Merge pull request #30 from JuliaAI/simplification

Major revision to simplify; in particular, to remove `obsfit`, `obspredict`, `obstransform`

Author: ablaom

.github/workflows/ci.yml

@@ -17,7 +17,8 @@ jobs:
       fail-fast: false
       matrix:
         version:
-          - '1.6'
+          - '1.6'  # previous LTS release
+          - '1.10' # new LTS release
           - '1' # automatically expands to the latest stable 1.x release of Julia.
         os:
           - ubuntu-latest
@@ -65,4 +66,4 @@ jobs:
             using Documenter: DocMeta, doctest
             using LearnAPI
             DocMeta.setdocmeta!(LearnAPI, :DocTestSetup, :(using LearnAPI); recursive=true)
-            doctest(LearnAPI)'
+            doctest(LearnAPI)'

Project.toml

@@ -14,9 +14,8 @@ DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0"
 LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
 MLUtils = "f1d291b0-491e-4a28-83b9-f70985020b54"
 Serialization = "9e88b42a-f829-5b0c-bbe9-9e923198166b"
-SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"
 Tables = "bd369af6-aec1-5ad0-b16a-f7cc5008161c"
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 
 [targets]
-test = ["DataFrames", "LinearAlgebra", "MLUtils", "Serialization", "SparseArrays", "Tables", "Test"]
+test = ["DataFrames", "LinearAlgebra", "MLUtils", "Serialization", "Tables", "Test"]

docs/Project.toml

@@ -1,5 +1,6 @@
 [deps]
 Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
+LearnAPI = "92ad9a40-7767-427a-9ee6-6e577f1266cb"
 MLUtils = "f1d291b0-491e-4a28-83b9-f70985020b54"
 ScientificTypesBase = "30f210dd-8aff-4c5f-94ba-8e64358c1161"
 Tables = "bd369af6-aec1-5ad0-b16a-f7cc5008161c"

docs/make.jl

@@ -6,18 +6,24 @@ const  REPO = Remotes.GitHub("JuliaAI", "LearnAPI.jl")
 
 makedocs(
     modules=[LearnAPI,],
-    format=Documenter.HTML(prettyurls = get(ENV, "CI", nothing) == "true"),
+    format=Documenter.HTML(
+        prettyurls = get(ENV, "CI", nothing) == "true",
+        collapselevel = 1,
+    ),
     pages=[
         "Home" => "index.md",
         "Anatomy of an Implementation" => "anatomy_of_an_implementation.md",
-        "Reference" => "reference.md",
-        "Kinds of Target Proxy" => "kinds_of_target_proxy.md",
-        "fit" => "fit.md",
-        "predict, transform, and relatives" => "predict_transform.md",
-        "minimize" => "minimize.md",
-        "obs" => "obs.md",
-        "Accessor Functions" => "accessor_functions.md",
-        "Algorithm Traits" => "traits.md",
+        "Reference" => [
+            "Overview" => "reference.md",
+            "fit/update" => "fit_update.md",
+            "predict/transform" => "predict_transform.md",
+            "Kinds of Target Proxy" => "kinds_of_target_proxy.md",
+            "minimize" => "minimize.md",
+            "target/weights/features" => "target_weights_features.md",
+            "obs" => "obs.md",
+            "Accessor Functions" => "accessor_functions.md",
+            "Algorithm Traits" => "traits.md",
+        ],
         "Common Implementation Patterns" => "common_implementation_patterns.md",
         "Testing an Implementation" => "testing_an_implementation.md",
     ],

docs/src/accessor_functions.md

@@ -1,7 +1,7 @@
 # [Accessor Functions](@id accessor_functions)
 
-The sole argument of an accessor function is the output, `model`, of [`fit`](@ref) or
-[`obsfit`](@ref).
+The sole argument of an accessor function is the output, `model`, of
+[`fit`](@ref). Algorithms are free to implement any number of these, or none of them.
 
 - [`LearnAPI.algorithm(model)`](@ref)
 - [`LearnAPI.extras(model)`](@ref)
@@ -12,9 +12,13 @@ The sole argument of an accessor function is the output, `model`, of [`fit`](@re
 - [`LearnAPI.feature_importances(model)`](@ref)
 - [`LearnAPI.training_labels(model)`](@ref)
 - [`LearnAPI.training_losses(model)`](@ref)
+- [`LearnAPI.training_predictions(model)`](@ref)
 - [`LearnAPI.training_scores(model)`](@ref)
 - [`LearnAPI.components(model)`](@ref)
 
+Algorithm-specific accessor functions may also be implemented. The names of all accessor
+functions are included in the list returned by [`LearnAPI.functions(algorithm)`](@ref).
+
 ## Implementation guide
 
 All new implementations must implement [`LearnAPI.algorithm`](@ref). While, all others are
@@ -33,6 +37,7 @@ LearnAPI.tree
 LearnAPI.trees
 LearnAPI.feature_importances
 LearnAPI.training_losses
+LearnAPI.training_predictions
 LearnAPI.training_scores
 LearnAPI.training_labels
 LearnAPI.components