DeclareMissings is not a real Imputor

src/Impute.jl

@@ -19,6 +19,7 @@ using LinearAlgebra
 using LinearAlgebra: Diagonal
 
 include("utils.jl")
+include("declaremissings.jl")
 include("imputors.jl")
 include("filter.jl")
 include("validators.jl")

src/chain.jl

@@ -1,4 +1,5 @@
-const Transform = Union{Validator, Filter, Imputor}
+# This should maybe be a supertype at some point?
+const Transform = Union{Validator, DeclareMissings, Filter, Imputor}
 
 """
     Chain{T<:Tuple{Vararg{Transform}}} <: Function
@@ -69,6 +70,9 @@ function (C::Chain)(data; kwargs...)
         if isa(t, Validator)
             # Validators just return the input
             validate(X, t; kwargs...)
+        elseif isa(t, DeclareMissings)
+            # DeclareMissings isn't guaranteed to work in-place
+            X = apply(X, t)
         elseif isa(t, Filter)
             # Filtering doesn't always work in-place
             X = apply(X, t; kwargs...)

src/imputors/declaremissings.jl → src/declaremissings.jl

@@ -12,20 +12,20 @@ a `missing`.
 
 # Example
 ```jldoctest
-julia> using Impute: DeclareMissings, impute
+julia> using Impute: DeclareMissings, apply
 
 julia> M = [1.0 2.0 -9999.0 NaN 5.0; 1.1 2.2 3.3 0.0 5.5]
 2×5 Array{Float64,2}:
  1.0  2.0  -9999.0  NaN    5.0
  1.1  2.2      3.3    0.0  5.5
 
-julia> impute(M, DeclareMissings(; values=(NaN, -9999.0, 0.0)))
+julia> apply(M, DeclareMissings(; values=(NaN, -9999.0, 0.0)))
 2×5 Array{Union{Missing, Float64},2}:
  1.0  2.0   missing  missing  5.0
  1.1  2.2  3.3       missing  5.5
 ```
 """
-struct DeclareMissings{T<:Tuple} <: Imputor
+struct DeclareMissings{T<:Tuple}
     values::T
 end
 
@@ -34,25 +34,27 @@ function DeclareMissings(; values)
     return DeclareMissings{typeof(T)}(T)
 end
 
+apply!(data::AbstractArray{Missing}, imp::DeclareMissings) = data
+
 # Primary definition just calls `replace!`
-function _impute!(data::AbstractArray{Union{T, Missing}}, imp::DeclareMissings) where T
+function apply!(data::AbstractArray{Union{T, Missing}}, imp::DeclareMissings) where T
     # Reduce the possible set of values to those that could actually be found in the data
     # Useful, if we declare a `Replace` imputor that should be applied to multiple datasets.
     Base.replace!(data, (v => missing for v in imp.values if v isa T)...)
 end
 
 # Most of the time the in-place methods won't work because we need to change the
 # eltype with allowmissing
-impute(data::AbstractArray, imp::DeclareMissings) = _impute!(allowmissing(data), imp)
+apply(data::AbstractArray, imp::DeclareMissings) = apply!(allowmissing(data), imp)
 
 # Custom implementation of a non-mutating impute for tables
-function impute(table, imp::DeclareMissings)
-    istable(table) || throw(MethodError(impute, (table, imp)))
+function apply(table, imp::DeclareMissings)
+    istable(table) || throw(MethodError(apply, (table, imp)))
 
     ctable = Tables.columns(table)
 
     cnames = Tuple(propertynames(ctable))
-    cdata = Tuple(impute(getproperty(ctable, cname), imp) for cname in cnames)
+    cdata = Tuple(apply(getproperty(ctable, cname), imp) for cname in cnames)
     # Reconstruct as a ColumnTable
     result = NamedTuple{cnames}(cdata)
 
