Merge pull request #108 from frankschae/formatter

Use SciML format?

Author: ChrisRackauckas

.JuliaFormatter.toml

@@ -0,0 +1 @@
+style = "sciml"

.github/workflows/FormatCheck.yml

@@ -0,0 +1,42 @@
+name: format-check
+
+on:
+  push:
+    branches:
+      - 'master'
+      - 'release-'
+    tags: '*'
+  pull_request:
+
+jobs:
+  build:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        julia-version: [1]
+        julia-arch: [x86]
+        os: [ubuntu-latest]
+    steps:
+      - uses: julia-actions/setup-julia@latest
+        with:
+          version: ${{ matrix.julia-version }}
+
+      - uses: actions/checkout@v1
+      - name: Install JuliaFormatter and format
+        # This will use the latest version by default but you can set the version like so:
+        #
+        # julia  -e 'using Pkg; Pkg.add(PackageSpec(name="JuliaFormatter", version="0.13.0"))'
+        run: |
+          julia  -e 'using Pkg; Pkg.add(PackageSpec(name="JuliaFormatter"))'
+          julia  -e 'using JuliaFormatter; format(".", verbose=true)'
+      - name: Format check
+        run: |
+          julia -e '
+          out = Cmd(`git diff --name-only`) |> read |> String
+          if out == ""
+              exit(0)
+          else
+              @error "Some files have not been formatted !!!"
+              write(stdout, out)
+              exit(1)
+          end'

docs/make.jl

@@ -2,18 +2,14 @@ using Documenter, DiffEqNoiseProcess
 
 include("pages.jl")
 
-makedocs(
-    sitename="DiffEqNoiseProcess.jl",
-    authors="Chris Rackauckas",
-    modules=[DiffEqNoiseProcess],
-    clean=true,doctest=false,
-    format = Documenter.HTML(analytics = "UA-90474609-3",
-                             assets = ["assets/favicon.ico"],
-                             canonical="https://noise.sciml.ai/stable/"),
-    pages=pages
-)
+makedocs(sitename = "DiffEqNoiseProcess.jl",
+         authors = "Chris Rackauckas",
+         modules = [DiffEqNoiseProcess],
+         clean = true, doctest = false,
+         format = Documenter.HTML(analytics = "UA-90474609-3",
+                                  assets = ["assets/favicon.ico"],
+                                  canonical = "https://noise.sciml.ai/stable/"),
+         pages = pages)
 
-deploydocs(
-   repo = "github.com/SciML/DiffEqNoiseProcess.jl.git";
-   push_preview = true
-)
+deploydocs(repo = "github.com/SciML/DiffEqNoiseProcess.jl.git";
+           push_preview = true)

docs/pages.jl

@@ -1,7 +1,7 @@
 # Put in a separate page so it can be used by SciMLDocs.jl
 
-pages=[
+pages = [
     "Home" => "index.md",
     "noise_processes.md",
-    "abstract_noise_processes.md"
-]
+    "abstract_noise_processes.md",
+]

src/DiffEqNoiseProcess.jl

@@ -9,7 +9,7 @@ import RandomNumbers: Xorshifts
 import RandomNumbers, Random123
 
 import DiffEqBase: isinplace, solve, AbstractNoiseProcess,
-       DEIntegrator, AbstractNoiseProblem
+                   DEIntegrator, AbstractNoiseProblem
 
 import PoissonRandom, Distributions
 

src/bridges.jl

@@ -10,17 +10,17 @@ BrownianBridge!(t0,tend,W0,Wend,Z0=nothing,Zend=nothing;kwargs...)
 
 where `W(t0)=W₀`, `W(tend)=Wend`, and likewise for the `Z` process if defined.
 """
-function BrownianBridge(t0,tend,W0,Wend,Z0=nothing,Zend=nothing;kwargs...)
-  W = WienerProcess(t0,W0,Z0;kwargs...)
-  h = tend-t0
-  Wh = Wend-W0
-  if Z0 != nothing
-    Zh = Zend - Z0
-  else
-    Zh = nothing
-  end
-  push!(W.S₁,(h,Wh,Zh))
-  W
+function BrownianBridge(t0, tend, W0, Wend, Z0 = nothing, Zend = nothing; kwargs...)
+    W = WienerProcess(t0, W0, Z0; kwargs...)
+    h = tend - t0
+    Wh = Wend - W0
+    if Z0 != nothing
+        Zh = Zend - Z0
+    else
+        Zh = nothing
+    end
+    push!(W.S₁, (h, Wh, Zh))
+    W
 end
 
 @doc doc"""
@@ -35,57 +35,59 @@ BrownianBridge!(t0,tend,W0,Wend,Z0=nothing,Zend=nothing;kwargs...)
 
