Merge pull request #507 from SciML/fix-formatter-line-splits

Fix unnecessary line splits following Catalyst.jl PR #1306

Author: ChrisRackauckas

docs/make.jl

@@ -12,8 +12,7 @@ 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" => [["\$", "\$"], ["\\(", "\\)"]],
+mathengine = MathJax3(Dict(:loader => Dict("load" => ["[tex]/require", "[tex]/mathtools"]), :tex => Dict("inlineMath" => [["\$", "\$"], ["\\(", "\\)"]],
         "packages" => [
             "base",
             "ams",
@@ -22,9 +21,7 @@ mathengine = MathJax3(Dict(:loader => Dict("load" => ["[tex]/require", "[tex]/ma
             "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"],
         canonical = "https://docs.sciml.ai/JumpProcesses/",
@@ -36,5 +33,4 @@ makedocs(sitename = "JumpProcesses.jl",
         repolink = "https://github.com/SciML/JumpProcesses.jl"),
     pages = pages)
 
-deploydocs(repo = "github.com/SciML/JumpProcesses.jl.git";
-    push_preview = true)
+deploydocs(repo = "github.com/SciML/JumpProcesses.jl.git"; push_preview = true)

src/coupling.jl

@@ -158,8 +158,7 @@ function build_split_jumps(prob::DiffEqBase.AbstractJumpProblem,
         push!(jumps, ConstantRateJump(new_rate, new_affect!))
         # only prob
         new_affect! = affect!
-        new_rate = (u, p,
-            t) -> rate(u.u, p, t) -
+        new_rate = (u, p, t) -> rate(u.u, p, t) -
                   min(rate(u.u, p, t), rate_control(u.u_control, p, t))
         push!(jumps, ConstantRateJump(new_rate, new_affect!))
         # only prob_control
@@ -168,9 +167,7 @@ function build_split_jumps(prob::DiffEqBase.AbstractJumpProblem,
             affect!(integrator)
             flip_u!(integrator.u)
         end
-        new_rate = (u,
-            p,
-            t) -> rate_control(u.u_control, p, t) -
+        new_rate = (u, p, t) -> rate_control(u.u_control, p, t) -
                   min(rate(u.u, p, t), rate_control(u.u_control, p, t))
         push!(jumps, ConstantRateJump(new_rate, new_affect!))
     end

src/jumps.jl

@@ -300,13 +300,11 @@ p        = (β=1e-4, ν=.01)
 u0       = [999, 1, 0]       # (S,I,R)
 tspan    = (0.0, 250.0)
 rateidxs = [1, 2]           # i.e. [β,ν]
-reactant_stoich =
-[
+reactant_stoich = [
   [1 => 1, 2 => 1],         # 1*S and 1*I
   [2 => 1]                  # 1*I
 ]
-net_stoich =
-[
+net_stoich = [
   [1 => -1, 2 => 1],        # -1*S and 1*I
   [2 => -1, 3 => 1]         # -1*I and 1*R
 ]

src/spatial/flatten.jl

@@ -47,8 +47,7 @@ function flatten(netstoch::AbstractArray, reactstoch::AbstractArray,
     hop_constants = Matrix{Vector{F}}(undef, size(hopping_constants))
     for ci in CartesianIndices(hop_constants)
         (species, site) = Tuple(ci)
-        hop_constants[ci] = hopping_constants[species, site] *
-                            ones(outdegree(spatial_system, site))
+        hop_constants[ci] = hopping_constants[species, site] * ones(outdegree(spatial_system, site))
     end
     flatten(netstoch, reactstoch, rx_rates, spatial_system, u0, tspan, hop_constants;
         kwargs...)

src/spatial/hop_rates.jl

@@ -157,8 +157,7 @@ end
 return hopping rate of species at site
 """
 function evalhoprate(hop_rates::HopRatesGraphDs, u, species, site, spatial_system)
-    @inbounds u[species, site] * hop_rates.hopping_constants[species] *
-              outdegree(spatial_system, site)
+    @inbounds u[species, site] * hop_rates.hopping_constants[species] * outdegree(spatial_system, site)
 end
 
 ############## hopping rates of form D_{s,i} ################
@@ -197,8 +196,7 @@ end
 return hopping rate of species at site
 """
 function evalhoprate(hop_rates::HopRatesGraphDsi, u, species, site, spatial_system)
-    @inbounds u[species, site] * hop_rates.hopping_constants[species, site] *
-              outdegree(spatial_system, site)
+    @inbounds u[species, site] * hop_rates.hopping_constants[species, site] * outdegree(spatial_system, site)
 end
 
