reapply formatter

Author: ArnoStrouwen

.JuliaFormatter.toml

@@ -1,2 +1,3 @@
 style = "sciml"
-format_markdown = true
+format_markdown = true
+format_docstrings = true

docs/pages.jl

@@ -2,13 +2,15 @@
 
 pages = ["index.md",
     "getting_started.md",
-    "Tutorials" => Any["GPU Ensembles" => Any["tutorials/gpu_ensemble_basic.md",
+    "Tutorials" => Any[
+        "GPU Ensembles" => Any["tutorials/gpu_ensemble_basic.md",
             "tutorials/parallel_callbacks.md",
             "tutorials/multigpu.md",
             "tutorials/lower_level_api.md",
             "tutorials/weak_order_conv_sde.md"],
         "Within-Method GPU" => Any["tutorials/within_method_gpu.md"]],
-    "Examples" => Any["GPU Ensembles" => Any["examples/sde.md",
+    "Examples" => Any[
+        "GPU Ensembles" => Any["examples/sde.md",
             "examples/ad.md",
             "examples/reductions.md"],
         "Within-Method GPU" => Any["examples/reaction_diffusion.md",
@@ -17,5 +19,5 @@ pages = ["index.md",
         "manual/ensemblegpuarray.md",
         "manual/backends.md",
         "manual/optimal_trajectories.md",
-        "manual/choosing_ensembler.md"],
+        "manual/choosing_ensembler.md"]
 ]

docs/src/examples/sde.md

@@ -27,6 +27,7 @@ prob = SDEProblem(lorenz, multiplicative_noise, u0, tspan, p)
 const pre_p = [rand(Float32, 3) for i in 1:10_000]
 prob_func = (prob, i, repeat) -> remake(prob, p = pre_p[i] .* p)
 monteprob = EnsembleProblem(prob, prob_func = prob_func)
-sol = solve(monteprob, SOSRI(), EnsembleGPUArray(CUDA.CUDABackend()), trajectories = 10_000,
+sol = solve(
+    monteprob, SOSRI(), EnsembleGPUArray(CUDA.CUDABackend()), trajectories = 10_000,
     saveat = 1.0f0)
 ```

docs/src/tutorials/gpu_ensemble_basic.md

@@ -25,7 +25,8 @@ Changing this to being GPU-parallelized is as simple as changing the ensemble me
 `EnsembleGPUArray`:
 
 ```@example lorenz
-sol = solve(monteprob, Tsit5(), EnsembleGPUArray(CUDA.CUDABackend()), trajectories = 10_000,
+sol = solve(
+    monteprob, Tsit5(), EnsembleGPUArray(CUDA.CUDABackend()), trajectories = 10_000,
     saveat = 1.0f0);
 ```
 

docs/src/tutorials/lower_level_api.md

@@ -89,12 +89,14 @@ end
 
 ## Finally use the lower API for faster solves! (Fixed time-stepping)
 
-@time CUDA.@sync sol = DiffEqGPU.vectorized_map_solve(probs, Tsit5(), EnsembleGPUArray(0.0),
+@time CUDA.@sync sol = DiffEqGPU.vectorized_map_solve(
+    probs, Tsit5(), EnsembleGPUArray(0.0),
     batch, false, dt = 0.001f0,
     save_everystep = false, dense = false)
 
 ## Adaptive time-stepping (Notice the boolean argument)
-@time CUDA.@sync sol = DiffEqGPU.vectorized_map_solve(probs, Tsit5(), EnsembleGPUArray(0.0),
+@time CUDA.@sync sol = DiffEqGPU.vectorized_map_solve(
+    probs, Tsit5(), EnsembleGPUArray(0.0),
     batch, true, dt = 0.001f0,
     save_everystep = false, dense = false)
 ```

src/algorithms.jl

@@ -16,7 +16,7 @@ struct EnsembleCPUArray <: EnsembleArrayAlgorithm end
 
 """
 ```julia
-EnsembleGPUArray(backend,cpu_offload = 0.2)
+EnsembleGPUArray(backend, cpu_offload = 0.2)
 ```
 
 An `EnsembleArrayAlgorithm` which utilizes the GPU kernels to parallelize each ODE solve
@@ -73,13 +73,14 @@ function lorenz(du, u, p, t)
     du[3] = u[1] * u[2] - p[3] * u[3]
 end
 
