Move unsort/unorder to tests

Author: juliangehring

Project.toml

@@ -7,7 +7,6 @@ version = "0.5.0"
 
 [deps]
 Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f"
-Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
 SpecialFunctions = "276daf66-3868-5448-9aa4-cd146d93841b"
 StatsBase = "2913bbd2-ae8a-5f71-8c99-4fb6c76f3a91"
 
@@ -18,7 +17,8 @@ StatsBase = "0.24.0 - 0.33"
 julia = "1.4"
 
 [extras]
+Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 
 [targets]
-test = ["Test"]
+test = ["Test", "Random"]

src/MultipleTesting.jl

@@ -16,8 +16,6 @@ import Distributions: estimate
 
 import SpecialFunctions: digamma
 
-import Random: shuffle!
-
 export PValues,
     adjust,
     PValueAdjustment,

src/utils.jl

@@ -1,22 +1,5 @@
 ## utility functions ##
 
-function unsort(x; kws...)
-    y = copy(x)
-    while issorted(y; kws...)
-        shuffle!(y)
-    end
-    return y
-end
-
-function unorder(x; kws...)
-    ord = collect(1:length(x))
-    while issorted(x[ord]; kws...)
-        shuffle!(ord)
-    end
-    return ord
-end
-
-
 function valid_pvalues(x::AbstractVector{T}) where T <: AbstractFloat
     if !isin(x)
         throw(DomainError("p-values must all be in [0, 1]"))

test/test-pi0-estimators.jl

@@ -5,6 +5,8 @@ using MultipleTesting
 using Test
 using StatsBase
 
+include("utils.jl")
+
 
 @testset "π₀ estimators" begin
 
@@ -16,8 +18,6 @@ using StatsBase
 
     lambdas = collect(0.05:0.05:0.95)
 
-    unsort = MultipleTesting.unsort
-
 
     @testset "Storey π₀" begin
 

test/test-pval-adjustment.jl

@@ -4,6 +4,8 @@ module Test_pval_adjustment
 using MultipleTesting
 using Test
 
+include("utils.jl")
+
 
 @testset "p-Value adjustment" begin
 
@@ -75,7 +77,7 @@ using Test
 
         # unsorted inputs
         for i in 1:10
-            ord = MultipleTesting.unorder(pval1)
+            ord = unorder(pval1)
             @test isapprox(adjust(pval1[ord], method()), ref1[method][ord], atol = 1e-9)
         end
 
@@ -88,15 +90,15 @@ using Test
         # this test is not valid for ForwardStop
         if method != ForwardStop
             for i in 1:10
-                ord = MultipleTesting.unorder(ref2[method])
+                ord = unorder(ref2[method])
                 @test isapprox(adjust(pval2[ord], method()), ref2[method][ord], atol = 1e-9) # FIXME
             end
         end
 
         ## sorting order does not play a role
         for i in 1:10
             pval4 = sort(rand(10)) # all under H0
-            ord = MultipleTesting.unorder(pval4)
+            ord = unorder(pval4)
             @test adjust(pval4[ord], method()) == adjust(pval4, method())[ord]
         end
 
@@ -112,7 +114,7 @@ using Test
 
             # unsorted inputs
             for i in 1:10
-                ord = MultipleTesting.unorder(pval3)
+                ord = unorder(pval3)
                 @test adjust(pval3[ord], n3, method()) == (adjust(pval3pad, n3, method())[1:k3])[ord]
             end
 

test/test-utils.jl

@@ -4,6 +4,8 @@ module Test_utils
 using MultipleTesting
 using Test
 
+include("utils.jl")
+
 
 @testset "Utility functions" begin
 
@@ -57,6 +59,29 @@ using Test
     end
 
 
+    @testset "harmonic_number" begin
+
+        # Exact computation as reference
+        harm_n_exact(n::Integer) = sum([Rational(1, i) for i in 1:BigInt(n)])
+
+        n = [1:100; 200:200:1000; 10000]
+
+        max_d = 0.0
+        for i in n
+            hn1 = MultipleTesting.harmonic_number(i)
+            hn2 = harm_n_exact(i)
+            max_d = max(abs(hn1 - hn2), max_d)
+        end
+        # approximation error in the range of floating point inaccuracy
+        @test max_d < (10 * eps())
+
+    end
+
+end
+
+
+@testset "Helper functions for testing" begin
+
     @testset "unsort" begin
 
         n = 20
@@ -65,8 +90,6 @@ using Test
         xu = xs[[1:2:n - 1; 2:2:n]] # unsorted
         @test !issorted(xu)
 
-        unsort = MultipleTesting.unsort
-
         @test issorted(xs)
         @test !issorted(unsort(xs))
 
@@ -90,8 +113,6 @@ using Test
         xu = xs[[1:2:n - 1; 2:2:n]] # unsorted
         @test !issorted(xu)
 
-        unorder = MultipleTesting.unorder
-
         @test issorted(xs)
         ord = unorder(xs)
         @test !issorted(ord)
@@ -110,25 +131,6 @@ using Test
 
     end
 
-
-    @testset "harmonic_number" begin
-
-        # Exact computation as reference
-        harm_n_exact(n::Integer) = sum([Rational(1, i) for i in 1:BigInt(n)])
-
-        n = [1:100; 200:200:1000; 10000]
-
-        max_d = 0.0
-        for i in n
-            hn1 = MultipleTesting.harmonic_number(i)
-            hn2 = harm_n_exact(i)
-            max_d = max(abs(hn1 - hn2), max_d)
-        end
-        # approximation error in the range of floating point inaccuracy
-        @test max_d < (10 * eps())
-
-    end
-
 end
 
 end

test/utils.jl

@@ -0,0 +1,19 @@
+# helper functions
+
+import Random: shuffle!
+
+function unsort(x; kws...)
+    y = copy(x)
+    while issorted(y; kws...)
+        shuffle!(y)
+    end
+    return y
+end
+
+function unorder(x; kws...)
+    ord = collect(1:length(x))
+    while issorted(x[ord]; kws...)
+        shuffle!(ord)
+    end
+    return ord
+end