Merge pull request #190 from JuliaAI/dev

For a 1.9.5 release

Author: ablaom

.github/codecov.yml

@@ -2,4 +2,7 @@ coverage:
   status:
     project:
       default:
-        threshold: 0.5%
+        threshold: 0.5%
+    patch:
+      default:
+        target: 80%

Project.toml

@@ -1,19 +1,31 @@
 name = "MLJModelInterface"
 uuid = "e80e1ace-859a-464e-9ed9-23947d8ae3ea"
 authors = ["Thibaut Lienart and Anthony Blaom"]
-version = "1.9.4"
+version = "1.9.5"
 
 [deps]
 Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
 ScientificTypesBase = "30f210dd-8aff-4c5f-94ba-8e64358c1161"
 StatisticalTraits = "64bff920-2084-43da-a3e6-9bb72801c0c9"
 
 [compat]
-ScientificTypesBase = "3.0"
+Aqua = "0.8"
+CategoricalArrays = "0.10"
+DataFrames = "1"
+Distances = "0.10"
+InteractiveUtils = "<0.0.1, 1"
+Markdown = "<0.0.1, 1"
+OrderedCollections = "1"
+Random = "<0.0.1, 1"
+ScientificTypes = "3"
+ScientificTypesBase = "3"
 StatisticalTraits = "3.2"
+Tables = "1"
+Test = "<0.0.1, 1"
 julia = "1.6"
 
 [extras]
+Aqua = "4c88cf16-eb10-579e-8560-4a9242c79595"
 CategoricalArrays = "324d7699-5711-5eae-9e2f-1d82baa6b597"
 DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0"
 Distances = "b4f34e82-e78d-54a5-968a-f98e89d6e8f7"
@@ -25,4 +37,4 @@ Tables = "bd369af6-aec1-5ad0-b16a-f7cc5008161c"
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 
 [targets]
-test = ["CategoricalArrays", "DataFrames", "Distances", "InteractiveUtils", "Markdown", "OrderedCollections", "ScientificTypes", "Tables", "Test"]
+test = ["Aqua", "CategoricalArrays", "DataFrames", "Distances", "InteractiveUtils", "Markdown", "OrderedCollections", "ScientificTypes", "Tables", "Test"]

src/data_utils.jl

@@ -58,7 +58,7 @@ end
 # int
 
 """
-   int(x; type=nothing)
+   int(x)
 