-u0 = Float32[1.0;0.0;0.0]
-tspan = (0.0f0,100.0f0)
-p = [10.0f0,28.0f0,8/3f0]
-prob = ODEProblem(lorenz,u0,tspan,p)
-prob_func = (prob,i,repeat) -> remake(prob,p=rand(Float32,3).*p)
-monteprob = EnsembleProblem(prob, prob_func = prob_func, safetycopy=false)
-@time sol = solve(monteprob,Tsit5(),EnsembleGPUArray(CUDADevice()),trajectories=10_000,saveat=1.0f0)
+u0 = Float32[1.0; 0.0; 0.0]
+tspan = (0.0f0, 100.0f0)
+p = [10.0f0, 28.0f0, 8 / 3.0f0]
+prob = ODEProblem(lorenz, u0, tspan, p)
+prob_func = (prob, i, repeat) -> remake(prob, p = rand(Float32, 3) .* p)
+monteprob = EnsembleProblem(prob, prob_func = prob_func, safetycopy = false)
+@time sol = solve(monteprob, Tsit5(), EnsembleGPUArray(CUDADevice()),
+    trajectories = 10_000, saveat = 1.0f0)
 ```
 """
 struct EnsembleGPUArray{Backend} <: EnsembleArrayAlgorithm
@@ -89,7 +90,7 @@ end
 
 """
 ```julia
-EnsembleGPUKernel(backend,cpu_offload = 0.2)
+EnsembleGPUKernel(backend, cpu_offload = 0.2)
 ```
 
 A massively-parallel ensemble algorithm which generates a unique GPU kernel for the entire
@@ -146,7 +147,7 @@ prob_func = (prob, i, repeat) -> remake(prob, p = (@SVector rand(Float32, 3)) .*
 monteprob = EnsembleProblem(prob, prob_func = prob_func, safetycopy = false)
 
 @time sol = solve(monteprob, GPUTsit5(), EnsembleGPUKernel(), trajectories = 10_000,
-                  adaptive = false, dt = 0.1f0)
+    adaptive = false, dt = 0.1f0)
 ```
 """
 struct EnsembleGPUKernel{Dev} <: EnsembleKernelAlgorithm

src/ensemblegpuarray/lowerlevel_solve.jl

@@ -3,23 +3,22 @@ Lower level API for `EnsembleArrayAlgorithm`. Avoids conversion of solution to C
 
 ```julia
 vectorized_map_solve(probs, alg,
-                     ensemblealg::Union{EnsembleArrayAlgorithm}, I,
-                     adaptive)
+    ensemblealg::Union{EnsembleArrayAlgorithm}, I,
+    adaptive)
 ```
 
 ## Arguments
 
-- `probs`: the GPU-setup problems generated by the ensemble.
-- `alg`: the kernel-based differential equation solver. Most of the solvers from OrdinaryDiffEq.jl
-         are supported.
-- `ensemblealg`: The `EnsembleGPUArray()` algorithm.
-- `I`: The iterator argument. Can be set to for e.g. 1:10_000 to simulate 10,000 trajectories.
-- `adaptive`: The Boolean argument for time-stepping. Use `true` to enable adaptive time-stepping.
+  - `probs`: the GPU-setup problems generated by the ensemble.
+  - `alg`: the kernel-based differential equation solver. Most of the solvers from OrdinaryDiffEq.jl
+    are supported.
+  - `ensemblealg`: The `EnsembleGPUArray()` algorithm.
+  - `I`: The iterator argument. Can be set to for e.g. 1:10_000 to simulate 10,000 trajectories.
+  - `adaptive`: The Boolean argument for time-stepping. Use `true` to enable adaptive time-stepping.
 
