fix figure & cleanup #422

st-- · 2022-01-11T15:41:14Z

@theogf apologies I had made a mistake with Plots... and then I also cleaned up the code a bit more

st-- · 2022-01-11T15:49:06Z

I've taken the opportunity to bump the LIBSVM dependency, deprecating #413

codecov · 2022-01-11T15:49:39Z

Codecov Report

Merging #422 (acffc5e) into master (40cb59e) will not change coverage.
The diff coverage is n/a.

@@           Coverage Diff           @@
##           master     #422   +/-   ##
=======================================
  Coverage   92.74%   92.74%           
=======================================
  Files          52       52           
  Lines        1199     1199           
=======================================
  Hits         1112     1112           
  Misses         87       87

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devmotion · 2022-01-11T15:53:16Z

examples/support-vector-machine/script.jl

+X1 = [cos.(angle1) sin.(angle1)] .+ 0.1randn(n1, 2)
+X2 = [1 .- cos.(angle2) 1 .- sin.(angle2) .- 0.5] .+ 0.1randn(n2, 2)


0.1randn(n1, 2) creates two arrays that can be avoided:

Suggested change

X1 = [cos.(angle1) sin.(angle1)] .+ 0.1randn(n1, 2)

X2 = [1 .- cos.(angle2) 1 .- sin.(angle2) .- 0.5] .+ 0.1randn(n2, 2)

X1 = [cos.(angle1) sin.(angle1)] .+ 0.1 .* randn.()

X2 = [1 .- cos.(angle2) 1 .- sin.(angle2) .- 0.5] .+ 0.1 .* randn.()

Alternatively, with one allocation:

Suggested change

X1 = [cos.(angle1) sin.(angle1)] .+ 0.1randn(n1, 2)

X2 = [1 .- cos.(angle2) 1 .- sin.(angle2) .- 0.5] .+ 0.1randn(n2, 2)

X1 = [cos.(angle1) sin.(angle1)] .+ 0.1 .* randn(n1, 2)

X2 = [1 .- cos.(angle2) 1 .- sin.(angle2) .- 0.5] .+ 0.1 .* randn(n2, 2)

In this case, the number of allocations makes no practical difference... but not having to pass the shape is neat! I didn't know randn.() works like that, I would have thought it only shifts everything by the same amount.

Damn! This is nice! I never new about x .+ randn.() is it working because of broadcast fusion?

devmotion · 2022-01-11T15:53:52Z

examples/support-vector-machine/script.jl

@@ -49,7 +48,7 @@ model = svmtrain(kernelmatrix(k, x_train), y_train; kernel=LIBSVM.Kernel.Precomp
 y_pred, _ = svmpredict(model, kernelmatrix(k, x_train, x_test));

 # Visualize prediction on a grid:
-plot(; lim=extrema(test_range), aspect_ratio=1)
+plot(; xlim=extrema(test_range), ylim=extrema(test_range), aspect_ratio=1)


I guess you want

Suggested change

plot(; xlim=extrema(test_range), ylim=extrema(test_range), aspect_ratio=1)

plot(; widen=false, aspect_ratio=1)

?

No, that doesn't fix it.

Ah, I guess you might have to specify the keyword argument when you actually plot data since otherwise subsequent calls might update the limits. I missed that there's nothing plotted in this call here.

No, widen isn't actually needed. Looks like updating Plots.jl seems to have fixed it though 😅

examples/support-vector-machine/script.jl

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

Co-authored-by: David Widmann <devmotion@users.noreply.github.com>

st-- · 2022-01-12T07:37:55Z

Can I have an approve to merge while even the nightly build is passing? 😂

commit f9bbd84 Author: st-- <st--@users.noreply.github.com> 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 <devmotion@users.noreply.github.com> * 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 <devmotion@users.noreply.github.com> * Apply suggestions from code review Co-authored-by: Théo Galy-Fajou <theo.galyfajou@gmail.com> * Update src/approximations/nystrom.jl Co-authored-by: Théo Galy-Fajou <theo.galyfajou@gmail.com> * 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 <devmotion@users.noreply.github.com> Co-authored-by: Théo Galy-Fajou <theo.galyfajou@gmail.com> commit d1c68a9 Author: st-- <st--@users.noreply.github.com> 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 <compathelper_noreply@julialang.org> commit 93d33c2 Author: st-- <st--@users.noreply.github.com> 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 <compathelper_noreply@julialang.org> Co-authored-by: st-- <st--@users.noreply.github.com> 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 <compathelper_noreply@julialang.org> Co-authored-by: st-- <st--@users.noreply.github.com> commit 924925d Author: st-- <st--@users.noreply.github.com> 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 <compathelper_noreply@julialang.org> Co-authored-by: Théo Galy-Fajou <theo.galyfajou@gmail.com> Co-authored-by: st-- <st--@users.noreply.github.com> 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 <compathelper_noreply@julialang.org> Co-authored-by: Théo Galy-Fajou <theo.galyfajou@gmail.com> Co-authored-by: st-- <st--@users.noreply.github.com> 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 <compathelper_noreply@julialang.org> commit 05fe340 Author: st-- <st--@users.noreply.github.com> 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-- <st--@users.noreply.github.com> 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 <theo.galyfajou@gmail.com> 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 <devmotion@users.noreply.github.com> Co-authored-by: David Widmann <devmotion@users.noreply.github.com> commit 9955044 Author: st-- <st--@users.noreply.github.com> 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 <devmotion@users.noreply.github.com> commit 33d64d1 Author: Théo Galy-Fajou <theo.galyfajou@gmail.com> 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 <devmotion@users.noreply.github.com> Date: Tue Nov 2 11:09:58 2021 +0100 Update docstring of `GibbsKernel` (#395)

