reapply formatter

Author: ArnoStrouwen

.JuliaFormatter.toml

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

docs/make.jl

@@ -14,7 +14,7 @@ mathengine = MathJax3(Dict(:loader => Dict("load" => ["[tex]/require", "[tex]/ma
             "ams",
             "autoload",
             "mathtools",
-            "require",
+            "require"
         ])))
 
 makedocs(sitename = "JumpProcesses.jl",

docs/pages.jl

@@ -10,5 +10,5 @@ pages = ["index.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"
 ]

docs/src/applications/advanced_point_process.md

@@ -190,8 +190,7 @@ processes connected to it by ``alpha``. This influence will then decrease at
 rate ``\beta``.
 
 The conditional intensity of this process has a recursive formulation which we
-can use to our advantage to significantly speed simulation. Let ``t_{N_i} = \max
-\{t_{n_j} < t \mid j \in E_i\}`` and ``\phi_i^\ast(t)`` below.
+can use to our advantage to significantly speed simulation. Let ``t_{N_i} = \max \{t_{n_j} < t \mid j \in E_i\}`` and ``\phi_i^\ast(t)`` below.
 
 ```math
 \begin{split}
@@ -224,8 +223,7 @@ end
 nothing # hide
 ```
 
-We assume that each sup-process `i` is a marked TPP. With probability ``(1 -
-\omega^\ast(t))``, we draw a mark from a 2-dimensional Gaussian
+We assume that each sup-process `i` is a marked TPP. With probability ``(1 - \omega^\ast(t))``, we draw a mark from a 2-dimensional Gaussian
 distribution centered in ``\mu_i`` with ``\sigma_1`` standard deviation; and
 with probability ``\omega^\ast(t)`` we draw from a 2-dimensional Gaussian
 distribution centered on the last location visited by ``i`` with ``\sigma_2``
@@ -321,7 +319,7 @@ using Graphs
 using Distributions
 V = 10
 G = erdos_renyi(V, 0.2)
-g = [[[i] ; neighbors(G, i)] for i in 1:nv(G)]
+g = [[[i]; neighbors(G, i)] for i in 1:nv(G)]
 mark_dist = [MvNormal(rand(2), [0.2, 0.2]) for i in 1:nv(G)]
 jumps = [hawkes_jump(i, g, mark_dist) for i in 1:nv(G)]
 tspan = (0.0, 50.0)
@@ -330,7 +328,7 @@ hawkes = SciMLPointProcess{
     eltype(jumps),
     typeof(g),
     eltype(mark_dist),
-    eltype(tspan),
+    eltype(tspan)
 }(jumps,
     mark_dist,
     g,
@@ -342,8 +340,7 @@ hawkes = SciMLPointProcess{
 ## [Sampling](@id tpp_sampling)
 
 JumpProcesses shines in the simulation of SDEs with discontinuous jumps. The
-mapping we introduced in the [previous Section](@ref tpp_theory) whereby ``du =
-dN(t)`` implies that JumpProcesses also excels in simulating TPPs.
+mapping we introduced in the [previous Section](@ref tpp_theory) whereby ``du = dN(t)`` implies that JumpProcesses also excels in simulating TPPs.
 
 JumpProcesses offers a plethora of simulation algorithms for TPPs. The library
 call them _aggregators_ because these algorithms are methods for aggregating

docs/src/index.md

@@ -22,26 +22,26 @@ As jump and point processes are often considered from a variety of perspectives
 across different fields, JumpProcesses provides three tutorials on using the
 package for those with different backgrounds:
 
-- [Simulating basic Poisson processes](@ref poisson_proc_tutorial)
-- [Simulating jump processes via SSAs (i.e., Gillespie methods)](@ref ssa_tutorial)
-- [Simulating temporal point processes (TPPs)](@ref tpp_tutorial)
+  - [Simulating basic Poisson processes](@ref poisson_proc_tutorial)
+  - [Simulating jump processes via SSAs (i.e., Gillespie methods)](@ref ssa_tutorial)
+  - [Simulating temporal point processes (TPPs)](@ref tpp_tutorial)
 
