From 1b1a560698d30f1939d2e480ca9c8e3c73aecdf9 Mon Sep 17 00:00:00 2001 From: ST John Date: Wed, 16 Jun 2021 13:58:39 +0300 Subject: [PATCH 01/62] copy make.jl from st/examples --- docs/make.jl | 35 ++++++++++++++++++++++++++++------- 1 file changed, 28 insertions(+), 7 deletions(-) diff --git a/docs/make.jl b/docs/make.jl index c2c14f8f9..3b2a36d87 100644 --- a/docs/make.jl +++ b/docs/make.jl @@ -1,4 +1,5 @@ using Documenter +using Literate # Print `@debug` statements (https://github.com/JuliaDocs/Documenter.jl/issues/955) if haskey(ENV, "GITHUB_ACTIONS") @@ -7,6 +8,21 @@ end using KernelFunctions +const EXAMPLES_SRC = joinpath(@__DIR__, "..", "examples") +const EXAMPLES_OUT = joinpath(@__DIR__, "src", "examples") + +if ispath(EXAMPLES_OUT) + rm(EXAMPLES_OUT; recursive=true) +end + +for filename in readdir(EXAMPLES_SRC) + endswith(filename, ".jl") || continue + name = splitext(filename)[1] + Literate.markdown( + joinpath(EXAMPLES_SRC, filename), EXAMPLES_OUT; name=name, documenter=true + ) +end + DocMeta.setdocmeta!( KernelFunctions, :DocTestSetup, @@ -32,16 +48,21 @@ makedocs(; "theory.md", "create_kernel.md", "API" => "api.md", - "Examples" => "example.md", - "Design" => "design.md", + "Examples" => [ + "Kernel Ridge Regression" => "examples/kernel_ridge_regression.md", + "Training kernel parameters" => "examples/train_kernel_parameters.md", + "Gaussian process priors" => "examples/gaussianprocesspriors.md", + "SVM" => "examples/svm.md", + "Deep Kernel Learning" => "examples/deepkernellearning.md", + ], + "Kernel Functions" => "kernels.md", + "Input Transforms" => "transform.md", + "Metrics" => "metrics.md", + "Theory" => "theory.md", + "Custom Kernels" => "create_kernel.md", ], strict=true, checkdocs=:exports, - doctestfilters=[ - r"{([a-zA-Z0-9]+,\s?)+[a-zA-Z0-9]+}", - r"(Array{[a-zA-Z0-9]+,\s?1}|Vector{[a-zA-Z0-9]+})", - r"(Array{[a-zA-Z0-9]+,\s?2}|Matrix{[a-zA-Z0-9]+})", - ], ) deploydocs(; From 7cabf13c8c5f4f6889225c468806ab5563c13c00 Mon Sep 17 00:00:00 2001 From: ST John Date: Wed, 16 Jun 2021 17:43:30 +0300 Subject: [PATCH 02/62] add general docs dependencies --- docs/Project.toml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/docs/Project.toml b/docs/Project.toml index 3f90d2da6..72a830453 100644 --- a/docs/Project.toml +++ b/docs/Project.toml @@ -1,5 +1,7 @@ [deps] Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4" +KernelFunctions = "ec8451be-7e33-11e9-00cf-bbf324bd1392" +Literate = "98b081ad-f1c9-55d3-8b20-4c87d4299306" PDMats = "90014a1f-27ba-587c-ab20-58faa44d9150" [compat] From d2cefec21c36464de8317511dd9200644f12fc51 Mon Sep 17 00:00:00 2001 From: ST John Date: Wed, 16 Jun 2021 17:46:58 +0300 Subject: [PATCH 03/62] clean up --- docs/make.jl | 13 +++++-------- 1 file changed, 5 insertions(+), 8 deletions(-) diff --git a/docs/make.jl b/docs/make.jl index 3b2a36d87..206a74f25 100644 --- a/docs/make.jl +++ b/docs/make.jl @@ -15,12 +15,9 @@ if ispath(EXAMPLES_OUT) rm(EXAMPLES_OUT; recursive=true) end -for filename in readdir(EXAMPLES_SRC) - endswith(filename, ".jl") || continue - name = splitext(filename)[1] - Literate.markdown( - joinpath(EXAMPLES_SRC, filename), EXAMPLES_OUT; name=name, documenter=true - ) +for filepath in readdir(EXAMPLES_SRC; join=true) + endswith(filepath, ".jl") || continue + Literate.markdown(filepath, EXAMPLES_OUT; documenter=true) end DocMeta.setdocmeta!( @@ -36,9 +33,9 @@ DocMeta.setdocmeta!( ) makedocs(; - sitename="KernelFunctions", - format=Documenter.HTML(), modules=[KernelFunctions], + sitename="KernelFunctions.jl", + format=Documenter.HTML(), pages=[ "Home" => "index.md", "userguide.md", From 60acddb5ea694513ac37295edc14c1edb79e965c Mon Sep 17 00:00:00 2001 From: ST John Date: Wed, 16 Jun 2021 17:48:01 +0300 Subject: [PATCH 04/62] auto-collect examples as suggested --- docs/make.jl | 12 +++++------- 1 file changed, 5 insertions(+), 7 deletions(-) diff --git a/docs/make.jl b/docs/make.jl index 206a74f25..24427b8a4 100644 --- a/docs/make.jl +++ b/docs/make.jl @@ -18,6 +18,7 @@ end for filepath in readdir(EXAMPLES_SRC; join=true) endswith(filepath, ".jl") || continue Literate.markdown(filepath, EXAMPLES_OUT; documenter=true) + Literate.notebook(filepath, EXAMPLES_OUT; documenter=true) end DocMeta.setdocmeta!( @@ -45,18 +46,15 @@ makedocs(; "theory.md", "create_kernel.md", "API" => "api.md", - "Examples" => [ - "Kernel Ridge Regression" => "examples/kernel_ridge_regression.md", - "Training kernel parameters" => "examples/train_kernel_parameters.md", - "Gaussian process priors" => "examples/gaussianprocesspriors.md", - "SVM" => "examples/svm.md", - "Deep Kernel Learning" => "examples/deepkernellearning.md", - ], "Kernel Functions" => "kernels.md", "Input Transforms" => "transform.md", "Metrics" => "metrics.md", "Theory" => "theory.md", "Custom Kernels" => "create_kernel.md", + "Examples" => + joinpath.( + "examples", filter(filename -> endswith(filename, ".md"), readdir(EXAMPLES_OUT)) + ), ], strict=true, checkdocs=:exports, From 1831892d35e3265b15c52e329c03f91ef9214f37 Mon Sep 17 00:00:00 2001 From: ST John Date: Wed, 16 Jun 2021 17:48:12 +0300 Subject: [PATCH 05/62] add docs dependencies for notebooks --- docs/Project.toml | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/docs/Project.toml b/docs/Project.toml index 72a830453..8bb50d22d 100644 --- a/docs/Project.toml +++ b/docs/Project.toml @@ -1,8 +1,12 @@ [deps] +Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f" Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4" +Flux = "587475ba-b771-5e3f-ad9e-33799f191a9c" KernelFunctions = "ec8451be-7e33-11e9-00cf-bbf324bd1392" Literate = "98b081ad-f1c9-55d3-8b20-4c87d4299306" +MLDataUtils = "cc2ba9b6-d476-5e6d-8eaf-a92d5412d41d" PDMats = "90014a1f-27ba-587c-ab20-58faa44d9150" +Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f" [compat] Documenter = "0.27" From a5940086c9e72249c6932a31beca6ce7cb36cc5e Mon Sep 17 00:00:00 2001 From: ST John Date: Wed, 16 Jun 2021 17:48:38 +0300 Subject: [PATCH 06/62] fix direct notebook bug --- examples/svm.jl | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/examples/svm.jl b/examples/svm.jl index 34f7ec632..f9f9f4ee9 100644 --- a/examples/svm.jl +++ b/examples/svm.jl @@ -20,7 +20,7 @@ function f(x, k, λ) inv(kernelmatrix(k, X; obsdim=1) + exp(λ[1]) * I) * y end # Optimal prediction f -svmloss(y, ŷ) = ŷ -> sum(maximum.(0.0, 1 - y * ŷ)) - λ * norm(ŷ)(f(X, k, λ)) # Total svm loss with regularisation -pred = f(Xgrid, k, λ) #Compute prediction on a grid +svmloss(y, ŷ, λ) = ŷ -> sum(maximum.(0.0, 1 - y * ŷ)) - λ * norm(ŷ)(f(X, k, λ)) # Total svm loss with regularisation +pred = f(Xgrid, k, 0.1) #Compute prediction on a grid contourf(xgrid, xgrid, pred) scatter!(eachcol(X)...; color=y, lab="data") From 271d3d74f14504bd322c84989c5952cd7e94bdff Mon Sep 17 00:00:00 2001 From: ST John Date: Wed, 16 Jun 2021 17:49:05 +0300 Subject: [PATCH 07/62] add blacklist as pairwise() is broken --- docs/make.jl | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/docs/make.jl b/docs/make.jl index 24427b8a4..f9e7ed5a4 100644 --- a/docs/make.jl +++ b/docs/make.jl @@ -10,6 +10,11 @@ using KernelFunctions const EXAMPLES_SRC = joinpath(@__DIR__, "..", "examples") const EXAMPLES_OUT = joinpath(@__DIR__, "src", "examples") +const BLACKLIST = [ + "deepkernellearning", + "kernelridgeregression", + "svm", +] if ispath(EXAMPLES_OUT) rm(EXAMPLES_OUT; recursive=true) @@ -17,6 +22,7 @@ end for filepath in readdir(EXAMPLES_SRC; join=true) endswith(filepath, ".jl") || continue + any([occursin(blacklistname, filepath) for blacklistname in BLACKLIST]) && continue Literate.markdown(filepath, EXAMPLES_OUT; documenter=true) Literate.notebook(filepath, EXAMPLES_OUT; documenter=true) end From ef894a4512d7d5ffd0e3cb6a75637a4c19476e65 Mon Sep 17 00:00:00 2001 From: ST John Date: Wed, 16 Jun 2021 17:49:33 +0300 Subject: [PATCH 08/62] comment out examples as it breaks for non-existing directory (everything blacklisted right now) --- docs/make.jl | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/docs/make.jl b/docs/make.jl index f9e7ed5a4..f5f52f77f 100644 --- a/docs/make.jl +++ b/docs/make.jl @@ -57,10 +57,10 @@ makedocs(; "Metrics" => "metrics.md", "Theory" => "theory.md", "Custom Kernels" => "create_kernel.md", - "Examples" => - joinpath.( - "examples", filter(filename -> endswith(filename, ".md"), readdir(EXAMPLES_OUT)) - ), + # "Examples" => + # joinpath.( + # "examples", filter(filename -> endswith(filename, ".md"), readdir(EXAMPLES_OUT)) + # ), ], strict=true, checkdocs=:exports, From beb4adb35cbd1a7c83ca509a06c825838d801dab Mon Sep 17 00:00:00 2001 From: ST John Date: Wed, 16 Jun 2021 17:49:49 +0300 Subject: [PATCH 09/62] add docs README --- docs/README.md | 35 +++++++++++++++++++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 docs/README.md diff --git a/docs/README.md b/docs/README.md new file mode 100644 index 000000000..367dabb82 --- /dev/null +++ b/docs/README.md @@ -0,0 +1,35 @@ +# How to build the docs locally + +Assuming you are in this (docs/) directory: + +Install docs dependencies: +```bash +julia --project=. -e 'using Pkg; Pkg.instantiate()' +``` +This will use the last released KernelFunctions.jl for building the docs. + +If instead you want to reflect the local state of the Git repository in your built docs, make sure to change the dependency to the development version: +```bash +julia --project=. -e "using Pkg; Pkg.develop(path=\"$(readlink -f ..)\")" +``` +To undo the pinning to the local path by the previous command, run +```bash +julia --project=. -e 'using Pkg; Pkg.free("KernelFunctions")' +``` + +To actually build the docs, run +```bash +julia --project=. make.jl +``` +The built docs will be underneath build/ + +# How to contribute to the docs + +## To add additional docs dependencies + +```bash +julia --project=. -e 'using Pkg; Pkg.add("NewDependency")' +``` +and commit the changes to Project.toml + + From 00ccba9206c6d4728b50dd6466dde4b4e8124305 Mon Sep 17 00:00:00 2001 From: st-- Date: Wed, 16 Jun 2021 17:59:53 +0300 Subject: [PATCH 10/62] Apply suggestions from code review Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> --- docs/make.jl | 6 +----- 1 file changed, 1 insertion(+), 5 deletions(-) diff --git a/docs/make.jl b/docs/make.jl index f5f52f77f..4aa9ab13c 100644 --- a/docs/make.jl +++ b/docs/make.jl @@ -10,11 +10,7 @@ using KernelFunctions const EXAMPLES_SRC = joinpath(@__DIR__, "..", "examples") const EXAMPLES_OUT = joinpath(@__DIR__, "src", "examples") -const BLACKLIST = [ - "deepkernellearning", - "kernelridgeregression", - "svm", -] +const BLACKLIST = ["deepkernellearning", "kernelridgeregression", "svm"] if ispath(EXAMPLES_OUT) rm(EXAMPLES_OUT; recursive=true) From feda9e0fd9f0cd305cd9d4b0e660943b8d7dd26c Mon Sep 17 00:00:00 2001 From: ST John Date: Wed, 16 Jun 2021 18:01:02 +0300 Subject: [PATCH 11/62] remove duplicate doc entries --- docs/make.jl | 5 ----- 1 file changed, 5 deletions(-) diff --git a/docs/make.jl b/docs/make.jl index f5f52f77f..d756a8b54 100644 --- a/docs/make.jl +++ b/docs/make.jl @@ -52,11 +52,6 @@ makedocs(; "theory.md", "create_kernel.md", "API" => "api.md", - "Kernel Functions" => "kernels.md", - "Input Transforms" => "transform.md", - "Metrics" => "metrics.md", - "Theory" => "theory.md", - "Custom Kernels" => "create_kernel.md", # "Examples" => # joinpath.( # "examples", filter(filename -> endswith(filename, ".md"), readdir(EXAMPLES_OUT)) From 901b5d0b64d9c445cc4b61f28962c24944df13f2 Mon Sep 17 00:00:00 2001 From: ST John Date: Wed, 16 Jun 2021 18:02:48 +0300 Subject: [PATCH 12/62] revert deletion --- docs/make.jl | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/docs/make.jl b/docs/make.jl index 21df802f4..31e992d61 100644 --- a/docs/make.jl +++ b/docs/make.jl @@ -55,6 +55,11 @@ makedocs(; ], strict=true, checkdocs=:exports, + doctestfilters=[ + r"{([a-zA-Z0-9]+,\s?)