Refactor (#13)

sharanry · web-flow · commit 4ab6912d9cf0 · 2020-09-05T00:01:02.000+05:30
* Refactor

* fix test bug

* Rename to GPLikelihoods

* Remove kernelfunctions dependency
diff --git a/Project.toml b/Project.toml
@@ -1,20 +1,16 @@
-name = "LatentGPs"
-uuid = "45b822f7-b0f9-4a40-9473-dffa0412f8e7"
+name = "GPLikelihoods"
+uuid = "6031954c-0455-49d7-b3b9-3e1c99afaf40"
 authors = ["willtebbutt <wt0881@my.bristol.ac.uk>"]
 version = "0.1.0"
 
 [deps]
 AbstractGPs = "99985d1d-32ba-4be9-9821-2ec096f28918"
 Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f"
 Functors = "d9f16b24-f501-4c13-a1f2-28368ffc5196"
-KernelFunctions = "ec8451be-7e33-11e9-00cf-bbf324bd1392"
-LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
 Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
-Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
 
 [compat]
-AbstractGPs = "0.1.1"
+AbstractGPs = "0.2"
 Distributions = "0.19, 0.20, 0.21, 0.22, 0.23"
 Functors = "0.1"
-KernelFunctions = "0.4"
 julia = "1.3"
diff --git a/README.md b/README.md
@@ -1,8 +1,8 @@
-# LatentGPs
+# GPLikelihoods
 
-[![Stable](https://img.shields.io/badge/docs-stable-blue.svg)](https://JuliaGaussianProcesses.github.io/LatentGPs.jl/stable)
-[![Dev](https://img.shields.io/badge/docs-dev-blue.svg)](https://JuliaGaussianProcesses.github.io/LatentGPs.jl/dev)
-[![Build Status](https://travis-ci.com/JuliaGaussianProcesses/LatentGPs.jl.svg?branch=master)](https://travis-ci.com/JuliaGaussianProcesses/LatentGPs.jl)
-[![Codecov](https://codecov.io/gh/JuliaGaussianProcesses/LatentGPs.jl/branch/master/graph/badge.svg)](https://codecov.io/gh/JuliaGaussianProcesses/LatentGPs.jl)
+[![Stable](https://img.shields.io/badge/docs-stable-blue.svg)](https://JuliaGaussianProcesses.github.io/GPLikelihoods.jl/stable)
+[![Dev](https://img.shields.io/badge/docs-dev-blue.svg)](https://JuliaGaussianProcesses.github.io/GPLikelihoods.jl/dev)
+[![Build Status](https://travis-ci.com/JuliaGaussianProcesses/GPLikelihoods.jl.svg?branch=master)](https://travis-ci.com/JuliaGaussianProcesses/GPLikelihoods.jl)
+[![Codecov](https://codecov.io/gh/JuliaGaussianProcesses/GPLikelihoods.jl/branch/master/graph/badge.svg)](https://codecov.io/gh/JuliaGaussianProcesses/GPLikelihoods.jl)
 [![Code Style: Blue](https://img.shields.io/badge/code%20style-blue-4495d1.svg)](https://github.com/invenia/BlueStyle)
 [![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)
diff --git a/docs/make.jl b/docs/make.jl
@@ -1,17 +1,17 @@
-using Documenter, LatentGPs
+using Documenter, GPLikelihoods
 
 makedocs(;
-    modules=[LatentGPs],
+    modules=[GPLikelihoods],
     format=Documenter.HTML(),
     pages=[
         "Home" => "index.md",
     ],
-    repo="https://github.com/JuliaGaussianProcesses/LatentGPs.jl/blob/{commit}{path}#L{line}",
-    sitename="LatentGPs.jl",
+    repo="https://github.com/JuliaGaussianProcesses/GPLikelihoods.jl/blob/{commit}{path}#L{line}",
+    sitename="GPLikelihoods.jl",
     authors="willtebbutt <wt0881@my.bristol.ac.uk>",
     assets=String[],
 )
 
 deploydocs(;
-    repo="github.com/JuliaGaussianProcesses/LatentGPs.jl",
+    repo="github.com/JuliaGaussianProcesses/GPLikelihoods.jl",
 )
diff --git a/docs/src/index.md b/docs/src/index.md
@@ -1,8 +1,8 @@
-# LatentGPs.jl
+# GPLikelihoods.jl
 
 ```@index
 ```
 
 ```@autodocs
-Modules = [LatentGPs]
+Modules = [GPLikelihoods]
 ```
diff --git a/src/GPLikelihoods.jl b/src/GPLikelihoods.jl
@@ -1,24 +1,14 @@
-module LatentGPs
+module GPLikelihoods
 
 using Distributions
-using KernelFunctions
 using AbstractGPs
-using LinearAlgebra
 using Random
 using Functors
 