 ## Keyword Arguments
 
 Only a subset of the common solver arguments are supported.
-
 """
 function vectorized_map_solve end
 

src/ensemblegpukernel/callbacks.jl

@@ -46,7 +46,7 @@ struct GPUContinuousCallback{F1, F2, F3, F4, F5, F6, T, T2, T3, I, R} <:
             interp_points, save_positions::F6, dtrelax::R, abstol::T,
             reltol::T2,
             repeat_nudge::T3) where {F1, F2, F3, F4, F5, F6, T, T2,
-            T3, I, R,
+            T3, I, R
     }
         if save_positions != (false, false)
             error("Callback `save_positions` are incompatible with kernel-based GPU ODE solvers due requiring static sizing. Please ensure `save_positions = (false,false)` is set in all callback definitions used with such solvers.")

src/ensemblegpukernel/integrators/integrator_utils.jl

@@ -10,11 +10,12 @@ function build_adaptive_controller_cache(alg::A, ::Type{T}) where {A, T}
     return beta1, beta2, qmax, qmin, gamma, qoldinit, qold
 end
 
-@inline function savevalues!(integrator::DiffEqBase.AbstractODEIntegrator{
+@inline function savevalues!(
+        integrator::DiffEqBase.AbstractODEIntegrator{
             AlgType,
             IIP,
             S,
-            T,
+            T
         }, ts,
         us,
         force = false) where {AlgType <: GPUODEAlgorithm, IIP, S, T}
@@ -45,23 +46,25 @@ end
     saved, savedexactly
 end
 
-@inline function DiffEqBase.terminate!(integrator::DiffEqBase.AbstractODEIntegrator{AlgType,
+@inline function DiffEqBase.terminate!(
+        integrator::DiffEqBase.AbstractODEIntegrator{AlgType,
             IIP, S,
             T},
         retcode = ReturnCode.Terminated) where {
         AlgType <:
         GPUODEAlgorithm,
         IIP,
         S,
-        T,
+        T
 }
     integrator.retcode = retcode
 end
 
-@inline function apply_discrete_callback!(integrator::DiffEqBase.AbstractODEIntegrator{
+@inline function apply_discrete_callback!(
+        integrator::DiffEqBase.AbstractODEIntegrator{
             AlgType,
             IIP,
-            S, T,
+            S, T
         },
         ts, us,
         callback::GPUDiscreteCallback) where {
@@ -79,10 +82,11 @@ end
     integrator.u_modified, saved_in_cb
 end
 
-@inline function apply_discrete_callback!(integrator::DiffEqBase.AbstractODEIntegrator{
+@inline function apply_discrete_callback!(
+        integrator::DiffEqBase.AbstractODEIntegrator{
             AlgType,
             IIP,
-            S, T,
+            S, T
         },
         ts, us,
         callback::GPUDiscreteCallback,
@@ -93,10 +97,11 @@ end
         args...)
 end
 
-@inline function apply_discrete_callback!(integrator::DiffEqBase.AbstractODEIntegrator{
+@inline function apply_discrete_callback!(
+        integrator::DiffEqBase.AbstractODEIntegrator{
             AlgType,
             IIP,
-            S, T,
+            S, T
         },
         ts, us,
         discrete_modified::Bool,
@@ -110,10 +115,11 @@ end
     discrete_modified || bool, saved_in_cb || saved_in_cb2
 end
 
-@inline function apply_discrete_callback!(integrator::DiffEqBase.AbstractODEIntegrator{
+@inline function apply_discrete_callback!(
+        integrator::DiffEqBase.AbstractODEIntegrator{
             AlgType,
             IIP,
-            S, T,
+            S, T
         },
         ts, us,
         discrete_modified::Bool,
@@ -126,11 +132,12 @@ end
     discrete_modified || bool, saved_in_cb || saved_in_cb2
 end
 
-@inline function interpolate(integrator::DiffEqBase.AbstractODEIntegrator{
+@inline function interpolate(
+        integrator::DiffEqBase.AbstractODEIntegrator{
             AlgType,
             IIP,
             S,
-            T,
+            T
         },
         t) where {AlgType <: GPUODEAlgorithm, IIP, S, T}
     θ = (t - integrator.tprev) / integrator.dt
@@ -142,11 +149,12 @@ end
             b7θ * integrator.k7)
 end
 