 The positional integer of the `CategoricalString` or `CategoricalValue` `x`, in
 the ordering defined by the pool of `x`. The type of `int(x)` is the reference
@@ -96,9 +96,9 @@ julia> int(v)
 ```
 See also: [`decoder`](@ref).
 """
-function int(x; type::Union{Nothing, Type{T}}=nothing) where T <: Real
+function int(x; type=nothing)
     type === nothing && return int(get_interface_mode(), x)
-    return convert.(T, int(get_interface_mode(), x))
+    return convert.(type, int(get_interface_mode(), x))
 end
 
 int(::LightInterface, x) = errlight("int")

src/equality.jl

@@ -124,7 +124,7 @@ function is_same_except(m1::M1,
                         is_same_except(
                             getproperty(m1, name),
                             getproperty(m2, name)
-                        ) || 
+                        ) ||
                         getproperty(m1, name) isa AbstractRNG ||
                         getproperty(m2, name) isa AbstractRNG
                     ) || return false
@@ -155,7 +155,8 @@ function special_in(x, itr)::Union{Bool,Missing}
 end
 
 Base.in(x::MLJType, itr::Set) = special_in(x, itr)
-Base.in(x::MLJType, itr::AbstractVector) = special_in(x, itr)
+Base.in(x::MLJType, itr::AbstractVector{<:MLJType}) = special_in(x, itr)
+Base.in(x::MLJType, itr::AbstractRange{<:MLJType}) = special_in(x, itr)
 Base.in(x::MLJType, itr::Tuple) = special_in(x, itr)
 
 # A version of `in` that actually uses `==`:

src/model_traits.jl

@@ -97,50 +97,39 @@ end
 # in `prediction_type` for models which, historically, have not
 # implemented the trait.
 
+# Actually, this has proven more trouble than it's worth and should be removed in 2.0.
+# See https://discourse.julialang.org/t/deconstructing-unionall-types/108328 to appreciate
+# some of the complications.
+
 function StatTraits.predict_scitype(
     M::Type{<:Union{Probabilistic, ProbabilisticDetector}}
 )
     return _density(target_scitype(M))
 end
 
-_density(::Any) = Unknown
-
-for T in [:Continuous, :Count, :Textual]
-    eval(
-        quote
-            function _density(::Type{AbstractArray{$T, D}}) where D
-                return AbstractArray{Density{$T}, D}
-            end
-        end
-    )
-end
+const SCALAR_SCITYPES_EXS =
+    [:Finite, :Multiclass, :OrderedFactor, :Infinite, :Continuous, :Count, :Textual]
 
-for T in [:Finite, :Multiclass, :OrderedFactor, :Infinite, :Continuous, :Count, :Textual]
-    eval(
-        quote
-            function _density(::Type{AbstractArray{<:$T, D}}) where D
-                return AbstractArray{Density{<:$T}, D}
-            end
+const SCALAR_SCITYPES =
+    eval.([:Finite, :Multiclass, :OrderedFactor, :Infinite, :Continuous, :Count, :Textual])
 
-            _density(::Type{Table($T)}) = Table(Density{$T})
-        end
-    )
+function _density(t)
+    for T in SCALAR_SCITYPES
+        t == AbstractVector{<:T} && return AbstractVector{Density{<:T}}
+        t == AbstractMatrix{<:T} && return AbstractMatrix{Density{<:T}}
+        t == Table(T) && return Table{<:AbstractVector{<:Density{<:T}}}
+    end
+    for T in  [Finite, Multiclass, OrderedFactor]
+        t == Table(T{2}) && return Table(Density{<:T{2}})
+    end
+    return Unknown
 end
 
-
-for T in [:Finite, :Multiclass, :OrderedFactor]
-    eval(
+for T in SCALAR_SCITYPES_EXS
         quote
-            function _density(::Type{AbstractArray{<:$T{N}, D}}) where {N, D}
-                return AbstractArray{Density{<:$T{N}}, D}
-            end
-
-            function _density(::Type{AbstractArray{$T{N}, D}}) where {N, D}
-                return AbstractArray{Density{$T{N}}, D}
-            end
-
-            _density(::Type{Table($T{N})}) where N = Table(Density{$T{N}})
-        end
-    )
+            _density(::Type{<:AbstractArray{W, D}}) where {W<:$T, D} =
+                AbstractArray{Density{W}, D}
+            _density(::Type{<:Table{<:AbstractVector{W}}}) where W<:$T =
+                Table(Density{W})
+        end |> eval
 end
-

test/aqua.jl

@@ -0,0 +1,4 @@
+import Aqua
+import MLJModelInterface
+
+Aqua.test_all(MLJModelInterface, ambiguities=true)

test/data_utils.jl

@@ -23,14 +23,15 @@ end
     # needing the `FullInterface`.
     X = (1, 2, 3)
     @test_throws M.InterfaceError matrix(X)
-    
+
     X = (a=[1, 2, 3], b=[1, 2, 3])
     @test_throws M.InterfaceError matrix(X)
 end
 
 @testset "matrix-full" begin
     setfull()
-    M.matrix(::FI, ::Val{:table}, X; kw...) = Tables.matrix(X; kw...)
+    # next line commented out as already defined in test/mode.jl:
+    # M.matrix(::FI, ::Val{:table}, X; kw...) = Tables.matrix(X; kw...)
     X = (a=[1, 2, 3], b=[1, 2, 3])
     @test matrix(X) == hcat([1, 2, 3], [1, 2, 3])
 end
@@ -120,14 +121,14 @@ end
 # ------------------------------------------------------------------------
 @testset "istable" begin