 where `W(t0)=W₀`, `W(tend)=Wend`, and likewise for the `Z` process if defined.
 """
-function BrownianBridge!(t0,tend,W0,Wh,Z0=nothing,Zh=nothing;kwargs...)
-  W = WienerProcess!(t0,W0,Z0;kwargs...)
-  h = tend-t0
-  Wh .-= W0
-  if Z0 != nothing
-    Zh .-= Z0
-  else
-    Zh = nothing
-  end
-  push!(W.S₁,(h,Wh,Zh))
-  W
+function BrownianBridge!(t0, tend, W0, Wh, Z0 = nothing, Zh = nothing; kwargs...)
+    W = WienerProcess!(t0, W0, Z0; kwargs...)
+    h = tend - t0
+    Wh .-= W0
+    if Z0 != nothing
+        Zh .-= Z0
+    else
+        Zh = nothing
+    end
+    push!(W.S₁, (h, Wh, Zh))
+    W
 end
 
-function GeometricBrownianBridge(μ,σ,t0,tend,W0,Wend,Z0=nothing,Zend=nothing;kwargs...)
-  W = GeometricBrownianMotionProcess(μ,σ,t0,W0,Z0;kwargs...)
-  h = tend-t0
-  Wh = Wend-W0
-  if Z0 != nothing
-    Zh = Zend - Z0
-  else
-    Zh = nothing
-  end
-  push!(W.S₁,(h,Wh,Zh))
-  W
+function GeometricBrownianBridge(μ, σ, t0, tend, W0, Wend, Z0 = nothing, Zend = nothing;
+                                 kwargs...)
+    W = GeometricBrownianMotionProcess(μ, σ, t0, W0, Z0; kwargs...)
+    h = tend - t0
+    Wh = Wend - W0
+    if Z0 != nothing
+        Zh = Zend - Z0
+    else
+        Zh = nothing
+    end
+    push!(W.S₁, (h, Wh, Zh))
+    W
 end
 
-function GeometricBrownianBridge!(μ,σ,t0,tend,W0,Wh,Z0=nothing,Zh=nothing;kwargs...)
-  W = GeometricBrownianMotionProcess!(μ,σ,t0,W0,Z0;kwargs...)
-  h = tend-t0
-  Wh .-= W0
-  if Z0 != nothing
-    Zh .-= Z0
-  else
-    Zh = nothing
-  end
-  push!(W.S₁,(h,Wh,Zh))
-  W
+function GeometricBrownianBridge!(μ, σ, t0, tend, W0, Wh, Z0 = nothing, Zh = nothing;
+                                  kwargs...)
+    W = GeometricBrownianMotionProcess!(μ, σ, t0, W0, Z0; kwargs...)
+    h = tend - t0
+    Wh .-= W0
+    if Z0 != nothing
+        Zh .-= Z0
+    else
+        Zh = nothing
+    end
+    push!(W.S₁, (h, Wh, Zh))
+    W
 end
 
-function CompoundPoissonBridge(rate,t0,tend,W0,Wend;kwargs...)
-  W = CompoundPoissonProcess(rate,t0,W0;kwargs...)
-  h = tend-t0
-  Wh = Wend-W0
-  push!(W.S₁,(h,Wh,nothing))
-  W
+function CompoundPoissonBridge(rate, t0, tend, W0, Wend; kwargs...)
+    W = CompoundPoissonProcess(rate, t0, W0; kwargs...)
+    h = tend - t0
+    Wh = Wend - W0
+    push!(W.S₁, (h, Wh, nothing))
+    W
 end
 
-function CompoundPoissonBridge!(rate,t0,tend,W0,Wh;kwargs...)
-  W = CompoundPoissonProcess!(rate,t0,W0;kwargs...)
-  h = tend-t0
-  Wh .-= W0
-  push!(W.S₁,(h,Wh,nothing))
-  W
+function CompoundPoissonBridge!(rate, t0, tend, W0, Wh; kwargs...)
+    W = CompoundPoissonProcess!(rate, t0, W0; kwargs...)
+    h = tend - t0
+    Wh .-= W0
+    push!(W.S₁, (h, Wh, nothing))
+    W
 end

