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@tlienart When I tested the utilsmigration branch locally, with MLJBase#dev (now a pending tagged release 0.6.0) I had some problems (julia 1.0.5 and 1.2; haven't tested others). Did some other merges onto dev happen after you tested? Maybe easier to diagnose after MLJBase 0.6.0 is released. julia> Pkg.status()
Status `~/Dropbox/Julia7/MLJ/MLJModels/sandbox/junk/Project.toml`
[a7f614a8] MLJBase v0.6.0 #dev (https://github.com/alan-turing-institute/MLJBase.jl.git)
[d491faf4] MLJModels v0.4.0 #utilsmigration (https://github.com/alan-turing-institute/MLJModels.jl.git)
(junk) pkg> test MLJModels
Testing MLJModels
Resolving package versions...
Status `/var/folders/4n/gvbmlhdc8xj973001s6vdyw00000gq/T/tmpUKR73h/Manifest.toml`
[621f4979] AbstractFFTs v0.4.1
[7d9fca2a] Arpack v0.3.1
[4fba245c] ArrayInterface v1.2.1
[13072b0f] AxisAlgorithms v1.0.0
[9e28174c] BinDeps v0.8.10
[b99e7846] BinaryProvider v0.5.6
[a74b3585] Blosc v0.5.1
[631607c0] CMake v1.1.2
[d5fb7624] CMakeWrapper v0.2.3
[00ebfdb7] CSTParser v0.6.2
[336ed68f] CSV v0.5.12
[49dc2e85] Calculus v0.5.0
[324d7699] CategoricalArrays v0.5.2
[aaaa29a8] Clustering v0.13.3
[944b1d66] CodecZlib v0.5.2
[3da002f7] ColorTypes v0.8.0
[5ae59095] Colors v0.9.6
[bbf7d656] CommonSubexpressions v0.2.0
[34da2185] Compat v2.1.0
[8f4d0f93] Conda v1.3.0
[9a962f9c] DataAPI v1.0.1
[a93c6f00] DataFrames v0.18.4
[864edb3b] DataStructures v0.17.0
[e2d170a0] DataValueInterfaces v1.0.0
[7806a523] DecisionTree v0.8.3
[01453d9d] DiffEqDiffTools v1.3.0
[163ba53b] DiffResults v0.0.4
[b552c78f] DiffRules v0.0.10
[b4f34e82] Distances v0.8.2
[31c24e10] Distributions v0.21.1
[fdbdab4c] ElasticArrays v0.4.0
[2904ab23] ElasticPDMats v0.2.1
[8f5d6c58] EzXML v0.9.4
[7a1cc6ca] FFTW v0.3.0
[442a2c76] FastGaussQuadrature v0.4.0
[5789e2e9] FileIO v1.0.7
[1a297f60] FillArrays v0.7.0
[53c48c17] FixedPointNumbers v0.6.1
[f6369f11] ForwardDiff v0.10.3
[38e38edf] GLM v1.3.2
[cc18c42c] GaussianMixtures v0.3.0
[891a1506] GaussianProcesses v0.9.0
[f67ccb44] HDF5 v0.12.3
[a98d9a8b] Interpolations v0.12.2
[c8e1da08] IterTools v1.2.0
[82899510] IteratorInterfaceExtensions v1.0.0
[4138dd39] JLD v0.9.1
[682c06a0] JSON v0.21.0
[5ab0869b] KernelDensity v0.5.1
[2d691ee1] LIBLINEAR v0.5.1
[b1bec4e5] LIBSVM v0.3.1
[b964fa9f] LaTeXStrings v1.0.3
[1b4a561d] LegacyStrings v0.4.1
[d3d80556] LineSearches v7.0.1
[a7f614a8] MLJBase v0.6.0 #dev (https://github.com/alan-turing-institute/MLJBase.jl.git)
[d491faf4] MLJModels v0.4.0 #utilsmigration (https://github.com/alan-turing-institute/MLJModels.jl.git)
[1914dd2f] MacroTools v0.5.1