@@ -65,16 +67,7 @@ function impute(table, imp::DeclareMissings)
 end
 
 # Specialcase for rowtable
-function impute(data::T, imp::DeclareMissings) where T <: AbstractVector{<:NamedTuple}
+function apply(data::T, imp::DeclareMissings) where T <: AbstractVector{<:NamedTuple}
     # We use columntable here so that we don't call `materialize` more often than needed.
-    return materializer(data)(impute(Tables.columntable(data), imp))
-end
-
-# Awkward imputor overrides necessary because we intercepted the higher level
-# `impute` calls
-_impute!(data::AbstractArray{Missing}, imp::DeclareMissings) = data
-
-# Skip custom dims stuff cause it isn't necessary here.
-function impute!(data::AbstractMatrix{Union{T, Missing}}, imp::DeclareMissings) where {T}
-    return _impute!(data, imp)
+    return materializer(data)(apply(Tables.columntable(data), imp))
 end

src/functional.jl

@@ -49,7 +49,6 @@ const global imputation_methods = (
     nocb = NOCB,
     replace = Replace,
     srs = SRS,
-    declaremissings = DeclareMissings,
     substitute = Substitute,
     svd = SVD,
     knn = KNN,
@@ -83,6 +82,9 @@ for (func, type) in pairs(imputation_methods)
     end
 end
 
+declaremissings(data; kwargs...) = apply(data, DeclareMissings(; kwargs...))
+declaremissings!(data; kwargs...) = apply!(data, DeclareMissings(; kwargs...))
+
 # Provide a specific functional API for Impute.Filter.
 filter(data; kwargs...) = apply(data, Filter(); kwargs...)
 filter!(data; kwargs...) = apply!(data, Filter(); kwargs...)

src/imputors.jl

@@ -241,7 +241,6 @@ files = [
     "nocb.jl",
     "replace.jl",
     "srs.jl",
-    "declaremissings.jl",
     "substitute.jl",
     "svd.jl",
 ]

test/chain.jl

@@ -110,6 +110,7 @@
         # Filter out colunns with more than 400 missing values, Fill with 0, and check that
         # everything was replaced
         C = Chain(
+            Impute.DeclareMissings(; values=(NaN, Inf, -Inf)),
             Impute.Filter(c -> count(ismissing, c) < 400),
             Impute.Replace(; values=0.0),
             Impute.Threshold(),

test/imputors/declaremissings.jl → test/declaremissings.jl

@@ -10,36 +10,39 @@
             a = collect(1.0:1.0:20.0)
             a[[2, 3, 7]] .= [NaN, 0.0, NaN]
 
-            result = impute(a, imp)
+            result = apply(a, imp)
             @test eltype(result) == Union{Float64, Missing}
             @test all(ismissing, result[[2, 3, 7]])
 
             # In-place operation don't work when the source array doesn't allow missings.
             b = copy(a)
-            result2 = impute!(b, imp)
-            @test eltype(result2) == Float64
-            @test isequal(result2[[2, 3, 7]], [NaN, 0.0, NaN])
+            @test_throws MethodError apply!(b, imp)
         end
 
         @testset "allowmissing" begin
             a = allowmissing(collect(1.0:1.0:20.0))
             a[[2, 3, 7]] .= [NaN, 0.0, NaN]
 
-            result = impute(a, imp)
+            result = apply(a, imp)
             @test eltype(result) == Union{Float64, Missing}
             @test all(ismissing, result[[2, 3, 7]])
 
-            # In-place operation don't work when the source array doesn't allow missings.
+            # In-place operation work when the source array allows missings.
             b = copy(a)
-            result2 = impute!(b, imp)
+            result2 = apply!(b, imp)
             @test eltype(result2) == Union{Float64, Missing}
             @test all(ismissing, result2[[2, 3, 7]])
+
+            c = copy(a)
+            result3 = Impute.declaremissings!(c; values=values)
+            @test eltype(result3) == Union{Float64, Missing}
+            @test all(ismissing, result3[[2, 3, 7]])
         end
 
         @testset "All missing" begin
             # Test having only missing data
             c = fill(missing, 10)
-            @test isequal(impute(c, imp), c)
+            @test isequal(apply(c, imp), c)
         end
     end
 
@@ -49,37 +52,35 @@
             a[[2, 3, 7]] .= [NaN, 0.0, NaN]
             m = collect(reshape(a, 5, 4))
 
