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reapply formatter #473

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4 changes: 3 additions & 1 deletion .JuliaFormatter.toml
Original file line number Diff line number Diff line change
@@ -1 +1,3 @@
style = "sciml"
style = "sciml"
format_markdown = true
format_docstrings = true
28 changes: 10 additions & 18 deletions CONTRIBUTING.md
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@@ -1,21 +1,13 @@
# Contributing

1. Fork the repository on github. (Click the `Fork` button in the top-right corner)

2. Clone the repository you have just forked. `git clone https://github.com/YOUR_USERNAME/Surrogates.jl.git`

3. `cd Surrogates.jl` Enter the repository's directory.

4. `julia` Open the Julia REPL.

5. `]` Enter package mode

6. Activate the local environment `activate .`

7. Install the dependencies. `instantiate`

8. Perform your edits (Atom with Juno, or VSCode with the Julia plugin are good editor choices)

9. Stage, Commit, and Push your changes

1. Fork the repository on github. (Click the `Fork` button in the top-right corner)

2. Clone the repository you have just forked. `git clone https://github.com/YOUR_USERNAME/Surrogates.jl.git`
3. `cd Surrogates.jl` Enter the repository's directory.
4. `julia` Open the Julia REPL.
5. `]` Enter package mode
6. Activate the local environment `activate .`
7. Install the dependencies. `instantiate`
8. Perform your edits (Atom with Juno, or VSCode with the Julia plugin are good editor choices)
9. Stage, Commit, and Push your changes
10. [Open a Pull Request](https://help.github.com/en/github/collaborating-with-issues-and-pull-requests/creating-a-pull-request-from-a-fork)
6 changes: 3 additions & 3 deletions LICENSE.md
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@@ -1,18 +1,18 @@
The Surrogates.jl package is licensed under the MIT "Expat" License:

> Copyright (c) 2019-20: Ludovico Bessi, Julia Computing.
>
>
> Permission is hereby granted, free of charge, to any person obtaining
> a copy of this software and associated documentation files (the
> "Software"), to deal in the Software without restriction, including
> without limitation the rights to use, copy, modify, merge, publish,
> distribute, sublicense, and/or sell copies of the Software, and to
> permit persons to whom the Software is furnished to do so, subject to
> the following conditions:
>
>
> The above copyright notice and this permission notice shall be
> included in all copies or substantial portions of the Software.
>
>
> THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
> EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
> MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.
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53 changes: 27 additions & 26 deletions README.md
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Expand Up @@ -6,47 +6,48 @@
[![codecov](https://codecov.io/gh/SciML/Surrogates.jl/branch/master/graph/badge.svg)](https://codecov.io/gh/SciML/Surrogates.jl)
[![Build Status](https://github.com/SciML/Surrogates.jl/workflows/CI/badge.svg)](https://github.com/SciML/Surrogates.jl/actions?query=workflow%3ACI)

[![ColPrac: Contributor's Guide on Collaborative Practices for Community Packages](https://img.shields.io/badge/ColPrac-Contributor's%20Guide-blueviolet)](https://github.com/SciML/ColPrac)
[![ColPrac: Contributor's Guide on Collaborative Practices for Community Packages](https://img.shields.io/badge/ColPrac-Contributor%27s%20Guide-blueviolet)](https://github.com/SciML/ColPrac)
[![SciML Code Style](https://img.shields.io/static/v1?label=code%20style&message=SciML&color=9558b2&labelColor=389826)](https://github.com/SciML/SciMLStyle)

A surrogate model is an approximation method that mimics the behavior of a computationally
expensive simulation. In more mathematical terms: suppose we are attempting to optimize a function
`f(p)`, but each calculation of `f` is very expensive. It may be the case we need to solve a PDE for each point or use advanced numerical linear algebra machinery, which is usually costly. The idea is then to develop a surrogate model `g` which approximates `f` by training on previous data collected from evaluations of `f`.
The construction of a surrogate model can be seen as a three-step process:

1. Sample selection
2. Construction of the surrogate model
3. Surrogate optimization
1. Sample selection
2. Construction of the surrogate model
3. Surrogate optimization

Sampling can be done through [QuasiMonteCarlo.jl](https://github.com/SciML/QuasiMonteCarlo.jl), all the functions available there can be used in Surrogates.jl.

## ALL the currently available surrogate models:

- Kriging
- Kriging using Stheno
- Radial Basis
- Wendland
- Linear
- Second Order Polynomial
- Support Vector Machines (Wait for LIBSVM resolution)
- Neural Networks
- Random Forests
- Lobachevsky
- Inverse-distance
- Polynomial expansions
- Variable fidelity
- Mixture of experts (Waiting GaussianMixtures package to work on v1.5)
- Earth
- Gradient Enhanced Kriging
- Kriging
- Kriging using Stheno
- Radial Basis
- Wendland
- Linear
- Second Order Polynomial
- Support Vector Machines (Wait for LIBSVM resolution)
- Neural Networks
- Random Forests
- Lobachevsky
- Inverse-distance
- Polynomial expansions
- Variable fidelity
- Mixture of experts (Waiting GaussianMixtures package to work on v1.5)
- Earth
- Gradient Enhanced Kriging

## ALL the currently available optimization methods:

- SRBF
- LCBS
- DYCORS
- EI
- SOP
- Multi-optimization: SMB and RTEA
- SRBF
- LCBS
- DYCORS
- EI
- SOP
- Multi-optimization: SMB and RTEA

## Installing Surrogates package

```julia
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78 changes: 39 additions & 39 deletions docs/pages.jl
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@@ -1,40 +1,40 @@
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",
"Improved Branin function" => "ImprovedBraninFunction.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",
"Improved Branin function" => "ImprovedBraninFunction.md",
"Ackley function" => "ackley.md",
"Gramacy & Lee Function" => "gramacylee.md",
"Salustowicz Benchmark" => "Salustowicz.md",
"Multi objective optimization" => "multi_objective_opt.md"
]]
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