-@inline function _change_t_via_interpolation!(integrator::DiffEqBase.AbstractODEIntegrator{
+@inline function _change_t_via_interpolation!(
+        integrator::DiffEqBase.AbstractODEIntegrator{
             AlgType,
             IIP,
             S,
-            T,
+            T
         },
         t,
         modify_save_endpoint::Type{Val{T1}}) where {
@@ -155,7 +163,7 @@ end
         IIP,
         S,
         T,
-        T1,
+        T1
 }
     # Can get rid of an allocation here with a function
     # get_tmp_arr(integrator.cache) which gives a pointer to some
@@ -169,11 +177,12 @@ end
         #integrator.dt = integrator.t - integrator.tprev
     end
 end
-@inline function DiffEqBase.change_t_via_interpolation!(integrator::DiffEqBase.AbstractODEIntegrator{
+@inline function DiffEqBase.change_t_via_interpolation!(
+        integrator::DiffEqBase.AbstractODEIntegrator{
             AlgType,
             IIP,
             S,
-            T,
+            T
         },
         t,
         modify_save_endpoint::Type{Val{T1}} = Val{
@@ -184,12 +193,13 @@ end
         IIP,
         S,
         T,
-        T1,
+        T1
 }
     _change_t_via_interpolation!(integrator, t, modify_save_endpoint)
 end
 
-@inline function apply_callback!(integrator::DiffEqBase.AbstractODEIntegrator{AlgType, IIP,
+@inline function apply_callback!(
+        integrator::DiffEqBase.AbstractODEIntegrator{AlgType, IIP,
             S, T},
         callback::GPUContinuousCallback,
         cb_time, prev_sign, event_idx, ts,
@@ -219,7 +229,8 @@ end
     true, saved_in_cb
 end
 
-@inline function handle_callbacks!(integrator::DiffEqBase.AbstractODEIntegrator{AlgType,
+@inline function handle_callbacks!(
+        integrator::DiffEqBase.AbstractODEIntegrator{AlgType,
             IIP, S, T},
         ts, us) where {AlgType <: GPUODEAlgorithm, IIP, S, T}
     discrete_callbacks = integrator.callback.discrete_callbacks
@@ -232,7 +243,8 @@ end
     if !(continuous_callbacks isa Tuple{})
         event_occurred = false
 
-        time, upcrossing, event_occurred, event_idx, idx, counter = DiffEqBase.find_first_continuous_callback(integrator,
+        time, upcrossing, event_occurred, event_idx, idx, counter = DiffEqBase.find_first_continuous_callback(
+            integrator,
             continuous_callbacks...)
 
         if event_occurred
@@ -256,16 +268,18 @@ end
     return false, saved_in_cb
 end
 
-@inline function DiffEqBase.find_callback_time(integrator::DiffEqBase.AbstractODEIntegrator{
+@inline function DiffEqBase.find_callback_time(
+        integrator::DiffEqBase.AbstractODEIntegrator{
             AlgType,
             IIP,
             S,
-            T,
+            T
         },
         callback::DiffEqGPU.GPUContinuousCallback,
         counter) where {AlgType <: GPUODEAlgorithm,
         IIP, S, T}
-    event_occurred, interp_index, prev_sign, prev_sign_index, event_idx = DiffEqBase.determine_event_occurance(integrator,
+    event_occurred, interp_index, prev_sign, prev_sign_index, event_idx = DiffEqBase.determine_event_occurance(
+        integrator,
         callback,
         counter)
 
@@ -321,15 +335,16 @@ end
         GPUODEAlgorithm,
         IIP,
         S,
-        T,
+        T
 }
     return nothing
 end
 
-@inline function DiffEqBase.get_condition(integrator::DiffEqBase.AbstractODEIntegrator{
+@inline function DiffEqBase.get_condition(
+        integrator::DiffEqBase.AbstractODEIntegrator{
             AlgType,
             IIP,
-            S, T,
+            S, T
         },
         callback,
         abst) where {AlgType <: GPUODEAlgorithm, IIP, S, T
@@ -345,11 +360,12 @@ end
 end
 
 # interp_points = 0 or equivalently nothing
-@inline function DiffEqBase.determine_event_occurance(integrator::DiffEqBase.AbstractODEIntegrator{
+@inline function DiffEqBase.determine_event_occurance(
+        integrator::DiffEqBase.AbstractODEIntegrator{
             AlgType,
             IIP,
             S,
-            T,
+            T
         },
         callback::DiffEqGPU.GPUContinuousCallback,
         counter) where {