+[a-zA-Z0-9]+}", + r"(Array{[a-zA-Z0-9]+,\s?1}|Vector{[a-zA-Z0-9]+})", + r"(Array{[a-zA-Z0-9]+,\s?2}|Matrix{[a-zA-Z0-9]+})", + ], ) deploydocs(; From a1718a37181baee5347977672e64687992ec4358 Mon Sep 17 00:00:00 2001 From: ST John Date: Thu, 17 Jun 2021 14:41:49 +0300 Subject: [PATCH 13/62] separate examples into individual diretories with own Project.toml --- docs/Project.toml | 7 +++--- docs/make.jl | 23 +++++++++++++------ examples/deep-kernel-learning/Project.toml | 8 +++++++ .../script.jl} | 0 examples/kernel-ridge-regression/Project.toml | 8 +++++++ .../script.jl} | 0 examples/support-vector-machine/Project.toml | 8 +++++++ .../script.jl} | 0 8 files changed, 43 insertions(+), 11 deletions(-) create mode 100644 examples/deep-kernel-learning/Project.toml rename examples/{deepkernellearning.jl => deep-kernel-learning/script.jl} (100%) create mode 100644 examples/kernel-ridge-regression/Project.toml rename examples/{kernelridgeregression.jl => kernel-ridge-regression/script.jl} (100%) create mode 100644 examples/support-vector-machine/Project.toml rename examples/{svm.jl => support-vector-machine/script.jl} (100%) diff --git a/docs/Project.toml b/docs/Project.toml index 8bb50d22d..64f61e7b5 100644 --- a/docs/Project.toml +++ b/docs/Project.toml @@ -1,12 +1,11 @@ [deps] -Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f" Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4" -Flux = "587475ba-b771-5e3f-ad9e-33799f191a9c" KernelFunctions = "ec8451be-7e33-11e9-00cf-bbf324bd1392" +LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e" Literate = "98b081ad-f1c9-55d3-8b20-4c87d4299306" -MLDataUtils = "cc2ba9b6-d476-5e6d-8eaf-a92d5412d41d" PDMats = "90014a1f-27ba-587c-ab20-58faa44d9150" -Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f" +Pkg = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f" +Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c" [compat] Documenter = "0.27" diff --git a/docs/make.jl b/docs/make.jl index 31e992d61..e2257b6e5 100644 --- a/docs/make.jl +++ b/docs/make.jl @@ -8,19 +8,28 @@ end using KernelFunctions -const EXAMPLES_SRC = joinpath(@__DIR__, "..", "examples") +const PACKAGE_DIR = joinpath(@__DIR__, "..") +const EXAMPLES_SRC = joinpath(PACKAGE_DIR, "examples") const EXAMPLES_OUT = joinpath(@__DIR__, "src", "examples") -const BLACKLIST = ["deepkernellearning", "kernelridgeregression", "svm"] +const BLACKLIST = [ + "deep-kernel-learning", + "kernel-ridge-regression", + "support-vector-machine", +] if ispath(EXAMPLES_OUT) rm(EXAMPLES_OUT; recursive=true) end -for filepath in readdir(EXAMPLES_SRC; join=true) - endswith(filepath, ".jl") || continue - any([occursin(blacklistname, filepath) for blacklistname in BLACKLIST]) && continue - Literate.markdown(filepath, EXAMPLES_OUT; documenter=true) - Literate.notebook(filepath, EXAMPLES_OUT; documenter=true) +for exampledir in readdir(EXAMPLES_SRC; join=true) + any([occursin(blacklistname, exampledir) for blacklistname in BLACKLIST]) && continue + Pkg.activate(exampledir) do + Pkg.develop(path=PACKAGE_DIR) + Pkg.instantiate() + filepath = joinpath(exampledir, "script.jl") + Literate.markdown(filepath, EXAMPLES_OUT; documenter=true) + Literate.notebook(filepath, EXAMPLES_OUT; documenter=true) + end end DocMeta.setdocmeta!( diff --git a/examples/deep-kernel-learning/Project.toml b/examples/deep-kernel-learning/Project.toml new file mode 100644 index 000000000..15222757e --- /dev/null +++ b/examples/deep-kernel-learning/Project.toml @@ -0,0 +1,8 @@ +[deps] +Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f" +Flux = "587475ba-b771-5e3f-ad9e-33799f191a9c" +KernelFunctions = "ec8451be-7e33-11e9-00cf-bbf324bd1392" +LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e" +MLDataUtils = "cc2ba9b6-d476-5e6d-8eaf-a92d5412d41d" +Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80" +Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f" diff --git a/examples/deepkernellearning.jl b/examples/deep-kernel-learning/script.jl similarity index 100% rename from examples/deepkernellearning.jl rename to examples/deep-kernel-learning/script.jl diff --git a/examples/kernel-ridge-regression/Project.toml b/examples/kernel-ridge-regression/Project.toml new file mode 100644 index 000000000..15222757e --- /dev/null +++ b/examples/kernel-ridge-regression/Project.toml @@ -0,0 +1,8 @@ +[deps] +Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f" +Flux = "587475ba-b771-5e3f-ad9e-33799f191a9c" +KernelFunctions = "ec8451be-7e33-11e9-00cf-bbf324bd1392" +LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e" +MLDataUtils = "cc2ba9b6-d476-5e6d-8eaf-a92d5412d41d" +Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80" +Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f" diff --git a/examples/kernelridgeregression.jl b/examples/kernel-ridge-regression/script.jl similarity index 100% rename from examples/kernelridgeregression.jl rename to examples/kernel-ridge-regression/script.jl diff --git a/examples/support-vector-machine/Project.toml b/examples/support-vector-machine/Project.toml new file mode 100644 index 000000000..15222757e --- /dev/null +++ b/examples/support-vector-machine/Project.toml @@ -0,0 +1,8 @@ +[deps] +Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f" +Flux = "587475ba-b771-5e3f-ad9e-33799f191a9c" +KernelFunctions = "ec8451be-7e33-11e9-00cf-bbf324bd1392" +LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e" +MLDataUtils = "cc2ba9b6-d476-5e6d-8eaf-a92d5412d41d" +Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80" +Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f" diff --git a/examples/svm.jl b/examples/support-vector-machine/script.jl similarity index 100% rename from examples/svm.jl rename to examples/support-vector-machine/script.jl From 66706c00f28c8cfb670cf029e796b40ec2a51c5e Mon Sep 17 00:00:00 2001 From: ST John Date: Thu, 17 Jun 2021 14:44:05 +0300 Subject: [PATCH 14/62] handle empty examples directory --- docs/make.jl | 13 ++++++------- 1 file changed, 6 insertions(+), 7 deletions(-) diff --git a/docs/make.jl b/docs/make.jl index e2257b6e5..1a55e75c0 100644 --- a/docs/make.jl +++ b/docs/make.jl @@ -17,9 +17,8 @@ const BLACKLIST = [ "support-vector-machine", ] -if ispath(EXAMPLES_OUT) - rm(EXAMPLES_OUT; recursive=true) -end +ispath(EXAMPLES_OUT) && rm(EXAMPLES_OUT; recursive=true) +mkpath(EXAMPLES_OUT) for exampledir in readdir(EXAMPLES_SRC; join=true) any([occursin(blacklistname, exampledir) for blacklistname in BLACKLIST]) && continue @@ -57,10 +56,10 @@ makedocs(; "theory.md", "create_kernel.md", "API" => "api.md", - # "Examples" => - # joinpath.( - # "examples", filter(filename -> endswith(filename, ".md"), readdir(EXAMPLES_OUT)) - # ), + "Examples" => + joinpath.( + "examples", filter(filename -> endswith(filename, ".md"), readdir(EXAMPLES_OUT)) + ), ], strict=true, checkdocs=:exports, From bddbea88ea5651db96c5cfc54ec6ecd74d42fb52 Mon Sep 17 00:00:00 2001 From: ST John Date: Thu, 17 Jun 2021 14:45:01 +0300 Subject: [PATCH 15/62] update README for non-unix systems --- docs/README.md | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/docs/README.md b/docs/README.md index 367dabb82..04311069f 100644 --- a/docs/README.md +++ b/docs/README.md @@ -10,6 +10,10 @@ This will use the last released KernelFunctions.jl for building the docs. If instead you want to reflect the local state of the Git repository in your built docs, make sure to change the dependency to the development version: ```bash +julia --project=. -e "using Pkg; Pkg.develop(path=\"/path/to/KernelFunctions.jl/\")" +``` +In a bash-like shell on Unix, you can also use the following command from the docs/ directory to get the absolute path: +```bash julia --project=. -e "using Pkg; Pkg.develop(path=\"$(readlink -f ..)\")" ``` To undo the pinning to the local path by the previous command, run @@ -31,5 +35,3 @@ The built docs will be underneath build/ julia --project=. -e 'using Pkg; Pkg.add("NewDependency")' ``` and commit the changes to Project.toml - - From c4a36f8b2817d8d01ece96a60bf24752eb0fb86a Mon Sep 17 00:00:00 2001 From: st-- Date: Thu, 17 Jun 2021 14:59:32 +0300 Subject: [PATCH 16/62] Apply suggestions from code review Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> --- docs/make.jl | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/docs/make.jl b/docs/make.jl index 1a55e75c0..7c31560ba 100644 --- a/docs/make.jl +++ b/docs/make.jl @@ -12,9 +12,7 @@ const PACKAGE_DIR = joinpath(@__DIR__, "..") const EXAMPLES_SRC = joinpath(PACKAGE_DIR, "examples") const EXAMPLES_OUT = joinpath(@__DIR__, "src", "examples") const BLACKLIST = [ - "deep-kernel-learning", - "kernel-ridge-regression", - "support-vector-machine", + "deep-kernel-learning", "kernel-ridge-regression", "support-vector-machine" ] ispath(EXAMPLES_OUT) && rm(EXAMPLES_OUT; recursive=true) From 384ac9c6f87e50b7b218aa757ae316f41b02daf7 Mon Sep 17 00:00:00 2001 From: st-- Date: Thu, 17 Jun 2021 15:00:03 +0300 Subject: [PATCH 17/62] Apply suggestions from code review Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> --- docs/make.jl | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/docs/make.jl b/docs/make.jl index 7c31560ba..46c921a2a 100644 --- a/docs/make.jl +++ b/docs/make.jl @@ -21,7 +21,7 @@ mkpath(EXAMPLES_OUT) for exampledir in readdir(EXAMPLES_SRC; join=true) any([occursin(blacklistname, exampledir) for blacklistname in BLACKLIST]) && continue Pkg.activate(exampledir) do - Pkg.develop(path=PACKAGE_DIR) + Pkg.develop(; path=PACKAGE_DIR) Pkg.instantiate() filepath = joinpath(exampledir, "script.jl") Literate.markdown(filepath, EXAMPLES_OUT; documenter=true) @@ -56,7 +56,8 @@ makedocs(; "API" => "api.md", "Examples" => joinpath.( - "examples", filter(filename -> endswith(filename, ".md"), readdir(EXAMPLES_OUT)) + "examples", + filter(filename -> endswith(filename, ".md"), readdir(EXAMPLES_OUT)), ), ], strict=true, From 80deae76b18906fb63038c0f24e1a757564d7dca Mon Sep 17 00:00:00 2001 From: ST John Date: Thu, 17 Jun 2021 15:01:41 +0300 Subject: [PATCH 18/62] revert removed doc --- docs/make.jl | 1 + 1 file changed, 1 insertion(+) diff --git a/docs/make.jl b/docs/make.jl index 1a55e75c0..2f489174d 100644 --- a/docs/make.jl +++ b/docs/make.jl @@ -56,6 +56,7 @@ makedocs(; "theory.md", "create_kernel.md", "API" => "api.md", + "Design" => "design.md", "Examples" => joinpath.( "examples", filter(filename -> endswith(filename, ".md"), readdir(EXAMPLES_OUT)) From cd0bc2bd1635a6032b0b193a0a337789d8637c5d Mon Sep 17 00:00:00 2001 From: st-- Date: Mon, 21 Jun 2021 12:48:12 +0300 Subject: [PATCH 19/62] Apply suggestions from code review Co-authored-by: willtebbutt --- docs/README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/README.md b/docs/README.md index 04311069f..3911b92fe 100644 --- a/docs/README.md +++ b/docs/README.md @@ -25,7 +25,7 @@ To actually build the docs, run ```bash julia --project=. make.jl ``` -The built docs will be underneath build/ +The built docs will be underneath build/, and are best viewed in a browser. # How to contribute to the docs From 75db97df60c0fc4814b2a66ccd99fcb980cde5e6 Mon Sep 17 00:00:00 2001 From: ST John Date: Mon, 21 Jun 2021 14:16:44 +0300 Subject: [PATCH 20/62] remove unused dependencies from svm example --- examples/support-vector-machine/Project.toml | 3 --- examples/support-vector-machine/script.jl | 25 +++++++++----------- 2 files changed, 11 insertions(+), 17 deletions(-) diff --git a/examples/support-vector-machine/Project.toml b/examples/support-vector-machine/Project.toml index 15222757e..d1b9295cc 100644 --- a/examples/support-vector-machine/Project.toml +++ b/examples/support-vector-machine/Project.toml @@ -1,8 +1,5 @@ [deps] Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f" -Flux = "587475ba-b771-5e3f-ad9e-33799f191a9c" KernelFunctions = "ec8451be-7e33-11e9-00cf-bbf324bd1392" LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e" -MLDataUtils = "cc2ba9b6-d476-5e6d-8eaf-a92d5412d41d" Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80" -Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f" diff --git a/examples/support-vector-machine/script.jl b/examples/support-vector-machine/script.jl index f9f9f4ee9..966f4d4fe 100644 --- a/examples/support-vector-machine/script.jl +++ b/examples/support-vector-machine/script.jl @@ -1,26 +1,23 @@ using KernelFunctions -using MLDataUtils -using Zygote -using Flux using Distributions, LinearAlgebra using Plots -N = 100 #Number of samples -μ = randn(2, 2) # Random Centers -xgrid = range(-3, 3; length=100) # Create a grid -Xgrid = hcat(collect.(Iterators.product(xgrid, xgrid))...)' #Combine into a 2D grid -y = rand([-1, 1], N) # Select randomly between the two classes +N = 100 # Number of samples +μ = randn(2, 2) # Random Centers +xgrid = range(-3, 3; length=100) # Create a grid +Xgrid = hcat(collect.(Iterators.product(xgrid, xgrid))...)' # Combine into a 2D grid +y = rand([-1, 1], N) # Select randomly between the two classes X = zeros(N, 2) -X[y .== 1, :] = rand(MvNormal(μ[:, 1], I), count(y .== 1))' #Attribute samples from class 1 -X[y .== -1, :] = rand(MvNormal(μ[:, 2], I), count(y .== -1))' # Attribute samples from class 2 +X[y .