diff --git a/.github/workflows/CompatHelper.yml b/.github/workflows/CompatHelper.yml index b17575afa..c13c749eb 100644 --- a/.github/workflows/CompatHelper.yml +++ b/.github/workflows/CompatHelper.yml @@ -1,16 +1,35 @@ name: CompatHelper + on: schedule: - - cron: '00 00 * * *' + - cron: 0 0 * * * workflow_dispatch: + jobs: CompatHelper: runs-on: ubuntu-latest steps: - - name: Pkg.add("CompatHelper") - run: julia -e 'using Pkg; Pkg.add("CompatHelper")' - - name: CompatHelper.main() + - uses: actions/checkout@v2 + - name: "Install CompatHelper" + run: | + import Pkg + name = "CompatHelper" + uuid = "aa819f21-2bde-4658-8897-bab36330d9b7" + version = "2" + Pkg.add(; name, uuid, version) + shell: julia --color=yes {0} + - name: "Run CompatHelper" + run: | + import CompatHelper + subdirs = ["", "test", "docs"] + for f in readdir("examples"; join=true) + if isdir(f) + push!(subdirs, joinpath("examples", basename(f))) + end + end + @info "CompatHelper directories" subdirs + CompatHelper.main(; subdirs=subdirs) + shell: julia --color=yes {0} env: GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} COMPATHELPER_PRIV: ${{ secrets.DOCUMENTER_KEY }} - run: julia -e 'using CompatHelper; CompatHelper.main(; subdirs = ["", "docs", "test"])' diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index d9d9ad787..8eeb12b4b 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -6,7 +6,7 @@ on: pull_request: jobs: test: - name: Julia ${{ matrix.version }} - ${{ matrix.os }} - ${{ matrix.arch }} - ${{ github.event_name }} + name: Julia ${{ matrix.version }} - ${{ matrix.group }} runs-on: ${{ matrix.os }} continue-on-error: ${{ matrix.version == 'nightly' }} strategy: @@ -18,10 +18,14 @@ jobs: - 'nightly' os: - ubuntu-latest - - macOS-latest - - windows-latest arch: - x64 + group: + - 'Transform' + - 'BaseKernels' + - 'Kernels' + - 'MultiOutput' + - 'Others' steps: - uses: actions/checkout@v2 - uses: julia-actions/setup-julia@v1 @@ -40,10 +44,26 @@ jobs: ${{ runner.os }}- - uses: julia-actions/julia-buildpkg@v1 - uses: julia-actions/julia-runtest@v1 + with: + coverage: ${{ matrix.version == '1' && matrix.os == 'ubuntu-latest' }} + env: + GROUP: ${{ matrix.group }} - uses: julia-actions/julia-processcoverage@v1 - - name: Send coverage if: matrix.version == '1' && matrix.os == 'ubuntu-latest' + - name: Coveralls parallel + if: matrix.version == '1' && matrix.os == 'ubuntu-latest' + uses: coverallsapp/github-action@master + with: + github-token: ${{ secrets.GITHUB_TOKEN }} + path-to-lcov: ./lcov.info + flag-name: run-${{ matrix.group }} + parallel: true + finish: + needs: test + runs-on: ubuntu-latest + steps: + - name: Send coverage uses: coverallsapp/github-action@master with: - github-token: ${{ secrets.GITHUB_TOKEN }} - path-to-lcov: ./lcov.info + github-token: ${{ secrets.github_token }} + parallel-finished: true diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml index e47f93896..2b57c0c99 100644 --- a/.github/workflows/docs.yml +++ b/.github/workflows/docs.yml @@ -19,6 +19,8 @@ jobs: run: julia --project=docs/ -e 'using Pkg; Pkg.develop(PackageSpec(path=pwd())); Pkg.instantiate()' - name: Build and deploy env: + GKSwstype: nul # turn off GR's interactive plotting for notebooks GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} # For authentication with GitHub Actions token DOCUMENTER_KEY: ${{ secrets.DOCUMENTER_KEY }} # For authentication with SSH deploy key + JULIA_DEBUG: Documenter # Print `@debug` statements (https://github.com/JuliaDocs/Documenter.jl/issues/955) run: julia --project=docs/ docs/make.jl diff --git a/.gitignore b/.gitignore index 3bd1d529e..eefb4afce 100644 --- a/.gitignore +++ b/.gitignore @@ -1,6 +1,6 @@ *.json *.cov -Manifest.toml +/Manifest.toml +/test/Manifest.toml coverage/ -src/update_v0.8.0 .DS_store diff --git a/Project.toml b/Project.toml index 6d5a50658..3e3387030 100644 --- a/Project.toml +++ b/Project.toml @@ -1,6 +1,6 @@ name = "KernelFunctions" uuid = "ec8451be-7e33-11e9-00cf-bbf324bd1392" -version = "0.10.5" +version = "0.10.7" [deps] ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" 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/ diff --git a/docs/Manifest.toml b/docs/Manifest.toml new file mode 100644 index 000000000..bd968e75c --- /dev/null +++ b/docs/Manifest.toml @@ -0,0 +1,355 @@ +# This file is machine-generated - editing it directly is not advised + +[[AbstractFFTs]] +deps = ["LinearAlgebra"] +git-tree-sha1 = "485ee0867925449198280d4af84bdb46a2a404d0" +uuid = "621f4979-c628-5d54-868e-fcf4e3e8185c" +version = "1.0.1" + +[[ArgTools]] +uuid = "0dad84c5-d112-42e6-8d28-ef12dabb789f" + +[[Artifacts]] +uuid = "56f22d72-fd6d-98f1-02f0-08ddc0907c33" + +[[Base64]] +uuid = "2a0f44e3-6c83-55bd-87e4-b1978d98bd5f" + +[[ChainRulesCore]] +deps = ["Compat", "LinearAlgebra", "SparseArrays"] +git-tree-sha1 = "be770c08881f7bb928dfd86d1ba83798f76cf62a" +uuid = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" +version = "0.10.9" + +[[Compat]] +deps = ["Base64", "Dates", "DelimitedFiles", "Distributed", "InteractiveUtils", "LibGit2", "Libdl", "LinearAlgebra", "Markdown", "Mmap", "Pkg", "Printf", "REPL", "Random", "SHA", "Serialization", "SharedArrays", "Sockets", "SparseArrays", "Statistics", "Test", "UUIDs", "Unicode"] +git-tree-sha1 = "dc7dedc2c2aa9faf59a55c622760a25cbefbe941" +uuid = "34da2185-b29b-5c13-b0c7-acf172513d20" +version = "3.31.0" + +[[CompilerSupportLibraries_jll]] +deps = ["Artifacts", "Libdl"] +uuid = "e66e0078-7015-5450-92f7-15fbd957f2ae" + +[[CompositionsBase]] +git-tree-sha1 = "f3955eb38944e5dd0fabf8ca1e267d94941d34a5" +uuid = "a33af91c-f02d-484b-be07-31d278c5ca2b" +version = "0.1.0" + +[[DataAPI]] +git-tree-sha1 = "ee400abb2298bd13bfc3df1c412ed228061a2385" +uuid = "9a962f9c-6df0-11e9-0e5d-c546b8b5ee8a" +version = "1.7.0" + +[[DataStructures]] +deps = ["Compat", "InteractiveUtils", "OrderedCollections"] +git-tree-sha1 = "4437b64df1e0adccc3e5d1adbc3ac741095e4677" +uuid = "864edb3b-99cc-5e75-8d2d-829cb0a9cfe8" +version = "0.18.9" + +[[Dates]] +deps = ["Printf"] +uuid = "ade2ca70-3891-5945-98fb-dc099432e06a" + +[[DelimitedFiles]] +deps = ["Mmap"] +uuid = "8bb1440f-4735-579b-a4ab-409b98df4dab" + +[[Distances]] +deps = ["LinearAlgebra", "Statistics", "StatsAPI"] +git-tree-sha1 = "abe4ad222b26af3337262b8afb28fab8d215e9f8" +uuid = "b4f34e82-e78d-54a5-968a-f98e89d6e8f7" +version = "0.10.3" + +[[Distributed]] +deps = ["Random", "Serialization", "Sockets"] +uuid = "8ba89e20-285c-5b6f-9357-94700520ee1b" + +[[DocStringExtensions]] +deps = ["LibGit2"] +git-tree-sha1 = "a32185f5428d3986f47c2ab78b1f216d5e6cc96f" +uuid = "ffbed154-4ef7-542d-bbb7-c09d3a79fcae" +version = "0.8.5" + +[[Documenter]] +deps = ["Base64", "Dates", "DocStringExtensions", "IOCapture", "InteractiveUtils", "JSON", "LibGit2", "Logging", "Markdown", "REPL", "Test", "Unicode"] +git-tree-sha1 = "47f13b6305ab195edb73c86815962d84e31b0f48" +uuid = "e30172f5-a6a5-5a46-863b-614d45cd2de4" +version = "0.27.3" + +[[Downloads]] +deps = ["ArgTools", "LibCURL", "NetworkOptions"] +uuid = "f43a241f-c20a-4ad4-852c-f6b1247861c6" + +[[FillArrays]] +deps = ["LinearAlgebra", "Random", "SparseArrays"] +git-tree-sha1 = "a603e79b71bb3c1efdb58f0ee32286efe2d1a255" +uuid = "1a297f60-69ca-5386-bcde-b61e274b549b" +version = "0.11.8" + +[[Functors]] +deps = ["MacroTools"] +git-tree-sha1 = "a7bb2af991c43dcf5c3455d276dd83976799634f" +uuid = "d9f16b24-f501-4c13-a1f2-28368ffc5196" +version = "0.2.1" + +[[IOCapture]] +deps = ["Logging", "Random"] +git-tree-sha1 = "f7be53659ab06ddc986428d3a9dcc95f6fa6705a" +uuid = "b5f81e59-6552-4d32-b1f0-c071b021bf89" +version = "0.2.2" + +[[InteractiveUtils]] +deps = ["Markdown"] +uuid = "b77e0a4c-d291-57a0-90e8-8db25a27a240" + +[[JLLWrappers]] +deps = ["Preferences"] +git-tree-sha1 = "642a199af8b68253517b80bd3bfd17eb4e84df6e" +uuid = "692b3bcd-3c85-4b1f-b108-f13ce0eb3210" +version = "1.3.0" + +[[JSON]] +deps = ["Dates", "Mmap", "Parsers", "Unicode"] +git-tree-sha1 = "81690084b6198a2e1da36fcfda16eeca9f9f24e4" +uuid = "682c06a0-de6a-54ab-a142-c8b1cf79cde6" +version = "0.21.1" + +[[KernelFunctions]] +deps = ["ChainRulesCore", "Compat", "CompositionsBase", "Distances", "FillArrays", "Functors", "LinearAlgebra", "Random", "Requires", "SpecialFunctions", "StatsBase", "StatsFuns", "TensorCore", "Test", "ZygoteRules"] +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" + +[[LibCURL_jll]] +deps = ["Artifacts", "LibSSH2_jll", "Libdl", "MbedTLS_jll", "Zlib_jll", "nghttp2_jll"] +uuid = "deac9b47-8bc7-5906-a0fe-35ac56dc84c0" + +[[LibGit2]] +deps = ["Base64", "NetworkOptions", "Printf", "SHA"] +uuid = "76f85450-5226-5b5a-8eaa-529ad045b433" + +[[LibSSH2_jll]] +deps = ["Artifacts", "Libdl", "MbedTLS_jll"] +uuid = "29816b5a-b9ab-546f-933c-edad1886dfa8" + +[[Libdl]] +uuid = "8f399da3-3557-5675-b5ff-fb832c97cbdb" + +[[LinearAlgebra]] +deps = ["Libdl"] +uuid = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e" + +[[LogExpFunctions]] +deps = ["DocStringExtensions", "LinearAlgebra"] +git-tree-sha1 = "1ba664552f1ef15325e68dc4c05c3ef8c2d5d885" +uuid = "2ab3a3ac-af41-5b50-aa03-7779005ae688" +version = "0.2.4" + +[[Logging]] +uuid = "56ddb016-857b-54e1-b83d-db4d58db5568" + +[[MacroTools]] +deps = ["Markdown", "Random"] +git-tree-sha1 = "6a8a2a625ab0dea913aba95c11370589e0239ff0" +uuid = "1914dd2f-81c6-5fcd-8719-6d5c9610ff09" +version = "0.5.6" + +[[Markdown]] +deps = ["Base64"] +uuid = "d6f4376e-aef5-505a-96c1-9c027394607a" + +[[MbedTLS_jll]] +deps = ["Artifacts", "Libdl"] +uuid = "c8ffd9c3-330d-5841-b78e-0817d7145fa1" + +[[Missings]] +deps = ["DataAPI"] +git-tree-sha1 = "4ea90bd5d3985ae1f9a908bd4500ae88921c5ce7" +uuid = "e1d29d7a-bbdc-5cf2-9ac0-f12de2c33e28" +version = "1.0.0" + +[[Mmap]] +uuid = "a63ad114-7e13-5084-954f-fe012c677804" + +[[MozillaCACerts_jll]] +uuid = "14a3606d-f60d-562e-9121-12d972cd8159" + +[[NamedDims]] +deps = ["AbstractFFTs", "LinearAlgebra", "Pkg", "Requires", "Statistics"] +git-tree-sha1 = "572b7af3ee53328eec29392d3b133804925595a1" +uuid = "356022a1-0364-5f58-8944-0da4b18d706f" +version = "0.2.34" + +[[NetworkOptions]] +uuid = "ca575930-c2e3-43a9-ace4-1e988b2c1908" + +[[OpenSpecFun_jll]] +deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "Libdl", "Pkg"] +git-tree-sha1 = "13652491f6856acfd2db29360e1bbcd4565d04f1" +uuid = "efe28fd5-8261-553b-a9e1-b2916fc3738e" +version = "0.5.5+0" + +[[OrderedCollections]] +git-tree-sha1 = "85f8e6578bf1f9ee0d11e7bb1b1456435479d47c" +uuid = "bac558e1-5e72-5ebc-8fee-abe8a469f55d" +version = "1.4.1" + +[[PDMats]] +deps = ["LinearAlgebra", "SparseArrays", "SuiteSparse"] +git-tree-sha1 = "4dd403333bcf0909341cfe57ec115152f937d7d8" +uuid = "90014a1f-27ba-587c-ab20-58faa44d9150" +version = "0.11.1" + +[[Parsers]] +deps = ["Dates"] +git-tree-sha1 = "c8abc88faa3f7a3950832ac5d6e690881590d6dc" +uuid = "69de0a69-1ddd-5017-9359-2bf0b02dc9f0" +version = "1.1.0" + +[[Pkg]] +deps = ["Artifacts", "Dates", "Downloads", "LibGit2", "Libdl", "Logging", "Markdown", "Printf", "REPL", "Random", "SHA", "Serialization", "TOML", "Tar", "UUIDs", "p7zip_jll"] +uuid = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f" + +[[Preferences]] +deps = ["TOML"] +git-tree-sha1 = "00cfd92944ca9c760982747e9a1d0d5d86ab1e5a" +uuid = "21216c6a-2e73-6563-6e65-726566657250" +version = "1.2.2" + +[[Printf]] +deps = ["Unicode"] +uuid = "de0858da-6303-5e67-8744-51eddeeeb8d7" + +[[REPL]] +deps = ["InteractiveUtils", "Markdown", "Sockets", "Unicode"] +uuid = "3fa0cd96-eef1-5676-8a61-b3b8758bbffb" + +[[Random]] +deps = ["Serialization"] +uuid = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c" + +[[Requires]] +deps = ["UUIDs"] +git-tree-sha1 = "4036a3bd08ac7e968e27c203d45f5fff15020621" +uuid = "ae029012-a4dd-5104-9daa-d747884805df" +version = "1.1.3" + +[[Rmath]] +deps = ["Random", "Rmath_jll"] +git-tree-sha1 = "bf3188feca147ce108c76ad82c2792c57abe7b1f" +uuid = "79098fc4-a85e-5d69-aa6a-4863f24498fa" +version = "0.7.0" + +[[Rmath_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] +git-tree-sha1 = "68db32dff12bb6127bac73c209881191bf0efbb7" +uuid = "f50d1b31-88e8-58de-be2c-1cc44531875f" +version = "0.3.0+0" + +[[SHA]] +uuid = "ea8e919c-243c-51af-8825-aaa63cd721ce" + +[[Serialization]] +uuid = "9e88b42a-f829-5b0c-bbe9-9e923198166b" + +[[SharedArrays]] +deps = ["Distributed", "Mmap", "Random", "Serialization"] +uuid = "1a1011a3-84de-559e-8e89-a11a2f7dc383" + +[[Sockets]] +uuid = "6462fe0b-24de-5631-8697-dd941f90decc" + +[[SortingAlgorithms]] +deps = ["DataStructures"] +git-tree-sha1 = "2ec1962eba973f383239da22e75218565c390a96" +uuid = "a2af1166-a08f-5f64-846c-94a0d3cef48c" +version = "1.0.0" + +[[SparseArrays]] +deps = ["LinearAlgebra", "Random"] +uuid = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" + +[[SpecialFunctions]] +deps = ["ChainRulesCore", "LogExpFunctions", "OpenSpecFun_jll"] +git-tree-sha1 = "a50550fa3164a8c46747e62063b4d774ac1bcf49" +uuid = "276daf66-3868-5448-9aa4-cd146d93841b" +version = "1.5.1" + +[[Statistics]] +deps = ["LinearAlgebra", "SparseArrays"] +uuid = "10745b16-79ce-11e8-11f9-7d13ad32a3b2" + +[[StatsAPI]] +git-tree-sha1 = "1958272568dc176a1d881acb797beb909c785510" +uuid = "82ae8749-77ed-4fe6-ae5f-f523153014b0" +version = "1.0.0" + +[[StatsBase]] +deps = ["DataAPI", "DataStructures", "LinearAlgebra", "Missings", "Printf", "Random", "SortingAlgorithms", "SparseArrays", "Statistics", "StatsAPI"] +git-tree-sha1 = "2f6792d523d7448bbe2fec99eca9218f06cc746d" +uuid = "2913bbd2-ae8a-5f71-8c99-4fb6c76f3a91" +version = "0.33.8" + +[[StatsFuns]] +deps = ["LogExpFunctions", "Rmath", "SpecialFunctions"] +git-tree-sha1 = "30cd8c360c54081f806b1ee14d2eecbef3c04c49" +uuid = "4c63d2b9-4356-54db-8cca-17b64c39e42c" +version = "0.9.8" + +[[SuiteSparse]] +deps = ["Libdl", "LinearAlgebra", "Serialization", "SparseArrays"] +uuid = "4607b0f0-06f3-5cda-b6b1-a6196a1729e9" + +[[TOML]] +deps = ["Dates"] +uuid = "fa267f1f-6049-4f14-aa54-33bafae1ed76" + +[[Tar]] +deps = ["ArgTools", "SHA"] +uuid = "a4e569a6-e804-4fa4-b0f3-eef7a1d5b13e" + +[[TensorCore]] +deps = ["LinearAlgebra"] +git-tree-sha1 = "1feb45f88d133a655e001435632f019a9a1bcdb6" +uuid = "62fd8b95-f654-4bbd-a8a5-9c27f68ccd50" +version = "0.1.1" + +[[Test]] +deps = ["InteractiveUtils", "Logging", "Random", "Serialization"] +uuid = "8dfed614-e22c-5e08-85e1-65c5234f0b40" + +[[UUIDs]] +deps = ["Random", "SHA"] +uuid = "cf7118a7-6976-5b1a-9a39-7adc72f591a4" + +[[Unicode]] +uuid = "4ec0a83e-493e-50e2-b9ac-8f72acf5a8f5" + +[[Zlib_jll]] +deps = ["Libdl"] +uuid = "83775a58-1f1d-513f-b197-d71354ab007a" + +[[ZygoteRules]] +deps = ["MacroTools"] +git-tree-sha1 = "9e7a1e8ca60b742e508a315c17eef5211e7fbfd7" +uuid = "700de1a5-db45-46bc-99cf-38207098b444" +version = "0.2.1" + +[[nghttp2_jll]] +deps = ["Artifacts", "Libdl"] +uuid = "8e850ede-7688-5339-a07c-302acd2aaf8d" + +[[p7zip_jll]] +deps = ["Artifacts", "Libdl"] +uuid = "3f19e933-33d8-53b3-aaab-bd5110c3b7a0" diff --git a/docs/Project.toml b/docs/Project.toml index 3f90d2da6..4f10fcafa 100644 --- a/docs/Project.toml +++ b/docs/Project.toml @@ -1,7 +1,12 @@ [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" [compat] Documenter = "0.27" +KernelFunctions = "0.10" +Kronecker = "0.4" PDMats = "0.11" +julia = "1.3" diff --git a/docs/README.md b/docs/README.md new file mode 100644 index 000000000..32e47f700 --- /dev/null +++ b/docs/README.md @@ -0,0 +1,63 @@ +# How to build the docs locally + +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. + +If you want to build the documentation, navigate to this (docs/) directory and open a Julia REPL. + +## Instantiation + +First activate the documentation environment: +```julia +julia> ] activate . +``` +Alternatively, you can start Julia with `julia --project=.`. + +Then install all packages: +```julia +julia> ] instantiate +``` +By default, this will use the development version of KernelFunctions in the parent directory. + +## Build + +To build the documentation, run (after activating the documentation environment) +```julia +julia> include("make.jl") +``` +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 make any changes, you can run +```julia +julia> include("make.jl") +``` +again to rebuild the documentation. + +# How to contribute to the docs + +## To add additional docs dependencies + +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. + + +## To add examples + +See [../examples](../examples/README.md) diff --git a/docs/literate.jl b/docs/literate.jl new file mode 100644 index 000000000..452d1cdf2 --- /dev/null +++ b/docs/literate.jl @@ -0,0 +1,53 @@ +# Retrieve name of example and output directory +if length(ARGS) != 2 + error("please specify the name of the example and the output directory") +end +const EXAMPLE = ARGS[1] +const OUTDIR = ARGS[2] + +# Activate environment +# Note that each example's Project.toml must include Literate as a dependency +using Pkg: Pkg +const EXAMPLEPATH = joinpath(@__DIR__, "..", "examples", EXAMPLE) +Pkg.activate(EXAMPLEPATH) +Pkg.instantiate() +using Literate: Literate + +function preprocess(content) + # Add link to nbviewer below the first heading of level 1 + sub = SubstitutionString( + """ +#md # ```@meta +#md # EditURL = "@__REPO_ROOT_URL__/examples/@__NAME__/script.jl" +#md # ``` +#md # +\\0 +# +#md # [![](https://img.shields.io/badge/show-nbviewer-579ACA.svg)](@__NBVIEWER_ROOT_URL__/examples/@__NAME__.ipynb) +#md # +# *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). +#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__/).