     # Nothing stops someone from implementing a Tables.jl
-    # interface that subtypes `AbstractArray`, so therefore 
+    # interface that subtypes `AbstractArray`, so therefore
     # `istable` should throw an error for `LightInterface`
     setlight()
     X = rand(5)
     @test_throws M.InterfaceError M.istable(X)
     X = randn(5, 5)
     @test_throws M.InterfaceError M.istable(X)
-    
+
     # The method runs in `FullInterface`
     setfull()
     X = rand(5)
@@ -184,10 +185,10 @@ end
     X = ones(5)
     @test nrows(X) == 5
     X = ones(5, 3)
-    @test nrows(X) == 5 
-    # It doesn't make sense to get the numbers of rows for 
-    # `AbstractArray`'s of dimension 3 or more. Except if these are 
-    # defined as Tables. Hence `FullInterface` would be required to check this 
+    @test nrows(X) == 5
+    # It doesn't make sense to get the numbers of rows for
+    # `AbstractArray`'s of dimension 3 or more. Except if these are
+    # defined as Tables. Hence `FullInterface` would be required to check this
     X = ones(5, 3, 2)
     @test_throws ArgumentError nrows(X)
     M.nrows(::FI, ::Val{:table}, X) = Tables.rowcount(X)
@@ -220,13 +221,13 @@ end
 
 @testset "select-full" begin
     setfull()
-   
+
     # test fallback
     X = nothing
     @test selectrows(X, 1) === nothing
     @test selectcols(X, 1) === nothing
     @test select(X, 1, 2) === nothing
-    
+
     # vector
     X = ones(5)
     @test selectrows(X, 1) == [1.0]
@@ -273,11 +274,11 @@ end
 
     project(t::NamedTuple, label::Colon) = t
     project(t::NamedTuple, label::Symbol) = project(t, [label,])
-    
+
     function project(t::NamedTuple, indices::AbstractArray{<:Integer})
         return NamedTuple{tuple(keys(t)[indices]...)}(tuple([t[i] for i in indices]...))
     end
-    
+
     project(t::NamedTuple, i::Integer) = project(t, [i,])
 
     X = (x=[1, 2, 3], y=[4, 5, 6], z=[0, 0, 0])
@@ -292,7 +293,7 @@ end
     @test select(X, :, 1) == [1, 2, 3]
     @test selectcols(X, :x) == [1, 2, 3]
     @test select(X, 1:2, :z) == [0, 0]
-    
+
     # extra tests by Anthony
     X = (x=[1, 2, 3], y=[10, 20, 30], z= [:a, :b, :c])
     @test select(X, 2, :y) == 20

test/metadata_utils.jl

@@ -198,12 +198,6 @@ metadata_pkg(FooRegressor2,
     is_wrapper=false
     )
 
-# this is added in MLJBase but not in MLJModelInterface, to avoid
-# InteractiveUtils as dependency:
-setfull()
-M.implemented_methods(::FI, M::Type{<:MLJType}) =
-    getfield.(methodswith(M), :name)
-
 const HEADER2 = MLJModelInterface.doc_header(FooRegressor2, augment=true)
 
 @doc """

test/model_traits.jl

@@ -114,10 +114,6 @@ M.human_name(::Type{<:U1}) = "funky model"
 
     setfull()
 
-    function M.implemented_methods(::FI, M::Type{<:MLJType})
-        return getfield.(methodswith(M), :name)
-    end
-
     @test Set(implemented_methods(mp)) == Set([:clean!,:bar,:foo])
 end
 
@@ -140,19 +136,15 @@ end
             M._density(AbstractVector{<:T}),
             AbstractVector{Density{<:T}}
         )
-        @test M._density(Table(T)) == Table(Density{T})
+        @test M._density(Table(T)) == Table(Density{<:T})
     end
 
     for T in [Finite, Multiclass, OrderedFactor]
-        @test ==(
-            M._density(AbstractArray{<:T{2},3}),
-            AbstractArray{Density{<:T{2}},3}
-        )
         @test ==(
             M._density(AbstractArray{T{2},3}),
             AbstractArray{Density{T{2}},3}
         )
-        @test M._density(Table(T{2})) == Table(Density{T{2}})
+        @test M._density(Table(T{2})) == Table(Density{<:T{2}})
     end
 end
 

test/runtests.jl

@@ -4,18 +4,45 @@ using Tables, Distances, CategoricalArrays, InteractiveUtils
 import DataFrames: DataFrame
 import Markdown
 import OrderedCollections
+import Aqua
 
 const M  = MLJModelInterface
 const FI = M.FullInterface
 
 setlight() = M.set_interface_mode(M.LightInterface())
 setfull() = M.set_interface_mode(M.FullInterface())
 
-include("mode.jl")
-include("parameter_inspection.jl")
-include("data_utils.jl")
-include("metadata_utils.jl")
-include("model_def.jl")
-include("model_api.jl")
-include("model_traits.jl")
-include("equality.jl")
+@testset "mode.jl" begin
+    include("mode.jl")
+end
+
+@testset "parameter_inspection.jl" begin
+    include("parameter_inspection.jl")
+end
+
+@testset "data_utils.jl" begin
+    include("data_utils.jl")
+end
+
+@testset "metadata_utils.jl" begin
+    include("metadata_utils.jl")
+end
+@testset "model_def.jl" begin
+    include("model_def.jl")
+end
+
+@testset "model_api.jl" begin
+    include("model_api.jl")
+end
+
+@testset "model_traits.jl" begin
+    include("model_traits.jl")
+end
+
+@testset "equality.jl" begin
+    include("equality.jl")
+end
+
+@testset "aqua.jl" begin
+    include("aqua.jl")
+end