Add ExplicitImports.jl tests (#21)

Author: adrhill

Project.toml

@@ -5,8 +5,10 @@ version = "3.0.0-DEV"
 
 [deps]
 Flux = "587475ba-b771-5e3f-ad9e-33799f191a9c"
+MLUtils = "f1d291b0-491e-4a28-83b9-f70985020b54"
 MacroTools = "1914dd2f-81c6-5fcd-8719-6d5c9610ff09"
 Markdown = "d6f4376e-aef5-505a-96c1-9c027394607a"
+NNlib = "872c559c-99b0-510c-b3b7-b6c96a88d5cd"
 Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
 Reexport = "189a3867-3050-52da-a836-e630ba90ab69"
 Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
@@ -15,8 +17,10 @@ Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f"
 
 [compat]
 Flux = "0.14"
+MLUtils = "0.4.4"
 MacroTools = "0.5"
 Markdown = "1"
+NNlib = "0.9.24"
 Random = "1"
 Reexport = "1"
 Statistics = "1"

docs/src/developer.md

@@ -100,7 +100,7 @@ Using the [Zygote.jl](https://github.com/FluxML/Zygote.jl) AD system,
 we obtain the output $z$ of a modified layer and its pullback `back` in a single function call:
 
 ```julia
-z, back = Zygote.pullback(modified_layer, aᵏ)
+z, back = pullback(modified_layer, aᵏ)
 ```
 We then call the pullback with the vector $s$ to obtain $c$:
 ```julia
@@ -201,7 +201,7 @@ function lrp!(Rᵏ, rule, layer, modified_layer, aᵏ, Rᵏ⁺¹)
    layer = isnothing(modified_layer) ? layer : modified_layer
 
    ãᵏ = modify_input(rule, aᵏ)
-   z, back = Zygote.pullback(modified_layer, ãᵏ)
+   z, back = pullback(modified_layer, ãᵏ)
    s = Rᵏ⁺¹ ./ modify_denominator(rule, z)
    Rᵏ .= ãᵏ .* only(back(s))
 end

src/RelevancePropagation.jl

@@ -1,18 +1,27 @@
 module RelevancePropagation
 
-using Reexport
-@reexport using XAIBase
+using Base.Iterators
+using Reexport: @reexport
 import XAIBase: call_analyzer
+using XAIBase: XAIBase, AbstractXAIMethod, Explanation
+using XAIBase: AbstractOutputSelector, AbstractFeatureSelector, number_of_features
 
-using XAIBase: AbstractFeatureSelector, number_of_features
-using Base.Iterators
 using MacroTools: @forward
-using Flux
-using Flux: Scale, normalise
-using Zygote
-using Markdown
+using Flux: Flux, Chain, Parallel, SkipConnection
+using Flux: Dense, Conv, ConvTranspose, CrossCor
+using Flux: BatchNorm, GroupNorm, InstanceNorm, LayerNorm, Scale
+using Flux:
+    MaxPool, MeanPool, AdaptiveMaxPool, AdaptiveMeanPool, GlobalMaxPool, GlobalMeanPool
+using Flux: AlphaDropout, Dropout, dropout
+using NNlib: relu, gelu, swish, mish, softmax, softmax!
+using MLUtils: MLUtils
+
+using Zygote: pullback
+using Markdown: @md_str
 using Statistics: mean, std
 
+@reexport using XAIBase
+
 include("bibliography.jl")
 include("layer_types.jl")
 include("layer_utils.jl")

src/layer_types.jl

@@ -5,10 +5,10 @@ const DataflowLayer = Union{Chain,Parallel,SkipConnection}
 const ConvLayer = Union{Conv,ConvTranspose,CrossCor}
 
 """Union type for dropout layers."""
-const DropoutLayer = Union{Dropout,typeof(Flux.dropout),AlphaDropout}