-            result = impute(m, imp)
+            result = apply(m, imp)
             @test eltype(result) == Union{Float64, Missing}
             @test all(ismissing, result[[2, 3, 7]])
 
             # In-place operation don't work when the source array doesn't allow missings.
             n = copy(m)
-            result2 = impute!(n, imp)
-            @test eltype(result2) == Float64
-            @test isequal(result2[[2, 3, 7]], [NaN, 0.0, NaN])
+            @test_throws MethodError apply!(n, imp)
         end
 
         @testset "allowmissing" begin
             a = allowmissing(collect(1.0:1.0:20.0))
             a[[2, 3, 7]] .= [NaN, 0.0, NaN]
             m = collect(reshape(a, 5, 4))
 
-            result = impute(m, imp)
+            result = apply(m, imp)
             @test eltype(result) == Union{Float64, Missing}
             @test all(ismissing, result[[2, 3, 7]])
 
             # In-place operation don't work when the source array doesn't allow missings.
             n = copy(m)
-            result2 = impute!(n, imp)
+            result2 = apply!(n, imp)
             @test eltype(result2) == Union{Float64, Missing}
             @test all(ismissing, result2[[2, 3, 7]])
         end
 
         @testset "All missing" begin
             # Test having only missing data
             c = fill(missing, 5, 4)
-            @test isequal(impute(c, imp), c)
+            @test isequal(apply(c, imp), c)
         end
     end
     @testset "Tables" begin
@@ -106,21 +107,8 @@
                 :desc => ["foo", "bar", missing],
             )
 
-            @testset "disallowmissing" begin
-                result = impute(table, imp)
-                @test isequal(result, expected)
-
-                result2 = impute!(deepcopy(table), imp)
-                @test !isequal(result2, expected)
-            end
-
-            @testset "allowmissing" begin
-                result = impute(mtable, imp)
-                @test isequal(result, expected)
-
-                result2 = impute!(deepcopy(mtable), imp)
-                @test isequal(result2, expected)
-            end
+            result = apply(table, imp)
+            @test isequal(result, expected)
         end
 
         @testset "Column Table" begin
@@ -146,21 +134,8 @@
                 desc = ["foo", "bar", missing],
             )
 
-            @testset "disallowmissing" begin
-                result = impute(table, imp)
-                @test isequal(result, expected)
-
-                result2 = impute!(deepcopy(table), imp)
-                @test !isequal(result2, expected)
-            end
-
-            @testset "allowmissing" begin
-                result = impute(mtable, imp)
-                @test isequal(result, expected)
-
-                result2 = impute!(deepcopy(mtable), imp)
-                @test isequal(result2, expected)
-            end
+            result = apply(table, imp)
+            @test isequal(result, expected)
         end
 
         @testset "Row Table" begin
@@ -186,21 +161,8 @@
                 desc = ["foo", "bar", missing],
             ))
 
-            @testset "disallowmissing" begin
-                result = impute(table, imp)
-                @test isequal(result, expected)
-
-                result2 = impute!(deepcopy(table), imp)
-                @test !isequal(result2, expected)
-            end
-
-            @testset "allowmissing" begin
-                result = impute(mtable, imp)
-                @test isequal(result, expected)
-
-                result2 = impute!(deepcopy(mtable), imp)
-                @test isequal(result2, expected)
-            end
+            result = apply(table, imp)
+            @test isequal(result, expected)
         end
     end
 end

test/runtests.jl

@@ -36,6 +36,7 @@ using Impute:
     Threshold,
     ThresholdError,
     apply,
+    apply!,
     impute,
     impute!,
     interp,
@@ -48,6 +49,7 @@ using Impute:
     include("testutils.jl")
 
     include("validators.jl")
+    include("declaremissings.jl")
     include("chain.jl")
     include("data.jl")
     include("deprecated.jl")
@@ -58,7 +60,6 @@ using Impute:
     include("imputors/nocb.jl")
     include("imputors/replace.jl")
     include("imputors/srs.jl")
-    include("imputors/declaremissings.jl")
     include("imputors/substitute.jl")
     include("imputors/svd.jl")
     include("utils.jl")