From 3bd0f8a7e97b4693e5bd333aef1793317bc94d13 Mon Sep 17 00:00:00 2001
From: "Anthony D. Blaom" <anthony.blaom@gmail.com>
Date: Wed, 25 Mar 2026 14:01:42 +1300
Subject: [PATCH 1/3] swap out CompatHelper for dependabot GH action

---
 .github/dependabot.yml             | 12 ++++++++++++
 .github/workflows/CompatHelper.yml | 16 ----------------
 2 files changed, 12 insertions(+), 16 deletions(-)
 create mode 100644 .github/dependabot.yml
 delete mode 100644 .github/workflows/CompatHelper.yml

diff --git a/.github/dependabot.yml b/.github/dependabot.yml
new file mode 100644
index 00000000..9c3da475
--- /dev/null
+++ b/.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"
diff --git a/.github/workflows/CompatHelper.yml b/.github/workflows/CompatHelper.yml
deleted file mode 100644
index d1217f23..00000000
--- a/.github/workflows/CompatHelper.yml
+++ /dev/null
@@ -1,16 +0,0 @@
-name: CompatHelper
-on:
-  schedule:
-    - cron: '00 00 * * *'
-  workflow_dispatch:
-jobs:
-  CompatHelper:
-    runs-on: ubuntu-latest
-    steps:
-      - name: Pkg.add("CompatHelper")
-        run: julia -e 'using Pkg; Pkg.add("CompatHelper")'
-      - name: CompatHelper.main()
-        env:
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-          COMPATHELPER_PRIV: ${{ secrets.DOCUMENTER_KEY }}
-        run: julia -e 'using CompatHelper; CompatHelper.main(; master_branch = "dev")'

From 59302e18c20c25ded02a137678dd58a08437191b Mon Sep 17 00:00:00 2001
From: "Anthony D. Blaom" <anthony.blaom@gmail.com>
Date: Wed, 25 Mar 2026 14:02:26 +1300
Subject: [PATCH 2/3] "modernize" runtests

---
 test/runtests.jl | 41 ++++++++++++++++++-----------------------
 1 file changed, 18 insertions(+), 23 deletions(-)

diff --git a/test/runtests.jl b/test/runtests.jl
index da955718..7550b512 100755
--- a/test/runtests.jl
+++ b/test/runtests.jl
@@ -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

From 2e1ac79f71553e3fdf9a476c9561b06114d884c8 Mon Sep 17 00:00:00 2001
From: "Anthony D. Blaom" <anthony.blaom@gmail.com>
Date: Wed, 25 Mar 2026 14:08:55 +1300
Subject: [PATCH 3/3] fix bug to resolve #606

---
 src/builtins/ThresholdPredictors.jl  |  8 +++++++-
 test/builtins/ThresholdPredictors.jl | 15 +++++++++++++++
 2 files changed, 22 insertions(+), 1 deletion(-)

diff --git a/src/builtins/ThresholdPredictors.jl b/src/builtins/ThresholdPredictors.jl
index 9b06f8a5..c0b82423 100644
--- a/src/builtins/ThresholdPredictors.jl
+++ b/src/builtins/ThresholdPredictors.jl
@@ -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
diff --git a/test/builtins/ThresholdPredictors.jl b/test/builtins/ThresholdPredictors.jl
index f8525d69..e074325e 100644
--- a/test/builtins/ThresholdPredictors.jl
+++ b/test/builtins/ThresholdPredictors.jl
@@ -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