+const DropoutLayer = Union{Dropout,typeof(dropout),AlphaDropout}
 
 """Union type for reshaping layers such as `flatten`."""
-const ReshapingLayer = Union{typeof(Flux.flatten),typeof(Flux.MLUtils.flatten)}
+const ReshapingLayer = Union{typeof(Flux.flatten),typeof(MLUtils.flatten)}
 
 """Union type for max pooling layers."""
 const MaxPoolLayer = Union{MaxPool,AdaptiveMaxPool,GlobalMaxPool}

src/rules.jl

@@ -12,7 +12,7 @@ const LRP_DEFAULT_BETA = 1.0f0
 function lrp!(Rᵏ, rule::AbstractLRPRule, layer, modified_layer, aᵏ, Rᵏ⁺¹)
     layer = isnothing(modified_layer) ? layer : modified_layer
     ãᵏ = modify_input(rule, aᵏ)
-    z, back = Zygote.pullback(layer, ãᵏ)
+    z, back = pullback(layer, ãᵏ)
     s = Rᵏ⁺¹ ./ modify_denominator(rule, z)
     c = only(back(s))
     Rᵏ .= ãᵏ .* c
@@ -338,9 +338,9 @@ function lrp!(Rᵏ, rule::ZBoxRule, layer, modified_layers, aᵏ, Rᵏ⁺¹)
     l = zbox_input(aᵏ, rule.low)
     h = zbox_input(aᵏ, rule.high)
 
-    z, back = Zygote.pullback(layer, aᵏ)
-    z⁺, back⁺ = Zygote.pullback(modified_layers.layer⁺, l)
-    z⁻, back⁻ = Zygote.pullback(modified_layers.layer⁻, h)
+    z, back = pullback(layer, aᵏ)
+    z⁺, back⁺ = pullback(modified_layers.layer⁺, l)
+    z⁻, back⁻ = pullback(modified_layers.layer⁻, h)
 
     s = Rᵏ⁺¹ ./ modify_denominator(rule, z - z⁺ - z⁻)
     c = only(back(s))
@@ -402,8 +402,8 @@ function lrp!(Rᵏ, rule::AlphaBetaRule, _layer, modified_layers, aᵏ, Rᵏ⁺
     aᵏ⁺ = keep_positive(aᵏ)
     aᵏ⁻ = keep_negative(aᵏ)
 
-    zᵅ⁺, back⁺ = Zygote.pullback(modified_layers.layerᵅ⁺, aᵏ⁺)
-    zᵅ⁻, back⁻ = Zygote.pullback(modified_layers.layerᵅ⁻, aᵏ⁻)
+    zᵅ⁺, back⁺ = pullback(modified_layers.layerᵅ⁺, aᵏ⁺)
+    zᵅ⁻, back⁻ = pullback(modified_layers.layerᵅ⁻, aᵏ⁻)
     # No need to linearize again: Wᵝ⁺ = Wᵅ⁺ and Wᵝ⁻ = Wᵅ⁻
     zᵝ⁺ = modified_layers.layerᵝ⁺(aᵏ⁻)
     zᵝ⁻ = modified_layers.layerᵝ⁻(aᵏ⁺)
@@ -451,8 +451,8 @@ function lrp!(Rᵏ, rule::ZPlusRule, _layer, modified_layers, aᵏ, Rᵏ⁺¹)
     aᵏ⁺ = keep_positive(aᵏ)
     aᵏ⁻ = keep_negative(aᵏ)
 
-    z⁺, back⁺ = Zygote.pullback(modified_layers.layer⁺, aᵏ⁺)
-    z⁻, back⁻ = Zygote.pullback(modified_layers.layer⁻, aᵏ⁻)
+    z⁺, back⁺ = pullback(modified_layers.layer⁺, aᵏ⁺)
+    z⁻, back⁻ = pullback(modified_layers.layer⁻, aᵏ⁻)
 
     s = Rᵏ⁺¹ ./ modify_denominator(rule, z⁺ + z⁻)
     c⁺ = only(back⁺(s))
@@ -504,8 +504,8 @@ function lrp!(Rᵏ, rule::GeneralizedGammaRule, layer, modified_layers, aᵏ, R
     aᵏ⁺ = keep_positive(aᵏ)
     aᵏ⁻ = keep_negative(aᵏ)
 
-    zˡ⁺, back⁺ = Zygote.pullback(modified_layers.layerˡ⁺, aᵏ⁺)
-    zˡ⁻, back⁻ = Zygote.pullback(modified_layers.layerˡ⁻, aᵏ⁻)
+    zˡ⁺, back⁺ = pullback(modified_layers.layerˡ⁺, aᵏ⁺)
+    zˡ⁻, back⁻ = pullback(modified_layers.layerˡ⁻, aᵏ⁻)
     # No need to linearize again: Wˡ⁺ = Wʳ⁺ and Wˡ⁻ = Wʳ⁻
     zʳ⁺ = modified_layers.layerʳ⁺(aᵏ⁻)