* +# + """, + ) + content = replace(content, r"^# # [^\n]*"m => sub; count=1) + + # remove VSCode `##` block delimiter lines + content = replace(content, r"^##$."ms => "") + + return content +end + +# Convert to markdown and notebook +const SCRIPTJL = joinpath(EXAMPLEPATH, "script.jl") +Literate.markdown( + SCRIPTJL, OUTDIR; name=EXAMPLE, documenter=false, execute=true, preprocess=preprocess +) +Literate.notebook( + SCRIPTJL, OUTDIR; name=EXAMPLE, documenter=false, execute=true, preprocess=preprocess +) diff --git a/docs/make.jl b/docs/make.jl index c2c14f8f9..8aca5486d 100644 --- a/docs/make.jl +++ b/docs/make.jl @@ -1,26 +1,59 @@ -using Documenter +### Process examples +# Always rerun examples +const EXAMPLES_OUT = joinpath(@__DIR__, "src", "examples") +ispath(EXAMPLES_OUT) && rm(EXAMPLES_OUT; recursive=true) +mkpath(EXAMPLES_OUT) -# Print `@debug` statements (https://github.com/JuliaDocs/Documenter.jl/issues/955) -if haskey(ENV, "GITHUB_ACTIONS") - ENV["JULIA_DEBUG"] = "Documenter" +# Install and precompile all packages +# Workaround for https://github.com/JuliaLang/Pkg.jl/issues/2219 +examples = filter!(isdir, readdir(joinpath(@__DIR__, "..", "examples"); join=true)) +let script = "using Pkg; Pkg.activate(ARGS[1]); Pkg.instantiate()" + for example in examples + if !success(`$(Base.julia_cmd()) -e $script $example`) + error( + "project environment of example ", + basename(example), + " could not be instantiated", + ) + end + end +end +# Run examples asynchronously +processes = let literatejl = joinpath(@__DIR__, "literate.jl") + map(examples) do example + return run( + pipeline( + `$(Base.julia_cmd()) $literatejl $(basename(example)) $EXAMPLES_OUT`; + stdin=devnull, + stdout=devnull, + stderr=stderr, + ); + wait=false, + )::Base.Process + end end +# Check that all examples were run successfully +isempty(processes) || success(processes) || error("some examples were not run successfully") + +### Build documentation +using Documenter + using KernelFunctions +using PDMats, Kronecker # we have to load all optional packages to generate the full API documentation +# Doctest setup DocMeta.setdocmeta!( KernelFunctions, :DocTestSetup, quote using KernelFunctions - using LinearAlgebra - using Random - using PDMats: PDMats - end; + end; # we have to load all packages used (implicitly) within jldoctest blocks in the API docstrings recursive=true, ) makedocs(; - sitename="KernelFunctions", + sitename="KernelFunctions.jl", format=Documenter.HTML(), modules=[KernelFunctions], pages=[ @@ -29,11 +62,13 @@ makedocs(; "kernels.md", "transform.md", "metrics.md", - "theory.md", "create_kernel.md", "API" => "api.md", - "Examples" => "example.md", "Design" => "design.md", + "Examples" => + map(filter!(filename -> endswith(filename, ".md"), readdir(EXAMPLES_OUT))) do x + return joinpath("examples", x) + end, ], strict=true, checkdocs=:exports, 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/docs/src/example.md b/docs/src/example.md deleted file mode 100644 index 14601f1e8..000000000 --- a/docs/src/example.md +++ /dev/null @@ -1,21 +0,0 @@ -# Examples (WIP) - -Here are a few examples of known complex kernels and how to do them. Or how to use kernels in a certain context - -## Kernel Ridge Regression - -Make a simple example of kernel ridge regression - -## Gaussian Process Regression - -Make a simple example of gaussian process regression - -## Deep Kernel Learning - -Put a Flux neural net in front of the kernel -cf. Wilson paper - -## Kernel Selection - -Create a large collection of kernels and optimize the weights -cf AISTATS 2018 paper diff --git a/docs/src/index.md b/docs/src/index.md index 719e6bb79..697fb1577 100644 --- a/docs/src/index.md +++ b/docs/src/index.md @@ -1,17 +1,12 @@ # KernelFunctions.jl -Model-agnostic kernel functions compatible with automatic differentiation - -**KernelFunctions.jl** is a general purpose kernel package. +**KernelFunctions.jl** is a general purpose [kernel](https://en.wikipedia.org/wiki/Positive-definite_kernel) package. It aims at providing a flexible framework for creating kernels and manipulating them. -The main goals of this package compared to its predecessors/concurrents in [MLKernels.jl](https://github.com/trthatcher/MLKernels.jl), [Stheno.jl](https://github.com/willtebbutt/Stheno.jl), [GaussianProcesses.jl](https://github.com/STOR-i/GaussianProcesses.jl) and [AugmentedGaussianProcesses.jl](https://github.com/theogf/AugmentedGaussianProcesses.jl) are: -- **Automatic Differentation** compatibility: all kernel functions should be differentiable via packages like [ForwardDiff.jl](https://github.com/JuliaDiff/ForwardDiff.jl) or [Zygote.jl](https://github.com/FluxML/Zygote.jl) +The main goals of this package are: - **Flexibility**: operations between kernels should be fluid and easy without breaking. - **Plug-and-play**: including the kernels before/after other steps should be straightforward. +- **Automatic Differentation** compatibility: all kernel functions which _ought_ to be differentiable using AD packages like [ForwardDiff.jl](https://github.com/JuliaDiff/ForwardDiff.jl) or [Zygote.jl](https://github.com/FluxML/Zygote.jl) _should_ be. -The methodology of how kernels are computed is quite simple and is done in three phases : -- A `Transform` object is applied sample-wise on every sample -- The pairwise matrix is computed using [Distances.jl](https://github.com/JuliaStats/Distances.jl) by using a `Metric` proper to each kernel -- The `Kernel` function is applied element-wise on the pairwise matrix +This package builds on top of lots of excellent existing work in packages such as [MLKernels.jl](https://github.com/trthatcher/MLKernels.jl), [Stheno.jl](https://github.com/willtebbutt/Stheno.jl), [GaussianProcesses.jl](https://github.com/STOR-i/GaussianProcesses.jl), and [AugmentedGaussianProcesses.jl](https://github.com/theogf/AugmentedGaussianProcesses.jl). -For a quick introduction on how to use it go to [User guide](@ref) +See the [User guide](@ref) for a brief introduction. diff --git a/docs/src/kernels.md b/docs/src/kernels.md index ffc92f501..ae0f0843a 100644 --- a/docs/src/kernels.md +++ b/docs/src/kernels.md @@ -134,4 +134,5 @@ MOKernel IndependentMOKernel LatentFactorMOKernel IntrinsicCoregionMOKernel +LinearMixingModelKernel ``` diff --git a/docs/src/theory.md b/docs/src/theory.md deleted file mode 100644 index 71717e87e..000000000 --- a/docs/src/theory.md +++ /dev/null @@ -1,3 +0,0 @@ -# Theory - -See [Wikipedia article](https://en.wikipedia.org/wiki/Positive-definite_kernel) diff --git a/docs/src/transform.md b/docs/src/transform.md index 9ed878a84..1237642c7 100644 --- a/docs/src/transform.md +++ b/docs/src/transform.md @@ -36,3 +36,9 @@ SelectTransform ChainTransform PeriodicTransform ``` + +## Convenience functions + +```@docs +with_lengthscale +``` diff --git a/docs/src/userguide.md b/docs/src/userguide.md index b3539dc64..e3db6ffc3 100644 --- a/docs/src/userguide.md +++ b/docs/src/userguide.md @@ -15,6 +15,11 @@ For example, a squared exponential kernel is created by k = SqExponentialKernel() ∘ ScaleTransform(2.0) k = compose(SqExponentialKernel(), ScaleTransform(2.0)) ``` + Alternatively, you can use the convenience function [`with_lengthscale`](@ref): + ```julia + k = with_lengthscale(SqExponentialKernel(), 0.5) + ``` + [`with_lengthscale`](@ref) also works with vector-valued lengthscales for ARD. Check the [Input Transforms](@ref input_transforms) page for more details. !!! tip "How do I set the kernel variance?" @@ -73,18 +78,37 @@ kernelmatrix(k, ColVecs(X)) # returns a 5×5 matrix -- each column of X treated ``` This is the mechanism used throughout KernelFunctions.jl to handle multi-dimensional inputs. -You can also utilise the `obsdim` keyword argument if you prefer: +You can utilise the `obsdim` keyword argument if you prefer: ```julia kernelmatrix(k, X; obsdim=1) # same as RowVecs(X) kernelmatrix(k, X; obsdim=2) # same as ColVecs(X) ``` This is similar to the convention used in [Distances.jl](https://github.com/JuliaStats/Distances.jl). -See [Input Types](@ref) for a more thorough discussion of these two approaches. +### So what type should I use to represent a collection of inputs? +The central assumption made by KernelFunctions.jl is that all collections of `N` inputs are represented by `AbstractVector`s of length `N`. +Abstraction is then used to ensure that efficiency is retained, `ColVecs` and `RowVecs` +being the most obvious examples of this. + +Concretely: +1. For `Real`-valued inputs (scalars), a `Vector{<:Real}` is fine. +1. For vector-valued inputs, consider a `ColVecs` or `RowVecs`. +1. For a new input type, simply represent collections of inputs of this type as an `AbstractVector`. + +See [Input Types](@ref) and [Design](@ref) for a more thorough discussion of the +considerations made when this design was adopted. + +The `obsdim` kwarg mentioned above is a special case for vector-valued inputs stored in a +matrix. +It is implemented as a lightweight wrapper that constructs either a `RowVecs` or `ColVecs` +from your inputs, and passes this on. + +### Output Types -We also support specific kernel matrix outputs: +In addition to plain `Matrix`-like output, KernelFunctions.jl supports specific output +types: - For a positive-definite matrix object of type `PDMat` from [`PDMats.jl`](https://github.com/JuliaStats/PDMats.jl), you can call the following: ```julia using PDMats diff --git a/examples/README.md b/examples/README.md new file mode 100644 index 000000000..de6ea3569 --- /dev/null +++ b/examples/README.md @@ -0,0 +1,52 @@ +# Example notebooks + +The examples in this directory are stored in [Literate.jl](https://github.com/fredrikekre/Literate.jl) format. + +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") +``` +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 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") +``` +(see the [Literate.jl docs](https://fredrikekre.github.io/Literate.jl/v2/) for additional options) or run +```shell +julia docs/literate.jl myexample 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 + +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 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. diff --git a/examples/deep-kernel-learning/Manifest.toml b/examples/deep-kernel-learning/Manifest.toml new file mode 100644 index 000000000..c3a4f40f2 --- /dev/null +++ b/examples/deep-kernel-learning/Manifest.toml @@ -0,0 +1,1156 @@ +# This file is machine-generated - editing it directly is not advised + +[[AbstractFFTs]] +deps = ["LinearAlgebra"] +git-tree-sha1 = 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"1.5.2+4" + +[[Xorg_libXrender_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libX11_jll"] +git-tree-sha1 = "19560f30fd49f4d4efbe7002a1037f8c43d43b96" +uuid = "ea2f1a96-1ddc-540d-b46f-429655e07cfa" +version = "0.9.10+4" + +[[Xorg_libpthread_stubs_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] +git-tree-sha1 = "6783737e45d3c59a4a4c4091f5f88cdcf0908cbb" +uuid = "14d82f49-176c-5ed1-bb49-ad3f5cbd8c74" +version = "0.1.0+3" + +[[Xorg_libxcb_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "XSLT_jll", "Xorg_libXau_jll", "Xorg_libXdmcp_jll", "Xorg_libpthread_stubs_jll"] +git-tree-sha1 = "daf17f441228e7a3833846cd048892861cff16d6" +uuid = "c7cfdc94-dc32-55de-ac96-5a1b8d977c5b" +version = "1.13.0+3" + +[[Xorg_libxkbfile_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libX11_jll"] +git-tree-sha1 = "926af861744212db0eb001d9e40b5d16292080b2" +uuid = "cc61e674-0454-545c-8b26-ed2c68acab7a" +version = "1.1.0+4" + +[[Xorg_xcb_util_image_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_xcb_util_jll"] +git-tree-sha1 = "0fab0a40349ba1cba2c1da699243396ff8e94b97" +uuid = "12413925-8142-5f55-bb0e-6d7ca50bb09b" +version = "0.4.0+1" + +[[Xorg_xcb_util_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libxcb_jll"] +git-tree-sha1 = "e7fd7b2881fa2eaa72717420894d3938177862d1" +uuid = "2def613f-5ad1-5310-b15b-b15d46f528f5" +version = "0.4.0+1" + +[[Xorg_xcb_util_keysyms_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_xcb_util_jll"] +git-tree-sha1 = "d1151e2c45a544f32441a567d1690e701ec89b00" +uuid = "975044d2-76e6-5fbe-bf08-97ce7c6574c7" +version = "0.4.0+1" + +[[Xorg_xcb_util_renderutil_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_xcb_util_jll"] +git-tree-sha1 = "dfd7a8f38d4613b6a575253b3174dd991ca6183e" +uuid = "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" + +[[ZipFile]] +deps = ["Libdl", "Printf", "Zlib_jll"] +git-tree-sha1 = "c3a5637e27e914a7a445b8d0ad063d701931e9f7" +uuid = "a5390f91-8eb1-5f08-bee0-b1d1ffed6cea" +version = "0.9.3" + +[[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" + +[[Zygote]] +deps = ["AbstractFFTs", "ChainRules", "ChainRulesCore", "DiffRules", "Distributed", "FillArrays", "ForwardDiff", "IRTools", "InteractiveUtils", "LinearAlgebra", "MacroTools", "NaNMath", "Random", "Requires", "SpecialFunctions", "Statistics", "ZygoteRules"] +git-tree-sha1 = "b1d95edd4e693066c38c13a10aab0a8f6a6e2f65" +uuid = "e88e6eb3-aa80-5325-afca-941959d7151f" +version = "0.6.12" + +[[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" diff --git a/examples/deep-kernel-learning/Project.toml b/examples/deep-kernel-learning/Project.toml new file mode 100644 index 000000000..f3b3a5b77 --- /dev/null +++ b/examples/deep-kernel-learning/Project.toml @@ -0,0 +1,19 @@ +[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" +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" +Literate = "2" +MLDataUtils = "0.5" +Plots = "1" +Zygote = "0.6" +julia = "1.3" diff --git a/examples/deepkernellearning.jl b/examples/deep-kernel-learning/script.jl similarity index 54% rename from examples/deepkernellearning.jl rename to examples/deep-kernel-learning/script.jl index 94346eea2..14c1560c3 100644 --- a/examples/deepkernellearning.jl +++ b/examples/deep-kernel-learning/script.jl @@ -1,3 +1,10 @@ +# # Deep Kernel Learning +# +# !!! warning +# This example is under construction + +# Setup + using KernelFunctions using MLDataUtils using Zygote @@ -10,31 +17,52 @@ 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)) +k = SqExponentialKernel() ∘ FunctionTransform(neuralnet) + +# Generate date + xmin = -3; 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 = RowVecs(reshape(x, :, 1)) +X_test = RowVecs(reshape(x_test, :, 1)) λ = [0.1] -function f(x, k, λ) - return kernelmatrix(k, X, x; obsdim=1) * - inv(kernelmatrix(k, X; obsdim=1) + exp(λ[1]) * I) * - y -end +#md nothing #hide + +# + +f(x, k, λ) = kernelmatrix(k, x, X) / (kernelmatrix(k, X) + exp(λ[1]) * I) * y 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, size=(300, 1500)) diff --git a/examples/gaussian-process-priors/Manifest.toml b/examples/gaussian-process-priors/Manifest.toml new file mode 100644 index 000000000..1b421a0ce --- /dev/null +++ b/examples/gaussian-process-priors/Manifest.toml @@ -0,0 +1,921 @@ +# This file is machine-generated - editing it directly is not advised + +[[Adapt]] +deps = ["LinearAlgebra"] +git-tree-sha1 = "84918055d15b3114ede17ac6a7182f68870c16f7" +uuid = "79e6a3ab-5dfb-504d-930d-738a2a938a0e" +version = "3.3.1" + +[[ArgTools]] +uuid = "0dad84c5-d112-42e6-8d28-ef12dabb789f" + +[[Artifacts]] +uuid = "56f22d72-fd6d-98f1-02f0-08ddc0907c33" + +[[Base64]] +uuid = "2a0f44e3-6c83-55bd-87e4-b1978d98bd5f" + +[[Bzip2_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] +git-tree-sha1 = "c3598e525718abcc440f69cc6d5f60dda0a1b61e" +uuid = "6e34b625-4abd-537c-b88f-471c36dfa7a0" +version = "1.0.6+5" + +[[Cairo_jll]] +deps = ["Artifacts", "Bzip2_jll", "Fontconfig_jll", "FreeType2_jll", "Glib_jll", "JLLWrappers", "LZO_jll", "Libdl", "Pixman_jll", "Pkg", "Xorg_libXext_jll", "Xorg_libXrender_jll", "Zlib_jll", "libpng_jll"] +git-tree-sha1 = "e2f47f6d8337369411569fd45ae5753ca10394c6" +uuid = "83423d85-b0ee-5818-9007-b63ccbeb887a" +version = "1.16.0+6" + +[[ChainRulesCore]] +deps = ["Compat", "LinearAlgebra", "SparseArrays"] +git-tree-sha1 = "be770c08881f7bb928dfd86d1ba83798f76cf62a" +uuid = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" +version = "0.10.9" + +[[ColorSchemes]] +deps = ["ColorTypes", "Colors", "FixedPointNumbers", "Random", "StaticArrays"] +git-tree-sha1 = "c8fd01e4b736013bc61b704871d20503b33ea402" +uuid = "35d6a980-a343-548e-a6ea-1d62b119f2f4" +version = "3.12.1" + +[[ColorTypes]] +deps = ["FixedPointNumbers", "Random"] +git-tree-sha1 = "024fe24d83e4a5bf5fc80501a314ce0d1aa35597" +uuid = "3da002f7-5984-5a60-b8a6-cbb66c0b333f" +version = "0.11.0" + +[[Colors]] +deps = ["ColorTypes", "FixedPointNumbers", "Reexport"] +git-tree-sha1 = "417b0ed7b8b838aa6ca0a87aadf1bb9eb111ce40" +uuid = "5ae59095-9a9b-59fe-a467-6f913c188581" +version = "0.12.8" + +[[Compat]] +deps = ["Base64", "Dates", "DelimitedFiles", "Distributed", "InteractiveUtils", "LibGit2", "Libdl", "LinearAlgebra", "Markdown", "Mmap", "Pkg", "Printf", "REPL", "Random", "SHA", "Serialization", "SharedArrays", "Sockets", "SparseArrays", "Statistics", "Test", "UUIDs", "Unicode"] +git-tree-sha1 = "dc7dedc2c2aa9faf59a55c622760a25cbefbe941" +uuid = "34da2185-b29b-5c13-b0c7-acf172513d20" +version = "3.31.0" + +[[CompilerSupportLibraries_jll]] +deps = ["Artifacts", "Libdl"] +uuid = "e66e0078-7015-5450-92f7-15fbd957f2ae" + +[[CompositionsBase]] +git-tree-sha1 = "f3955eb38944e5dd0fabf8ca1e267d94941d34a5" +uuid = "a33af91c-f02d-484b-be07-31d278c5ca2b" +version = "0.1.0" + +[[Contour]] +deps = ["StaticArrays"] +git-tree-sha1 = "9f02045d934dc030edad45944ea80dbd1f0ebea7" +uuid = "d38c429a-6771-53c6-b99e-75d170b6e991" +version = "0.5.7" + +[[DataAPI]] +git-tree-sha1 = "ee400abb2298bd13bfc3df1c412ed228061a2385" +uuid = "9a962f9c-6df0-11e9-0e5d-c546b8b5ee8a" +version = "1.7.0" + +[[DataStructures]] +deps = ["Compat", "InteractiveUtils", "OrderedCollections"] +git-tree-sha1 = "4437b64df1e0adccc3e5d1adbc3ac741095e4677" +uuid = "864edb3b-99cc-5e75-8d2d-829cb0a9cfe8" +version = "0.18.9" + +[[DataValueInterfaces]] +git-tree-sha1 = "bfc1187b79289637fa0ef6d4436ebdfe6905cbd6" +uuid = "e2d170a0-9d28-54be-80f0-106bbe20a464" +version = "1.0.0" + +[[Dates]] +deps = ["Printf"] +uuid = "ade2ca70-3891-5945-98fb-dc099432e06a" + +[[DelimitedFiles]] +deps = ["Mmap"] +uuid = "8bb1440f-4735-579b-a4ab-409b98df4dab" + +[[Distances]] 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b/examples/gaussian-process-priors/Project.toml @@ -0,0 +1,13 @@ +[deps] +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" +Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c" + +[compat] +Distributions = "0.25" +KernelFunctions = "0.10" +Literate = "2" +Plots = "1" diff --git a/examples/gaussian-process-priors/script.jl b/examples/gaussian-process-priors/script.jl new file mode 100644 index 000000000..b1ba3dcee --- /dev/null +++ b/examples/gaussian-process-priors/script.jl @@ -0,0 +1,128 @@ +# # Gaussian process prior samples +# +# The kernels defined in this package can also be used to specify the +# covariance of a Gaussian process prior. +# A Gaussian process (GP) is defined by its mean function $m(\cdot)$ and its covariance function or kernel $k(\cdot, \cdot')$: +# ```math +# f \sim \mathcal{GP}\big(m(\cdot), k(\cdot, \cdot')\big) +# ``` +# In this notebook we show how the choice of kernel affects the samples from a GP (with zero mean). + +## Load required packages +using KernelFunctions, LinearAlgebra +using Plots, Plots.PlotMeasures +default(; lw=1.0, legendfontsize=8.0) +using Random: seed! +seed!(42); # reproducibility + +## +# ## Evaluation at finite set of points +# +# The function values $\mathbf{f} = \{f(x_n)\}_{n=1}^N$ of the GP at a finite number $N$ of points $X = \{x_n\}_{n=1}^N$ follow a multivariate normal distribution $\mathbf{f} \sim \mathcal{MVN}(\mathbf{m}, \mathrm{K})$ with mean vector $\mathbf{m}$ and covariance matrix $\mathrm{K}$, where +# ```math +# \begin{aligned} +# \mathbf{m}_i &= m(x_i) \\ +# \mathrm{K}_{i,j} &= k(x_i, x_j) +# \end{aligned} +# ``` +# with $1 \le i, j \le N$. +# +# We can visualize the infinite-dimensional GP by evaluating it on a fine grid to approximate the dense real line: +num_inputs = 101 +xlim = (-5, 5) +X = range(xlim...; length=num_inputs); + +# Given a kernel `k`, we can compute the kernel matrix as `K = kernelmatrix(k, X)`. + +## +# ## Random samples +# +# To sample from the multivariate normal distribution $p(\mathbf{f}) = \mathcal{MVN}(0, \mathrm{K})$, we could make use of Distributions.jl and call `rand(MvNormal(K))`. +# Alternatively, we could use the [AbstractGPs.jl](https://github.com/JuliaGaussianProcesses/AbstractGPs.jl) package and construct a `GP` object which we evaluate at the points of interest and from which we can then sample: `rand(GP(k)(X))`. + +# Here, we will explicitly construct samples using the Cholesky factorization $\mathrm{L} = \operatorname{cholesky}(\mathrm{K})$, +# with $\mathbf{f} = \mathrm{L} \mathbf{v}$, where $\mathbf{v} \sim \mathcal{N}(0, \mathbf{I})$ is a vector of standard-normal random variables. + +# We will use the same randomness $\mathbf{v}$ to generate comparable samples across different kernels. +num_samples = 7 +v = randn(num_inputs, num_samples); + +# Mathematically, a kernel matrix is by definition positive semi-definite, but due to finite-precision inaccuracies, the computed kernel matrix might not be exactly positive definite. To avoid Cholesky errors, we add a small "nugget" term on the diagonal: +function mvn_sample(K) + L = cholesky(K + 1e-6 * I) + f = L.L * v + return f +end; + +## +# ## Visualization +# We now define a function that visualizes a kernel for us. + +function visualize(k::Kernel) + K = kernelmatrix(k, X) + f = mvn_sample(K) + + p_kernel_2d = heatmap( + X, + X, + K; + yflip=true, + colorbar=false, + ylabel=string(nameof(typeof(k))), + ylim=xlim, + yticks=([xlim[1], 0, xlim[end]], ["\u22125", raw"$x'$", "5"]), + vlim=(0, 1), + title=raw"$k(x, x')$", + aspect_ratio=:equal, + left_margin=5mm, + ) + + p_kernel_cut = plot( + X, + k.(X, 0.0); + title=string(raw"$k(x, x_\mathrm{ref})$"), + label=raw"$x_\mathrm{ref}=0.0$", + legend=:topleft, + foreground_color_legend=nothing, + ) + plot!(X, k.(X, 1.5); label=raw"$x_\mathrm{ref}=1.5$") + + p_samples = plot(X, f; c="blue", title=raw"$f(x)$", ylim=(-3, 3), label=nothing) + + return plot( + p_kernel_2d, + p_kernel_cut, + p_samples; + layout=(1, 3), + xlabel=raw"$x$", + xlim=xlim, + xticks=collect(xlim), + ) +end; + +## +# We can now visualize a kernel and show samples from +# a Gaussian process with a given kernel: + +plot(visualize(SqExponentialKernel()); size=(800, 210), bottommargin=5mm, topmargin=5mm) + +## +# ## Kernel comparison +# This also allows us to compare different kernels: + +kernels = [ + Matern12Kernel(), + Matern32Kernel(), + Matern52Kernel(), + SqExponentialKernel(), + WhiteKernel(), + ConstantKernel(), + LinearKernel(), + compose(PeriodicKernel(), ScaleTransform(0.2)), + NeuralNetworkKernel(), +] +plot( + [visualize(k) for k in kernels]...; + layout=(length(kernels), 1), + size=(800, 220 * length(kernels) + 100), +) diff --git a/examples/kernel-ridge-regression/Manifest.toml b/examples/kernel-ridge-regression/Manifest.toml new file mode 100644 index 000000000..8b8a2d648 --- /dev/null +++ b/examples/kernel-ridge-regression/Manifest.toml @@ -0,0 +1,921 @@ +# This file is machine-generated - editing it directly is 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"d8fb68d0-12a3-5cfd-a85a-d49703b185fd" +version = "0.9.1+5" diff --git a/examples/kernel-ridge-regression/Project.toml b/examples/kernel-ridge-regression/Project.toml new file mode 100644 index 000000000..13219d95c --- /dev/null +++ b/examples/kernel-ridge-regression/Project.toml @@ -0,0 +1,13 @@ +[deps] +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" + +[compat] +Distributions = "0.25" +KernelFunctions = "0.10" +Literate = "2" +Plots = "1" +julia = "1.3" diff --git a/examples/kernel-ridge-regression/script.jl b/examples/kernel-ridge-regression/script.jl new file mode 100644 index 000000000..62afc5944 --- /dev/null +++ b/examples/kernel-ridge-regression/script.jl @@ -0,0 +1,162 @@ +# # Kernel Ridge Regression +# +# Building on linear regression, we can fit non-linear data sets by introducing a feature space. In a higher-dimensional feature space, we can overfit the data; ridge regression introduces regularization to avoid this. In this notebook we show how we can use KernelFunctions.jl for *kernel* ridge regression. + +## Loading and setup of required packages +using KernelFunctions +using LinearAlgebra +using Distributions + +## Plotting +using Plots; +default(; lw=2.0, legendfontsize=11.0, ylims=(-150, 500)); + +using Random: seed! +seed!(42); + +## +# ## Toy data +# Here we use a one-dimensional toy problem. We generate data using the fourth-order polynomial $f(x) = (x+4)(x+1)(x-1)(x-3)$: + +f_truth(x) = (x + 4) * (x + 1) * (x - 1) * (x - 3) + +x_train = -5:0.5:5 +x_test = -7:0.1:7 + +noise = rand(Uniform(-20, 20), length(x_train)) +y_train = f_truth.