[e1d29d7a] Missings v0.4.2
[78c3b35d] Mocking v0.7.0
[6f286f6a] MultivariateStats v0.7.0
[0db19996] NBInclude v2.1.0
[d41bc354] NLSolversBase v7.4.1
[77ba4419] NaNMath v0.3.2
[9bbee03b] NaiveBayes v0.4.0
[b8a86587] NearestNeighbors v0.4.3
[6fe1bfb0] OffsetArrays v0.11.1
[429524aa] Optim v0.19.3
[bac558e1] OrderedCollections v1.1.0
[90014a1f] PDMats v0.9.10
[d96e819e] Parameters v0.12.0
[69de0a69] Parsers v0.3.7
[2dfb63ee] PooledArrays v0.5.2
[85a6dd25] PositiveFactorizations v0.2.2
[438e738f] PyCall v1.91.2
[d330b81b] PyPlot v2.8.2
[1fd47b50] QuadGK v2.0.3
[df47a6cb] RData v0.6.3
[ce6b1742] RDatasets v0.6.3
[c84ed2f1] Ratios v0.3.1
[3cdcf5f2] RecipesBase v0.7.0
[731186ca] RecursiveArrayTools v0.18.6
[189a3867] Reexport v0.2.0
[ae029012] Requires v0.5.2
[79098fc4] Rmath v0.5.0
[321657f4] ScientificTypes v0.2.0
[3646fa90] ScikitLearn v0.5.1
[6e75b9c4] ScikitLearnBase v0.5.0
[1277b4bf] ShiftedArrays v0.5.0
[b85f4697] SoftGlobalScope v1.0.10
[a2af1166] SortingAlgorithms v0.3.1
[276daf66] SpecialFunctions v0.7.2
[90137ffa] StaticArrays v0.11.0
[2913bbd2] StatsBase v0.32.0
[4c63d2b9] StatsFuns v0.8.0
[3eaba693] StatsModels v0.6.3
[3783bdb8] TableTraits v1.0.0
[bd369af6] Tables v0.2.11
[f269a46b] TimeZones v0.10.0
[0796e94c] Tokenize v0.5.6
[3bb67fe8] TranscodingStreams v0.9.5
[30578b45] URIParser v0.4.0
[81def892] VersionParsing v1.1.3
[ea10d353] WeakRefStrings v0.6.1
[efce3f68] WoodburyMatrices v0.4.1
[009559a3] XGBoost v0.4.1
[2a0f44e3] Base64 [`@stdlib/Base64`]
[ade2ca70] Dates [`@stdlib/Dates`]
[8bb1440f] DelimitedFiles [`@stdlib/DelimitedFiles`]
[8ba89e20] Distributed [`@stdlib/Distributed`]
[9fa8497b] Future [`@stdlib/Future`]
[b77e0a4c] InteractiveUtils [`@stdlib/InteractiveUtils`]
[76f85450] LibGit2 [`@stdlib/LibGit2`]
[8f399da3] Libdl [`@stdlib/Libdl`]
[37e2e46d] LinearAlgebra [`@stdlib/LinearAlgebra`]
[56ddb016] Logging [`@stdlib/Logging`]
[d6f4376e] Markdown [`@stdlib/Markdown`]
[a63ad114] Mmap [`@stdlib/Mmap`]
[44cfe95a] Pkg [`@stdlib/Pkg`]
[de0858da] Printf [`@stdlib/Printf`]
[9abbd945] Profile [`@stdlib/Profile`]
[3fa0cd96] REPL [`@stdlib/REPL`]
[9a3f8284] Random [`@stdlib/Random`]
[ea8e919c] SHA [`@stdlib/SHA`]
[9e88b42a] Serialization [`@stdlib/Serialization`]
[1a1011a3] SharedArrays [`@stdlib/SharedArrays`]
[6462fe0b] Sockets [`@stdlib/Sockets`]
[2f01184e] SparseArrays [`@stdlib/SparseArrays`]
[10745b16] Statistics [`@stdlib/Statistics`]
[4607b0f0] SuiteSparse [`@stdlib/SuiteSparse`]
[8dfed614] Test [`@stdlib/Test`]
[cf7118a7] UUIDs [`@stdlib/UUIDs`]
[4ec0a83e] Unicode [`@stdlib/Unicode`]
[ Info: Model metadata loaded from registry.
