Squashed commit of the following:

commit f9bbd84
Author: st-- <[email protected]>
Date:   Fri Jan 28 09:11:50 2022 +0100

    make nystrom work with AbstractVector (#427)

    * make nystrom work with AbstractVector

    * add test

    * Update test/approximations/nystrom.jl

    Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>

    * patch bump

    * Update test/approximations/nystrom.jl

    Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>

    * Apply suggestions from code review

    Co-authored-by: David Widmann <[email protected]>

    * Apply suggestions from code review

    * deprecate

    * Apply suggestions from code review

    Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>

    * Apply suggestions from code review

    Co-authored-by: David Widmann <[email protected]>

    * Apply suggestions from code review

    Co-authored-by: Théo Galy-Fajou <[email protected]>

    * Update src/approximations/nystrom.jl

    Co-authored-by: Théo Galy-Fajou <[email protected]>

    * Update src/approximations/nystrom.jl

    Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>

    Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
    Co-authored-by: David Widmann <[email protected]>
    Co-authored-by: Théo Galy-Fajou <[email protected]>

commit d1c68a9
Author: st-- <[email protected]>
Date:   Thu Jan 13 22:33:43 2022 +0100

    fix Distances compat (#423)

    * CompatHelper: bump compat for Distances to 0.10 for package test, (keep existing compat)

    * try out Theo's fix

    * fix test compat

    * use ForwardDiff for chain rule test of SqMahalanobis

    * test on 1.4 instead of 1.3 - see if the chainrules test passes there

    * revert version branch

    * revert to 1.3

    * test_broken for older Julia versions

    Co-authored-by: CompatHelper Julia <[email protected]>

commit 93d33c2
Author: st-- <[email protected]>
Date:   Wed Jan 12 14:11:14 2022 +0100

    fix figure & cleanup (#422)

    * fix figure & cleanup

    * bump LIBSVM compat & Manifest

    * improve writing, replaces #321

commit 40cb59e
Author: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
Date:   Wed Jan 12 09:39:01 2022 +0200

    CompatHelper: bump compat for Kronecker to 0.5 for package docs, (keep existing compat) (#367)

    * CompatHelper: bump compat for Kronecker to 0.5 for package docs, (keep existing compat)

    * ] up

    Co-authored-by: CompatHelper Julia <[email protected]>
    Co-authored-by: st-- <[email protected]>

commit 7204529
Author: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
Date:   Tue Jan 11 18:37:23 2022 +0200

    CompatHelper: bump compat for Kronecker to 0.5 for package test, (keep existing compat) (#366)

    Co-authored-by: CompatHelper Julia <[email protected]>
    Co-authored-by: st-- <[email protected]>

commit 924925d
Author: st-- <[email protected]>
Date:   Tue Jan 11 16:26:02 2022 +0100

    switch SVM example to half-moon dataset (#421)

commit 992b665
Author: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
Date:   Fri Dec 24 12:18:56 2021 +0200

    CompatHelper: bump compat for SpecialFunctions to 2 for package test, (keep existing compat) (#412)

    Co-authored-by: CompatHelper Julia <[email protected]>
    Co-authored-by: Théo Galy-Fajou <[email protected]>
    Co-authored-by: st-- <[email protected]>

commit 04fa7f7
Author: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
Date:   Thu Dec 23 13:33:59 2021 +0200

    CompatHelper: bump compat for SpecialFunctions to 2, (keep existing compat) (#411)

    Co-authored-by: CompatHelper Julia <[email protected]>
    Co-authored-by: Théo Galy-Fajou <[email protected]>
    Co-authored-by: st-- <[email protected]>

commit c0fc3e1
Author: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
Date:   Thu Dec 23 01:10:40 2021 +0200

    CompatHelper: add new compat entry for Compat at version 3 for package test, (keep existing compat) (#418)

    Co-authored-by: CompatHelper Julia <[email protected]>

commit 05fe340
Author: st-- <[email protected]>
Date:   Tue Dec 21 00:49:37 2021 +0200

    use only() instead of first() (#403)

    * use only() instead of first() for 1-"vectors" that were for the benefit of Flux

    * fix one test that should not have worked as it was

    * add missing scalar Sinus constructor

commit 2d17212
Author: st-- <[email protected]>
Date:   Sat Dec 18 23:43:30 2021 +0200

    Zygote AD failure workarounds & test cleanup (#414)

    Zygote AD failures:

    * revert #409 (test_utils workaround for broken Zygote - now working again)

    * disable broken Zygote AD test for ChainTransform

    Improved tests:

    * finer-grained testsets

    * add missing test cases to test_AD

    * replace test_FiniteDiff with test_AD(..., :FiniteDiff, ...)