(x_train) + noise +y_test = f_truth.(x_test) + +plot(x_test, y_test; label=raw"$f(x)$") +scatter!(x_train, y_train; seriescolor=1, label="observations") + +## +# ## Linear regression +# For training inputs $\mathrm{X}=(\mathbf{x}_n)_{n=1}^N$ and observations $\mathbf{y}=(y_n)_{n=1}^N$, the linear regression weights $\mathbf{w}$ using the least-squares estimator are given by +# ```math +# \mathbf{w} = (\mathrm{X}^\top \mathrm{X})^{-1} \mathrm{X}^\top \mathbf{y} +# ``` +# We predict at test inputs $\mathbf{x}_*$ using +# ```math +# \hat{y}_* = \mathbf{x}_*^\top \mathbf{w} +# ``` +# This is implemented by `linear_regression`: + +function linear_regression(X, y, Xstar) + weights = (X' * X) \ (X' * y) + return Xstar * weights +end; + +# A linear regression fit to the above data set: + +y_pred = linear_regression(x_train, y_train, x_test) +scatter(x_train, y_train; label="observations") +plot!(x_test, y_pred; label="linear fit") + +## +# ## Featurization +# We can improve the fit by including additional features, i.e. generalizing to $\tilde{\mathrm{X}} = (\phi(x_n))_{n=1}^N$, where $\phi(x)$ constructs a feature vector for each input $x$. Here we include powers of the input, $\phi(x) = (1, x, x^2, \dots, x^d)$: + +function featurize_poly(x; degree=1) + return repeat(x, 1, degree + 1) .^ (0:degree)' +end + +function featurized_fit_and_plot(degree) + X = featurize_poly(x_train; degree=degree) + Xstar = featurize_poly(x_test; degree=degree) + y_pred = linear_regression(X, y_train, Xstar) + scatter(x_train, y_train; legend=false, title="fit of order $degree") + return plot!(x_test, y_pred) +end + +plot((featurized_fit_and_plot(degree) for degree in 1:4)...) + +## +# Note that the fit becomes perfect when we include exactly as many orders in the features as we have in the underlying polynomial (4). +# +# However, when increasing the number of features, we can quickly overfit to noise in the data set: + +featurized_fit_and_plot(20) + +## +# ## Ridge regression +# To counteract this unwanted behaviour, we can introduce regularization. This leads to *ridge regression* with $L_2$ regularization of the weights ([Tikhonov regularization](https://en.wikipedia.org/wiki/Tikhonov_regularization)). +# Instead of the weights in linear regression, +# ```math +# \mathbf{w} = (\mathrm{X}^\top \mathrm{X})^{-1} \mathrm{X}^\top \mathbf{y} +# ``` +# we introduce the ridge parameter $\lambda$: +# ```math +# \mathbf{w} = (\mathrm{X}^\top \mathrm{X} + \lambda \mathbb{1})^{-1} \mathrm{X}^\top \mathbf{y} +# ``` +# As before, we predict at test inputs $\mathbf{x}_*$ using +# ```math +# \hat{y}_* = \mathbf{x}_*^\top \mathbf{w} +# ``` +# This is implemented by `ridge_regression`: + +function ridge_regression(X, y, Xstar, lambda) + weights = (X' * X + lambda * I) \ (X' * y) + return Xstar * weights +end + +function regularized_fit_and_plot(degree, lambda) + X = featurize_poly(x_train; degree=degree) + Xstar = featurize_poly(x_test; degree=degree) + y_pred = ridge_regression(X, y_train, Xstar, lambda) + scatter(x_train, y_train; legend=false, title="\$\\lambda=$lambda\$") + return plot!(x_test, y_pred) +end + +plot((regularized_fit_and_plot(20, lambda) for lambda in (1e-3, 1e-2, 1e-1, 1))...) + +## +# ## Kernel ridge regression +# Instead of constructing the feature matrix explicitly, we can use *kernels* to replace inner products of feature vectors with a kernel evaluation: $\langle \phi(x), \phi(x') \rangle = k(x, x')$ or $\tilde{\mathrm{X}} \tilde{\mathrm{X}}^\top = \mathrm{K}$, where $\mathrm{K}_{ij} = k(x_i, x_j)$. +# +# To apply this "kernel trick" to ridge regression, we can rewrite the ridge estimate for the weights +# ```math +# \mathbf{w} = (\mathrm{X}^\top \mathrm{X} + \lambda \mathbb{1})^{-1} \mathrm{X}^\top \mathbf{y} +# ``` +# using the [matrix inversion lemma](https://tlienart.github.io/pub/csml/mtheory/matinvlem.html#basic_lemmas) +# as +# ```math +# \mathbf{w} = \mathrm{X}^\top (\mathrm{X} \mathrm{X}^\top + \lambda \mathbb{1})^{-1} \mathbf{y} +# ``` +# where we can now replace the inner product with the kernel matrix, +# ```math +# \mathbf{w} = \mathrm{X}^\top (\mathrm{K} + \lambda \mathbb{1})^{-1} \mathbf{y} +# ``` +# And the prediction yields another inner product, +# ```math +# \hat{y}_* = \mathbf{x}_*^\top \mathbf{w} = \langle \mathbf{x}_*, \mathbf{w} \rangle = \mathbf{k}_* (\mathrm{K} + \lambda \mathbb{1})^{-1} \mathbf{y} +# ``` +# where $(\mathbf{k}_*)_n = k(x_*, x_n)$. +# +# This is implemented by `kernel_ridge_regression`: + +function kernel_ridge_regression(k, X, y, Xstar, lambda) + K = kernelmatrix(k, X) + kstar = kernelmatrix(k, Xstar, X) + return kstar * ((K + lambda * I) \ y) +end; + +# Now, instead of explicitly constructing features, we can simply pass in a `PolynomialKernel` object: + +function kernelized_fit_and_plot(kernel, lambda=1e-4) + y_pred = kernel_ridge_regression(kernel, x_train, y_train, x_test, lambda) + if kernel isa PolynomialKernel + title = string("order ", kernel.degree) + else + title = string(nameof(typeof(kernel))) + end + scatter(x_train, y_train; label=nothing) + return plot!(x_test, y_pred; label=nothing, title=title) +end + +plot((kernelized_fit_and_plot(PolynomialKernel(; degree=degree, c=1)) for degree in 1:4)...) + +## +# However, we can now also use kernels that would have an infinite-dimensional feature expansion, such as the squared exponential kernel: + +kernelized_fit_and_plot(SqExponentialKernel()) diff --git a/examples/kernelridgeregression.jl b/examples/kernelridgeregression.jl deleted file mode 100644 index 0bc02f25a..000000000 --- a/examples/kernelridgeregression.jl +++ /dev/null @@ -1,40 +0,0 @@ -using KernelFunctions -using MLDataUtils -using Zygote -using Flux -using Distributions, LinearAlgebra -using Plots - -Flux.@functor SqExponentialKernel -Flux.@functor ScaleTransform -Flux.@functor KernelSum -Flux.@functor Matern32Kernel - -xmin = -3; -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) -k = SqExponentialKernel(1.0)#+Matern32Kernel(2.0) -λ = [-1.0] -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, 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) -## -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) -end diff --git a/examples/support-vector-machine/Manifest.toml b/examples/support-vector-machine/Manifest.toml new file mode 100644 index 000000000..8b8a2d648 --- /dev/null +++ b/examples/support-vector-machine/Manifest.toml @@ -0,0 +1,921 @@ +# This file is machine-generated - editing it directly is not advised + +[[Adapt]] +deps = ["LinearAlgebra"] +git-tree-sha1 = 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"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" diff --git a/examples/support-vector-machine/Project.toml b/examples/support-vector-machine/Project.toml new file mode 100644 index 000000000..13219d95c --- /dev/null +++ b/examples/support-vector-machine/Project.toml @@ -0,0 +1,13 @@ +[deps] +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" + +[compat] +Distributions = "0.25" +KernelFunctions = "0.10" +Literate = "2" +Plots = "1" +julia = "1.3" diff --git a/examples/support-vector-machine/script.jl b/examples/support-vector-machine/script.jl new file mode 100644 index 000000000..7cf80cac4 --- /dev/null +++ b/examples/support-vector-machine/script.jl @@ -0,0 +1,42 @@ +# # Support Vector Machine +# +# !!! warning +# This example is under construction + +using KernelFunctions +using Distributions +using Plots + +using LinearAlgebra +using Random + +## Set plotting theme +theme(:wong) + +## Set seed +Random.seed!(1234); + +# Number of samples: +N = 100; + +# Select randomly between two classes: +y = rand([-1, 1], N); + +# Random attributes for both classes: +X = Matrix{Float64}(undef, 2, N) +rand!(MvNormal(randn(2), I), view(X, :, y .== 1)) +rand!(MvNormal(randn(2), I), view(X, :, y .== -1)); + +# Create a 2D grid: +xgrid = range(floor(Int, minimum(X)), ceil(Int, maximum(X)); length=100) +Xgrid = ColVecs(mapreduce(collect, hcat, Iterators.product(xgrid, xgrid))); + +# Create kernel function: +k = SqExponentialKernel() ∘ ScaleTransform(2.0) + +# Optimal prediction: +f(x, X, k, λ) = kernelmatrix(k, x, X) / (kernelmatrix(k, X) + exp(λ) * I) * y + +# Compute prediction on a grid: +contourf(xgrid, xgrid, f(Xgrid, ColVecs(X), k, 0.1)) +scatter!