Merge pull request #361 from SciML/format

setup SciML Style

.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

@@ -2,15 +2,10 @@ using Documenter, Surrogates
 
 include("pages.jl")
 
-makedocs(
-    sitename="Surrogates.jl",
-    format = Documenter.HTML(analytics = "UA-90474609-3",
-                         assets = ["assets/favicon.ico"],
-                         canonical="https://surrogates.sciml.ai/stable/"),
-    pages = pages
-)
+makedocs(sitename = "Surrogates.jl",
+         format = Documenter.HTML(analytics = "UA-90474609-3",
+                                  assets = ["assets/favicon.ico"],
+                                  canonical = "https://surrogates.sciml.ai/stable/"),
+         pages = pages)
 
-
-deploydocs(
-   repo = "github.com/SciML/Surrogates.jl.git",
-)
+deploydocs(repo = "github.com/SciML/Surrogates.jl.git")

docs/pages.jl

@@ -1,39 +1,37 @@
-pages = [
-    "index.md"
-    "Tutorials" => [
-        "Basics" => "tutorials.md",
-        "Radials" => "radials.md",
-        "Kriging" => "kriging.md",
-        "Gaussian Process" =>"abstractgps.md",
-        "Lobachevsky" => "lobachevsky.md",
-        "Linear" => "LinearSurrogate.md",
-        "InverseDistance" => "InverseDistance.md",
-        "RandomForest" => "randomforest.md",
-        "SecondOrderPolynomial" => "secondorderpoly.md",
-        "NeuralSurrogate" => "neural.md",
-        "Wendland" => "wendland.md",
-        "Polynomial Chaos" => "polychaos.md",
-        "Variable Fidelity" => "variablefidelity.md",
-        "Gradient Enhanced Kriging" => "gek.md"
-       ]
-    "User guide" => [
-        "Samples" => "samples.md",
-        "Surrogates" => "surrogate.md",
-        "Optimization" => "optimizations.md"
-        ]
-    "Benchmarks" => [
-        "Sphere function" => "sphere_function.md",
-        "Lp norm" => "lp.md",
-        "Rosenbrock" => "rosenbrock.md",
-        "Tensor product" => "tensor_prod.md",
-        "Cantilever beam" => "cantilever.md",
-        "Water Flow function" => "water_flow.md",
-        "Welded beam function" => "welded_beam.md",
-        "Branin function" => "BraninFunction.md",
-        "Ackley function" => "ackley.md",
-        "Gramacy & Lee Function" => "gramacylee.md",
-        "Salustowicz Benchmark" => "Salustowicz.md",
-        "Multi objective optimization" => "multi_objective_opt.md"
-        ]
-    "Contributing" => "contributing.md"
-    ]
+pages = ["index.md"
+         "Tutorials" => [
+             "Basics" => "tutorials.md",
+             "Radials" => "radials.md",
+             "Kriging" => "kriging.md",
+             "Gaussian Process" => "abstractgps.md",
+             "Lobachevsky" => "lobachevsky.md",
+             "Linear" => "LinearSurrogate.md",
+             "InverseDistance" => "InverseDistance.md",
+             "RandomForest" => "randomforest.md",
+             "SecondOrderPolynomial" => "secondorderpoly.md",
+             "NeuralSurrogate" => "neural.md",
+             "Wendland" => "wendland.md",
+             "Polynomial Chaos" => "polychaos.md",
+             "Variable Fidelity" => "variablefidelity.md",
+             "Gradient Enhanced Kriging" => "gek.md",
+         ]
+         "User guide" => [
+             "Samples" => "samples.md",
+             "Surrogates" => "surrogate.md",
+             "Optimization" => "optimizations.md",
+         ]
+         "Benchmarks" => [
+             "Sphere function" => "sphere_function.md",
+             "Lp norm" => "lp.md",
+             "Rosenbrock" => "rosenbrock.md",
+             "Tensor product" => "tensor_prod.md",
+             "Cantilever beam" => "cantilever.md",
+             "Water Flow function" => "water_flow.md",
+             "Welded beam function" => "welded_beam.md",
+             "Branin function" => "BraninFunction.md",
+             "Ackley function" => "ackley.md",
+             "Gramacy & Lee Function" => "gramacylee.md",
+             "Salustowicz Benchmark" => "Salustowicz.md",
+             "Multi objective optimization" => "multi_objective_opt.md",
+         ]
+         "Contributing" => "contributing.md"]

lib/SurrogatesAbstractGPs/src/SurrogatesAbstractGPs.jl

@@ -8,15 +8,15 @@ using AbstractGPs
 mutable struct AbstractGPSurrogate{X, Y, GP, GP_P, S} <: AbstractSurrogate
     x::X
     y::Y
-    gp::GP 
+    gp::GP
     gp_posterior::GP_P
     Σy::S
- end
+end
 
 # constructor
 function AbstractGPSurrogate(x, y; gp = GP(Matern52Kernel()), Σy = 0.1)
-    AbstractGPSurrogate(x, y, gp, posterior(gp(x, Σy),y), Σy)
- end
+    AbstractGPSurrogate(x, y, gp, posterior(gp(x, Σy), y), Σy)
+end
 
 # predictor 
 function (g::AbstractGPSurrogate)(val)
@@ -34,7 +34,7 @@ function add_point!(g::AbstractGPSurrogate, new_x, new_y)
     x_copy = copy(g.x)
     push!(x_copy, new_x)
     y_copy = copy(g.y)
-    push!(y_copy, new_y) 
+    push!(y_copy, new_y)
     updated_posterior = posterior(g.gp(x_copy, g.Σy), y_copy)
     g.x, g.y, g.gp_posterior = x_copy, y_copy, updated_posterior
     nothing