 ############## hopping rates of form D_{s,i,j} ################
@@ -344,8 +342,7 @@ function sample_target_site(hop_rates::HopRatesGraphDsLij, site, species, rng,
 end
 
 function evalhoprate(hop_rates::HopRatesGraphDsLij, u, species, site, spatial_system)
-    @inbounds u[species, site] * hop_rates.species_hop_constants[species] *
-              hop_rates.hop_const_cumulative_sums[site][end]
+    @inbounds u[species, site] * hop_rates.species_hop_constants[species] * hop_rates.hop_const_cumulative_sums[site][end]
 end
 
 ############## hopping rates of form D_s * L_{i,j} optimized for cartesian grid ################
@@ -398,8 +395,7 @@ function sample_target_site(hop_rates::HopRatesGridDsLij, site, species, rng, gr
 end
 
 function evalhoprate(hop_rates::HopRatesGridDsLij, u, species, site, grid)
-    @inbounds u[species, site] * hop_rates.species_hop_constants[species] *
-              hop_rates.hop_const_cumulative_sums[end, site]
+    @inbounds u[species, site] * hop_rates.species_hop_constants[species] * hop_rates.hop_const_cumulative_sums[end, site]
 end
 
 ############## hopping rates of form D_{s,i} * L_{i,j} ################
@@ -441,8 +437,7 @@ function sample_target_site(hop_rates::HopRatesGraphDsiLij, site, species, rng,
 end
 
 function evalhoprate(hop_rates::HopRatesGraphDsiLij, u, species, site, spatial_system)
-    @inbounds u[species, site] * hop_rates.species_hop_constants[species, site] *
-              hop_rates.hop_const_cumulative_sums[site][end]
+    @inbounds u[species, site] * hop_rates.species_hop_constants[species, site] * hop_rates.hop_const_cumulative_sums[site][end]
 end
 
 ############## hopping rates of form D_{s,i} * L_{i,j} optimized for cartesian grid ################
@@ -497,6 +492,5 @@ function sample_target_site(hop_rates::HopRatesGridDsiLij, site, species, rng, g
 end
 
 function evalhoprate(hop_rates::HopRatesGridDsiLij, u, species, site, grid)
-    @inbounds u[species, site] * hop_rates.species_hop_constants[species, site] *
-              hop_rates.hop_const_cumulative_sums[end, site]
+    @inbounds u[species, site] * hop_rates.species_hop_constants[species, site] * hop_rates.hop_const_cumulative_sums[end, site]
 end

test/bracketing.jl

@@ -37,10 +37,8 @@ netstoch = [[1 => -1]]
 majump = MassActionJump(majump_rates, reactstoch,
     netstoch)
 reaction_index = 1
-@test JP.get_majump_brackets(ulow, uhigh, reaction_index, majump)[1] ==
-      majump_rates[1] * ulow[1] # low
-@test JP.get_majump_brackets(ulow, uhigh, reaction_index, majump)[2] ==
-      majump_rates[1] * uhigh[1] # high
+@test JP.get_majump_brackets(ulow, uhigh, reaction_index, majump)[1] == majump_rates[1] * ulow[1] # low
+@test JP.get_majump_brackets(ulow, uhigh, reaction_index, majump)[2] == majump_rates[1] * uhigh[1] # high
 
 # constant rate
 rate(u, params, t) = 1 / u[1]

test/degenerate_rx_cases.jl

@@ -97,8 +97,7 @@ dep_graph = [
 ]
 spec_to_dep_jumps = [[2]]
 jump_to_dep_specs = [[1], [1]]
-namedpars = (dep_graph = dep_graph, vartojumps_map = spec_to_dep_jumps,
-    jumptovars_map = jump_to_dep_specs)
+namedpars = (dep_graph = dep_graph, vartojumps_map = spec_to_dep_jumps, jumptovars_map = jump_to_dep_specs)
 
 for method in methods
     local jump_prob = JumpProblem(prob, method, jump, jump2; rng = rng, namedpars...)
@@ -109,8 +108,7 @@ for method in methods
     end
 
     if doprint
-        println("Mix of constant and mass action jumps, method = ", typeof(method),
-            ", sol[end] = ", sol[end, end])
+        println("Mix of constant and mass action jumps, method = ", typeof(method), ", sol[end] = ", sol[end, end])
     end
     @test sol[end, end] > 200
 end