[ Info: MLJModels.Constant.ConstantRegressor
import MLJModels ✔
import DecisionTree ✔
import MLJModels.DecisionTree_.DecisionTreeClassifier ✔
Test Summary: | Pass Total
metadata | 48 48
┌ Warning: `T` is deprecated, use `nonmissingtype` instead.
│ caller = catvaluetype at array.jl:555 [inlined]
└ @ Core ~/.julia/packages/CategoricalArrays/ucKV2/src/array.jl:555
┌ Warning: `T` is deprecated, use `nonmissingtype` instead.
│ caller = catvaluetype at array.jl:555 [inlined]
└ @ Core ~/.julia/packages/CategoricalArrays/ucKV2/src/array.jl:555
┌ Warning: `T` is deprecated, use `nonmissingtype` instead.
│ caller = catvaluetype at array.jl:555 [inlined]
└ @ Core ~/.julia/packages/CategoricalArrays/ucKV2/src/array.jl:555
[ Info: Spawning 3 sub-features to one-hot encode feature :favourite_number.
Test Summary: | Pass Total
built-in models | 40 40
Test Summary: | Pass Total
MultivariateStats | 7 7
virginica : 50/150
Test Summary: | Pass Total
DecisionTree | 7 7
Test Summary: | Pass Total
GaussianProcesses | 3 3
Test Summary: | Pass Total
Clustering | 15 15
┌ Warning: `T` is deprecated, use `nonmissingtype` instead.
│ caller = catvaluetype at array.jl:555 [inlined]
└ @ Core ~/.julia/packages/CategoricalArrays/ucKV2/src/array.jl:555
Test Summary: | Pass Total
GLM | 16 16
┌ Warning: `T` is deprecated, use `nonmissingtype` instead.
│ caller = catvaluetype at array.jl:555 [inlined]
└ @ Core ~/.julia/packages/CategoricalArrays/ucKV2/src/array.jl:555
LogRegClf: Error During Test at /Users/anthony/.julia/packages/MLJModels/0i1tm/test/ScikitLearn/linear-classifiers.jl:4
Got exception outside of a @test
PyError ($(Expr(:escape, :(ccall(#= /Users/anthony/.julia/packages/PyCall/ttONZ/src/pyfncall.jl:44 =# @pysym(:PyObject_Call), PyPtr, (PyPtr, PyPtr, PyPtr), o, pyargsptr, kw))))) <class 'TypeError'>
TypeError("__init__() got an unexpected keyword argument 'l1_ratio'")
Stacktrace:
[1] pyerr_check at /Users/anthony/.julia/packages/PyCall/ttONZ/src/exception.jl:60 [inlined]
[2] pyerr_check at /Users/anthony/.julia/packages/PyCall/ttONZ/src/exception.jl:64 [inlined]
[3] macro expansion at /Users/anthony/.julia/packages/PyCall/ttONZ/src/exception.jl:84 [inlined]
[4] __pycall!(::PyCall.PyObject, ::Ptr{PyCall.PyObject_struct}, ::PyCall.PyObject, ::PyCall.PyObject) at /Users/anthony/.julia/packages/PyCall/ttONZ/src/pyfncall.jl:44
[5] _pycall!(::PyCall.PyObject, ::PyCall.PyObject, ::Tuple{}, ::Int64, ::PyCall.PyObject) at /Users/anthony/.julia/packages/PyCall/ttONZ/src/pyfncall.jl:29
[6] _pycall!(::PyCall.PyObject, ::PyCall.PyObject, ::Tuple{}, ::Base.Iterators.Pairs{Symbol,Any,NTuple{15,Symbol},NamedTuple{(:penalty, :dual, :tol, :C, :fit_intercept, :intercept_scaling, :class_weight, :random_state, :solver, :max_iter, :multi_class, :verbose, :warm_start, :n_jobs, :l1_ratio),Tuple{String,Bool,Float64,Float64,Bool,Float64,Nothing,Nothing,String,Int64,String,Int64,Bool,Nothing,Nothing}}}) at /Users/anthony/.julia/packages/PyCall/ttONZ/src/pyfncall.jl:11
