Merge pull request #614 from JuliaAI/dev

For a 0.18.5 release

Author: ablaom

.github/dependabot.yml

@@ -0,0 +1,12 @@
+# https://docs.github.com/github/administering-a-repository/configuration-options-for-dependency-updates
+version: 2
+updates:
+  - package-ecosystem: "github-actions"
+    directory: "/" # Location of package manifests
+    schedule:
+      interval: "monthly"
+  - package-ecosystem: "julia"
+    directories: # Location of Julia projects
+      - "/"
+    schedule:
+      interval: "weekly"

.github/workflows/CompatHelper.yml

@@ -24,12 +24,12 @@ jobs:
         arch:
           - x64
     steps:
-      - uses: actions/checkout@v2
-      - uses: julia-actions/setup-julia@v1
+      - uses: actions/checkout@v6
+      - uses: julia-actions/setup-julia@v2
         with:
           version: ${{ matrix.version }}
           arch: ${{ matrix.arch }}
-      - uses: julia-actions/cache@v1
+      - uses: julia-actions/cache@v3
         env:
           cache-name: cache-artifacts
         with:
@@ -45,7 +45,7 @@ jobs:
           # This environment variable enables the integration tests:
           MLJ_TEST_REGISTRY: "false"
       - uses: julia-actions/julia-processcoverage@v1
-      - uses: codecov/codecov-action@v4
+      - uses: codecov/codecov-action@v6
         with:
           token: ${{ secrets.CODECOV_TOKEN }}
           fail_ci_if_error: false

.github/workflows/ci.yml

@@ -1,7 +1,7 @@
 name = "MLJModels"
 uuid = "d491faf4-2d78-11e9-2867-c94bc002c0b7"
 authors = ["Anthony D. Blaom <anthony.blaom@gmail.com>"]
-version = "0.18.4"
+version = "0.18.5"
 
 [deps]
 CategoricalArrays = "324d7699-5711-5eae-9e2f-1d82baa6b597"

Project.toml

@@ -245,8 +245,14 @@ function MMI.fitted_params(model::ThresholdUnion, fitresult)
         )
 end
 
+# to strip off any "report" part of the atomic model's output of `predict`:
+prediction_part(output, atomic_model) =
+    prediction_part(output, Val(:predict in MMI.reporting_operations(atomic_model)))
+prediction_part(output, ::Val{true}) = first(output)
+prediction_part(output, ::Val{false}) = output
+
 function MMI.predict(model::ThresholdUnion, fitresult, X)
-    yhat = MMI.predict(model.model, fitresult[1], X)
+    yhat = prediction_part(MMI.predict(model.model, fitresult[1], X), model.model)
     threshold = (1 - fitresult[2], fitresult[2])
     return _predict_threshold(yhat, threshold)
 end

src/builtins/ThresholdPredictors.jl

@@ -18,7 +18,6 @@ MLJGLMInterface = "caf8df21-4939-456d-ac9c-5fefbfb04c0c"
 MLJIteration = "614be32b-d00c-4edb-bd02-1eb411ab5e55"
 MLJLIBSVMInterface = "61c7150f-6c77-4bb1-949c-13197eac2a52"
 MLJLinearModels = "6ee0df7b-362f-4a72-a706-9e79364fb692"
-MLJModelRegistryTools = "0a96183e-380b-4aa6-be10-c555140810f2"
 MLJModels = "d491faf4-2d78-11e9-2867-c94bc002c0b7"
 MLJMultivariateStatsInterface = "1b6a4a23-ba22-4f51-9698-8599985d3728"
 MLJNaiveBayesInterface = "33e4bacb-b9e2-458e-9a13-5d9a90b235fa"

src/registry/Metadata.toml

@@ -323,6 +323,21 @@ end
     @test MLJBase.predict(mach2, (; x = rand(2))) ==  yhat
 end
 
+@testset "wrapping models with non-empty `reporting_observations`" begin
+    # to resolve https://github.com/JuliaAI/MLJModels.jl/issues/606
+
+    X = (x = rand(3),)
+    y = coerce([0, 1, 0], OrderedFactor)
+    mode_class = y[1] # `0`
+
+    clf = ConstantClassifier()
+    pipe = Standardizer() |> clf
+    point_predictor = BinaryThresholdPredictor(pipe)
+
+    mach = MLJBase.machine(point_predictor, X, y) |> MLJBase.fit!
+    @test MLJBase.predict(mach, X) == fill(mode_class, 3)
+end
+
 end # module
 
 true

src/registry/Project.toml

@@ -2,33 +2,28 @@ import Pkg
 
 using Test, MLJModels, MLJTransforms
 
-@testset "metadata" begin
-    @testset "metadata.jl" begin
-        @test include("metadata.jl")
-    end
-    @testset "model search" begin
-        @test include("model_search.jl")
-    end
-    @testset "loading model code" begin
-        @test include("loading.jl")
-    end
-end
-
-@testset "built-in models" begin
-    @testset "Constant.jl" begin
-        @test include("builtins/Constant.jl")
-    end
-    @testset "ThresholdPredictors" begin
-        @test include("builtins/ThresholdPredictors.jl")
-    end
-end
+test_files = [
+    "metadata.jl",
+    "model_search.jl",
+    "loading.jl",
+    joinpath("builtins", "Constant.jl"),
+    joinpath("builtins", "ThresholdPredictors.jl"),
+]
 
 if parse(Bool, get(ENV, "MLJ_TEST_REGISTRY", "false"))
-    @testset "registry" begin
-        @test include("registry.jl")
-    end
+    push!(test_files, "registry.jl")
 else
     @info "Test of the MLJ Registry is being skipped. Set environment variable "*
         "MLJ_TEST_REGISTRY = \"true\" to include them.\n"*
         "The Registry test takes about ten minutes. "
 end
+
+files = isempty(ARGS) ? test_files : ARGS
+
+for file in files
+    quote
+        @testset $file begin
+            include($file)
+        end
+    end |> eval
+end