fix Distances compat #423

st-- · 2022-01-11T16:34:15Z

Aims to resolve #390 and #391

…ep existing compat)

…21-941-03135690217

devmotion · 2022-01-11T16:40:00Z

test/chainrules.jl

@@ -21,7 +21,13 @@
    compare_gradient(:Zygote, [x, y]) do xy
        KernelFunctions.Sinus(r)(xy[1], xy[2])
    end
-    compare_gradient(:Zygote, [Q, x, y]) do xy
-        SqMahalanobis(xy[1])(xy[2], xy[3])
+    if VERSION < v"1.6"


What's the reason for this check?

The tests seemed to pass fine as is on 1.6, and I don't want to skip checks if I can avoid it.

Sure, but how is the Julia version relevant here? It does not affect the version of Distances that is used, so why can't we use the same test for all Julia versions? It also seems tests fail on Julia 1.3 currently.

Relevant because it only fails in 1.3 (and 1.4). It passes with 1.6 and 1.7. [not tested on 1.5]

Should we just skip the test for 1.3? Or raise julia compat to ~~1.4 (part of Ubuntu 20.04) or~~ 1.6 (LTS)?

codecov · 2022-01-11T16:46:23Z

Codecov Report

Merging #423 (ae34ff2) into master (93d33c2) will not change coverage.
The diff coverage is n/a.

@@           Coverage Diff           @@
##           master     #423   +/-   ##
=======================================
  Coverage   92.74%   92.74%           
=======================================
  Files          52       52           
  Lines        1199     1199           
=======================================
  Hits         1112     1112           
  Misses         87       87

Impacted Files	Coverage Δ
src/chainrules.jl	`87.65% <ø> (ø)`

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…tions.jl into st/fix_distances

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)

* 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-- <[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) * 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-- <[email protected]> * Apply suggestions from code review Co-authored-by: st-- <[email protected]> * 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-- <[email protected]> * format Co-authored-by: ST John <[email protected]> Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>

CompatHelper Julia and others added 4 commits October 26, 2021 00:42

CompatHelper: bump compat for Distances to 0.10 for package test, (ke…

a6e2264

…ep existing compat)

Merge branch 'master' into compathelper/new_version/2021-10-26-00-42-…

98815a4

…21-941-03135690217

try out Theo's fix

b398577

fix test compat

f124818

devmotion reviewed Jan 11, 2022

View reviewed changes

st-- added 6 commits January 12, 2022 15:13

Merge branch 'master' of github.com:JuliaGaussianProcesses/KernelFunc…

a7e7452

…tions.jl into st/fix_distances

use ForwardDiff for chain rule test of SqMahalanobis

01530b6

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

740dcb5

revert version branch

733cfcc

revert to 1.3

f692b4d

test_broken for older Julia versions

ae34ff2

st-- mentioned this pull request Jan 13, 2022

Known AD Failures #116

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st-- requested a review from theogf January 13, 2022 16:35

theogf approved these changes Jan 13, 2022

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st-- merged commit d1c68a9 into master Jan 13, 2022

st-- deleted the st/fix_distances branch January 13, 2022 21:33

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fix Distances compat #423

fix Distances compat #423

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devmotion Jan 11, 2022

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fix Distances compat #423

fix Distances compat #423

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