(X[1, :], X[2, :]; color=y, lab="data", widen=false) diff --git a/examples/svm.jl b/examples/svm.jl deleted file mode 100644 index 34f7ec632..000000000 --- a/examples/svm.jl +++ /dev/null @@ -1,26 +0,0 @@ -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 -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 -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) = 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 -contourf(xgrid, xgrid, pred) -scatter!(eachcol(X)...; color=y, lab="data") diff --git a/src/KernelFunctions.jl b/src/KernelFunctions.jl index 670c1c8f6..248993573 100644 --- a/src/KernelFunctions.jl +++ b/src/KernelFunctions.jl @@ -27,6 +27,7 @@ export Transform, IdentityTransform, FunctionTransform, PeriodicTransform +export with_lengthscale export NystromFact, nystrom @@ -36,7 +37,8 @@ export spectral_mixture_kernel, spectral_mixture_product_kernel export ColVecs, RowVecs export MOInput -export IndependentMOKernel, LatentFactorMOKernel, IntrinsicCoregionMOKernel +export IndependentMOKernel, + LatentFactorMOKernel, IntrinsicCoregionMOKernel, LinearMixingModelKernel # Reexports export tensor, ⊗, compose @@ -74,6 +76,7 @@ include(joinpath("transform", "selecttransform.jl")) include(joinpath("transform", "chaintransform.jl")) include(joinpath("transform", "periodic_transform.jl")) include(joinpath("kernels", "transformedkernel.jl")) +include(joinpath("transform", "with_lengthscale.jl")) include(joinpath("basekernels", "constant.jl")) include(joinpath("basekernels", "cosine.jl")) @@ -106,6 +109,7 @@ include(joinpath("mokernels", "moinput.jl")) include(joinpath("mokernels", "independent.jl")) include(joinpath("mokernels", "slfm.jl")) include(joinpath("mokernels", "intrinsiccoregion.jl")) +include(joinpath("mokernels", "lmm.jl")) include("chainrules.jl") include("zygoterules.jl") diff --git a/src/matrix/kernelmatrix.jl b/src/matrix/kernelmatrix.jl index da42bec37..888026a23 100644 --- a/src/matrix/kernelmatrix.jl +++ b/src/matrix/kernelmatrix.jl @@ -24,9 +24,16 @@ kernelmatrix! """ kernelmatrix(κ::Kernel, x::AbstractVector) + +Compute the kernel `κ` for each pair of inputs in `x`. +Returns a matrix of size `(length(x), length(x))` satisfying +`kernelmatrix(κ, x)[p, q] == κ(x[p], x[q])`. + kernelmatrix(κ::Kernel, x::AbstractVector, y::AbstractVector) -Calculate the kernel matrix of `x` (and `y`) with respect to kernel `κ`. +Compute the kernel `κ` for each pair of inputs in `x` and `y`. +Returns a matrix of size `(length(x), length(y))` satisfying +`kernelmatrix(κ, x, y)[p, q] == κ(x[p], y[q])`. kernelmatrix(κ::Kernel, X::AbstractMatrix; obsdim::Int=2) kernelmatrix(κ::Kernel, X::AbstractMatrix, Y::AbstractMatrix; obsdim::Int=2) @@ -65,11 +72,11 @@ kernelmatrix_diag! """ kernelmatrix_diag(κ::Kernel, x::AbstractVector) -Calculate the diagonal matrix of `x` with respect to kernel `κ`. +Compute the diagonal of `kernelmatrix(κ, x)` efficiently. kernelmatrix_diag(κ::Kernel, x::AbstractVector, y::AbstractVector) -Calculate the diagonal of `kernelmatrix(κ, x, y)` efficiently. +Compute the diagonal of `kernelmatrix(κ, x, y)` efficiently. Requires that `x` and `y` are the same length. kernelmatrix_diag(κ::Kernel, X::AbstractMatrix; obsdim::Int=2) 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)) diff --git a/src/mokernels/intrinsiccoregion.jl b/src/mokernels/intrinsiccoregion.jl index 9e38ba09b..cf8e6879c 100644 --- a/src/mokernels/intrinsiccoregion.jl +++ b/src/mokernels/intrinsiccoregion.jl @@ -1,5 +1,5 @@ @doc raw""" - IntrinsicIntrinsicCoregionMOKernel(; kernel::Kernel, B::AbstractMatrix) + IntrinsicCoregionMOKernel(; kernel::Kernel, B::AbstractMatrix) Kernel associated with the intrinsic coregionalization model. diff --git a/src/mokernels/lmm.jl b/src/mokernels/lmm.jl new file mode 100644 index 000000000..1427d2a1c --- /dev/null +++ b/src/mokernels/lmm.jl @@ -0,0 +1,45 @@ +@doc raw""" + LinearMixingModelKernel(g, e::MOKernel, A::AbstractMatrix) + +Kernel associated with the linear mixing model. + +# Definition + +For inputs ``x, x'`` and output dimensions ``p_x, p_{x'}'``, the kernel is defined as[^BPTHST] +```math +k\big((x, p_x), (x, p_{x'})\big) = H_{:,p_{x}}K(x, x')H_{:,p_{x'}} +``` +where ``K(x, x') = Diag(k_1(x, x'), ..., k_m(x, x'))`` with zero off-diagonal entries. +``H_{:,p_{x}}`` is the ``p_x``-th column (`p_x`-th output) of ``H \in \mathbb{R}^{m \times p}`` +representing ``m`` basis vectors for the ``p`` dimensional output space of ``f``. +``k_1, \ldots, k_m`` are ``m`` kernels, one for each latent process, ``H`` is a +mixing matrix of ``m`` basis vectors spanning the output space. + +[^BPTHST]: Wessel P. Bruinsma, Eric Perim, Will Tebbutt, J. Scott Hosking, Arno Solin, Richard E. Turner (2020). [Scalable Exact Inference in Multi-Output Gaussian Processes](https://arxiv.org/pdf/1911.06287.pdf). +""" +struct LinearMixingModelKernel{Tk<:AbstractVector{<:Kernel},Th<:AbstractMatrix} <: MOKernel + K::Tk + H::Th +end + +function LinearMixingModelKernel(k::Kernel, H::AbstractMatrix) + return LinearMixingModelKernel(Fill(k, size(H, 1)), H) +end + +function (κ::LinearMixingModelKernel)((x, px)::Tuple{Any,Int}, (y, py)::Tuple{Any,Int}) + (px > size(κ.H, 2) || py > size(κ.H, 2) || px < 1 || py < 1) && + error("`px` and `py` must be within the range of the number of outputs") + return sum(κ.H[i, px] * κ.K[i](x, y) * κ.H[i, py] for i in 1:length(κ.K)) +end + +function Base.show(io::IO, k::LinearMixingModelKernel) + return print(io, "Linear Mixing Model Multi-Output Kernel") +end + +function Base.show(io::IO, mime::MIME"text/plain", k::LinearMixingModelKernel) + print(io, "Linear Mixing Model Multi-Output Kernel. Kernels:") + for k in k.K + print(io, "\n\t") + show(io, mime, k) + end +end diff --git a/src/transform/with_lengthscale.jl b/src/transform/with_lengthscale.jl new file mode 100644 index 000000000..72360dba8 --- /dev/null +++ b/src/transform/with_lengthscale.jl @@ -0,0 +1,43 @@ +""" + with_lengthscale(kernel::Kernel, lengthscale::Real) + +Construct a transformed kernel with `lengthscale`. + +# Examples + +```jldoctest +julia> kernel = with_lengthscale(SqExponentialKernel(), 2.5); + +julia> x = rand(2); + +julia> y = rand(2); + +julia> kernel(x, y) ≈ (SqExponentialKernel() ∘ ScaleTransform(0.4))(x, y) +true +``` +""" +function with_lengthscale(kernel::Kernel, lengthscale::Real) + return kernel ∘ ScaleTransform(inv(lengthscale)) +end + +""" + with_lengthscale(kernel::Kernel, lengthscales::AbstractVector{<:Real}) + +Construct a transformed "ARD" kernel with different `lengthscales` for each dimension. + +# Examples + +```jldoctest +julia> kernel = with_lengthscale(SqExponentialKernel(), [0.5, 2.5]); + +julia> x = rand(2); + +julia> y = rand(2); + +julia> kernel(x, y) ≈ (SqExponentialKernel() ∘ ARDTransform([2, 0.4]))(x, y) +true +``` +""" +function with_lengthscale(kernel::Kernel, lengthscales::AbstractVector{<:Real}) + return kernel ∘ ARDTransform(map(inv, lengthscales)) +end diff --git a/test/mokernels/lmm.jl b/test/mokernels/lmm.jl new file mode 100644 index 000000000..645304c76 --- /dev/null +++ b/test/mokernels/lmm.jl @@ -0,0 +1,48 @@ +@testset "lmm" begin + rng = MersenneTwister(123) + FDM = FiniteDifferences.central_fdm(5, 1) + N = 10 + in_dim = 3 + out_dim = 6 + x1 = MOInput([rand(rng, in_dim) for _ in 1:N], out_dim) + x2 = MOInput([rand(rng, in_dim) for _ in 1:N], out_dim) + H = rand(4, 6) + + k = LinearMixingModelKernel( + [Matern32Kernel(), SqExponentialKernel(), FBMKernel(), Matern32Kernel()], H + ) + @test k isa LinearMixingModelKernel + @test k isa MOKernel + @test k isa Kernel + @test k(x1[1], x2[1]) isa Real + + @test string(k) == "Linear Mixing Model Multi-Output Kernel" + @test repr("text/plain", k) == ( + "Linear Mixing Model Multi-Output Kernel. Kernels:\n" * + "\tMatern 3/2 Kernel (metric = Euclidean(0.0))\n" * + "\tSquared Exponential Kernel (metric = Euclidean(0.0))\n" * + "\tFractional Brownian Motion Kernel (h = 0.5)\n" * + "\tMatern 3/2 Kernel (metric = Euclidean(0.0))" + ) + + k = LinearMixingModelKernel(SEKernel(), H) + + @test k isa LinearMixingModelKernel + @test k isa MOKernel + @test k isa Kernel + @test length(k.K) == 4 + for kernel in k.K + @test isa(kernel, SEKernel) + end + + @test string(k) == "Linear Mixing Model Multi-Output Kernel" + @test repr("text/plain", k) == ( + "Linear Mixing Model Multi-Output Kernel. Kernels:\n" * + "\tSquared Exponential Kernel (metric = Euclidean(0.0))\n" * + "\tSquared Exponential Kernel (metric = Euclidean(0.0))\n" * + "\tSquared Exponential Kernel (metric = Euclidean(0.0))\n" * + "\tSquared Exponential Kernel (metric = Euclidean(0.0))" + ) + + test_ADs(k) +end