[7] #call#111 at /Users/anthony/.julia/packages/PyCall/ttONZ/src/pyfncall.jl:89 [inlined]
[8] (::getfield(PyCall, Symbol("#kw#PyObject")))(::NamedTuple{(:penalty, :dual, :tol, :C, :fit_intercept, :intercept_scaling, :class_weight, :random_state, :solver, :max_iter, :multi_class, :verbose, :warm_start, :n_jobs, :l1_ratio),Tuple{String,Bool,Float64,Float64,Bool,Float64,Nothing,Nothing,String,Int64,String,Int64,Bool,Nothing,Nothing}}, ::PyCall.PyObject) at ./none:0
[9] fit(::MLJModels.ScikitLearn_.LogisticClassifier, ::Int64, ::Tables.MatrixTable{Array{Float64,2}}, ::CategoricalArrays.CategoricalArray{String,1,UInt32,String,CategoricalArrays.CategoricalString{UInt32},Union{}}) at /Users/anthony/.julia/packages/MLJModels/0i1tm/src/ScikitLearn/ScikitLearn.jl:80
[10] #simple_test_classif_prob#9(::Bool, ::Bool, ::Float64, ::Function, ::MLJModels.ScikitLearn_.LogisticClassifier, ::Tables.MatrixTable{Array{Float64,2}}, ::CategoricalArrays.CategoricalArray{String,1,UInt32,String,CategoricalArrays.CategoricalString{UInt32},Union{}}) at /Users/anthony/.julia/packages/MLJModels/0i1tm/test/testutils.jl:107
[11] simple_test_classif_prob(::MLJModels.ScikitLearn_.LogisticClassifier, ::Tables.MatrixTable{Array{Float64,2}}, ::CategoricalArrays.CategoricalArray{String,1,UInt32,String,CategoricalArrays.CategoricalString{UInt32},Union{}}) at /Users/anthony/.julia/packages/MLJModels/0i1tm/test/testutils.jl:107
[12] macro expansion at /Users/anthony/.julia/packages/MLJModels/0i1tm/test/ScikitLearn/linear-classifiers.jl:5 [inlined]
[13] macro expansion at /Users/julia/buildbot/worker/package_macos64/build/usr/share/julia/stdlib/v1.0/Test/src/Test.jl:1083 [inlined]
[14] top-level scope at /Users/anthony/.julia/packages/MLJModels/0i1tm/test/ScikitLearn/linear-classifiers.jl:5
[15] include at ./boot.jl:317 [inlined]
[16] include_relative(::Module, ::String) at ./loading.jl:1044
[17] include at ./sysimg.jl:29 [inlined]
[18] include(::String) at /Users/anthony/.julia/packages/MLJModels/0i1tm/test/ScikitLearn/ScikitLearn.jl:1
[19] top-level scope at none:0
[20] include at ./boot.jl:317 [inlined]
[21] include_relative(::Module, ::String) at ./loading.jl:1044
[22] include(::Module, ::String) at ./sysimg.jl:29
[23] include(::String) at ./client.jl:392
[24] macro expansion at /Users/anthony/.julia/packages/MLJModels/0i1tm/test/runtests.jl:57 [inlined]
[25] macro expansion at /Users/julia/buildbot/worker/package_macos64/build/usr/share/julia/stdlib/v1.0/Test/src/Test.jl:1083 [inlined]
[26] top-level scope at /Users/anthony/.julia/packages/MLJModels/0i1tm/test/runtests.jl:57
[27] include at ./boot.jl:317 [inlined]
[28] include_relative(::Module, ::String) at ./loading.jl:1044
[29] include(::Module, ::String) at ./sysimg.jl:29
[30] include(::String) at ./client.jl:392
[31] top-level scope at none:0
[32] eval(::Module, ::Any) at ./boot.jl:319
[33] exec_options(::Base.JLOptions) at ./client.jl:243
[34] _start() at ./client.jl:425
LogRegCVClf: Error During Test at /Users/anthony/.julia/packages/MLJModels/0i1tm/test/ScikitLearn/linear-classifiers.jl:14