== 1, :] = rand(MvNormal(μ[:, 1], I), count(y .== 1))' # Attribute samples from class 1 +X[y .== -1, :] = rand(MvNormal(μ[:, 2], I), count(y .== -1))' # Attribute samples from class 2 -k = SqExponentialKernel(2.0) # Create kernel function +k = SqExponentialKernel(2.0) # Create kernel function function f(x, k, λ) return kernelmatrix(k, x, X; obsdim=1) * inv(kernelmatrix(k, X; obsdim=1) + exp(λ[1]) * I) * y -end # Optimal prediction f -svmloss(y, ŷ, λ) = ŷ -> sum(maximum.(0.0, 1 - y * ŷ)) - λ * norm(ŷ)(f(X, k, λ)) # Total svm loss with regularisation -pred = f(Xgrid, k, 0.1) #Compute prediction on a grid +end # Optimal prediction f +svmloss(y, ŷ, λ) = ŷ -> sum(maximum.(0.0, 1 - y * ŷ)) - λ * norm(ŷ)(f(X, k, λ)) # Total svm loss with regularisation +pred = f(Xgrid, k, 0.1) # Compute prediction on a grid contourf(xgrid, xgrid, pred) scatter!(eachcol(X)...; color=y, lab="data") From 8c657bc218d742d2f578d3cfcfa0c80eb56a40cc Mon Sep 17 00:00:00 2001 From: ST John Date: Mon, 21 Jun 2021 14:24:41 +0300 Subject: [PATCH 21/62] fix bug in svm notebook --- docs/make.jl | 3 ++- examples/support-vector-machine/script.jl | 2 +- 2 files changed, 3 insertions(+), 2 deletions(-) diff --git a/docs/make.jl b/docs/make.jl index 347f1d6ec..1f136170c 100644 --- a/docs/make.jl +++ b/docs/make.jl @@ -1,5 +1,6 @@ using Documenter using Literate +using Pkg # Print `@debug` statements (https://github.com/JuliaDocs/Documenter.jl/issues/955) if haskey(ENV, "GITHUB_ACTIONS") @@ -12,7 +13,7 @@ const PACKAGE_DIR = joinpath(@__DIR__, "..") const EXAMPLES_SRC = joinpath(PACKAGE_DIR, "examples") const EXAMPLES_OUT = joinpath(@__DIR__, "src", "examples") const BLACKLIST = [ - "deep-kernel-learning", "kernel-ridge-regression", "support-vector-machine" + "deep-kernel-learning", "kernel-ridge-regression" ] ispath(EXAMPLES_OUT) && rm(EXAMPLES_OUT; recursive=true) diff --git a/examples/support-vector-machine/script.jl b/examples/support-vector-machine/script.jl index 966f4d4fe..8f8257d88 100644 --- a/examples/support-vector-machine/script.jl +++ b/examples/support-vector-machine/script.jl @@ -11,7 +11,7 @@ X = zeros(N, 2) X[y .== 1, :] = rand(MvNormal(μ[:, 1], I), count(y .== 1))' # Attribute samples from class 1 X[y .== -1, :] = rand(MvNormal(μ[:, 2], I), count(y .== -1))' # Attribute samples from class 2 -k = SqExponentialKernel(2.0) # Create kernel function +k = SqExponentialKernel() # Create kernel function function f(x, k, λ) return kernelmatrix(k, x, X; obsdim=1) * inv(kernelmatrix(k, X; obsdim=1) + exp(λ[1]) * I) * From 001dfc3b00f885598148591b62fbef779ea037cc Mon Sep 17 00:00:00 2001 From: st-- Date: Mon, 21 Jun 2021 14:32:58 +0300 Subject: [PATCH 22/62] Apply suggestions from code review MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Théo Galy-Fajou --- docs/make.jl | 4 +--- examples/support-vector-machine/script.jl | 2 +- 2 files changed, 2 insertions(+), 4 deletions(-) diff --git a/docs/make.jl b/docs/make.jl index 1f136170c..39329f2bf 100644 --- a/docs/make.jl +++ b/docs/make.jl @@ -12,9 +12,7 @@ using KernelFunctions const PACKAGE_DIR = joinpath(@__DIR__, "..") const EXAMPLES_SRC = joinpath(PACKAGE_DIR, "examples") const EXAMPLES_OUT = joinpath(@__DIR__, "src", "examples") -const BLACKLIST = [ - "deep-kernel-learning", "kernel-ridge-regression" -] +const BLACKLIST = ["deep-kernel-learning", "kernel-ridge-regression"] ispath(EXAMPLES_OUT) && rm(EXAMPLES_OUT; recursive=true) mkpath(EXAMPLES_OUT) diff --git a/examples/support-vector-machine/script.jl b/examples/support-vector-machine/script.jl index 8f8257d88..b5178fdd8 100644 --- a/examples/support-vector-machine/script.jl +++ b/examples/support-vector-machine/script.jl @@ -11,7 +11,7 @@ X = zeros(N, 2) X[y .== 1, :] = rand(MvNormal(μ[:, 1], I), count(y .== 1))' # Attribute samples from class 1 X[y .== -1, :] = rand(MvNormal(μ[:, 2], I), count(y .== -1))' # Attribute samples from class 2 -k = SqExponentialKernel() # Create kernel function +k = compose(SqExponentialKernel(), ScaleTransform(2.0)) # Create kernel function function f(x, k, λ) return kernelmatrix(k, x, X; obsdim=1) * inv(kernelmatrix(k, X; obsdim=1) + exp(λ[1]) * I) * From a60e230b9b66b84c3086c61a45de6b0a8cf330ba Mon Sep 17 00:00:00 2001 From: ST John Date: Mon, 21 Jun 2021 15:30:54 +0300 Subject: [PATCH 23/62] fix examples scripts compose --- examples/deep-kernel-learning/script.jl | 2 +- examples/kernel-ridge-regression/script.jl | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/examples/deep-kernel-learning/script.jl b/examples/deep-kernel-learning/script.jl index 94346eea2..010e02a57 100644 --- a/examples/deep-kernel-learning/script.jl +++ b/examples/deep-kernel-learning/script.jl @@ -11,7 +11,7 @@ Flux.@functor Matern32Kernel Flux.@functor FunctionTransform neuralnet = Chain(Dense(1, 3), Dense(3, 2)) -k = SqExponentialKernel(FunctionTransform(neuralnet)) +k = SqExponentialKernel() ∘ FunctionTransform(neuralnet) xmin = -3; xmax = 3; x = range(xmin, xmax; length=100) diff --git a/examples/kernel-ridge-regression/script.jl b/examples/kernel-ridge-regression/script.jl index 0bc02f25a..b7536e6f7 100644 --- a/examples/kernel-ridge-regression/script.jl +++ b/examples/kernel-ridge-regression/script.jl @@ -17,7 +17,7 @@ x_test = range(xmin, xmax; length=300) x, y = noisy_function(sinc, x; noise=0.1) X = reshape(x, :, 1) X_test = reshape(x_test, :, 1) -k = SqExponentialKernel(1.0)#+Matern32Kernel(2.0) +k = SqExponentialKernel() + Matern32Kernel() ∘ ScaleTransform(2.0) λ = [-1.0] function f(x, k, λ) return kernelmatrix(k, x, X; obsdim=1) * From 14ad37d859c216203dc412ef75ea3e4b44669632 Mon Sep 17 00:00:00 2001 From: ST John Date: Mon, 21 Jun 2021 15:35:50 +0300 Subject: [PATCH 24/62] fix script output name --- docs/make.jl | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/docs/make.jl b/docs/make.jl index 39329f2bf..6b808d59b 100644 --- a/docs/make.jl +++ b/docs/make.jl @@ -17,14 +17,14 @@ const BLACKLIST = ["deep-kernel-learning", "kernel-ridge-regression"] ispath(EXAMPLES_OUT) && rm(EXAMPLES_OUT; recursive=true) mkpath(EXAMPLES_OUT) -for exampledir in readdir(EXAMPLES_SRC; join=true) +for example in readdir(EXAMPLES_SRC) any([occursin(blacklistname, exampledir) for blacklistname in BLACKLIST]) && continue - Pkg.activate(exampledir) do + Pkg.activate(joinpath(EXAMPLES_SRC, example)) do Pkg.develop(; path=PACKAGE_DIR) Pkg.instantiate() - filepath = joinpath(exampledir, "script.jl") - Literate.markdown(filepath, EXAMPLES_OUT; documenter=true) - Literate.notebook(filepath, EXAMPLES_OUT; documenter=true) + filepath = joinpath(EXAMPLES_SRC, example, "script.jl") + Literate.markdown(filepath, EXAMPLES_OUT; name=example, documenter=true) + Literate.notebook(filepath, EXAMPLES_OUT; name=example, documenter=true) end end From 715e0a5f6b5b005c06517faf3aea4c653cf97e68 Mon Sep 17 00:00:00 2001 From: ST John Date: Mon, 21 Jun 2021 15:39:45 +0300 Subject: [PATCH 25/62] bugfix --- docs/make.jl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/make.jl b/docs/make.jl index 6b808d59b..bc63a82ae 100644 --- a/docs/make.jl +++ b/docs/make.jl @@ -18,7 +18,7 @@ ispath(EXAMPLES_OUT) && rm(EXAMPLES_OUT; recursive=true) mkpath(EXAMPLES_OUT) for example in readdir(EXAMPLES_SRC) - any([occursin(blacklistname, exampledir) for blacklistname in BLACKLIST]) && continue + any([occursin(blacklisted, example) for blacklisted in BLACKLIST]) && continue Pkg.activate(joinpath(EXAMPLES_SRC, example)) do Pkg.develop(; path=PACKAGE_DIR) Pkg.instantiate() From 09990f8de509e3a38feed9bed60aed1252a638f6 Mon Sep 17 00:00:00 2001 From: ST John Date: Mon, 21 Jun 2021 16:16:29 +0300 Subject: [PATCH 26/62] include preprocessor for Documenter@setup --- docs/make.jl | 23 +++++++++++++++++++++-- 1 file changed, 21 insertions(+), 2 deletions(-) diff --git a/docs/make.jl b/docs/make.jl index bc63a82ae..e656dc947 100644 --- a/docs/make.jl +++ b/docs/make.jl @@ -17,14 +17,33 @@ const BLACKLIST = ["deep-kernel-learning", "kernel-ridge-regression"] ispath(EXAMPLES_OUT) && rm(EXAMPLES_OUT; recursive=true) mkpath(EXAMPLES_OUT) +# preprocessor for Literate example scripts: +# - add Documenter @setup snippet that activates each example's own project environment +function preprocess(content) + sub = SubstitutionString( + """ +\\0 +# +#md # +#md # ```@setup @__NAME__ +#md # using Pkg: Pkg +#md # Pkg.activate("$(INPUT)/@__NAME__") +#md # Pkg.instantiate() +#md # ``` +# + """, + ) + return replace(content, r"^# # [^\n]*"m => sub; count=1) +end + for example in readdir(EXAMPLES_SRC) any([occursin(blacklisted, example) for blacklisted in BLACKLIST]) && continue Pkg.activate(joinpath(EXAMPLES_SRC, example)) do Pkg.develop(; path=PACKAGE_DIR) Pkg.instantiate() filepath = joinpath(EXAMPLES_SRC, example, "script.jl") - Literate.markdown(filepath, EXAMPLES_OUT; name=example, documenter=true) - Literate.notebook(filepath, EXAMPLES_OUT; name=example, documenter=true) + Literate.markdown(filepath, EXAMPLES_OUT; name=example, documenter=true, preprocess=preprocess) + Literate.notebook(filepath, EXAMPLES_OUT; name=example, documenter=true, preprocess=preprocess) end end From 4f34f3717b4c3957134641f8189f22d8cfb14918 Mon Sep 17 00:00:00 2001 From: st-- Date: Mon, 21 Jun 2021 16:19:06 +0300 Subject: [PATCH 27/62] Apply suggestions from code review MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Théo Galy-Fajou --- docs/make.jl | 34 ++++++++++++++++++---------------- 1 file changed, 18 insertions(+), 16 deletions(-) diff --git a/docs/make.jl b/docs/make.jl index e656dc947..1af722cd5 100644 --- a/docs/make.jl +++ b/docs/make.jl @@ -20,30 +20,32 @@ mkpath(EXAMPLES_OUT) # preprocessor for Literate example scripts: # - add Documenter @setup snippet that activates each example's own project environment function preprocess(content) - sub = SubstitutionString( - """ -\\0 -# -#md # -#md # ```@setup @__NAME__ -#md # using Pkg: Pkg -#md # Pkg.activate("$(INPUT)/@__NAME__") -#md # Pkg.instantiate() -#md # ``` -# - """, - ) + sub = SubstitutionString(""" + \\0 + # + #md # + #md # ```@setup @__NAME__ + #md # using Pkg: Pkg + #md # Pkg.activate("$(INPUT)/@__NAME__") + #md # Pkg.instantiate() + #md # ``` + # + """) return replace(content, r"^# # [^\n]*"m => sub; count=1) end for example in readdir(EXAMPLES_SRC) - any([occursin(blacklisted, example) for blacklisted in BLACKLIST]) && continue + example ∈ BLACKLIST && continue Pkg.activate(joinpath(EXAMPLES_SRC, example)) do Pkg.develop(; path=PACKAGE_DIR) Pkg.instantiate() filepath = joinpath(EXAMPLES_SRC, example, "script.jl") - Literate.markdown(filepath, EXAMPLES_OUT; name=example, documenter=true, preprocess=preprocess) - Literate.notebook(filepath, EXAMPLES_OUT; name=example, documenter=true, preprocess=preprocess) + Literate.markdown( + filepath, EXAMPLES_OUT; name=example, documenter=true, preprocess=preprocess + ) + Literate.notebook( + filepath, EXAMPLES_OUT; name=example, documenter=true, preprocess=preprocess + ) end end From f2db1ea681d06accdafde1256f88e6fab0323f41 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Th=C3=A9o=20Galy-Fajou?= Date: Mon, 21 Jun 2021 15:42:19 +0200 Subject: [PATCH 28/62] Correct file_path for environment --- docs/make.jl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/make.jl b/docs/make.jl index 1af722cd5..6fd937de1 100644 --- a/docs/make.jl +++ b/docs/make.jl @@ -26,7 +26,7 @@ function preprocess(content) #md # #md # ```@setup @__NAME__ #md # using Pkg: Pkg - #md # Pkg.activate("$(INPUT)/@__NAME__") + #md # Pkg.activate("$(EXAMPLES_SRC)/@__NAME__") #md # Pkg.instantiate() #md # ``` # From c8298ecd68204e5ec09bcd2b3db9650b0c07560f Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Th=C3=A9o=20Galy-Fajou?