diff --git a/test/runtests.jl b/test/runtests.jl index e878d8158..2f74221a8 100644 --- a/test/runtests.jl +++ b/test/runtests.jl @@ -19,6 +19,10 @@ using KernelFunctions: SimpleKernel, metric, kappa, ColVecs, RowVecs, TestUtils using KernelFunctions.TestUtils: test_interface +# The GROUP is used to run different sets of tests in parallel on the GitHub Actions CI. +# If you want to introduce a new group, ensure you also add it to .github/workflows/ci.yml +const GROUP = get(ENV, "GROUP", "") + # Writing tests: # 1. The file structure of the test should match precisely the file structure of src. # Amongst other things, this means that there should be exactly 1 test file per src file. @@ -54,122 +58,135 @@ using KernelFunctions.TestUtils: test_interface include("test_utils.jl") @testset "KernelFunctions" begin - include("utils.jl") - - @testset "distances" begin - include(joinpath("distances", "pairwise.jl")) - include(joinpath("distances", "dotproduct.jl")) - include(joinpath("distances", "delta.jl")) - include(joinpath("distances", "sinus.jl")) + if GROUP == "" || GROUP == "Transform" + @testset "transform" begin + include(joinpath("transform", "transform.jl")) + print(" ") + include(joinpath("transform", "scaletransform.jl")) + print(" ") + include(joinpath("transform", "ardtransform.jl")) + print(" ") + include(joinpath("transform", "lineartransform.jl")) + print(" ") + include(joinpath("transform", "functiontransform.jl")) + print(" ") + include(joinpath("transform", "selecttransform.jl")) + print(" ") + include(joinpath("transform", "chaintransform.jl")) + print(" ") + include(joinpath("transform", "periodic_transform.jl")) + print(" ") + include(joinpath("transform", "with_lengthscale.jl")) + print(" ") + end + @info "Ran tests on Transform" end - @info "Ran tests on Distances" - @testset "transform" begin - include(joinpath("transform", "transform.jl")) - print(" ") - include(joinpath("transform", "scaletransform.jl")) - print(" ") - include(joinpath("transform", "ardtransform.jl")) - print(" ") - include(joinpath("transform", "lineartransform.jl")) - print(" ") - include(joinpath("transform", "functiontransform.jl")) - print(" ") - include(joinpath("transform", "selecttransform.jl")) - print(" ") - include(joinpath("transform", "chaintransform.jl")) - print(" ") - include(joinpath("transform", "periodic_transform.jl")) - print(" ") + if GROUP == "" || GROUP == "BaseKernels" + @testset "basekernels" begin + include(joinpath("basekernels", "constant.jl")) + print(" ") + include(joinpath("basekernels", "cosine.jl")) + print(" ") + include(joinpath("basekernels", "exponential.jl")) + print(" ") + include(joinpath("basekernels", "exponentiated.jl")) + print(" ") + include(joinpath("basekernels", "fbm.jl")) + print(" ") + include(joinpath("basekernels", "gabor.jl")) + print(" ") + include(joinpath("basekernels", "matern.jl")) + print(" ") + include(joinpath("basekernels", "nn.jl")) + print(" ") + include(joinpath("basekernels", "periodic.jl")) + print(" ") + include(joinpath("basekernels", "piecewisepolynomial.jl")) + print(" ") + include(joinpath("basekernels", "polynomial.jl")) + print(" ") + include(joinpath("basekernels", "rational.jl")) + print(" ") + include(joinpath("basekernels", "sm.jl")) + print(" ") + include(joinpath("basekernels", "wiener.jl")) + print(" ") + end + @info "Ran tests on BaseKernel" end - @info "Ran tests on Transform" - @testset "basekernels" begin - include(joinpath("basekernels", "constant.jl")) - print(" ") - include(joinpath("basekernels", "cosine.jl")) - print(" ") - include(joinpath("basekernels", "exponential.jl")) - print(" ") - include(joinpath("basekernels", "exponentiated.jl")) - print(" ") - include(joinpath("basekernels", "fbm.jl")) - print(" ") - include(joinpath("basekernels", "gabor.jl")) - print(" ") - include(joinpath("basekernels", "matern.jl")) - print(" ") - include(joinpath("basekernels", "nn.jl")) - print(" ") - include(joinpath("basekernels", "periodic.jl")) - print(" ") - include(joinpath("basekernels", "piecewisepolynomial.jl")) - print(" ") - include(joinpath("basekernels", "polynomial.jl")) - print(" ") - include(joinpath("basekernels", "rational.jl")) - print(" ") - include(joinpath("basekernels", "sm.jl")) - print(" ") - include(joinpath("basekernels", "wiener.jl")) - print(" ") + if GROUP == "" || GROUP == "Kernels" + @testset "kernels" begin + include(joinpath("kernels", "kernelproduct.jl")) + include(joinpath("kernels", "kernelsum.jl")) + include(joinpath("kernels", "kerneltensorproduct.jl")) + include(joinpath("kernels", "overloads.jl")) + include(joinpath("kernels", "scaledkernel.jl")) + include(joinpath("kernels", "transformedkernel.jl")) + include(joinpath("kernels", "normalizedkernel.jl")) + include(joinpath("kernels", "neuralkernelnetwork.jl")) + end + @info "Ran tests on Kernel" end - @info "Ran tests on BaseKernel" - @testset "kernels" begin - include(joinpath("kernels", "kernelproduct.jl")) - include(joinpath("kernels", "kernelsum.jl")) - include(joinpath("kernels", "kerneltensorproduct.jl")) - include(joinpath("kernels", "overloads.jl")) - include(joinpath("kernels", "scaledkernel.jl")) - include(joinpath("kernels", "transformedkernel.jl")) - include(joinpath("kernels", "normalizedkernel.jl")) - include(joinpath("kernels", "neuralkernelnetwork.jl")) + if GROUP == "" || GROUP == "MultiOutput" + @testset "multi_output" begin + include(joinpath("mokernels", "moinput.jl")) + include(joinpath("mokernels", "independent.jl")) + include(joinpath("mokernels", "slfm.jl")) + include(joinpath("mokernels", "intrinsiccoregion.jl")) + include(joinpath("mokernels", "lmm.jl")) + end + @info "Ran tests on Multi-Output Kernels" end - @info "Ran tests on Kernel" - @testset "matrix" begin - include(joinpath("matrix", "kernelmatrix.jl")) - include(joinpath("matrix", "kernelkroneckermat.jl")) - include(joinpath("matrix", "kernelpdmat.jl")) - end - @info "Ran tests on matrix" + if GROUP == "" || GROUP == "Others" + include("utils.jl") - @testset "multi_output" begin - include(joinpath("mokernels", "moinput.jl")) - include(joinpath("mokernels", "independent.jl")) - include(joinpath("mokernels", "slfm.jl")) - include(joinpath("mokernels", "intrinsiccoregion.jl")) - end - @info "Ran tests on Multi-Output Kernels" + @testset "distances" begin + include(joinpath("distances", "pairwise.jl")) + include(joinpath("distances", "dotproduct.jl")) + include(joinpath("distances", "delta.jl")) + include(joinpath("distances", "sinus.jl")) + end + @info "Ran tests on Distances" - @testset "approximations" begin - include(joinpath("approximations", "nystrom.jl")) - end + @testset "matrix" begin + include(joinpath("matrix", "kernelmatrix.jl")) + include(joinpath("matrix", "kernelkroneckermat.jl")) + include(joinpath("matrix", "kernelpdmat.jl")) + end + @info "Ran tests on matrix" + + @testset "approximations" begin + include(joinpath("approximations", "nystrom.jl")) + end - include("generic.jl") - include("chainrules.jl") - include("zygoterules.jl") + include("generic.jl") + include("chainrules.jl") + include("zygoterules.jl") - @testset "doctests" begin - DocMeta.setdocmeta!( - KernelFunctions, - :DocTestSetup, - quote - using KernelFunctions - using LinearAlgebra - using Random - using PDMats: PDMats - end; - recursive=true, - ) - doctest( - KernelFunctions; - 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]+})", - ], - ) + @testset "doctests" begin + DocMeta.setdocmeta!( + KernelFunctions, + :DocTestSetup, + quote + using KernelFunctions + using LinearAlgebra + using Random + using PDMats: PDMats + end; + recursive=true, + ) + doctest( + KernelFunctions; + 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]+})", + ], + ) + end end end diff --git a/test/transform/with_lengthscale.jl b/test/transform/with_lengthscale.jl new file mode 100644 index 000000000..60d401e82 --- /dev/null +++ b/test/transform/with_lengthscale.jl @@ -0,0 +1,17 @@ +@testset "with_lengthscale" begin + @testset "ScaleTransform" begin + l = exp(rand()) + kernel = @inferred(with_lengthscale(SqExponentialKernel(), l)) + + @test kernel isa TransformedKernel{<:SqExponentialKernel,<:ScaleTransform} + @test kernel.transform.s[1] ≈ inv(l) + end + + @testset "ARDTransform" begin + l = map(exp, rand(5)) + kernel = @inferred(with_lengthscale(SqExponentialKernel(), l)) + + @test kernel isa TransformedKernel{<:SqExponentialKernel,<:ARDTransform} + @test kernel.transform.v ≈ map(inv, l) + end +end