 These tutorials also explain the types of jump/point processes that can be
 mathematically modelled with JumpProcesses.jl. For more complicated models that
 couple ODEs and/or SDEs with continuous noise to jump processes, we provide a
 tutorial on
 
-- [Simulating jump-diffusion processes](@ref jump_diffusion_tutorial)
+  - [Simulating jump-diffusion processes](@ref jump_diffusion_tutorial)
 
 For jump processes that involve spatial transport on a graph/mesh, such
 as Reaction-Diffusion Master Equation models, we provide a tutorial on
 
-- [Spatial SSAs](@ref Spatial-SSAs-with-JumpProcesses.jl)
+  - [Spatial SSAs](@ref Spatial-SSAs-with-JumpProcesses.jl)
 
 Finally, we provide application tutorials which are more extensive tutorials that
 interface with other libraries going deeper into a topic.
 
-- [Temporal Point Processes (TPP) with JumpProcesses and PointProcesses](@ref tpp_advanced)
+  - [Temporal Point Processes (TPP) with JumpProcesses and PointProcesses](@ref tpp_advanced)
 
 We provide a mathematical overview of the library below, but note users may also
 skip to the appropriate tutorial listed above to get started with using
@@ -73,6 +73,7 @@ can then generate exact realizations of pure jump processes of the form
 ```math
 du = \sum_{i=1}^I h_i(u,p,t) \, dN_i(t),
 ```
+
 where ``h_i(u,p,t)`` represents the amount that ``u(t)`` changes when ``N_i(t)``
 jumps. JumpProcesses encodes such changes via a user-provided `affect!`
 function, which allows even more general changes to the state, ``u(t)``, when
@@ -146,7 +147,7 @@ Pkg.add("JumpProcesses")
 
   - See the [SciML Style Guide](https://github.com/SciML/SciMLStyle) for common coding practices and other style decisions.
   - There are a few community forums for getting help and asking questions:
-
+    
       + The #diffeq-bridged and #sciml-bridged channels in the
         [Julia Slack](https://julialang.org/slack/)
       + The #diffeq-bridged and #sciml-bridged channels in the

docs/src/tutorials/discrete_stochastic_example.md

@@ -453,11 +453,11 @@ latter determining the affect function.
 rateidxs = [1, 2]           # i.e., [β, ν]
 reactant_stoich = [
     [1 => 1, 2 => 1],         # 1*S and 1*I
-    [2 => 1],                  # 1*I
+    [2 => 1]                  # 1*I
 ]
 net_stoich = [
     [1 => -1, 2 => 1],        # -1*S and 1*I
-    [2 => -1, 3 => 1],         # -1*I and 1*R
+    [2 => -1, 3 => 1]         # -1*I and 1*R
 ]
 mass_act_jump = MassActionJump(reactant_stoich, net_stoich; param_idxs = rateidxs)
 ```

docs/src/tutorials/point_process_simulation.md

@@ -231,7 +231,7 @@ and hence the dependencies of `seasonal_process` are only `[2]`.
 Therefore, we obtain the following dependency graph:
 