= Date: Mon, 21 Jun 2021 15:56:02 +0200 Subject: [PATCH 29/62] Adding the necessary header for the @setup replacement --- examples/support-vector-machine/script.jl | 1 + 1 file changed, 1 insertion(+) diff --git a/examples/support-vector-machine/script.jl b/examples/support-vector-machine/script.jl index b5178fdd8..1ce2522ed 100644 --- a/examples/support-vector-machine/script.jl +++ b/examples/support-vector-machine/script.jl @@ -1,3 +1,4 @@ +# # Support Vector Machine using KernelFunctions using Distributions, LinearAlgebra using Plots From 754a8dbb6a447c582d77dd9dac6a59f972e7c6f6 Mon Sep 17 00:00:00 2001 From: ST John Date: Tue, 22 Jun 2021 23:13:38 +0300 Subject: [PATCH 30/62] correct headers for remaining examples scripts --- examples/deep-kernel-learning/script.jl | 1 + examples/kernel-ridge-regression/script.jl | 1 + 2 files changed, 2 insertions(+) diff --git a/examples/deep-kernel-learning/script.jl b/examples/deep-kernel-learning/script.jl index 010e02a57..d962dd593 100644 --- a/examples/deep-kernel-learning/script.jl +++ b/examples/deep-kernel-learning/script.jl @@ -1,3 +1,4 @@ +# # Deep Kernel Learning using KernelFunctions using MLDataUtils using Zygote diff --git a/examples/kernel-ridge-regression/script.jl b/examples/kernel-ridge-regression/script.jl index b7536e6f7..f34b2a282 100644 --- a/examples/kernel-ridge-regression/script.jl +++ b/examples/kernel-ridge-regression/script.jl @@ -1,3 +1,4 @@ +# # Kernel Ridge Regression using KernelFunctions using MLDataUtils using Zygote From 8641c78e429e5fc59542e99dde834954616da5e6 Mon Sep 17 00:00:00 2001 From: ST John Date: Tue, 22 Jun 2021 23:14:09 +0300 Subject: [PATCH 31/62] fix KRR notebook and swap it with SVM in blacklist --- docs/make.jl | 2 +- examples/kernel-ridge-regression/script.jl | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/docs/make.jl b/docs/make.jl index 6fd937de1..e4438e067 100644 --- a/docs/make.jl +++ b/docs/make.jl @@ -12,7 +12,7 @@ using KernelFunctions const PACKAGE_DIR = joinpath(@__DIR__, "..") const EXAMPLES_SRC = joinpath(PACKAGE_DIR, "examples") const EXAMPLES_OUT = joinpath(@__DIR__, "src", "examples") -const BLACKLIST = ["deep-kernel-learning", "kernel-ridge-regression"] +const BLACKLIST = ["deep-kernel-learning", "support-vector-machine"] ispath(EXAMPLES_OUT) && rm(EXAMPLES_OUT; recursive=true) mkpath(EXAMPLES_OUT) diff --git a/examples/kernel-ridge-regression/script.jl b/examples/kernel-ridge-regression/script.jl index f34b2a282..76beca606 100644 --- a/examples/kernel-ridge-regression/script.jl +++ b/examples/kernel-ridge-regression/script.jl @@ -26,7 +26,7 @@ function f(x, k, λ) y end f(X, k, 1.0) -loss(k, λ) = ŷ -> sum(y - ŷ) / length(y) + exp(λ[1]) * norm(ŷ)(f(X, k, λ)) +loss(k, λ) = (ŷ -> sum(y - ŷ) / length(y) + exp(λ[1]) * norm(ŷ))(f(X, k, λ)) loss(k, λ) ps = Flux.params(k) push!(ps, λ) From 407d6f058c5dc9e8610fd65f6359c62402d35339 Mon Sep 17 00:00:00 2001 From: ST John Date: Tue, 22 Jun 2021 23:14:26 +0300 Subject: [PATCH 32/62] do not execute notebook --- docs/make.jl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/make.jl b/docs/make.jl index e4438e067..b20279a99 100644 --- a/docs/make.jl +++ b/docs/make.jl @@ -44,7 +44,7 @@ for example in readdir(EXAMPLES_SRC) filepath, EXAMPLES_OUT; name=example, documenter=true, preprocess=preprocess ) Literate.notebook( - filepath, EXAMPLES_OUT; name=example, documenter=true, preprocess=preprocess + filepath, EXAMPLES_OUT; name=example, documenter=true, preprocess=preprocess, execute=false ) end end From 3e452ae595b3230a40fe58c2fdaa3169f7239147 Mon Sep 17 00:00:00 2001 From: ST John Date: Tue, 22 Jun 2021 23:15:54 +0300 Subject: [PATCH 33/62] update .gitignore --- .gitignore | 1 - docs/.gitignore | 3 +-- 2 files changed, 1 insertion(+), 3 deletions(-) diff --git a/.gitignore b/.gitignore index 3bd1d529e..02bcc5a34 100644 --- a/.gitignore +++ b/.gitignore @@ -2,5 +2,4 @@ *.cov Manifest.toml coverage/ -src/update_v0.8.0 .DS_store diff --git a/docs/.gitignore b/docs/.gitignore index 90fb8a549..909052372 100644 --- a/docs/.gitignore +++ b/docs/.gitignore @@ -1,4 +1,3 @@ build/ site/ - -#Temp to avoid to many changes +src/examples/ From 262ceefbc28389d430379628a9c07b34d19cad59 Mon Sep 17 00:00:00 2001 From: st-- Date: Tue, 22 Jun 2021 23:21:51 +0300 Subject: [PATCH 34/62] Update docs/make.jl Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> --- docs/make.jl | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/docs/make.jl b/docs/make.jl index b20279a99..f26f703c5 100644 --- a/docs/make.jl +++ b/docs/make.jl @@ -44,7 +44,12 @@ for example in readdir(EXAMPLES_SRC) filepath, EXAMPLES_OUT; name=example, documenter=true, preprocess=preprocess ) Literate.notebook( - filepath, EXAMPLES_OUT; name=example, documenter=true, preprocess=preprocess, execute=false + filepath, + EXAMPLES_OUT; + name=example, + documenter=true, + preprocess=preprocess, + execute=false, ) end end From 495bf19a28b0181d8489174c7818ee08d96023ff Mon Sep 17 00:00:00 2001 From: ST John Date: Wed, 23 Jun 2021 09:54:54 +0300 Subject: [PATCH 35/62] update docs and examples README and ignore examples/README in docs/make.jl --- docs/README.md | 23 +++++++++++++++++++---- docs/make.jl | 6 ++++-- examples/README.md | 16 ++++++++++++++++ 3 files changed, 39 insertions(+), 6 deletions(-) create mode 100644 examples/README.md diff --git a/docs/README.md b/docs/README.md index 3911b92fe..008354134 100644 --- a/docs/README.md +++ b/docs/README.md @@ -2,13 +2,15 @@ Assuming you are in this (docs/) directory: -Install docs dependencies: +## Setup + +First, make sure the docs dependencies are installed: ```bash julia --project=. -e 'using Pkg; Pkg.instantiate()' ``` -This will use the last released KernelFunctions.jl for building the docs. +This will use the last *released* KernelFunctions.jl for building the docs. -If instead you want to reflect the local state of the Git repository in your built docs, make sure to change the dependency to the development version: +If instead you want to reflect the *local* state of the Git repository in your built docs, next change the dependency to the development version: ```bash julia --project=. -e "using Pkg; Pkg.develop(path=\"/path/to/KernelFunctions.jl/\")" ``` @@ -16,17 +18,25 @@ In a bash-like shell on Unix, you can also use the following command from the do ```bash julia --project=. -e "using Pkg; Pkg.develop(path=\"$(readlink -f ..)\")" ``` -To undo the pinning to the local path by the previous command, run + +You can undo the pinning to the local path that was created by `Pkg.develop` through running ```bash julia --project=. -e 'using Pkg; Pkg.free("KernelFunctions")' ``` +## Build + To actually build the docs, run ```bash julia --project=. make.jl ``` The built docs will be underneath build/, and are best viewed in a browser. +If you want to iteratively edit and view the docs, it will be faster to re-run from within the same Julia REPL: +```julia +julia> include("make.jl") +``` + # How to contribute to the docs ## To add additional docs dependencies @@ -35,3 +45,8 @@ The built docs will be underneath build/, and are best viewed in a browser. julia --project=. -e 'using Pkg; Pkg.add("NewDependency")' ``` and commit the changes to Project.toml + + +## To add examples + +See [../examples](../examples/README.md) diff --git a/docs/make.jl b/docs/make.jl index f26f703c5..d8f083cb3 100644 --- a/docs/make.jl +++ b/docs/make.jl @@ -36,10 +36,12 @@ end for example in readdir(EXAMPLES_SRC) example ∈ BLACKLIST && continue - Pkg.activate(joinpath(EXAMPLES_SRC, example)) do + exampledir = joinpath(EXAMPLES_SRC, example) + isdir(exampledir) || continue + Pkg.activate(exampledir) do Pkg.develop(; path=PACKAGE_DIR) Pkg.instantiate() - filepath = joinpath(EXAMPLES_SRC, example, "script.jl") + filepath = joinpath(exampledir, "script.jl") Literate.markdown( filepath, EXAMPLES_OUT; name=example, documenter=true, preprocess=preprocess ) diff --git a/examples/README.md b/examples/README.md new file mode 100644 index 000000000..2d2d60b07 --- /dev/null +++ b/examples/README.md @@ -0,0 +1,16 @@ +# Example notebooks + +The examples in this directory are stored in [Literate.jl](https://github.com/fredrikekre/Literate.jl) format. +To run them locally, simply `include("script.jl")` in the Julia REPL. + +You can convert them to markdown and Jupyter notebook formats, respectively, by executing +```julia +julia> using Literate +julia> Literate.markdown("script.jl", "output_directory") +julia> Literate.notebook("script.jl", "output_directory") +``` + +## Add a new example + +Create a new subdirectory in here, and put your code in a file called `script.jl` so that it will get picked up by the automatic docs build. +You should also add a `Project.toml` file with all your script's dependencies (including KernelFunctions.jl). From 34c97fa2c936345a72a5c6d7f1412dbf89558c74 Mon Sep 17 00:00:00 2001 From: ST John Date: Wed, 23 Jun 2021 10:56:12 +0300 Subject: [PATCH 36/62] fix plotting --- examples/kernel-ridge-regression/script.jl | 31 ++++++++++++++++++++-- 1 file changed, 29 insertions(+), 2 deletions(-) diff --git a/examples/kernel-ridge-regression/script.jl b/examples/kernel-ridge-regression/script.jl index 76beca606..3c634ab83 100644 --- a/examples/kernel-ridge-regression/script.jl +++ b/examples/kernel-ridge-regression/script.jl @@ -1,4 +1,7 @@ # # Kernel Ridge Regression + +# Setup + using KernelFunctions using MLDataUtils using Zygote @@ -11,6 +14,8 @@ Flux.@functor ScaleTransform Flux.@functor KernelSum Flux.@functor Matern32Kernel +# Generate date + xmin = -3; xmax = 3; x = range(xmin, xmax; length=100) @@ -18,24 +23,46 @@ x_test = range(xmin, xmax; length=300) x, y = noisy_function(sinc, x; noise=0.1) X = reshape(x, :, 1) X_test = reshape(x_test, :, 1) +#md nothing #hide + +# Set up kernel and regularisation parameter + k = SqExponentialKernel() + Matern32Kernel() ∘ ScaleTransform(2.0) λ = [-1.0] +#md nothing #hide + +# + function f(x, k, λ) return kernelmatrix(k, x, X; obsdim=1) * inv(kernelmatrix(k, X; obsdim=1) + exp(λ[1]) * I) * y end f(X, k, 1.0) + +# + loss(k, λ) = (ŷ -> sum(y - ŷ) / length(y) + exp(λ[1]) * norm(ŷ))(f(X, k, λ)) loss(k, λ) + +# + ps = Flux.params(k) push!(ps, λ) opt = Flux.Momentum(0.1) -## +#md nothing #hide + +plots = [] for i in 1:10 grads = Zygote.gradient(() -> loss(k, λ), ps) Flux.Optimise.update!(opt, ps, grads) p = Plots.scatter(x, y; lab="data", title="Loss = $(loss(k,λ))") Plots.plot!(x_test, f(X_test, k, λ); lab="Prediction", lw=3.0) - display(p) + push!(plots, p) end + +# + +l = @layout grid(10, 1) +plot(plots..., layout=l) +plot!(size=(300, 1500)) From 87da65929a5c8815c828eefcee829043dc26df7d Mon Sep 17 00:00:00 2001 From: st-- Date: Wed, 23 Jun 2021 11:03:35 +0300 Subject: [PATCH 37/62] Update examples/kernel-ridge-regression/script.jl Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> --- examples/kernel-ridge-regression/script.jl | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/examples/kernel-ridge-regression/script.jl b/examples/kernel-ridge-regression/script.jl index 3c634ab83..f2c7d174c 100644 --- a/examples/kernel-ridge-regression/script.jl +++ b/examples/kernel-ridge-regression/script.jl @@ -64,5 +64,5 @@ end # l = @layout grid(10, 1) -plot(plots..., layout=l) -plot!(size=(300, 1500)) +plot(plots...; layout=l) +plot!(; size=(300, 1500)) From e8513072e81cf020612357abbe43ac8c2a51065a Mon Sep 17 00:00:00 2001 From: ST John Date: Wed, 23 Jun 2021 12:33:33 +0300 Subject: [PATCH 38/62] add under-construction warnings to examples --- examples/deep-kernel-learning/script.jl | 4 ++++ examples/kernel-ridge-regression/script.jl | 3 +++ examples/support-vector-machine/script.jl | 4 ++++ 3 files changed, 11 insertions(+) diff --git a/examples/deep-kernel-learning/script.jl b/examples/deep-kernel-learning/script.jl index d962dd593..4641a9128 100644 --- a/examples/deep-kernel-learning/script.jl +++ b/examples/deep-kernel-learning/script.jl @@ -1,4 +1,8 @@ # # Deep Kernel Learning +# +# !!! warning +# This example is under construction + using KernelFunctions using MLDataUtils using Zygote diff --git a/examples/kernel-ridge-regression/script.jl b/examples/kernel-ridge-regression/script.jl index f2c7d174c..b85dd1398 100644 --- a/examples/kernel-ridge-regression/script.jl +++ b/examples/kernel-ridge-regression/script.jl @@ -1,4 +1,7 @@ # # Kernel Ridge Regression +# +# !!! warning +# This example is under construction # Setup diff --git a/examples/support-vector-machine/script.jl b/examples/support-vector-machine/script.jl index 1ce2522ed..adbc11ca3 100644 --- a/examples/support-vector-machine/script.jl +++ b/examples/support-vector-machine/script.jl @@ -1,4 +1,8 @@ # # Support Vector Machine +# +# !!! warning +# This example is under construction + using KernelFunctions using Distributions, LinearAlgebra using Plots From b3c8aa6664e6ed82a747fa1b005441a77005c2e3 Mon Sep 17 00:00:00 2001 From: ST John Date: Wed, 23 Jun 2021 12:37:54 +0300 Subject: [PATCH 39/62] copy over fixes from KRR example --- examples/deep-kernel-learning/script.jl | 33 ++++++++++++++++++++++--- 1 file changed, 30 insertions(+), 3 deletions(-) diff --git a/examples/deep-kernel-learning/script.jl b/examples/deep-kernel-learning/script.jl index 4641a9128..699fd45be 100644 --- a/examples/deep-kernel-learning/script.jl +++ b/examples/deep-kernel-learning/script.jl @@ -3,6 +3,8 @@ # !!! warning # This example is under construction +# Setup + using KernelFunctions using MLDataUtils using Zygote @@ -15,8 +17,13 @@ Flux.