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Merge pull request #452 from sathvikbhagavan/sb/doc1
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Update makedocs syntax and few cleanups
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ChrisRackauckas authored Dec 13, 2023
2 parents 665b85d + a9c4fa0 commit 7a66e2e
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Showing 30 changed files with 452 additions and 377 deletions.
1 change: 0 additions & 1 deletion .github/workflows/CI.yml
Original file line number Diff line number Diff line change
Expand Up @@ -15,7 +15,6 @@ jobs:
- Core
version:
- '1'
- '1.6'
steps:
- uses: actions/checkout@v4
- uses: julia-actions/setup-julia@v1
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18 changes: 6 additions & 12 deletions docs/make.jl
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Expand Up @@ -10,17 +10,11 @@ using Plots
include("pages.jl")

makedocs(sitename = "Surrogates.jl",
strict = [
:doctest,
:linkcheck,
:parse_error,
:example_block,
# Other available options are
# :autodocs_block, :cross_references, :docs_block, :eval_block, :example_block, :footnote, :meta_block, :missing_docs, :setup_block
],
format = Documenter.HTML(analytics = "UA-90474609-3",
assets = ["assets/favicon.ico"],
canonical = "https://docs.sciml.ai/Surrogates/stable/"),
pages = pages)
linkcheck = true,
warnonly = [:missing_docs],
format = Documenter.HTML(analytics = "UA-90474609-3",
assets = ["assets/favicon.ico"],
canonical = "https://docs.sciml.ai/Surrogates/stable/"),
pages = pages)

deploydocs(repo = "github.com/SciML/Surrogates.jl.git")
76 changes: 38 additions & 38 deletions docs/pages.jl
Original file line number Diff line number Diff line change
@@ -1,39 +1,39 @@
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",
"GEKPLS" => "gekpls.md",
"MOE" => "moe.md",
"Parallel Optimization" => "parallel.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",
]]
"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",
"GEKPLS" => "gekpls.md",
"MOE" => "moe.md",
"Parallel Optimization" => "parallel.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",
]]
45 changes: 24 additions & 21 deletions docs/src/index.md
Original file line number Diff line number Diff line change
Expand Up @@ -113,56 +113,59 @@ surrogate_optimize(f,SRBF(),lb,ub,my_lobachevsky,RandomSample())
value = my_lobachevsky(5.0)
```
## Reproducibility

```@raw html
<details><summary>The documentation of this SciML package was built using these direct dependencies,</summary>
```

```@example
using Pkg # hide
Pkg.status() # hide
```

```@raw html
</details>
```

```@raw html
<details><summary>and using this machine and Julia version.</summary>
```

```@example
using InteractiveUtils # hide
versioninfo() # hide
```

```@raw html
</details>
```

```@raw html
<details><summary>A more complete overview of all dependencies and their versions is also provided.</summary>
```

```@example
using Pkg # hide
Pkg.status(;mode = PKGMODE_MANIFEST) # hide
Pkg.status(; mode = PKGMODE_MANIFEST) # hide
```

```@raw html
</details>
```
```@raw html
You can also download the
<a href="
```
```@eval
using TOML
version = TOML.parse(read("../../Project.toml",String))["version"]
name = TOML.parse(read("../../Project.toml",String))["name"]
link = "https://github.com/SciML/"*name*".jl/tree/gh-pages/v"*version*"/assets/Manifest.toml"
```
```@raw html
">manifest</a> file and the
<a href="
```