 ```@example tpp-tutorial
-dep_graph = [[1,2], [2]]
+dep_graph = [[1, 2], [2]]
 ```
 
 We can then construct the corresponding problem `JumpProblem`, passing our

ext/JumpProcessFastBroadcastExt.jl

@@ -3,30 +3,30 @@ module JumpProcessFastBroadcastExt
 using JumpProcesses, FastBroadcast
 
 @inline function FastBroadcast.fast_materialize!(::FastBroadcast.False, ::DB, dst::EJA,
-                                                 bc::Base.Broadcast.Broadcasted{S}) where {
-                                                                                           S,
-                                                                                           DB,
-                                                                                           EJA <:
-                                                                                           ExtendedJumpArray
-                                                                                           }
+        bc::Base.Broadcast.Broadcasted{S}) where {
+        S,
+        DB,
+        EJA <:
+        ExtendedJumpArray
+}
     FastBroadcast.fast_materialize!(FastBroadcast.False(), DB(), dst.u,
-                                    JumpProcesses.repack(bc, Val(:u)))
+        JumpProcesses.repack(bc, Val(:u)))
     FastBroadcast.fast_materialize!(FastBroadcast.False(), DB(), dst.jump_u,
-                                    JumpProcesses.repack(bc, Val(:jump_u)))
+        JumpProcesses.repack(bc, Val(:jump_u)))
     dst
 end
 
 @inline function FastBroadcast.fast_materialize!(::FastBroadcast.True, ::DB, dst::EJA,
-                                                 bc::Base.Broadcast.Broadcasted{S}) where {
-                                                                                           S,
-                                                                                           DB,
-                                                                                           EJA <:
-                                                                                           ExtendedJumpArray
-                                                                                           }
+        bc::Base.Broadcast.Broadcasted{S}) where {
+        S,
+        DB,
+        EJA <:
+        ExtendedJumpArray
+}
     FastBroadcast.fast_materialize!(FastBroadcast.True(), DB(), dst.u,
-                                    JumpProcesses.repack(bc, Val(:u)))
+        JumpProcesses.repack(bc, Val(:u)))
     FastBroadcast.fast_materialize!(FastBroadcast.True(), DB(), dst.jump_u,
-                                    JumpProcesses.repack(bc, Val(:jump_u)))
+        JumpProcesses.repack(bc, Val(:jump_u)))
     dst
 end
 

src/SSA_stepper.jl

@@ -108,8 +108,8 @@ function DiffEqBase.u_modified!(integrator::SSAIntegrator, bool::Bool)
 end
 
 function DiffEqBase.__solve(jump_prob::JumpProblem,
-                            alg::SSAStepper;
-                            kwargs...)
+        alg::SSAStepper;
+        kwargs...)
     integrator = init(jump_prob, alg; kwargs...)
     solve!(integrator)
     integrator.sol
@@ -145,15 +145,15 @@ function DiffEqBase.solve!(integrator::SSAIntegrator)
 end
 
 function DiffEqBase.__init(jump_prob::JumpProblem,
-                           alg::SSAStepper;
-                           save_start = true,
-                           save_end = true,
-                           seed = nothing,
-                           alias_jump = Threads.threadid() == 1,
-                           saveat = nothing,
-                           callback = nothing,
-                           tstops = eltype(jump_prob.prob.tspan)[],
-                           numsteps_hint = 100)
+        alg::SSAStepper;
+        save_start = true,
+        save_end = true,
+        seed = nothing,
+        alias_jump = Threads.threadid() == 1,
+        saveat = nothing,
+        callback = nothing,
+        tstops = eltype(jump_prob.prob.tspan)[],
+        numsteps_hint = 100)
     if !(jump_prob.prob isa DiscreteProblem)
         error("SSAStepper only supports DiscreteProblems.")
     end
@@ -184,9 +184,9 @@ function DiffEqBase.__init(jump_prob::JumpProblem,
     end
 
     sol = DiffEqBase.build_solution(prob, alg, t, u, dense = false,
-                                    calculate_error = false,
-                                    stats = DiffEqBase.Stats(0),
-                                    interp = DiffEqBase.ConstantInterpolation(t, u))
+        calculate_error = false,
+        stats = DiffEqBase.Stats(0),
+        interp = DiffEqBase.ConstantInterpolation(t, u))
     save_everystep = any(cb.save_positions)
 
     if saveat isa Number
@@ -217,8 +217,8 @@ function DiffEqBase.__init(jump_prob::JumpProblem,