@functor KernelSum Flux.@functor Matern32Kernel Flux.@functor FunctionTransform +# set up a kernel with a neural network feature extractor: + neuralnet = Chain(Dense(1, 3), Dense(3, 2)) k = SqExponentialKernel() ∘ FunctionTransform(neuralnet) + +# Generate date + xmin = -3; xmax = 3; x = range(xmin, xmax; length=100) @@ -24,22 +31,42 @@ x_test = rand(Uniform(xmin, xmax), 200) x, y = noisy_function(sinc, x; noise=0.1) X = reshape(x, :, 1) λ = [0.1] +#md nothing #hide + +# + function f(x, k, λ) return kernelmatrix(k, X, x; obsdim=1) * inv(kernelmatrix(k, X; obsdim=1) + exp(λ[1]) * I) * y end f(X, k, 1.0) -loss(k, λ) = ŷ -> sum(y - ŷ) / length(y) + exp(λ[1]) * norm(ŷ)(f(X, k, λ)) + +# + +loss(k, λ) = (ŷ -> sum(y - ŷ) / length(y) + exp(λ[1]) * norm(ŷ))(f(X, k, λ)) loss(k, λ) + +# + ps = Flux.params(k) # push!(ps,λ) opt = Flux.Momentum(1.0) -## +#md nothing #hide + +# + +plots = [] for i in 1:10 grads = Zygote.gradient(() -> loss(k, λ), ps) Flux.Optimise.update!(opt, ps, grads) p = Plots.scatter(x, y; lab="data", title="Loss = $(loss(k,λ))") Plots.plot!(x, f(X, k, λ); lab="Prediction", lw=3.0) - display(p) + push!(plots, p) end + +# + +l = @layout grid(10, 1) +plot(plots...; layout=l) +plot!(; size=(300, 1500)) From 6fd8175a8124630161048ae3bf2475cedef74e57 Mon Sep 17 00:00:00 2001 From: st-- Date: Wed, 23 Jun 2021 14:53:21 +0300 Subject: [PATCH 40/62] Apply suggestions from code review Co-authored-by: David Widmann --- examples/README.md | 21 +++++++++++++++++++-- examples/deep-kernel-learning/script.jl | 3 +-- examples/kernel-ridge-regression/script.jl | 3 +-- 3 files changed, 21 insertions(+), 6 deletions(-) diff --git a/examples/README.md b/examples/README.md index 2d2d60b07..33604f0ee 100644 --- a/examples/README.md +++ b/examples/README.md @@ -1,7 +1,21 @@ # Example notebooks The examples in this directory are stored in [Literate.jl](https://github.com/fredrikekre/Literate.jl) format. -To run them locally, simply `include("script.jl")` in the Julia REPL. + +To run them locally, navigate to the directory with the example that you want to run and +start the Julia REPL and activate the project environment of the example: +```julia +julia> ] activate . +``` +Alternatively, you can start Julia with `julia --project=.`. Then install all required +packages with +```julia +julia> ] instantiate +``` +Afterwards simply run +```julia +julia> include("script.jl") +``` You can convert them to markdown and Jupyter notebook formats, respectively, by executing ```julia @@ -13,4 +27,7 @@ julia> Literate.notebook("script.jl", "output_directory") ## Add a new example Create a new subdirectory in here, and put your code in a file called `script.jl` so that it will get picked up by the automatic docs build. -You should also add a `Project.toml` file with all your script's dependencies (including KernelFunctions.jl). + +Every example uses a separate project environment. Therefore you should also create a new +project environment in the directory of the example, install all required package there (including KernelFunctions.jl), and +commit the `Project.toml` and a `Manifest.toml` file. diff --git a/examples/deep-kernel-learning/script.jl b/examples/deep-kernel-learning/script.jl index 699fd45be..b158a1cae 100644 --- a/examples/deep-kernel-learning/script.jl +++ b/examples/deep-kernel-learning/script.jl @@ -68,5 +68,4 @@ end # l = @layout grid(10, 1) -plot(plots...; layout=l) -plot!(; size=(300, 1500)) +plot(plots...; layout=l, size=(300, 1500)) diff --git a/examples/kernel-ridge-regression/script.jl b/examples/kernel-ridge-regression/script.jl index b85dd1398..93d2f8289 100644 --- a/examples/kernel-ridge-regression/script.jl +++ b/examples/kernel-ridge-regression/script.jl @@ -67,5 +67,4 @@ end # l = @layout grid(10, 1) -plot(plots...; layout=l) -plot!(; size=(300, 1500)) +plot(plots...; layout=l, size=(300, 1500)) From f034c638b3c5a20ced98097aa1972e3d4d5529f9 Mon Sep 17 00:00:00 2001 From: ST John Date: Tue, 29 Jun 2021 13:08:39 +0300 Subject: [PATCH 41/62] commit examples/*/Manifest.toml --- examples/deep-kernel-learning/Manifest.toml | 1144 +++++++++++++++++ .../kernel-ridge-regression/Manifest.toml | 1144 +++++++++++++++++ examples/support-vector-machine/Manifest.toml | 909 +++++++++++++ 3 files changed, 3197 insertions(+) create mode 100644 examples/deep-kernel-learning/Manifest.toml create mode 100644 examples/kernel-ridge-regression/Manifest.toml create mode 100644 examples/support-vector-machine/Manifest.toml diff --git a/examples/deep-kernel-learning/Manifest.toml b/examples/deep-kernel-learning/Manifest.toml new file mode 100644 index 000000000..f4df6dec9 --- /dev/null +++ b/examples/deep-kernel-learning/Manifest.toml @@ -0,0 +1,1144 @@ +# This file is machine-generated - editing it directly is not advised + +[[AbstractFFTs]] +deps = ["LinearAlgebra"] +git-tree-sha1 = 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"0d47668e-0667-5a69-a72c-f761630bfb7e" +version = "0.3.9+1" + +[[Xorg_xcb_util_wm_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_xcb_util_jll"] +git-tree-sha1 = "e78d10aab01a4a154142c5006ed44fd9e8e31b67" +uuid = "c22f9ab0-d5fe-5066-847c-f4bb1cd4e361" +version = "0.4.1+1" + +[[Xorg_xkbcomp_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libxkbfile_jll"] +git-tree-sha1 = "4bcbf660f6c2e714f87e960a171b119d06ee163b" +uuid = "35661453-b289-5fab-8a00-3d9160c6a3a4" +version = "1.4.2+4" + +[[Xorg_xkeyboard_config_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_xkbcomp_jll"] +git-tree-sha1 = "5c8424f8a67c3f2209646d4425f3d415fee5931d" +uuid = "33bec58e-1273-512f-9401-5d533626f822" +version = "2.27.0+4" + +[[Xorg_xtrans_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] +git-tree-sha1 = "79c31e7844f6ecf779705fbc12146eb190b7d845" +uuid = "c5fb5394-a638-5e4d-96e5-b29de1b5cf10" +version = "1.4.0+3" + +[[Zlib_jll]] +deps = ["Libdl"] +uuid = "83775a58-1f1d-513f-b197-d71354ab007a" + +[[Zstd_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] +git-tree-sha1 = "cc4bf3fdde8b7e3e9fa0351bdeedba1cf3b7f6e6" +uuid = "3161d3a3-bdf6-5164-811a-617609db77b4" +version = "1.5.0+0" + +[[ZygoteRules]] +deps = ["MacroTools"] +git-tree-sha1 = "9e7a1e8ca60b742e508a315c17eef5211e7fbfd7" +uuid = "700de1a5-db45-46bc-99cf-38207098b444" +version = "0.2.1" + +[[libass_jll]] +deps = ["Artifacts", "Bzip2_jll", "FreeType2_jll", "FriBidi_jll", "JLLWrappers", "Libdl", "Pkg", "Zlib_jll"] +git-tree-sha1 = "acc685bcf777b2202a904cdcb49ad34c2fa1880c" +uuid = "0ac62f75-1d6f-5e53-bd7c-93b484bb37c0" +version = "0.14.0+4" + +[[libfdk_aac_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] +git-tree-sha1 = "7a5780a0d9c6864184b3a2eeeb833a0c871f00ab" +uuid = "f638f0a6-7fb0-5443-88ba-1cc74229b280" +version = "0.1.6+4" + +[[libpng_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Zlib_jll"] +git-tree-sha1 = "94d180a6d2b5e55e447e2d27a29ed04fe79eb30c" +uuid = "b53b4c65-9356-5827-b1ea-8c7a1a84506f" +version = "1.6.38+0" + +[[libvorbis_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Ogg_jll", "Pkg"] +git-tree-sha1 = "c45f4e40e7aafe9d086379e5578947ec8b95a8fb" +uuid = "f27f6e37-5d2b-51aa-960f-b287f2bc3b7a" +version = "1.3.7+0" + +[[nghttp2_jll]] +deps = ["Artifacts", "Libdl"] +uuid = "8e850ede-7688-5339-a07c-302acd2aaf8d" + +[[p7zip_jll]] +deps = ["Artifacts", "Libdl"] +uuid = "3f19e933-33d8-53b3-aaab-bd5110c3b7a0" + +[[x264_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] +git-tree-sha1 = "d713c1ce4deac133e3334ee12f4adff07f81778f" +uuid = "1270edf5-f2f9-52d2-97e9-ab00b5d0237a" +version = "2020.7.14+2" + +[[x265_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] +git-tree-sha1 = "487da2f8f2f0c8ee0e83f39d13037d6bbf0a45ab" +uuid = "dfaa095f-4041-5dcd-9319-2fabd8486b76" +version = "3.0.0+3" + +[[xkbcommon_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Wayland_jll", "Wayland_protocols_jll", "Xorg_libxcb_jll", "Xorg_xkeyboard_config_jll"] +git-tree-sha1 = "ece2350174195bb31de1a63bea3a41ae1aa593b6" +uuid = "d8fb68d0-12a3-5cfd-a85a-d49703b185fd" +version = "0.9.1+5" From 2fa2f1bcbf004c80f73f1fe71a0e343e2e18aa49 Mon Sep 17 00:00:00 2001 From: ST John Date: Tue, 29 Jun 2021 13:26:40 +0300 Subject: [PATCH 42/62] fix optional package loading --- docs/Manifest.toml | 18 ++++++++++++++++++ docs/Project.toml | 2 +- docs/make.jl | 7 +++---- 3 files changed, 22 insertions(+), 5 deletions(-) diff --git a/docs/Manifest.toml b/docs/Manifest.toml index cfe901179..dc7c0498b 100644 --- a/docs/Manifest.toml +++ b/docs/Manifest.toml @@ -1,5 +1,11 @@ # This file is machine-generated - editing it directly is not advised +[[AbstractFFTs]] +deps = ["LinearAlgebra"] +git-tree-sha1 = "051c95d6836228d120f5f4b984dd5aba1624f716" +uuid = "621f4979-c628-5d54-868e-fcf4e3e8185c" +version = "0.5.0" + [[ArgTools]] uuid = "0dad84c5-d112-42e6-8d28-ef12dabb789f" @@ -115,6 +121,12 @@ path = ".." uuid = "ec8451be-7e33-11e9-00cf-bbf324bd1392" version = "0.10.6" +[[Kronecker]] +deps = ["FillArrays", "LinearAlgebra", "NamedDims", "SparseArrays", "StatsBase"] +git-tree-sha1 = "90e082a267982069e624ea0f825d324c86a01b4e" +uuid = "2c470bb0-bcc8-11e8-3dad-c9649493f05e" +version = "0.4.3" + [[LibCURL]] deps = ["LibCURL_jll", "MozillaCACerts_jll"] uuid = "b27032c2-a3e7-50c8-80cd-2d36dbcbfd21" @@ -173,6 +185,12 @@ uuid = "a63ad114-7e13-5084-954f-fe012c677804" [[MozillaCACerts_jll]] uuid = "14a3606d-f60d-562e-9121-12d972cd8159" +[[NamedDims]] +deps = ["AbstractFFTs", "LinearAlgebra", "Pkg", "Requires", "Statistics"] +git-tree-sha1 = "e91d3ee8ac1514651b6e85686ca31257d17b1eb2" +uuid = "356022a1-0364-5f58-8944-0da4b18d706f" +version = "0.2.33" + [[NetworkOptions]] uuid = "ca575930-c2e3-43a9-ace4-1e988b2c1908" diff --git a/docs/Project.toml b/docs/Project.toml index bb0a04983..3f3371a33 100644 --- a/docs/Project.toml +++ b/docs/Project.toml @@ -1,9 +1,9 @@ [deps] Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4" KernelFunctions = "ec8451be-7e33-11e9-00cf-bbf324bd1392" +Kronecker = "2c470bb0-bcc8-11e8-3dad-c9649493f05e" PDMats = "90014a1f-27ba-587c-ab20-58faa44d9150" Pkg = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f" -Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c" [compat] Documenter = "0.27" diff --git a/docs/make.jl b/docs/make.jl index ab0da26c1..cf6a13ab0 100644 --- a/docs/make.jl +++ b/docs/make.jl @@ -38,11 +38,10 @@ DocMeta.setdocmeta!( KernelFunctions, :DocTestSetup, quote + using PDMats + using Kronecker using KernelFunctions - using LinearAlgebra - using Random - using PDMats: PDMats - end; + end; # we load all optional packages to generate the full API documentation recursive=true, ) From 6b3238ba26424f3c6c9cdc743512c83aa808728a Mon Sep 17 00:00:00 2001 From: ST John Date: Tue, 29 Jun 2021 13:26:55 +0300 Subject: [PATCH 43/62] doc fixes --- docs/src/create_kernel.md | 2 +- src/matrix/kernelpdmat.jl | 8 ++++---- 2 files changed, 5 insertions(+), 5 deletions(-) diff --git a/docs/src/create_kernel.md b/docs/src/create_kernel.md index d7a10c4db..c7234b41f 100644 --- a/docs/src/create_kernel.md +++ b/docs/src/create_kernel.md @@ -10,7 +10,7 @@ Here are a few ways depending on how complicated your kernel is: If your kernel function is of the form `k(x, y) = f(d(x, y))` where `d(x, y)` is a `PreMetric`, you can construct your custom kernel by defining `kappa` and `metric` for your kernel. -Here is for example how one can define the `SqExponentialKernel` again : +Here is for example how one can define the `SqExponentialKernel` again: ```julia struct MyKernel <: KernelFunctions.SimpleKernel end diff --git a/src/matrix/kernelpdmat.jl b/src/matrix/kernelpdmat.jl index 8348d454a..e0146c863 100644 --- a/src/matrix/kernelpdmat.jl +++ b/src/matrix/kernelpdmat.jl @@ -6,10 +6,10 @@ export kernelpdmat kernelpdmat(k::Kernel, X::AbstractMatrix; obsdim::Int=2) kernelpdmat(k::Kernel, X::AbstractVector) -Compute a positive-definite matrix in the form of a `PDMat` matrix see [PDMats.jl](https://github.com/JuliaStats/PDMats.jl) -with the cholesky decomposition precomputed. -The algorithm recursively tries to add recursively a diagonal nugget until positive -definiteness is achieved or until the noise is too big. +Compute a positive-definite matrix in the form of a `PDMat` matrix (see [PDMats.jl](https://github.com/JuliaStats/PDMats.jl)), +with the Cholesky decomposition precomputed. +The algorithm adds a diagonal "nugget" term to the kernel matrix which is increased