* initial version of training kernel parameters example from st/examples (#234) * update script * Apply suggestions from code review Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> * fix out-of-domain initial value * initial version of training kernel parameters example from st/examples (#234) * update script * Apply suggestions from code review Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> * fix out-of-domain initial value * Add ParameterHandling * Extend example * Failed attempts with default Flux opt * Add Flux.destructure example * Add some nothing * Squashed commit of the following: commit f9bbd84 Author: st-- <st--@users.noreply.github.com> 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 <devmotion@users.noreply.github.com> * 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 <devmotion@users.noreply.github.com> * Apply suggestions from code review Co-authored-by: Théo Galy-Fajou <theo.galyfajou@gmail.com> * Update src/approximations/nystrom.jl Co-authored-by: Théo Galy-Fajou <theo.galyfajou@gmail.com> * 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 <devmotion@users.noreply.github.com> Co-authored-by: Théo Galy-Fajou <theo.galyfajou@gmail.com> commit d1c68a9 Author: st-- <st--@users.noreply.github.com> 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 <compathelper_noreply@julialang.org> commit 93d33c2 Author: st-- <st--@users.noreply.github.com> 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 <compathelper_noreply@julialang.org> Co-authored-by: st-- <st--@users.noreply.github.com> 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 <compathelper_noreply@julialang.org> Co-authored-by: st-- <st--@users.noreply.github.com> commit 924925d Author: st-- <st--@users.noreply.github.com> 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 <compathelper_noreply@julialang.org> Co-authored-by: Théo Galy-Fajou <theo.galyfajou@gmail.com> Co-authored-by: st-- <st--@users.noreply.github.com> 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 <compathelper_noreply@julialang.org> Co-authored-by: Théo Galy-Fajou <theo.galyfajou@gmail.com> Co-authored-by: st-- <st--@users.noreply.github.com> 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 <compathelper_noreply@julialang.org> commit 05fe340 Author: st-- <st--@users.noreply.github.com> 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-- <st--@users.noreply.github.com> 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 <theo.galyfajou@gmail.com> 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 <devmotion@users.noreply.github.com> Co-authored-by: David Widmann <devmotion@users.noreply.github.com> commit 9955044 Author: st-- <st--@users.noreply.github.com> 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 <devmotion@users.noreply.github.com> commit 33d64d1 Author: Théo Galy-Fajou <theo.galyfajou@gmail.com> 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 <devmotion@users.noreply.github.com> Date: Tue Nov 2 11:09:58 2021 +0100 Update docstring of `GibbsKernel` (#395) * change title * Update manifest * Formatter * Some small updates * Add BenchmarkTools * Move Benchmarks to the correct manifest * Formatter * Fix missed comment * Add ParameterHandling too * Change gif embed * Forgot # * Formatter Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> * Compat and gif kwargs * , for ; * different commit msg * Some more clarification * Change display * Final changes * Apply suggestions from code review Co-authored-by: st-- <st--@users.noreply.github.com> * Apply suggestions from code review Co-authored-by: st-- <st--@users.noreply.github.com> * Address comments * Missed one * Manifest issue * Apply suggestions from formatter Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> * Local formatter * Delete loss description. Co-authored-by: st-- <st--@users.noreply.github.com> * format Co-authored-by: ST John <st--@users.noreply.github.com> Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>

fix figure & cleanup

7c06c94

st-- requested a review from theogf January 11, 2022 15:41

bump LIBSVM compat & Manifest

5b4580e

devmotion reviewed Jan 11, 2022

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bugfix & improve writing, replaces #321

1c71067

github-actions bot reviewed Jan 11, 2022

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examples/support-vector-machine/script.jl Outdated Show resolved Hide resolved

st-- and others added 4 commits January 11, 2022 17:07

Update examples/support-vector-machine/script.jl

9397bf7

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

Update examples/support-vector-machine/script.jl

8fd0601

Co-authored-by: David Widmann <devmotion@users.noreply.github.com>

revert to just lim=

eb5ee62

Merge branch 'master' into st/svm_example

88b534a

Merge branch 'master' into st/svm_example

acffc5e

theogf approved these changes Jan 12, 2022

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st-- merged commit 93d33c2 into master Jan 12, 2022

st-- deleted the st/svm_example branch January 12, 2022 13:11

st-- mentioned this pull request Jan 12, 2022

CompatHelper: bump compat for LIBSVM to 0.8 for package support-vector-machine, (keep existing compat) #413

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fix figure & cleanup #422

fix figure & cleanup #422

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		X1 = [cos.(angle1) sin.(angle1)] .+ 0.1randn(n1, 2)
		X2 = [1 .- cos.(angle2) 1 .- sin.(angle2) .- 0.5] .+ 0.1randn(n2, 2)

	plot(; xlim=extrema(test_range), ylim=extrema(test_range), aspect_ratio=1)
	plot(; widen=false, aspect_ratio=1)

fix figure & cleanup #422

fix figure & cleanup #422

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