func(
+                    SciMLBase.build_solution(
+                        probs[i].prob,
+                        alg,
+                        ts[1:sol_idx],
+                        [us[j, :] for j in 1:sol_idx],
+                        k = nothing,
+                        stats = nothing,
+                        calculate_error = false,
+                        retcode = sol_idx !=
+                        length(ts) ?
+                        ReturnCode.Terminated :
+                        ReturnCode.Success
+                    ),
+                    i
+                )[1]
+            end
+            for i in eachindex(probs)
+    ]
     return SciMLBase.EnsembleSolution(sol, time, true)
 end
 
@@ -82,7 +92,8 @@ end
 @kernel function simple_tau_leaping_kernel(
         @Const(probs_data), _us, _ts, dt, @Const(rj_data),
         current_u_buf, rate_cache_buf, counts_buf, local_dc_buf,
-        seed::UInt64)
+        seed::UInt64
+    )
     i = @index(Global, Linear)
 
     # Get thread-local buffers
@@ -114,7 +125,7 @@ end
 
     # Get input/output arrays
     ts_view = @inbounds view(_ts, :, i)
-    us_view = @inbounds view(_us,:,:,i)
+    us_view = @inbounds view(_us, :, :, i)
 
     # Initialize first time step and state
     @inbounds ts_view[1] = tspan[1]
@@ -124,7 +135,7 @@ end
 
     # Main loop
     for j in 2:n
-        tprev = tspan[1] + (j-2) * dt
+        tprev = tspan[1] + (j - 2) * dt
 
         # Compute rates and scale by dt
         rate(rate_cache, current_u, p, tprev)
@@ -143,20 +154,24 @@ end
         @inbounds for k in 1:state_dim
             us_view[j, k] = current_u[k]
         end
-        @inbounds ts_view[j] = tspan[1] + (j-1) * dt
+        @inbounds ts_view[j] = tspan[1] + (j - 1) * dt
     end
 end
 
 # Vectorized solve function
-function vectorized_solve(probs, prob::JumpProblem, alg::SimpleTauLeaping;
-        backend, trajectories, seed, dt, kwargs...)
+function vectorized_solve(
+        probs, prob::JumpProblem, alg::SimpleTauLeaping;
+        backend, trajectories, seed, dt, kwargs...
+    )
     # Extract common jump data
     rj = prob.regular_jump
     rj_data = JumpData(rj.rate, rj.c, rj.numjumps)
 
     # Extract trajectory-specific data without static typing
-    probs_data = [TrajectoryData(SA{eltype(p.prob.u0)}[p.prob.u0...], p.prob.p, p.prob.tspan)
-                  for p in probs]
+    probs_data = [
+        TrajectoryData(SA{eltype(p.prob.u0)}[p.prob.u0...], p.prob.p, p.prob.tspan)
+            for p in probs
+    ]
 
     # Adapt to GPU
     probs_data_gpu = adapt(backend, probs_data)
@@ -197,13 +212,15 @@ function vectorized_solve(probs, prob::JumpProblem, alg::SimpleTauLeaping;
     KernelAbstractions.synchronize(backend)
 
     # Seed for Poisson sampling
-    seed = seed === nothing ? UInt64(12345) : UInt64(seed);
+    seed = seed === nothing ? UInt64(12345) : UInt64(seed)
 
     # Launch main kernel
     kernel = simple_tau_leaping_kernel(backend)
-    main_event = kernel(probs_data_gpu, us, ts, dt, rj_data_gpu,
+    main_event = kernel(
+        probs_data_gpu, us, ts, dt, rj_data_gpu,
         current_u_buf, rate_cache_buf, counts_buf, local_dc_buf, seed;
-        ndrange = n_trajectories)
+        ndrange = n_trajectories
+    )
     KernelAbstractions.synchronize(backend)
 
     return ts, us

diff --git a/src/JumpProcesses.jl b/src/JumpProcesses.jl
@@ -33,18 +33,18 @@ import SymbolicIndexingInterface as SII
 
 # 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!
+    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} <:
-              DEIntegrator{Alg, IIP, U, T} end
+DEIntegrator{Alg, IIP, U, T} end
 
 const DEFAULT_RNG = Random.default_rng()
 
@@ -126,7 +126,7 @@ export init, solve, solve!
 include("SSA_stepper.jl")
 export SSAStepper
 
-# leaping: 
+# leaping:
 include("simple_regular_solve.jl")
 export SimpleTauLeaping, EnsembleGPUKernel