until positive +definiteness is achieved. The algorithm gives up with an error if the nugget becomes larger than 1% of the largest value in the kernel matrix. """ function kernelpdmat(κ::Kernel, X::AbstractMatrix; obsdim::Int=defaultobs) return kernelpdmat(κ, vec_of_vecs(X; obsdim=obsdim)) From 1ea5c6c138ab42f522927a3e9107d2e650855111 Mon Sep 17 00:00:00 2001 From: ST John Date: Tue, 29 Jun 2021 13:35:03 +0300 Subject: [PATCH 44/62] explicit Pkg.add of Literate --- docs/literate.jl | 1 + 1 file changed, 1 insertion(+) diff --git a/docs/literate.jl b/docs/literate.jl index 97223eef1..cde18ed41 100644 --- a/docs/literate.jl +++ b/docs/literate.jl @@ -8,6 +8,7 @@ const OUTDIR = ARGS[2] # Activate environment using Pkg: Pkg Pkg.activate(dirname(SCRIPTJL)) +Pkg.add("Literate"; preserve=Pkg.PRESERVE_ALL) Pkg.instantiate() using Literate: Literate From 241cf62f43eaf9ac237d682624ca039d3fbc3ec8 Mon Sep 17 00:00:00 2001 From: st-- Date: Tue, 29 Jun 2021 13:36:33 +0300 Subject: [PATCH 45/62] Apply suggestions from code review --- docs/README.md | 2 +- examples/README.md | 4 +++- 2 files changed, 4 insertions(+), 2 deletions(-) diff --git a/docs/README.md b/docs/README.md index 008354134..57d30217b 100644 --- a/docs/README.md +++ b/docs/README.md @@ -44,7 +44,7 @@ julia> include("make.jl") ```bash julia --project=. -e 'using Pkg; Pkg.add("NewDependency")' ``` -and commit the changes to Project.toml +and commit the changes to Project.toml and Manifest.toml. ## To add examples diff --git a/examples/README.md b/examples/README.md index 33604f0ee..bc5e35c12 100644 --- a/examples/README.md +++ b/examples/README.md @@ -23,11 +23,13 @@ julia> using Literate julia> Literate.markdown("script.jl", "output_directory") julia> Literate.notebook("script.jl", "output_directory") ``` +or run +`julia --project=. ../../docs/literate.jl script.jl output_directory`. ## Add a new example Create a new subdirectory in here, and put your code in a file called `script.jl` so that it will get picked up by the automatic docs build. Every example uses a separate project environment. Therefore you should also create a new -project environment in the directory of the example, install all required package there (including KernelFunctions.jl), and +project environment in the directory of the example that contains all packages required by your script. Note that you must also include both the `KernelFunctions` and the `Literate` packages. Make sure to both commit the `Project.toml` and a `Manifest.toml` file. From df1c52655e0adf28db9d1c88cfe7dd406c156235 Mon Sep 17 00:00:00 2001 From: st-- Date: Tue, 29 Jun 2021 13:45:29 +0300 Subject: [PATCH 46/62] Update examples/README.md --- examples/README.md | 13 +++++++++++-- 1 file changed, 11 insertions(+), 2 deletions(-) diff --git a/examples/README.md b/examples/README.md index bc5e35c12..6a40a89b7 100644 --- a/examples/README.md +++ b/examples/README.md @@ -31,5 +31,14 @@ or run Create a new subdirectory in here, and put your code in a file called `script.jl` so that it will get picked up by the automatic docs build. Every example uses a separate project environment. Therefore you should also create a new -project environment in the directory of the example that contains all packages required by your script. Note that you must also include both the `KernelFunctions` and the `Literate` packages. Make sure to both -commit the `Project.toml` and a `Manifest.toml` file. +project environment in the directory of the example that contains all packages required by your script. +Note that the dependencies of your example must include the `Literate` package. +From a Julia REPL started in your example script's directory, you can run +```julia +julia> ] activate . +julia> ] add Literate +julia> ] add KernelFunctions +julia> # add any other example-specific dependencies +``` +to generate the project files. +Make sure to commit both the `Project.toml` and the `Manifest.toml` file when you want to contribute your example in a pull request. From cac9e7d8007829006b85f9ad077864c6e9be28fb Mon Sep 17 00:00:00 2001 From: ST John Date: Tue, 29 Jun 2021 13:57:24 +0300 Subject: [PATCH 47/62] update README --- docs/README.md | 50 ++++++++++++++++++++++++++++---------------------- docs/make.jl | 2 +- 2 files changed, 29 insertions(+), 23 deletions(-) diff --git a/docs/README.md b/docs/README.md index 57d30217b..eb759518b 100644 --- a/docs/README.md +++ b/docs/README.md @@ -1,41 +1,47 @@ # How to build the docs locally -Assuming you are in this (docs/) directory: +If you just want to modify or add an example, you can [build just the example](../examples/README.md) without having to build the full documentation locally. -## Setup +If you want to build the documentation, navigate to this (docs/) directory and open a Julia REPL. -First, make sure the docs dependencies are installed: -```bash -julia --project=. -e 'using Pkg; Pkg.instantiate()' -``` -This will use the last *released* KernelFunctions.jl for building the docs. +## Instantiation -If instead you want to reflect the *local* state of the Git repository in your built docs, next change the dependency to the development version: -```bash -julia --project=. -e "using Pkg; Pkg.develop(path=\"/path/to/KernelFunctions.jl/\")" -``` -In a bash-like shell on Unix, you can also use the following command from the docs/ directory to get the absolute path: -```bash -julia --project=. -e "using Pkg; Pkg.develop(path=\"$(readlink -f ..)\")" +First activate the documentation environment: +```julia +julia> ] activate . ``` +Alternatively, you can start Julia with `julia --project=.`. -You can undo the pinning to the local path that was created by `Pkg.develop` through running -```bash -julia --project=. -e 'using Pkg; Pkg.free("KernelFunctions")' +Then install all packages: +```julia +julia> ] instantiate ``` +By default, this will use the development version of KernelFunctions in the parent directory. ## Build -To actually build the docs, run -```bash -julia --project=. make.jl +To build the documentation, run (after activating the documentation environment) +```julia +julia> include("make.jl") ``` -The built docs will be underneath build/, and are best viewed in a browser. +You can speed up the process if you do not execute the examples and comment out the +relevant sections in `docs/make.jl`. + +The output is in the `docs/build/` directory and best viewed in a browser. +The documentation uses pretty URLs which can be a hindrance if you browse the documentation locally. +The [Documenter documentation](https://juliadocs.github.io/Documenter.jl/stable/man/guide/#Building-an-Empty-Document) suggests that + +> You can run a local web server out of the `docs/build` directory. One way to accomplish +> this is to install the [LiveServer](https://github.com/tlienart/LiveServer.jl) Julia +> package. You can then start the server with `julia -e 'using LiveServer; serve(dir="docs/build")'`. +> Alternatively, if you have Python installed, you can start one with +> `python3 -m http.server --bind localhost` (or `python -m SimpleHTTPServer` with Python 2). -If you want to iteratively edit and view the docs, it will be faster to re-run from within the same Julia REPL: +If you make any changes, you can run ```julia julia> include("make.jl") ``` +again to rebuild the documentation. # How to contribute to the docs diff --git a/docs/make.jl b/docs/make.jl index cf6a13ab0..01aa93c64 100644 --- a/docs/make.jl +++ b/docs/make.jl @@ -41,7 +41,7 @@ DocMeta.setdocmeta!( using PDMats using Kronecker using KernelFunctions - end; # we load all optional packages to generate the full API documentation + end; # we have to load all optional packages to generate the full API documentation recursive=true, ) From f2d8dcc7e9e396ed9726eae8e5deca2f9f9ae0d6 Mon Sep 17 00:00:00 2001 From: st-- Date: Tue, 29 Jun 2021 14:06:27 +0300 Subject: [PATCH 48/62] Update docs/Project.toml Co-authored-by: David Widmann --- docs/Project.toml | 1 - 1 file changed, 1 deletion(-) diff --git a/docs/Project.toml b/docs/Project.toml index 3f3371a33..c0b55a35f 100644 --- a/docs/Project.toml +++ b/docs/Project.toml @@ -3,7 +3,6 @@ Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4" KernelFunctions = "ec8451be-7e33-11e9-00cf-bbf324bd1392" Kronecker = "2c470bb0-bcc8-11e8-3dad-c9649493f05e" PDMats = "90014a1f-27ba-587c-ab20-58faa44d9150" -Pkg = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f" [compat] Documenter = "0.27" From 2b1627b0193b22d8ab96f73ee127d830c3aaa109 Mon Sep 17 00:00:00 2001 From: ST John Date: Tue, 29 Jun 2021 14:10:52 +0300 Subject: [PATCH 49/62] update examples *.toml --- examples/deep-kernel-learning/Manifest.toml | 16 ++++++++++++++-- examples/deep-kernel-learning/Project.toml | 1 + examples/kernel-ridge-regression/Manifest.toml | 14 +++++++++++++- examples/kernel-ridge-regression/Project.toml | 1 + examples/support-vector-machine/Manifest.toml | 16 ++++++++++++++-- examples/support-vector-machine/Project.toml | 1 + 6 files changed, 44 insertions(+), 5 deletions(-) diff --git a/examples/deep-kernel-learning/Manifest.toml b/examples/deep-kernel-learning/Manifest.toml index f4df6dec9..21e7dd974 100644 --- a/examples/deep-kernel-learning/Manifest.toml +++ b/examples/deep-kernel-learning/Manifest.toml @@ -337,6 +337,12 @@ git-tree-sha1 = "86ed84701fbfd1142c9786f8e53c595ff5a4def9" uuid = "cd3eb016-35fb-5094-929b-558a96fad6f3" version = "0.9.10" +[[IOCapture]] +deps = ["Logging", "Random"] +git-tree-sha1 = "f7be53659ab06ddc986428d3a9dcc95f6fa6705a" +uuid = "b5f81e59-6552-4d32-b1f0-c071b021bf89" +version = "0.2.2" + [[IRTools]] deps = ["InteractiveUtils", "MacroTools", "Test"] git-tree-sha1 = "c67e7515a11f726f44083e74f218d134396d6510" @@ -394,10 +400,10 @@ uuid = "e5e0dc1b-0480-54bc-9374-aad01c23163d" version = "0.8.4" [[KernelFunctions]] -deps = ["ChainRulesCore", "Compat", "CompositionsBase", "Distances", "Distributions", "FillArrays", "Functors", "LinearAlgebra", "Random", "Requires", "SpecialFunctions", "StatsBase", "StatsFuns", "TensorCore", "Test", "ZygoteRules"] +deps = ["ChainRulesCore", "Compat", "CompositionsBase", "Distances", "FillArrays", "Functors", "LinearAlgebra", "Random", "Requires", "SpecialFunctions", "StatsBase", "StatsFuns", "TensorCore", "Test", "ZygoteRules"] path = "/u/10/johnt1/unix/JuliaCode/KernelFunctions.jl/docs/.." uuid = "ec8451be-7e33-11e9-00cf-bbf324bd1392" -version = "0.10.5" +version = "0.10.6" [[LAME_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -515,6 +521,12 @@ version = "2.36.0+0" deps = ["Libdl"] uuid = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e" +[[Literate]] +deps = ["Base64", "IOCapture", "JSON", "REPL"] +git-tree-sha1 = "501a1a74a0c825037860d36d87d703e987d39dbc" +uuid = "98b081ad-f1c9-55d3-8b20-4c87d4299306" +version = "2.8.1" + [[LogExpFunctions]] deps = ["DocStringExtensions", "LinearAlgebra"] git-tree-sha1 = "1ba664552f1ef15325e68dc4c05c3ef8c2d5d885" diff --git a/examples/deep-kernel-learning/Project.toml b/examples/deep-kernel-learning/Project.toml index 15222757e..7d7efcd20 100644 --- a/examples/deep-kernel-learning/Project.toml +++ b/examples/deep-kernel-learning/Project.toml @@ -3,6 +3,7 @@ Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f" Flux = "587475ba-b771-5e3f-ad9e-33799f191a9c" KernelFunctions = "ec8451be-7e33-11e9-00cf-bbf324bd1392" LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e" +Literate = "98b081ad-f1c9-55d3-8b20-4c87d4299306" MLDataUtils = "cc2ba9b6-d476-5e6d-8eaf-a92d5412d41d" Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80" Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f" diff --git a/examples/kernel-ridge-regression/Manifest.toml b/examples/kernel-ridge-regression/Manifest.toml index aaa081e71..21e7dd974 100644 --- a/examples/kernel-ridge-regression/Manifest.toml +++ b/examples/kernel-ridge-regression/Manifest.toml @@ -337,6 +337,12 @@ git-tree-sha1 = "86ed84701fbfd1142c9786f8e53c595ff5a4def9" uuid = "cd3eb016-35fb-5094-929b-558a96fad6f3" version = "0.9.10" +[[IOCapture]] +deps = ["Logging", "Random"] +git-tree-sha1 = "f7be53659ab06ddc986428d3a9dcc95f6fa6705a" +uuid = "b5f81e59-6552-4d32-b1f0-c071b021bf89" +version = "0.2.2" + [[IRTools]] deps = ["InteractiveUtils", "MacroTools", "Test"] git-tree-sha1 = "c67e7515a11f726f44083e74f218d134396d6510" @@ -397,7 +403,7 @@ version = "0.8.4" deps = ["ChainRulesCore", "Compat", "CompositionsBase", "Distances", "FillArrays", "Functors", "LinearAlgebra", "Random", "Requires", "SpecialFunctions", "StatsBase", "StatsFuns", "TensorCore", "Test", "ZygoteRules"] path = "/u/10/johnt1/unix/JuliaCode/KernelFunctions.jl/docs/.." uuid = "ec8451be-7e33-11e9-00cf-bbf324bd1392" -version = "0.10.5" +version = "0.10.6" [[LAME_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -515,6 +521,12 @@ version = "2.36.0+0" deps = ["Libdl"] uuid = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e" +[[Literate]] +deps = ["Base64", "IOCapture", "JSON", "REPL"] +git-tree-sha1 = "501a1a74a0c825037860d36d87d703e987d39dbc" +uuid = "98b081ad-f1c9-55d3-8b20-4c87d4299306" +version = "2.8.1" + [[LogExpFunctions]] deps = ["DocStringExtensions", "LinearAlgebra"] git-tree-sha1 = "1ba664552f1ef15325e68dc4c05c3ef8c2d5d885" diff --git a/examples/kernel-ridge-regression/Project.toml b/examples/kernel-ridge-regression/Project.toml index 15222757e..7d7efcd20 100644 --- a/examples/kernel-ridge-regression/Project.toml +++ b/examples/kernel-ridge-regression/Project.toml @@ -3,6 +3,7 @@ Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f" Flux = "587475ba-b771-5e3f-ad9e-33799f191a9c" KernelFunctions = "ec8451be-7e33-11e9-00cf-bbf324bd1392" LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e" +Literate = "98b081ad-f1c9-55d3-8b20-4c87d4299306" MLDataUtils = "cc2ba9b6-d476-5e6d-8eaf-a92d5412d41d" Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80" Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f" diff --git a/examples/support-vector-machine/Manifest.toml b/examples/support-vector-machine/Manifest.toml index ab3beeee6..dabb58d5a 100644 --- a/examples/support-vector-machine/Manifest.toml +++ b/examples/support-vector-machine/Manifest.toml @@ -235,6 +235,12 @@ git-tree-sha1 = "86ed84701fbfd1142c9786f8e53c595ff5a4def9" uuid = "cd3eb016-35fb-5094-929b-558a96fad6f3" version = "0.9.10" +[[IOCapture]] +deps = ["Logging", "Random"] +git-tree-sha1 = "f7be53659ab06ddc986428d3a9dcc95f6fa6705a" +uuid = "b5f81e59-6552-4d32-b1f0-c071b021bf89" +version = "0.2.2" + [[IniFile]] deps = ["Test"] git-tree-sha1 = "098e4d2c533924c921f9f9847274f2ad89e018b8" @@ -274,10 +280,10 @@ uuid = "aacddb02-875f-59d6-b918-886e6ef4fbf8" version = "2.1.0+0" [[KernelFunctions]] -deps = ["ChainRulesCore", "Compat", "CompositionsBase", "Distances", "Distributions", "FillArrays", "Functors", "LinearAlgebra", "Random", "Requires", "SpecialFunctions", "StatsBase", "StatsFuns", "TensorCore", "Test", "ZygoteRules"] +deps = ["ChainRulesCore", "Compat", "CompositionsBase", "Distances", "FillArrays", "Functors", "LinearAlgebra", "Random", "Requires", "SpecialFunctions", "StatsBase", "StatsFuns", "TensorCore", "Test", "ZygoteRules"] path = "/u/10/johnt1/unix/JuliaCode/KernelFunctions.jl/docs/.." uuid = "ec8451be-7e33-11e9-00cf-bbf324bd1392" -version = "0.10.5" +version = "0.10.6" [[LAME_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -379,6 +385,12 @@ version = "2.36.0+0" deps = ["Libdl"] uuid = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e" +[[Literate]] +deps = ["Base64", "IOCapture", "JSON", "REPL"] +git-tree-sha1 = "501a1a74a0c825037860d36d87d703e987d39dbc" +uuid = "98b081ad-f1c9-55d3-8b20-4c87d4299306" +version = "2.8.1" + [[LogExpFunctions]] deps = ["DocStringExtensions", "LinearAlgebra"] git-tree-sha1 = "1ba664552f1ef15325e68dc4c05c3ef8c2d5d885" diff --git a/examples/support-vector-machine/Project.toml b/examples/support-vector-machine/Project.toml index d1b9295cc..16d77268d 100644 --- a/examples/support-vector-machine/Project.toml +++ b/examples/support-vector-machine/Project.toml @@ -2,4 +2,5 @@ Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f" KernelFunctions = "ec8451be-7e33-11e9-00cf-bbf324bd1392" LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e" +Literate = "98b081ad-f1c9-55d3-8b20-4c87d4299306" Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80" From a91edc969fbfda84ceb04d4ae43eb6065ba47256 Mon Sep 17 00:00:00 2001 From: ST John Date: Tue, 29 Jun 2021 14:11:06 +0300 Subject: [PATCH 50/62] use cleaner f form --- examples/deep-kernel-learning/script.jl | 9 +++------ examples/kernel-ridge-regression/script.jl | 10 +++------- 2 files changed, 6 insertions(+), 13 deletions(-) diff --git a/examples/deep-kernel-learning/script.jl b/examples/deep-kernel-learning/script.jl index b158a1cae..6db37e65b 100644 --- a/examples/deep-kernel-learning/script.jl +++ b/examples/deep-kernel-learning/script.jl @@ -29,17 +29,14 @@ xmax = 3; x = range(xmin, xmax; length=100) x_test = rand(Uniform(xmin, xmax), 200) x, y = noisy_function(sinc, x; noise=0.1) -X = reshape(x, :, 1) +X = ColVecs(reshape(x, :, 1)) +X_test = ColVecs(reshape(x_test, :, 1)) λ = [0.1] #md nothing #hide # -function f(x, k, λ) - return kernelmatrix(k, X, x; obsdim=1) * - inv(kernelmatrix(k, X; obsdim=1) + exp(λ[1]) * I) * - y -end +f(x, k, λ) = kernelmatrix(k, x, X) / (kernelmatrix(k, X) + exp(λ) * I) * y f(X, k, 1.0) # diff --git a/examples/kernel-ridge-regression/script.jl b/examples/kernel-ridge-regression/script.jl index 93d2f8289..ea3eca775 100644 --- a/examples/kernel-ridge-regression/script.jl +++ b/examples/kernel-ridge-regression/script.jl @@ -24,8 +24,8 @@ xmax = 3; x = range(xmin, xmax; length=100) x_test = range(xmin, xmax; length=300) x, y = noisy_function(sinc, x; noise=0.1) -X = reshape(x, :, 1) -X_test = reshape(x_test, :, 1) +X = ColVecs(reshape(x, :, 1)) +X_test = ColVecs(reshape(x_test, :, 1)) #md nothing #hide # Set up kernel and regularisation parameter @@ -36,11 +36,7 @@ k = SqExponentialKernel() + Matern32Kernel() ∘ ScaleTransform(2.0) # -function f(x, k, λ) - return kernelmatrix(k, x, X; obsdim=1) * - inv(kernelmatrix(k, X; obsdim=1) + exp(λ[1]) * I) * - y -end +f(x, k, λ) = kernelmatrix(k, x, X) / (kernelmatrix(k, X) + exp(λ) * I) * y f(X, k, 1.0) # From 1daf1c37c0c8f0ece36ecacca40bdcc943feb0e8 Mon Sep 17 00:00:00 2001 From: ST John Date: Tue, 29 Jun 2021 14:58:12 +0300 Subject: [PATCH 51/62] fix errors --- docs/make.jl | 12 ++++++------ examples/deep-kernel-learning/script.jl | 6 +++--- examples/kernel-ridge-regression/script.jl | 6 +++--- 3 files changed, 12 insertions(+), 12 deletions(-) diff --git a/docs/make.jl b/docs/make.jl index 01aa93c64..33ed2b8df 100644 --- a/docs/make.jl +++ b/docs/make.jl @@ -1,4 +1,4 @@ -# run examples +### Process examples const EXAMPLES_SRC = joinpath(@__DIR__, "..", "examples") const EXAMPLES_OUT = joinpath(@__DIR__, "src", "examples") const LITERATEJL = joinpath(@__DIR__, "literate.jl") @@ -24,10 +24,12 @@ end # Check that all examples were run successfully isempty(processes) || success(processes) || error("some examples were not run successfully") -# Build documentation -using KernelFunctions +### Build documentation using Documenter +using KernelFunctions +using PDMats, Kronecker # we have to load all optional packages to generate the full API documentation + # Print `@debug` statements (https://github.com/JuliaDocs/Documenter.jl/issues/955) if haskey(ENV, "GITHUB_ACTIONS") ENV["JULIA_DEBUG"] = "Documenter" @@ -38,10 +40,8 @@ DocMeta.setdocmeta!( KernelFunctions, :DocTestSetup, quote - using PDMats - using Kronecker using KernelFunctions - end; # we have to load all optional packages to generate the full API documentation + end; # we have to load all packages used (implicitly) within jldoctest blocks in the API docstrings recursive=true, ) diff --git a/examples/deep-kernel-learning/script.jl b/examples/deep-kernel-learning/script.jl index 6db37e65b..14c1560c3 100644 --- a/examples/deep-kernel-learning/script.jl +++ b/examples/deep-kernel-learning/script.jl @@ -29,14 +29,14 @@ xmax = 3; x = range(xmin, xmax; length=100) x_test = rand(Uniform(xmin, xmax), 200) x, y = noisy_function(sinc, x; noise=0.1) -X = ColVecs(reshape(x, :, 1)) -X_test = ColVecs(reshape(x_test, :, 1)) +X = RowVecs(reshape(x, :, 1)) +X_test = RowVecs(reshape(x_test, :, 1)) λ = [0.1] #md nothing #hide # -f(x, k, λ) = kernelmatrix(k, x, X) / (kernelmatrix(k, X) + exp(λ) * I) * y +f(x, k, λ) = kernelmatrix(k, x, X) / (kernelmatrix(k, X) + exp(λ[1]) * I) * y f(X, k, 1.0) # diff --git a/examples/kernel-ridge-regression/script.jl b/examples/kernel-ridge-regression/script.jl index ea3eca775..5064a8a45 100644 --- a/examples/kernel-ridge-regression/script.jl +++ b/examples/kernel-ridge-regression/script.jl @@ -24,8 +24,8 @@ xmax = 3; x = range(xmin, xmax; length=100) x_test = range(xmin, xmax; length=300) x, y = noisy_function(sinc, x; noise=0.1) -X = ColVecs(reshape(x, :, 1)) -X_test = ColVecs(reshape(x_test, :, 1)) +X = RowVecs(reshape(x, :, 1)) +X_test = RowVecs(reshape(x_test, :, 1)) #md nothing #hide # Set up kernel and regularisation parameter @@ -36,7 +36,7 @@ k = SqExponentialKernel() + Matern32Kernel() ∘ ScaleTransform(2.0) # -f(x, k, λ) = kernelmatrix(k, x, X) / (kernelmatrix(k, X) + exp(λ) * I) * y +f(x, k, λ) = kernelmatrix(k, x, X) / (kernelmatrix(k, X) + exp(λ[1]) * I) * y f(X, k, 1.0) # From b262ac0a1b8b3c45d37279c38be53df0da843f0f Mon Sep 17 00:00:00 2001 From: ST John Date: Tue, 29 Jun 2021 14:59:31 +0300 Subject: [PATCH 52/62] fix example Manifest.tomls --- examples/deep-kernel-learning/Manifest.toml | 2 +- examples/kernel-ridge-regression/Manifest.toml | 2 +- examples/support-vector-machine/Manifest.toml | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/examples/deep-kernel-learning/Manifest.toml b/examples/deep-kernel-learning/Manifest.toml index 21e7dd974..c3a4f40f2 100644 --- a/examples/deep-kernel-learning/Manifest.toml +++ b/examples/deep-kernel-learning/Manifest.toml @@ -401,7 +401,7 @@ version = "0.8.4" [[KernelFunctions]] deps = ["ChainRulesCore", "Compat", "CompositionsBase", "Distances", "FillArrays", "Functors", "LinearAlgebra", "Random", "Requires", "SpecialFunctions", "StatsBase", "StatsFuns", "TensorCore", "Test", "ZygoteRules"] -path = "/u/10/johnt1/unix/JuliaCode/KernelFunctions.jl/docs/.." +path = "../.." uuid = "ec8451be-7e33-11e9-00cf-bbf324bd1392" version = "0.10.6" diff --git a/examples/kernel-ridge-regression/Manifest.toml b/examples/kernel-ridge-regression/Manifest.toml index 21e7dd974..c3a4f40f2 100644 --- a/examples/kernel-ridge-regression/Manifest.toml +++ b/examples/kernel-ridge-regression/Manifest.toml @@ -401,7 +401,7 @@ version = "0.8.4" [[KernelFunctions]] deps = ["ChainRulesCore", "Compat", "CompositionsBase", "Distances", "FillArrays", "Functors", "LinearAlgebra", "Random", "Requires", "SpecialFunctions", "StatsBase", "StatsFuns", "TensorCore", "Test", "ZygoteRules"] -path = "/u/10/johnt1/unix/JuliaCode/KernelFunctions.jl/docs/.." +path = "../.." uuid = "ec8451be-7e33-11e9-00cf-bbf324bd1392" version = "0.10.6" diff --git a/examples/support-vector-machine/Manifest.toml b/examples/support-vector-machine/Manifest.toml index dabb58d5a..8b8a2d648 100644 --- a/examples/support-vector-machine/Manifest.toml +++ b/examples/support-vector-machine/Manifest.toml @@ -281,7 +281,7 @@ version = "2.1.0+0" [[KernelFunctions]] deps = ["ChainRulesCore", "Compat", "CompositionsBase", "Distances", "FillArrays", "Functors", "LinearAlgebra", "Random", "Requires", "SpecialFunctions", "StatsBase", "StatsFuns", "TensorCore", "Test", "ZygoteRules"] -path = "/u/10/johnt1/unix/JuliaCode/KernelFunctions.jl/docs/.." +path = "../.." uuid = "ec8451be-7e33-11e9-00cf-bbf324bd1392" version = "0.10.6" From 4cce78ee9b0e24ce955b1ee69faf1b2433e2331f Mon Sep 17 00:00:00 2001 From: st-- Date: Tue, 29 Jun 2021 15:16:18 +0300 Subject: [PATCH 53/62] Update examples/README.md Co-authored-by: David Widmann --- examples/README.md | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/examples/README.md b/examples/README.md index 6a40a89b7..04f97c7c7 100644 --- a/examples/README.md +++ b/examples/README.md @@ -24,7 +24,9 @@ julia> Literate.markdown("script.jl", "output_directory") julia> Literate.notebook("script.jl", "output_directory") ``` or run -`julia --project=. ../../docs/literate.jl script.jl output_directory`. +```shell +julia docs/literate.jl examples/myexample/script.jl output_directory +``` ## Add a new example From 64d5ef7d60c62a9881da3837668c0d0b4779452d Mon Sep 17 00:00:00 2001 From: ST John Date: Tue, 29 Jun 2021 15:37:18 +0300 Subject: [PATCH 54/62] better error messages? --- docs/literate.jl | 39 ++++++++++++++++++++++----------------- 1 file changed, 22 insertions(+), 17 deletions(-) diff --git a/docs/literate.jl b/docs/literate.jl index cde18ed41..2e5c71389 100644 --- a/docs/literate.jl +++ b/docs/literate.jl @@ -38,20 +38,25 @@ function preprocess(content) return replace(content, r"^# # [^\n]*"m => sub; count=1) end -# Convert to markdown and notebook -Literate.markdown( - SCRIPTJL, - OUTDIR; - name=basename(dirname(SCRIPTJL)), - documenter=false, - execute=true, - preprocess=preprocess, -) -Literate.notebook( - SCRIPTJL, - OUTDIR; - name=basename(dirname(SCRIPTJL)), - documenter=false, - execute=true, - preprocess=preprocess, -) +try + # Convert to markdown and notebook + Literate.markdown( + SCRIPTJL, + OUTDIR; + name=basename(dirname(SCRIPTJL)), + documenter=false, + execute=true, + preprocess=preprocess, + ) + Literate.notebook( + SCRIPTJL, + OUTDIR; + name=basename(dirname(SCRIPTJL)), + documenter=false, + execute=true, + preprocess=preprocess, + ) +catch e + # add script path to error message + throw(LoadError(SCRIPTJL, 0, e)) +end From 853b437582537c95947e0b07866304c9eaf40904 Mon Sep 17 00:00:00 2001 From: ST John Date: Tue, 29 Jun 2021 16:00:50 +0300 Subject: [PATCH 55/62] Revert "better error messages?" This reverts commit 64d5ef7d60c62a9881da3837668c0d0b4779452d. --- docs/literate.jl | 39 +++++++++++++++++---------------------- 1 file changed, 17 insertions(+), 22 deletions(-) diff --git a/docs/literate.jl b/docs/literate.jl index 2e5c71389..cde18ed41 100644 --- a/docs/literate.jl +++ b/docs/literate.jl @@ -38,25 +38,20 @@ function preprocess(content) return replace(content, r"^# # [^\n]*"m => sub; count=1) end -try - # Convert to markdown and notebook - Literate.markdown( - SCRIPTJL, - OUTDIR; - name=basename(dirname(SCRIPTJL)), - documenter=false, - execute=true, - preprocess=preprocess, - ) - Literate.notebook( - SCRIPTJL, - OUTDIR; - name=basename(dirname(SCRIPTJL)), - documenter=false, - execute=true, - preprocess=preprocess, - ) -catch e - # add script path to error message - throw(LoadError(SCRIPTJL, 0, e)) -end +# Convert to markdown and notebook +Literate.markdown( + SCRIPTJL, + OUTDIR; + name=basename(dirname(SCRIPTJL)), + documenter=false, + execute=true, + preprocess=preprocess, +) +Literate.notebook( + SCRIPTJL, + OUTDIR; + name=basename(dirname(SCRIPTJL)), + documenter=false, + execute=true, + preprocess=preprocess, +) From eff7c11a7fbb428097c8960ad290162ff36f6fa1 Mon Sep 17 00:00:00 2001 From: ST John Date: Tue, 29 Jun 2021 17:12:24 +0300 Subject: [PATCH 56/62] give responsibility for adding Literate dependency back to examples --- docs/literate.jl | 2 +- examples/README.md | 4 +++- 2 files changed, 4 insertions(+), 2 deletions(-) diff --git a/docs/literate.jl b/docs/literate.jl index cde18ed41..aec037869 100644 --- a/docs/literate.jl +++ b/docs/literate.jl @@ -8,7 +8,7 @@ const OUTDIR = ARGS[2] # Activate environment using Pkg: Pkg Pkg.activate(dirname(SCRIPTJL)) -Pkg.add("Literate"; preserve=Pkg.PRESERVE_ALL) +# Note that each example's Project.toml must include Literate as a dependency Pkg.instantiate() using Literate: Literate diff --git a/examples/README.md b/examples/README.md index 04f97c7c7..4c70185ed 100644 --- a/examples/README.md +++ b/examples/README.md @@ -34,7 +34,8 @@ Create a new subdirectory in here, and put your code in a file called `script.jl Every example uses a separate project environment. Therefore you should also create a new project environment in the directory of the example that contains all packages required by your script. -Note that the dependencies of your example must include the `Literate` package. +Note that the dependencies of your example *must* include the `Literate` package. + From a Julia REPL started in your example script's directory, you can run ```julia julia> ] activate . @@ -43,4 +44,5 @@ julia> ] add KernelFunctions julia> # add any other example-specific dependencies ``` to generate the project files. + Make sure to commit both the `Project.toml` and the `Manifest.toml` file when you want to contribute your example in a pull request. From a44d48f35205c3f5501fe9ffff146b1814aac483 Mon Sep 17 00:00:00 2001 From: ST John Date: Tue, 29 Jun 2021 17:20:12 +0300 Subject: [PATCH 57/62] preprocess header in italics --- docs/literate.jl | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) diff --git a/docs/literate.jl b/docs/literate.jl index aec037869..11511688b 100644 --- a/docs/literate.jl +++ b/docs/literate.jl @@ -24,14 +24,13 @@ function preprocess(content) # #md # [![](https://img.shields.io/badge/show-nbviewer-579ACA.svg)](@__NBVIEWER_ROOT_URL__/examples/@__NAME__.ipynb) #md # -# You are seeing the +# *You are seeing the #md # HTML output generated by [Documenter.jl](https://github.com/JuliaDocs/Documenter.jl) and #nb # notebook output generated by # [Literate.jl](https://github.com/fredrikekre/Literate.jl) from the # [Julia source file](@__REPO_ROOT_URL__/examples/@__NAME__/script.jl). -# The corresponding -#md # notebook can be viewed in [nbviewer](@__NBVIEWER_ROOT_URL__/examples/@__NAME__.ipynb). -#nb # HTML output can be viewed [here](https://juliagaussianprocesses.github.io/KernelFunctions.jl/dev/examples/@__NAME__/). +#md # The corresponding notebook can be viewed in [nbviewer](@__NBVIEWER_ROOT_URL__/examples/@__NAME__.ipynb).* +#nb # The rendered HTML can be viewed [in the docs](https://juliagaussianprocesses.github.io/KernelFunctions.jl/dev/examples/@__NAME__/).* # """, ) From fa0033becbd5d596024da7069455f5ddc33c74cd Mon Sep 17 00:00:00 2001 From: st-- Date: Wed, 30 Jun 2021 16:13:32 +0300 Subject: [PATCH 58/62] Apply suggestions from code review Co-authored-by: David Widmann --- docs/README.md | 7 ++++++- examples/README.md | 3 ++- 2 files changed, 8 insertions(+), 2 deletions(-) diff --git a/docs/README.md b/docs/README.md index eb759518b..32e47f700 100644 --- a/docs/README.md +++ b/docs/README.md @@ -47,7 +47,12 @@ again to rebuild the documentation. ## To add additional docs dependencies -```bash +To add additional dependencies, run (after activating the documentation environment) +```julia +julia> ] add NewDependency +``` +or, as a shell one-liner: +```shell julia --project=. -e 'using Pkg; Pkg.add("NewDependency")' ``` and commit the changes to Project.toml and Manifest.toml. diff --git a/examples/README.md b/examples/README.md index 4c70185ed..2ad8ce6e4 100644 --- a/examples/README.md +++ b/examples/README.md @@ -16,7 +16,8 @@ Afterwards simply run ```julia julia> include("script.jl") ``` - +In particular when editing an example, it can be convenient to (re-)run only some parts of +an example. Many editors with Julia support such as VSCode, Juno, and Emacs support the evaluation of individual lines or code chunks. You can convert them to markdown and Jupyter notebook formats, respectively, by executing ```julia julia> using Literate From 1fd657de216f4a0b5354c12e884431043c10e346 Mon Sep 17 00:00:00 2001 From: st-- Date: Wed, 30 Jun 2021 16:17:44 +0300 Subject: [PATCH 59/62] Update examples/README.md --- examples/README.md | 9 ++++++--- 1 file changed, 6 insertions(+), 3 deletions(-) diff --git a/examples/README.md b/examples/README.md index 2ad8ce6e4..8d07902eb 100644 --- a/examples/README.md +++ b/examples/README.md @@ -17,17 +17,20 @@ Afterwards simply run julia> include("script.jl") ``` In particular when editing an example, it can be convenient to (re-)run only some parts of -an example. Many editors with Julia support such as VSCode, Juno, and Emacs support the evaluation of individual lines or code chunks. -You can convert them to markdown and Jupyter notebook formats, respectively, by executing +an example. +Many editors with Julia support such as VSCode, Juno, and Emacs support the evaluation of individual lines or code chunks. + +You can convert a notebook to markdown and Jupyter notebook formats, respectively, by executing ```julia julia> using Literate julia> Literate.markdown("script.jl", "output_directory") julia> Literate.notebook("script.jl", "output_directory") ``` -or run +(see the [Literate.jl docs](https://fredrikekre.github.io/Literate.jl/v2/) for additional options) or run ```shell julia docs/literate.jl examples/myexample/script.jl output_directory ``` +which also executes the code and generates embedded plots etc. in the same way as in building the KernelFunctions documentation. ## Add a new example From 735b4375988dd219320550324f6490f5323d8189 Mon Sep 17 00:00:00 2001 From: ST John Date: Wed, 30 Jun 2021 16:20:38 +0300 Subject: [PATCH 60/62] compat for Kronecker in docs --- docs/Project.toml | 1 + 1 file changed, 1 insertion(+) diff --git a/docs/Project.toml b/docs/Project.toml index c0b55a35f..016e0db56 100644 --- a/docs/Project.toml +++ b/docs/Project.toml @@ -8,4 +8,5 @@ PDMats = "90014a1f-27ba-587c-ab20-58faa44d9150" Documenter = "0.27" KernelFunctions = "0.10" PDMats = "0.11" +Kronecker = "0.4" julia = "1.3" From 03a68405182ecf17e4a5d532bbf67d10fc33feb6 Mon Sep 17 00:00:00 2001 From: ST John Date: Wed, 30 Jun 2021 16:25:55 +0300 Subject: [PATCH 61/62] add [compat] --- examples/deep-kernel-learning/Project.toml | 11 +++++++++++ examples/kernel-ridge-regression/Project.toml | 11 +++++++++++ examples/support-vector-machine/Project.toml | 8 ++++++++ 3 files changed, 30 insertions(+) diff --git a/examples/deep-kernel-learning/Project.toml b/examples/deep-kernel-learning/Project.toml index 7d7efcd20..60232ed67 100644 --- a/examples/deep-kernel-learning/Project.toml +++ b/examples/deep-kernel-learning/Project.toml @@ -7,3 +7,14 @@ Literate = "98b081ad-f1c9-55d3-8b20-4c87d4299306" MLDataUtils = "cc2ba9b6-d476-5e6d-8eaf-a92d5412d41d" Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80" Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f" + +[compat] +Distributions = "0.25" +Flux = "0.12" +KernelFunctions = "0.10" +LinearAlgebra = "3" +Literate = "2" +MLDataUtils = "0.5" +Plots = "1" +Zygote = "0.6" +julia = "1.3" diff --git a/examples/kernel-ridge-regression/Project.toml b/examples/kernel-ridge-regression/Project.toml index 7d7efcd20..60232ed67 100644 --- a/examples/kernel-ridge-regression/Project.toml +++ b/examples/kernel-ridge-regression/Project.toml @@ -7,3 +7,14 @@ Literate = "98b081ad-f1c9-55d3-8b20-4c87d4299306" MLDataUtils = "cc2ba9b6-d476-5e6d-8eaf-a92d5412d41d" Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80" Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f" + +[compat] +Distributions = "0.25" +Flux = "0.12" +KernelFunctions = "0.10" +LinearAlgebra = "3" +Literate = "2" +MLDataUtils = "0.5" +Plots = "1" +Zygote = "0.6" +julia = "1.3" diff --git a/examples/support-vector-machine/Project.toml b/examples/support-vector-machine/Project.toml index 16d77268d..6abdde1a9 100644 --- a/examples/support-vector-machine/Project.toml +++ b/examples/support-vector-machine/Project.toml @@ -4,3 +4,11 @@ KernelFunctions = "ec8451be-7e33-11e9-00cf-bbf324bd1392" LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e" Literate = "98b081ad-f1c9-55d3-8b20-4c87d4299306" Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80" + +[compat] +Distributions = "0.25" +KernelFunctions = "0.10" +LinearAlgebra = "3" +Literate = "2" +Plots = "1" +julia = "1.3" From 7aebf8395482b3a2dbf4bda5a46ab2254aa4e9a5 Mon Sep 17 00:00:00 2001 From: st-- Date: Wed, 30 Jun 2021 17:05:51 +0300 Subject: [PATCH 62/62] Apply suggestions from code review Co-authored-by: David Widmann --- examples/deep-kernel-learning/Project.toml | 1 - examples/kernel-ridge-regression/Project.toml | 1 - examples/support-vector-machine/Project.toml | 1 - 3 files changed, 3 deletions(-) diff --git a/examples/deep-kernel-learning/Project.toml b/examples/deep-kernel-learning/Project.toml index 60232ed67..f3b3a5b77 100644 --- a/examples/deep-kernel-learning/Project.toml +++ b/examples/deep-kernel-learning/Project.toml @@ -12,7 +12,6 @@ Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f" Distributions = "0.25" Flux = "0.12" KernelFunctions = "0.10" -LinearAlgebra = "3" Literate = "2" MLDataUtils = "0.5" Plots = "1" diff --git a/examples/kernel-ridge-regression/Project.toml b/examples/kernel-ridge-regression/Project.toml index 60232ed67..f3b3a5b77 100644 --- a/examples/kernel-ridge-regression/Project.toml +++ b/examples/kernel-ridge-regression/Project.toml @@ -12,7 +12,6 @@ Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f" Distributions = "0.25" Flux = "0.12" KernelFunctions = "0.10" -LinearAlgebra = "3" Literate = "2" MLDataUtils = "0.5" Plots = "1" diff --git a/examples/support-vector-machine/Project.toml b/examples/support-vector-machine/Project.toml index 6abdde1a9..13219d95c 100644 --- a/examples/support-vector-machine/Project.toml +++ b/examples/support-vector-machine/Project.toml @@ -8,7 +8,6 @@ Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80" [compat] Distributions = "0.25" KernelFunctions = "0.10" -LinearAlgebra = "3" Literate = "2" Plots = "1" julia = "1.3"