     zʳ⁻ = modified_layers.layerʳ⁻(aᵏ⁺)

test/Project.toml

@@ -1,6 +1,7 @@
 [deps]
 Aqua = "4c88cf16-eb10-579e-8560-4a9242c79595"
 BenchmarkTools = "6e4b80f9-dd63-53aa-95a3-0cdb28fa8baf"
+ExplicitImports = "7d51a73a-1435-4ff3-83d9-f097790105c7"
 Flux = "587475ba-b771-5e3f-ad9e-33799f191a9c"
 JLD2 = "033835bb-8acc-5ee8-8aae-3f567f8a3819"
 JuliaFormatter = "98e50ef6-434e-11e9-1051-2b60c6c9e899"

test/runtests.jl

@@ -6,18 +6,9 @@ using Aqua
 
 @testset verbose = true "RelevancePropagation.jl" begin
     @testset verbose = true "Linting" begin
-        @testset "Code formatting" begin
-            @info "- Testing code formatting with JuliaFormatter..."
-            @test JuliaFormatter.format(
-                RelevancePropagation; verbose=false, overwrite=false
-            )
-        end
-        @testset "Aqua.jl" begin
-            @info "- Running Aqua.jl tests. These might print warnings from dependencies..."
-            Aqua.test_all(RelevancePropagation; ambiguities=false)
-        end
+        @info "Testing linting..."
+        include("test_linting.jl")
     end
-
     @testset "Utilities" begin
         @info "Testing utilities..."
         include("test_utils.jl")

test/test_linting.jl

@@ -0,0 +1,40 @@
+using RelevancePropagation
+using Test
+
+using JuliaFormatter: JuliaFormatter
+using Aqua: Aqua
+using ExplicitImports:
+    check_no_implicit_imports,
+    check_no_stale_explicit_imports,
+    check_all_explicit_imports_via_owners,
+    check_all_qualified_accesses_via_owners,
+    check_no_self_qualified_accesses
+
+@testset "Code formatting" begin
+    @info "...with JuliaFormatter.jl"
+    @test JuliaFormatter.format(RelevancePropagation; verbose=false, overwrite=false)
+end
+
+@testset "Aqua.jl" begin
+    @info "...with Aqua.jl"
+    Aqua.test_all(RelevancePropagation; ambiguities=false)
+end
+
+@testset "ExplicitImports tests" begin
+    @info "...with ExplicitImports.jl"
+    @testset "Improper implicit imports" begin
+        @test check_no_implicit_imports(RelevancePropagation) === nothing
+    end
+    @testset "Improper explicit imports" begin
+        @test check_no_stale_explicit_imports(RelevancePropagation;) === nothing
+        @test check_all_explicit_imports_via_owners(RelevancePropagation) === nothing
+        # TODO: test in the future when `public` is more common
+        # @test check_all_explicit_imports_are_public(RelevancePropagation) === nothing
+    end
+    @testset "Improper qualified accesses" begin
+        @test check_all_qualified_accesses_via_owners(RelevancePropagation) === nothing
+        @test check_no_self_qualified_accesses(RelevancePropagation) === nothing
+        # TODO: test in the future when `public` is more common
+        # @test check_all_qualified_accesses_are_public(RelevancePropagation) === nothing
+    end
+end