Fix tests for GLM v1.9 (#47)

* warning for wrong type for * print test_args * qrpred not exported by GLM v1.9.0 format undo format qrpred not fully defined in GLM v1.9 qrpred is not defined in GLM v1.9 * GHA: do not duplicate jobs * add julia-format action add julia-format action format docs files gha naming * docs add CategoricalArrays dep * refactor and improve treating edge cases * correct function entries in docs * refactorize input validation for fit method * fix doctest * use format-check from MixedModels.jl * add typos github action * run typos * follow .JuliaFormatter.toml * run format correct type correct type correct type * do not show QR pivoted warning when installing the package * fix docs fix docs * fix some docs
getzze · Sep 25, 2024 · 9796dad · 9796dad
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diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml
@@ -1,15 +1,71 @@
 name: CI
+
 on:
-  - push
-  - pull_request
+  push:
+    branches:
+      - 'main'
+      - 'release-'
+    tags: '*'
+  pull_request:
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+env:
+  FORCE_COLOR: "1"
+
+
 jobs:
+  format-check:
+    # note: keep in sync with `format/run.jl`
+    name: Style check (Julia ${{ matrix.julia-version }} - ${{ github.event_name }})
+    # Run on push's or non-draft PRs
+    if: (github.event_name == 'push') || (github.event.pull_request.draft == false)
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        julia-version: [1.6]
+    steps:
+      - uses: julia-actions/setup-julia@latest
+        with:
+          version: ${{ matrix.julia-version }}
+      - uses: actions/checkout@v4
+      - name: Instantiate `format` environment and format
+        run: |
+          julia --project=format -e 'using Pkg; Pkg.instantiate()'
+          julia --project=format 'format/run.jl'
+      - uses: reviewdog/action-suggester@v1
+        if: github.event_name == 'pull_request'
+        with:
+          tool_name: JuliaFormatter
+          fail_on_error: true
+
+  typos-check:
+    name: Spell Check with Typos
+    # Run on PRs
+    if: github.event_name == 'pull_request'
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout Actions Repository
+        uses: actions/checkout@v4
+      - name: Check spelling
+        uses: crate-ci/typos@master
+        with:
+            config: ./_typos.toml
+            write_changes: true
+      - uses: reviewdog/action-suggester@v1
+        with:
+          tool_name: Typos
+          fail_on_error: true
+
   test:
-    name: Julia ${{ matrix.version }} - ${{ matrix.os }} - ${{ matrix.arch }} - ${{ github.event_name }}
+    name: Julia ${{ matrix.julia-version }} - ${{ matrix.os }} - ${{ matrix.arch }} - ${{ github.event_name }}
     runs-on: ${{ matrix.os }}
     strategy:
       fail-fast: false
       matrix:
-        version:
+        julia-version:
           - '1.6'
           - '1'  # latest stable 1.x release
           - 'nightly'
@@ -18,10 +74,10 @@ jobs:
         arch:
           - x64
     steps:
-      - uses: actions/checkout@v2
-      - uses: julia-actions/setup-julia@v1
+      - uses: actions/checkout@v4
+      - uses: julia-actions/setup-julia@latest
         with:
-          version: ${{ matrix.version }}
+          version: ${{ matrix.julia-version }}
           arch: ${{ matrix.arch }}
       - uses: actions/cache@v1
         env:
@@ -43,8 +99,8 @@ jobs:
     name: Documentation
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
-      - uses: julia-actions/setup-julia@v1
+      - uses: actions/checkout@v4
+      - uses: julia-actions/setup-julia@latest
         with:
           version: '1'
       - name: Install dependencies

diff --git a/.github/workflows/format-check.yml b/.github/workflows/format-check.yml
diff --git a/README.md b/README.md
@@ -43,13 +43,13 @@ This package implements:
 
 ## Installation
 
-```julia
+```
 julia>] add RobustModels
 ```
 
 To install the last development version:
 
-```julia
+```
 julia>] add RobustModels#main
 ```
 

diff --git a/_typos.toml b/_typos.toml
@@ -0,0 +1,10 @@
+# https://github.com/crate-ci/typos#false-positives
+[default]
+
+[default.extend-identifiers]
+missings = "missings"
+Missings = "Missings"
+Artic = "Artic"
+
+[default.extend-words]
+qest = "qest"
diff --git a/docs/Project.toml b/docs/Project.toml
@@ -1,11 +1,14 @@
 [deps]
+CategoricalArrays = "324d7699-5711-5eae-9e2f-1d82baa6b597"
 DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0"
 Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f"
 Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
 GLM = "38e38edf-8417-5370-95a0-9cbb8c7f171a"
 LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
 RDatasets = "ce6b1742-4840-55fa-b093-852dadbb1d8b"
+RobustModels = "d6ea1423-9682-4bbd-952f-b1577cbf8c98"
 SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"
 Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
+StatsAPI = "82ae8749-77ed-4fe6-ae5f-f523153014b0"
 StatsBase = "2913bbd2-ae8a-5f71-8c99-4fb6c76f3a91"
 StatsModels = "3eaba693-59b7-5ba5-a881-562e759f1c8d"
diff --git a/docs/make.jl b/docs/make.jl
@@ -1,15 +1,18 @@
 using Documenter
-using GLM, StatsBase, SparseArrays, LinearAlgebra
+using GLM, StatsBase, StatsAPI, SparseArrays, LinearAlgebra
 using RobustModels
 