test/extended_jump_array.jl

@@ -7,17 +7,15 @@ rng = StableRNG(123)
 # Check that the new broadcast norm gives the same result as the old one
 rand_array = ExtendedJumpArray{Float64, 1, Vector{Float64}, Vector{Float64}}(rand(rng, 5),
     rand(rng, 2))
-old_norm = Base.FastMath.sqrt_fast(DiffEqBase.UNITLESS_ABS2(rand_array) /
-                                   max(DiffEqBase.recursive_length(rand_array), 1))
+old_norm = Base.FastMath.sqrt_fast(DiffEqBase.UNITLESS_ABS2(rand_array) / max(DiffEqBase.recursive_length(rand_array), 1))
 new_norm = DiffEqBase.ODE_DEFAULT_NORM(rand_array, 0.0)
 @test old_norm ≈ new_norm
 
 # Check for an ExtendedJumpArray where the types differ (Float64/Int64)
 rand_array = ExtendedJumpArray{Float64, 1, Vector{Float64}, Vector{Int64}}(rand(rng, 5),
     rand(rng, 1:1000,
         2))
-old_norm = Base.FastMath.sqrt_fast(DiffEqBase.UNITLESS_ABS2(rand_array) /
-                                   max(DiffEqBase.recursive_length(rand_array), 1))
+old_norm = Base.FastMath.sqrt_fast(DiffEqBase.UNITLESS_ABS2(rand_array) / max(DiffEqBase.recursive_length(rand_array), 1))
 new_norm = DiffEqBase.ODE_DEFAULT_NORM(rand_array, 0.0)
 @test old_norm ≈ new_norm
 

test/hawkes_test.jl

@@ -156,8 +156,7 @@ let alg = Coevolve()
     for vr_aggregator in (VR_FRM(), VR_Direct(), VR_DirectFW())
         oprob = ODEProblem(f!, u0, tspan, p)
         jumps = hawkes_jump(u0, g, h)
-        jprob = JumpProblem(oprob, alg, jumps...; vr_aggregator, dep_graph = g, rng,
-            use_vrj_bounds = false)
+        jprob = JumpProblem(oprob, alg, jumps...; vr_aggregator, dep_graph = g, rng, use_vrj_bounds = false)
         @test length(jprob.variable_jumps) == 1
         sols = Vector{ODESolution}(undef, Nsims)
         for n in 1:Nsims

test/spatial/hop_rates.jl

@@ -121,8 +121,7 @@ for hop_rates in hop_rates_structs
             target_propensities[target] = sum([hop_constants[species, site][i]
                                                for species in 1:num_species])
         end
-        statistical_test(hop_rates, spec_propensities, target_propensities, num_species, u,
-            site, g, rng, rel_tol)
+        statistical_test(hop_rates, spec_propensities, target_propensities, num_species, u, site, g, rng, rel_tol)
     end
 end
 test_reset(hop_rates, num_nodes)
@@ -153,8 +152,7 @@ for hop_rates in hop_rates_structs
                                                site_hop_constants[site][i]
                                                for species in 1:num_species])
         end
-        statistical_test(hop_rates, spec_propensities, target_propensities, num_species, u,
-            site, g, rng, rel_tol)
+        statistical_test(hop_rates, spec_propensities, target_propensities, num_species, u, site, g, rng, rel_tol)
     end
 end
 test_reset(hop_rates, num_nodes)
@@ -177,16 +175,14 @@ hop_rates_structs = [
 for hop_rates in hop_rates_structs
     show(io, "text/plain", hop_rates)
     for site in 1:num_nodes
-        spec_propensities = [species_hop_constants[species, site] *
-                             sum(site_hop_constants[site]) for species in 1:num_species]
+        spec_propensities = [species_hop_constants[species, site] * sum(site_hop_constants[site]) for species in 1:num_species]
         target_propensities = Dict{Int, Float64}()
         for (i, target) in enumerate(JP.neighbors(g, site))
             target_propensities[target] = sum([species_hop_constants[species, site] *
                                                site_hop_constants[site][i]
                                                for species in 1:num_species])
         end
-        statistical_test(hop_rates, spec_propensities, target_propensities, num_species, u,
-            site, g, rng, rel_tol)
+        statistical_test(hop_rates, spec_propensities, target_propensities, num_species, u, site, g, rng, rel_tol)
     end
 end
 test_reset(hop_rates, num_nodes)