src/compoundpoisson.jl

@@ -1,44 +1,55 @@
-function cpp_bridge(dW,cpp,W,W0,Wh,q,h,u,p,t,rng)
-  rand.(rng,Distributions.Binomial.(Int.(Wh),float.(q)))
-end
-function cpp_bridge!(rand_vec,cpp,W,W0,Wh,q,h,u,p,t,rng)
-  rand_vec .= rand.(rng,Distributions.Binomial.(Int.(Wh),float.(q)))
-end
-
-"""
-https://www.math.wisc.edu/~anderson/papers/AndPostleap.pdf
-Incorporating postleap checks in tau-leaping
-J. Chem. Phys. 128, 054103 (2008); https://doi.org/10.1063/1.2819665
-"""
-mutable struct CompoundPoissonProcess{R,CR}
-  rate::R
-  currate::CR
-  computerates::Bool
-  function CompoundPoissonProcess(rate,t0,W0;computerates=true,kwargs...)
-    cpp = new{typeof(rate),typeof(W0)}(rate,W0,computerates)
-    NoiseProcess{false}(t0,W0,nothing,cpp,(dW,W,W0,Wh,q,h,u,p,t,rng)->cpp_bridge(dW,cpp,W,W0,Wh,q,h,u,p,t,rng);continuous=false,cache=cpp,kwargs...)
-  end
-end
-function (P::CompoundPoissonProcess)(dW,W,dt,u,p,t,rng)
-  P.computerates && (P.currate = P.rate(u,p,t))
-  PoissonRandom.pois_rand.(rng,dt.*P.currate)
-end
-
-"""
-https://www.math.wisc.edu/~anderson/papers/AndPostleap.pdf
-Incorporating postleap checks in tau-leaping
-J. Chem. Phys. 128, 054103 (2008); https://doi.org/10.1063/1.2819665
-"""
-struct CompoundPoissonProcess!{R,CR}
-  rate::R
-  currate::CR
-  computerates::Bool
-  function CompoundPoissonProcess!(rate,t0,W0;computerates=true,kwargs...)
-    cpp = new{typeof(rate),typeof(W0)}(rate,copy(W0),computerates)
-    NoiseProcess{true}(t0,W0,nothing,cpp,(rand_vec,W,W0,Wh,q,h,u,p,t,rng)->cpp_bridge!(rand_vec,cpp,W,W0,Wh,q,h,u,p,t,rng);continuous=false,cache=cpp,kwargs...)
-  end
-end
-function (P::CompoundPoissonProcess!)(rand_vec,W,dt,u,p,t,rng)
-  P.computerates && P.rate(P.currate,u,p,t)
-  @. rand_vec = PoissonRandom.pois_rand(rng,dt*P.currate)
-end
+function cpp_bridge(dW, cpp, W, W0, Wh, q, h, u, p, t, rng)
+    rand.(rng, Distributions.Binomial.(Int.(Wh), float.(q)))
+end
+function cpp_bridge!(rand_vec, cpp, W, W0, Wh, q, h, u, p, t, rng)
+    rand_vec .= rand.(rng, Distributions.Binomial.(Int.(Wh), float.(q)))
+end
+
+"""
+https://www.math.wisc.edu/~anderson/papers/AndPostleap.pdf
+Incorporating postleap checks in tau-leaping
+J. Chem. Phys. 128, 054103 (2008); https://doi.org/10.1063/1.2819665
+"""
+mutable struct CompoundPoissonProcess{R, CR}
+    rate::R
+    currate::CR
+    computerates::Bool
+    function CompoundPoissonProcess(rate, t0, W0; computerates = true, kwargs...)
+        cpp = new{typeof(rate), typeof(W0)}(rate, W0, computerates)
+        NoiseProcess{false}(t0, W0, nothing, cpp,
+                            (dW, W, W0, Wh, q, h, u, p, t, rng) -> cpp_bridge(dW, cpp, W,
+                                                                              W0, Wh, q, h,
+                                                                              u, p, t, rng);
+                            continuous = false, cache = cpp, kwargs...)
+    end
+end
+function (P::CompoundPoissonProcess)(dW, W, dt, u, p, t, rng)
+    P.computerates && (P.currate = P.rate(u, p, t))
+    PoissonRandom.pois_rand.(rng, dt .* P.currate)
+end
+
+"""
+https://www.math.wisc.edu/~anderson/papers/AndPostleap.pdf
+Incorporating postleap checks in tau-leaping
+J. Chem. Phys. 128, 054103 (2008); https://doi.org/10.1063/1.2819665
+"""
+struct CompoundPoissonProcess!{R, CR}
+    rate::R
+    currate::CR
+    computerates::Bool
+    function CompoundPoissonProcess!(rate, t0, W0; computerates = true, kwargs...)
+        cpp = new{typeof(rate), typeof(W0)}(rate, copy(W0), computerates)
+        NoiseProcess{true}(t0, W0, nothing, cpp,
+                           (rand_vec, W, W0, Wh, q, h, u, p, t, rng) -> cpp_bridge!(rand_vec,
+                                                                                    cpp, W,
+                                                                                    W0, Wh,
+                                                                                    q, h, u,
+                                                                                    p, t,
+                                                                                    rng);
+                           continuous = false, cache = cpp, kwargs...)
+    end
+end
+function (P::CompoundPoissonProcess!)(rand_vec, W, dt, u, p, t, rng)
+    P.computerates && P.rate(P.currate, u, p, t)
+    @. rand_vec = PoissonRandom.pois_rand(rng, dt * P.currate)
+end