Got exception outside of a @test
PyError ($(Expr(:escape, :(ccall(#= /Users/anthony/.julia/packages/PyCall/ttONZ/src/pyfncall.jl:44 =# @pysym(:PyObject_Call), PyPtr, (PyPtr, PyPtr, PyPtr), o, pyargsptr, kw))))) <class 'TypeError'>
TypeError("__init__() got an unexpected keyword argument 'l1_ratios'")
Stacktrace:
[1] pyerr_check at /Users/anthony/.julia/packages/PyCall/ttONZ/src/exception.jl:60 [inlined]
[2] pyerr_check at /Users/anthony/.julia/packages/PyCall/ttONZ/src/exception.jl:64 [inlined]
[3] macro expansion at /Users/anthony/.julia/packages/PyCall/ttONZ/src/exception.jl:84 [inlined]
[4] __pycall!(::PyCall.PyObject, ::Ptr{PyCall.PyObject_struct}, ::PyCall.PyObject, ::PyCall.PyObject) at /Users/anthony/.julia/packages/PyCall/ttONZ/src/pyfncall.jl:44
[5] _pycall!(::PyCall.PyObject, ::PyCall.PyObject, ::Tuple{}, ::Int64, ::PyCall.PyObject) at /Users/anthony/.julia/packages/PyCall/ttONZ/src/pyfncall.jl:29
[6] _pycall!(::PyCall.PyObject, ::PyCall.PyObject, ::Tuple{}, ::Base.Iterators.Pairs{Symbol,Any,NTuple{17,Symbol},NamedTuple{(:Cs, :fit_intercept, :cv, :dual, :penalty, :scoring, :solver, :tol, :max_iter, :class_weight, :n_jobs, :verbose, :refit, :intercept_scaling, :multi_class, :random_state, :l1_ratios),Tuple{Int64,Bool,Int64,Bool,String,Nothing,String,Float64,Int64,Nothing,Nothing,Int64,Bool,Float64,String,Nothing,Nothing}}}) at /Users/anthony/.julia/packages/PyCall/ttONZ/src/pyfncall.jl:11
[7] #call#111 at /Users/anthony/.julia/packages/PyCall/ttONZ/src/pyfncall.jl:89 [inlined]
[8] (::getfield(PyCall, Symbol("#kw#PyObject")))(::NamedTuple{(:Cs, :fit_intercept, :cv, :dual, :penalty, :scoring, :solver, :tol, :max_iter, :class_weight, :n_jobs, :verbose, :refit, :intercept_scaling, :multi_class, :random_state, :l1_ratios),Tuple{Int64,Bool,Int64,Bool,String,Nothing,String,Float64,Int64,Nothing,Nothing,Int64,Bool,Float64,String,Nothing,Nothing}}, ::PyCall.PyObject) at ./none:0
[9] fit(::MLJModels.ScikitLearn_.LogisticCVClassifier, ::Int64, ::Tables.MatrixTable{Array{Float64,2}}, ::CategoricalArrays.CategoricalArray{String,1,UInt32,String,CategoricalArrays.CategoricalString{UInt32},Union{}}) at /Users/anthony/.julia/packages/MLJModels/0i1tm/src/ScikitLearn/ScikitLearn.jl:80
[10] #simple_test_classif_prob#9(::Bool, ::Bool, ::Float64, ::Function, ::MLJModels.ScikitLearn_.LogisticCVClassifier, ::Tables.MatrixTable{Array{Float64,2}}, ::CategoricalArrays.CategoricalArray{String,1,UInt32,String,CategoricalArrays.CategoricalString{UInt32},Union{}}) at /Users/anthony/.julia/packages/MLJModels/0i1tm/test/testutils.jl:107
[11] simple_test_classif_prob(::MLJModels.ScikitLearn_.LogisticCVClassifier, ::Tables.MatrixTable{Array{Float64,2}}, ::CategoricalArrays.CategoricalArray{String,1,UInt32,String,CategoricalArrays.CategoricalString{UInt32},Union{}}) at /Users/anthony/.julia/packages/MLJModels/0i1tm/test/testutils.jl:107
[12] macro expansion at /Users/anthony/.julia/packages/MLJModels/0i1tm/test/ScikitLearn/linear-classifiers.jl:15 [inlined]