```@eval
using TOML
version = TOML.parse(read("../../Project.toml",String))["version"]
name = TOML.parse(read("../../Project.toml",String))["name"]
link = "https://github.com/SciML/"*name*".jl/tree/gh-pages/v"*version*"/assets/Project.toml"
```
```@raw html
">project</a> file.
using Markdown
version = TOML.parse(read("../../Project.toml", String))["version"]
name = TOML.parse(read("../../Project.toml", String))["name"]
link_manifest = "https://github.com/SciML/" * name * ".jl/tree/gh-pages/v" * version *
"/assets/Manifest.toml"
link_project = "https://github.com/SciML/" * name * ".jl/tree/gh-pages/v" * version *
"/assets/Project.toml"
Markdown.parse("""You can also download the
[manifest]($link_manifest)
file and the
[project]($link_project)
file.
""")
```
4 changes: 2 additions & 2 deletions lib/SurrogatesAbstractGPs/test/runtests.jl
Original file line number Diff line number Diff line change
Expand Up @@ -27,7 +27,7 @@ using Surrogates: sample, SobolSample
x_points = sample(5, lb, ub, SobolSample())
y_points = f.(x_points)
agp1D = AbstractGPSurrogate([x_points[1]], [y_points[1]],
gp = GP(SqExponentialKernel()), Σy = 0.05)
gp = GP(SqExponentialKernel()), Σy = 0.05)
x_new = 2.5
y_actual = f.(x_new)
for i in 2:length(x_points)
Expand Down Expand Up @@ -88,7 +88,7 @@ using Surrogates: sample, SobolSample
b = 6
my_k_EI1 = AbstractGPSurrogate(x, y)
surrogate_optimize(objective_function, EI(), a, b, my_k_EI1, RandomSample(),
maxiters = 200, num_new_samples = 155)
maxiters = 200, num_new_samples = 155)
end

@testset "Optimization ND" begin
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6 changes: 3 additions & 3 deletions lib/SurrogatesFlux/src/SurrogatesFlux.jl
Original file line number Diff line number Diff line change
Expand Up @@ -26,8 +26,8 @@ NeuralSurrogate(x,y,lb,ub,model,loss,opt,n_echos)
"""
function NeuralSurrogate(x, y, lb, ub; model = Chain(Dense(length(x[1]), 1), first),
loss = (x, y) -> Flux.mse(model(x), y), opt = Descent(0.01),
n_echos::Int = 1)
loss = (x, y) -> Flux.mse(model(x), y), opt = Descent(0.01),
n_echos::Int = 1)
X = vec.(collect.(x))
data = zip(X, y)
ps = Flux.params(model)
Expand Down Expand Up @@ -59,7 +59,7 @@ function add_point!(my_n::NeuralSurrogate, x_new, y_new)
end
X = vec.(collect.(my_n.x))
data = zip(X, my_n.y)
for epoch in 1:my_n.n_echos
for epoch in 1:(my_n.n_echos)
Flux.train!(my_n.loss, my_n.ps, data, my_n.opt)
end
nothing
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16 changes: 8 additions & 8 deletions lib/SurrogatesFlux/test/runtests.jl
Original file line number Diff line number Diff line change
Expand Up @@ -19,7 +19,7 @@ using SafeTestsets
my_opt = Descent(0.01)
n_echos = 1
my_neural = NeuralSurrogate(x, y, a, b, model = my_model, loss = my_loss, opt = my_opt,
n_echos = 1)
n_echos = 1)
my_neural_kwargs = NeuralSurrogate(x, y, a, b)
add_point!(my_neural, 8.5, 20.0)
add_point!(my_neural, [3.2, 3.5], [7.4, 8.0])
Expand All @@ -37,7 +37,7 @@ using SafeTestsets
my_opt = Descent(0.01)
n_echos = 1
my_neural = NeuralSurrogate(x, y, lb, ub, model = my_model, loss = my_loss,
opt = my_opt, n_echos = 1)
opt = my_opt, n_echos = 1)
my_neural_kwargs = NeuralSurrogate(x, y, lb, ub)
my_neural((3.5, 1.49))
my_neural([3.4, 1.4])
Expand All @@ -54,7 +54,7 @@ using SafeTestsets
my_model = Chain(Dense(1, 2))
my_loss(x, y) = Flux.mse(my_model(x), y)
surrogate = NeuralSurrogate(x, y, lb, ub, model = my_model, loss = my_loss,
opt = my_opt, n_echos = 1)
opt = my_opt, n_echos = 1)
surr_kwargs = NeuralSurrogate(x, y, lb, ub)

f = x -> [x[1], x[2]^2]
Expand All @@ -66,7 +66,7 @@ using SafeTestsets
my_model = Chain(Dense(2, 2))
my_loss(x, y) = Flux.mse(my_model(x), y)
surrogate = NeuralSurrogate(x, y, lb, ub, model = my_model, loss = my_loss,
opt = my_opt, n_echos = 1)
opt = my_opt, n_echos = 1)
surrogate_kwargs = NeuralSurrogate(x, y, lb, ub)
surrogate((1.0, 2.0))
x_new = (2.0, 2.0)
Expand All @@ -85,7 +85,7 @@ using SafeTestsets
n_echos = 1
my_neural_ND_neural = NeuralSurrogate(x, y, lb, ub)
surrogate_optimize(objective_function_ND, SRBF(), lb, ub, my_neural_ND_neural,
SobolSample(), maxiters = 15)
SobolSample(), maxiters = 15)

# AD Compatibility
lb = 0.0
Expand All @@ -101,7 +101,7 @@ using SafeTestsets
my_opt = Descent(0.01)
n_echos = 1
my_neural = NeuralSurrogate(x, y, lb, ub, model = my_model, loss = my_loss,
opt = my_opt, n_echos = 1)
opt = my_opt, n_echos = 1)
g = x -> my_neural'(x)
g(3.4)
end
Expand All @@ -120,7 +120,7 @@ using SafeTestsets
my_opt = Descent(0.01)
n_echos = 1
my_neural = NeuralSurrogate(x, y, lb, ub, model = my_model, loss = my_loss,
opt = my_opt, n_echos = 1)
opt = my_opt, n_echos = 1)
g = x -> Zygote.gradient(my_neural, x)
g((2.0, 5.0))
end
Expand All @@ -141,7 +141,7 @@ using SafeTestsets
my_opt = Descent(0.01)
n_echos = 1
my_neural = NeuralSurrogate(x, y, lb, ub, model = my_model, loss = my_loss,
opt = my_opt, n_echos = 1)
opt = my_opt, n_echos = 1)
Zygote.gradient(x -> sum(my_neural(x)), (2.0, 5.0))

my_rad = RadialBasis(x, y, lb, ub, rad = linearRadial())
Expand Down
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