         error("The time interval to solve over is non-increasing, i.e. tspan[2] <= tspan[1]. This is not allowed for pure jump problem.")
 
     integrator = SSAIntegrator(prob.f, copy(prob.u0), prob.tspan[1], prob.tspan[1], tdir,
-                               prob.p, sol, 1, prob.tspan[1], cb, _saveat, save_everystep,
-                               save_end, cur_saveat, opts, tstops, 1, false, true)
+        prob.p, sol, 1, prob.tspan[1], cb, _saveat, save_everystep,
+        save_end, cur_saveat, opts, tstops, 1, false, true)
     cb.initialize(cb, integrator.u, prob.tspan[1], integrator)
     DiffEqBase.initialize!(opts.callback, integrator.u, prob.tspan[1], integrator)
     integrator
@@ -235,7 +235,7 @@ end
 # The Jump aggregators should not register the next jump through add_tstop! for SSAIntegrator
 # such that we can achieve maximum performance
 @inline function register_next_jump_time!(integrator::SSAIntegrator,
-                                          p::AbstractSSAJumpAggregator, t)
+        p::AbstractSSAJumpAggregator, t)
     integrator.tstop = p.next_jump_time
     nothing
 end
@@ -279,7 +279,7 @@ function DiffEqBase.step!(integrator::SSAIntegrator)
 
     if !(integrator.opts.callback.discrete_callbacks isa Tuple{})
         discrete_modified, saved_in_cb = DiffEqBase.apply_discrete_callback!(integrator,
-                                                                             integrator.opts.callback.discrete_callbacks...)
+            integrator.opts.callback.discrete_callbacks...)
     else
         saved_in_cb = false
     end

src/aggregators/aggregated_api.jl

@@ -11,41 +11,41 @@ Notes
     vector is unchanged, this can safely be set to false to improve performance.
 """
 function reset_aggregated_jumps!(integrator, uprev = nothing; update_jump_params = true,
-                                 kwargs...)
+        kwargs...)
     reset_aggregated_jumps!(integrator, uprev, integrator.opts.callback,
-                            update_jump_params = update_jump_params, kwargs...)
+        update_jump_params = update_jump_params, kwargs...)
     nothing
 end
 
 function reset_aggregated_jumps!(integrator, uprev, callback::Nothing;
-                                 update_jump_params = true, kwargs...)
+        update_jump_params = true, kwargs...)
     nothing
 end
 
 function reset_aggregated_jumps!(integrator, uprev, callback::CallbackSet;
-                                 update_jump_params = true, kwargs...)
+        update_jump_params = true, kwargs...)
     if !isempty(callback.discrete_callbacks)
         reset_aggregated_jumps!(integrator, uprev, callback.discrete_callbacks...,
-                                update_jump_params = update_jump_params, kwargs...)
+            update_jump_params = update_jump_params, kwargs...)
     end
     nothing
 end
 
 function reset_aggregated_jumps!(integrator, uprev, cb::DiscreteCallback, cbs...;
-                                 update_jump_params = true, kwargs...)
+        update_jump_params = true, kwargs...)
     if cb.condition isa AbstractSSAJumpAggregator
         maj = cb.condition.ma_jumps
         update_jump_params && using_params(maj) &&
             update_parameters!(cb.condition.ma_jumps, integrator.p; kwargs...)
         cb.condition(cb, integrator.u, integrator.t, integrator)
     end
     reset_aggregated_jumps!(integrator, uprev, cbs...;
-                            update_jump_params = update_jump_params, kwargs...)
+        update_jump_params = update_jump_params, kwargs...)
     nothing
 end
 
 function reset_aggregated_jumps!(integrator, uprev, cb::DiscreteCallback;
-                                 update_jump_params = true, kwargs...)
+        update_jump_params = true, kwargs...)
     if cb.condition isa AbstractSSAJumpAggregator
         maj = cb.condition.ma_jumps
         update_jump_params && using_params(maj) &&

src/aggregators/aggregators.jl

@@ -164,7 +164,7 @@ algorithm with optimal binning,  Journal of Chemical Physics 143, 074108
 struct DirectCRDirect <: AbstractAggregatorAlgorithm end
 
 const JUMP_AGGREGATORS = (Direct(), DirectFW(), DirectCR(), SortingDirect(), RSSA(), FRM(),
-                          FRMFW(), NRM(), RSSACR(), RDirect(), Coevolve())
+    FRMFW(), NRM(), RSSACR(), RDirect(), Coevolve())
 
 # For JumpProblem construction without an aggregator
 struct NullAggregator <: AbstractAggregatorAlgorithm end

src/aggregators/bracketing.jl

@@ -63,7 +63,7 @@ get brackets for the rate of reaction rx by first checking if the reaction is a
         return get_majump_brackets(p.ulow, p.uhigh, rx, ma_jumps)
     else
         @inbounds return get_cjump_brackets(p.ulow, p.uhigh, p.rates[rx - num_majumps],
-                                            params, t)
+            params, t)
     end
 end