    * remove code duplication

commit 3c49949
Author: Théo Galy-Fajou <[email protected]>
Date:   Wed Nov 24 18:32:19 2021 +0100

    Fix typo in valid_inputs error (#408)

    * Fix typo in valid_inputs error

    * Update src/utils.jl

    Co-authored-by: David Widmann <[email protected]>

    Co-authored-by: David Widmann <[email protected]>

commit 9955044
Author: st-- <[email protected]>
Date:   Wed Nov 24 18:55:18 2021 +0200

    Fix for Zygote 0.6.30 breaking our tests (#409)

    * restrict Zygote to <0.6.30

    * revert Zygote test restriction and add finer-grained testset

    * Update test/utils.jl

    Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>

    * revert testset

    * mark test_broken

    * Use `@test_throws` instead of `@test_broken`

    Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
    Co-authored-by: David Widmann <[email protected]>

commit 33d64d1
Author: Théo Galy-Fajou <[email protected]>
Date:   Thu Nov 4 14:23:57 2021 +0100

    Add benchmarking CI (#399)

    * Add benchmark file

    * delete old benchmarks

    * Add github action

    * Add Project

    * Apply suggestions from code review

    Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>

    * Missing end of line

    Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>

commit 360ce10
Author: David Widmann <[email protected]>
Date:   Tue Nov 2 11:09:58 2021 +0100

    Update docstring of `GibbsKernel` (#395)

.github/workflows/benchmark.yml

@@ -0,0 +1,24 @@
+name: Run benchmarks
+
+on:
+  pull_request:
+
+jobs:
+  Benchmark:
+    runs-on: ubuntu-latest
+    if: contains(github.event.pull_request.labels.*.name, 'performance critical')
+    env:
+      JULIA_DEBUG: BenchmarkCI
+    steps:
+      - uses: actions/checkout@v2
+      - uses: julia-actions/setup-julia@latest
+        with:
+          version: 1.6
+      - name: Install dependencies
+        run: julia -e 'using Pkg; pkg"add PkgBenchmark BenchmarkCI"'
+      - name: Run benchmarks
+        run: julia -e "using BenchmarkCI; BenchmarkCI.judge()"
+      - name: Post results
+        run: julia -e "using BenchmarkCI; BenchmarkCI.postjudge()"
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

.gitignore

@@ -4,3 +4,4 @@
 /test/Manifest.toml
 coverage/
 .DS_store
+benchmark/Manifest.toml

Project.toml

@@ -1,6 +1,6 @@
 name = "KernelFunctions"
 uuid = "ec8451be-7e33-11e9-00cf-bbf324bd1392"
-version = "0.10.26"
+version = "0.10.28"
 
 [deps]
 ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4"
@@ -30,7 +30,7 @@ Functors = "0.1, 0.2"
 IrrationalConstants = "0.1"
 LogExpFunctions = "0.2.1, 0.3"
 Requires = "1.0.1"
-SpecialFunctions = "0.8, 0.9, 0.10, 1"
+SpecialFunctions = "0.8, 0.9, 0.10, 1, 2"
 StatsBase = "0.32, 0.33"
 TensorCore = "0.1"
 ZygoteRules = "0.2"

benchmark/Project.toml

@@ -0,0 +1,3 @@
+[deps]
+BenchmarkTools = "6e4b80f9-dd63-53aa-95a3-0cdb28fa8baf"
+KernelFunctions = "ec8451be-7e33-11e9-00cf-bbf324bd1392"

benchmark/benchmarks.jl

@@ -1,23 +1,46 @@
 using BenchmarkTools
-using Random
-using Distances, LinearAlgebra
+using KernelFunctions
 
-const SUITE = BenchmarkGroup()
+N1 = 10
+N2 = 20
 
-Random.seed!(1234)
+X = rand(N1, N2)
+Xc = ColVecs(X)
+Xr = RowVecs(X)
+Xv = collect.(eachcol(X))
+Y = rand(N1, N2)
+Yc = ColVecs(Y)
+Yr = RowVecs(Y)
+Yv = collect.(eachcol(Y))
 
-dim = 50
-N1 = 1000;
-N2 = 500;
-alpha = 2.0
+# Create the general suite of benchmarks
+SUITE = BenchmarkGroup()
 
-X = rand(Float64, N1, dim)
-Y = rand(Float64, N2, dim)
+kernels = Dict(
+    "SqExponential" => SqExponentialKernel(), "Exponential" => ExponentialKernel()
+)
 
-KXY = rand(Float64, N1, N2)
-KX = rand(Float64, N1, N1)
-sKX = Symmetric(rand(Float64, N1, N1))
-kX = rand(Float64, N1)
+inputtypes = Dict("ColVecs" => (Xc, Yc), "RowVecs" => (Xr, Yr), "Vecs" => (Xv, Yv))
 
-include("kernelmatrix.jl")
-include("MLKernels.jl")
+functions = Dict(
+    "kernelmatrixX" => (kernel, X, Y) -> kernelmatrix(kernel, X),
+    "kernelmatrixXY" => (kernel, X, Y) -> kernelmatrix(kernel, X, Y),
+    "kernelmatrix_diagX" => (kernel, X, Y) -> kernelmatrix_diag(kernel, X),
+    "kernelmatrix_diagXY" => (kernel, X, Y) -> kernelmatrix_diag(kernel, X, Y),
+)
+
+for (kname, kernel) in kernels
+    SUITE[kname] = sk = BenchmarkGroup()
+    for (inputname, (X, Y)) in inputtypes
+        sk[inputname] = si = BenchmarkGroup()
+        for (fname, f) in functions
+            si[fname] = @benchmarkable $f($kernel, $X, $Y)
+        end
+    end
+end
+
+# Uncomment the following to run benchmark locally
+
+# tune!(SUITE)
+
+# results = run(SUITE, verbose=true)