[13] macro expansion at /Users/julia/buildbot/worker/package_macos64/build/usr/share/julia/stdlib/v1.0/Test/src/Test.jl:1083 [inlined]
[14] top-level scope at /Users/anthony/.julia/packages/MLJModels/0i1tm/test/ScikitLearn/linear-classifiers.jl:15
[15] include at ./boot.jl:317 [inlined]
[16] include_relative(::Module, ::String) at ./loading.jl:1044
[17] include at ./sysimg.jl:29 [inlined]
[18] include(::String) at /Users/anthony/.julia/packages/MLJModels/0i1tm/test/ScikitLearn/ScikitLearn.jl:1
[19] top-level scope at none:0
[20] include at ./boot.jl:317 [inlined]
[21] include_relative(::Module, ::String) at ./loading.jl:1044
[22] include(::Module, ::String) at ./sysimg.jl:29
[23] include(::String) at ./client.jl:392
[24] macro expansion at /Users/anthony/.julia/packages/MLJModels/0i1tm/test/runtests.jl:57 [inlined]
[25] macro expansion at /Users/julia/buildbot/worker/package_macos64/build/usr/share/julia/stdlib/v1.0/Test/src/Test.jl:1083 [inlined]
[26] top-level scope at /Users/anthony/.julia/packages/MLJModels/0i1tm/test/runtests.jl:57
[27] include at ./boot.jl:317 [inlined]
[28] include_relative(::Module, ::String) at ./loading.jl:1044
[29] include(::Module, ::String) at ./sysimg.jl:29
[30] include(::String) at ./client.jl:392
[31] top-level scope at none:0
[32] eval(::Module, ::Any) at ./boot.jl:319
[33] exec_options(::Base.JLOptions) at ./client.jl:243
[34] _start() at ./client.jl:425
Test Summary: | Pass Error Total
ScikitLearn | 262 2 264
SVM-infos | 7 7
SVCs | 3 3
SVRs | 3 3
ARD | 3 3
BayesianRidge | 3 3
ElasticNet | 3 3
ElasticNetCV | 3 3
Huber | 3 3
Lars | 3 3
LarsCV | 3 3
Lasso | 3 3
LassoCV | 3 3
LassoLars | 3 3
LassoLarsCV | 3 3
LassoLarsIC | 3 3
LinReg | 5 5
OMP | 3 3
OMPCV | 3 3
OMPCV | 3 3
PassAggr | 3 3
RANSAC | 3 3
Ridge | 3 3
RidgeCV | 4 4
SGDReg | 3 3
TheilSen | 3 3
MTLassoCV | 4 4
MTLassoCV | 3 3
MTElNet | 3 3
MTElNetCV | 3 3
LogRegClf | 1 1
LogRegCVClf | 1 1
PAClf | 7 7
PerceptronClf | 7 7
RidgeClf | 7 7
RidgeCVClf | 7 7
SGDClf | 13 13
GPRegressor | 3 3
GPClassif | 8 8
AdaBoostReg | 3 3
BaggingReg | 3 3
XTreeReg | 3 3
GBReg | 3 3
RFReg | 3 3
AdaboostClf | 8 8
BaggingClf | 8 8
GradBoostClf | 8 8
RForestClf | 8 8
XTreeClf | 8 8
DummyReg | 4 4
DummyClf | 7 7
GaussianNBClf | 8 8
KNNReg | 5 5
KNNClf | 8 8
BernNBClf | 7 7
MultiNBClf | 7 7
ComplNBClf | 7 7
ERROR: LoadError: Some tests did not pass: 262 passed, 0 failed, 2 errored, 0 broken.
in expression starting at /Users/anthony/.julia/packages/MLJModels/0i1tm/test/runtests.jl:56
ERROR: Package MLJModels errored during testing |
my dev branches were in synch so not sure what you're experiencing. But let's wait for MLJBase 0.6 to be tagged |
There are clean! methods in src/NearestNeighbors.jl. I guesss these are redundant since the @sk_macro generates clean! ? (If I remove, then I get rid of some bugs that crash MLJ tests - that |
this is now superseded by #72 |
This is a new PR to merge the contents of the utilsmigration branch onto master.