-import Statistics
 import Distributions
 
-export LatentGP
-
-export logpdf, rand
-
 export GaussianLikelihood, PoissonLikelihood
 
-
-include("latent_gp.jl")
-
 # Likelihoods
 include("likelihoods/gaussian.jl")
 include("likelihoods/poisson.jl")
diff --git a/src/latent_gp.jl b/src/latent_gp.jl
diff --git a/test/Project.toml b/test/Project.toml
@@ -2,13 +2,11 @@
 AbstractGPs = "99985d1d-32ba-4be9-9821-2ec096f28918"
 Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f"
 Functors = "d9f16b24-f501-4c13-a1f2-28368ffc5196"
-KernelFunctions = "ec8451be-7e33-11e9-00cf-bbf324bd1392"
-LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
 Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 
 [compat]
-AbstractGPs = "0.1.1"
+AbstractGPs = "0.2"
 Distributions = "0.19, 0.20, 0.21, 0.22, 0.23"
-KernelFunctions = "0.4"
+Functors = "0.1"
 julia = "1.3"
diff --git a/test/latent_gp.jl b/test/latent_gp.jl
diff --git a/test/likelihoods/gaussian.jl b/test/likelihoods/gaussian.jl
@@ -1,12 +1,13 @@
 @testset "GaussianLikelihood" begin
+    rng = MersenneTwister(123)
     gp = GP(SqExponentialKernel())
-    x = rand(10)
-    y = rand(10)
-    fx = gp(x, 1e-5)
-    lik = GaussianLikelihood(first(fx.Σy))
-    lgp = LatentGP(fx, lik)
-    
-    @test typeof(lik(rand(fx))) <: Distribution
-    @test length(rand(lik(rand(fx)))) == 10
+    x = rand(rng, 10)
+    y = rand(rng, 10)
+    lik = GaussianLikelihood(1e-5)
+    lgp = LatentGP(gp, lik, 1e-5)
+    lfgp = lgp(x)
+
+    @test typeof(lik(rand(rng, lfgp.fx))) <: Distribution
+    @test length(rand(rng, lik(rand(rng, lfgp.fx)))) == 10
     @test keys(Functors.functor(lik)[1]) == (:σ²,)
 end
diff --git a/test/likelihoods/poisson.jl b/test/likelihoods/poisson.jl
@@ -1,11 +1,13 @@
 @testset "PoissonLikelihood" begin
+    rng = MersenneTwister(123)
     gp = GP(SqExponentialKernel())
-    x = rand(10)
-    y = rand(10)
-    fx = gp(x, 1e-6)
+    x = rand(rng, 10)
+    y = rand(rng, 10)
     lik = PoissonLikelihood()
-    lgp = LatentGP(fx, lik)
+    lgp = LatentGP(gp, lik, 1e-5)
+    lfgp = lgp(x)
     
-    @test typeof(lik(rand(fx))) <: Distribution
-    @test length(rand(lik(rand(fx)))) == 10
+    @test typeof(lik(rand(rng, lfgp.fx))) <: Distribution
+    @test length(rand(rng, lik(rand(rng, lfgp.fx)))) == 10
+    @test Functors.functor(lik)[1] == ()
 end
diff --git a/test/runtests.jl b/test/runtests.jl
@@ -1,15 +1,11 @@
-using LatentGPs
-using KernelFunctions
+using GPLikelihoods
 using AbstractGPs
-using LinearAlgebra
 using Test
 using Random
 using Functors
 using Distributions
 
-@testset "LatentGPs.jl" begin
-
-    include("latent_gp.jl")
+@testset "GPLikelihoods.jl" begin
 
     @testset "likelihoods" begin
         include("likelihoods/gaussian.jl")