 DocMeta.setdocmeta!(
-    RobustModels, :DocTestSetup, :(using RobustModels, StatsBase, GLM); recursive=true
+    RobustModels,
+    :DocTestSetup,
+    :(using RobustModels, StatsBase, GLM, StatsAPI);
+    recursive=true,
 )
 
 prettyurls = get(ENV, "CI", "false") == "true"
 
 makedocs(;
-    modules=[RobustModels, GLM, StatsBase],
+    modules=[RobustModels, GLM, StatsBase, StatsAPI],
     sitename="RobustModels",
     authors="Bertrand Lacoste <[email protected]>",
     repo="https://github.com/getzze/RobustModels.jl/blob/{commit}{path}#{line}",
@@ -18,17 +21,18 @@ makedocs(;
         canonical="https://getzze.github.io/RobustModels.jl",
         assets=["assets/favicon.ico"],
     ),
+    #! format: off
     pages=[
-        "Home" => "index.md", 
-        "manual.md", 
-        "examples.md", 
+        "Home" => "index.md",
+        "manual.md",
+        "examples.md",
         "api.md",
     ],
+    #! format: on
+    ## Uncomment the line below to re-generate doctest outputs
     # doctest = :fix,
+    warnonly=[:missing_docs],
     debug=false,
 )
 
-deploydocs(; 
-    devbranch="main", 
-    repo="github.com/getzze/RobustModels.jl",
-)
+deploydocs(; devbranch="main", repo="github.com/getzze/RobustModels.jl")
diff --git a/docs/src/api.md b/docs/src/api.md
@@ -8,20 +8,23 @@ AbstractEstimator
 AbstractQuantileEstimator
 LossFunction
 RobustLinearModel
+RobustModels.RobustLinResp
+GLM.LinPred
 RobustModels.DensePredCG
 RobustModels.SparsePredCG
 GLM.DensePredChol
 GLM.SparsePredChol
+GLM.DensePredQR
 RobustModels.RidgePred
-RobustModels.RobustLinResp
+RobustModels.AbstractRegularizedPred
 QuantileRegression
 ```
 
 ## Constructors for models
 
 ```@docs
-fit(::Type{M}, ::Union{AbstractMatrix{T},SparseMatrixCSC{T}}, ::AbstractVector{T}, ::AbstractEstimator) where {T<:AbstractFloat, M<:RobustLinearModel}
-fit(::Type{M}, ::Union{AbstractMatrix{T},SparseMatrixCSC{T}}, ::AbstractVector{T}) where {T<:AbstractFloat, M<:QuantileRegression}
+fit(::Type{M}, ::Union{AbstractMatrix{T}}, ::AbstractVector{T}, ::AbstractMEstimator) where {T<:AbstractFloat, M<:RobustLinearModel}
+fit(::Type{M}, ::Union{AbstractMatrix{T}}, ::AbstractVector{T}) where {T<:AbstractFloat, M<:QuantileRegression}
 ```
 
 ```@docs
@@ -33,34 +36,45 @@ refit!
 
 ## Model methods
 ```@docs
-StatsBase.coef
-StatsBase.coeftable
-StatsBase.confint
+StatsModels.coef
+StatsAPI.coeftable
+StatsAPI.coefnames
+StatsModels.responsename
+StatsAPI.confint
 StatsBase.deviance
 StatsBase.nulldeviance
-StatsBase.dof
-StatsBase.dof_residual
-nobs(::StatisticalModel)
-StatsBase.isfitted
-StatsBase.islinear
-StatsBase.loglikelihood
-StatsBase.nullloglikelihood
-StatsBase.stderror
+StatsAPI.dof
+StatsAPI.dof_residual
+StatsBase.nobs
+wobs
+StatsAPI.isfitted
+StatsAPI.islinear
+StatsAPI.loglikelihood
+StatsAPI.nullloglikelihood
+StatsAPI.stderror
 StatsBase.vcov
 StatsBase.weights
 workingweights
-StatsBase.fitted
+StatsAPI.fitted
 StatsBase.predict
-StatsBase.leverage
-StatsBase.modelmatrix
+StatsModels.leverage
+leverage_weights
+StatsAPI.modelmatrix
 projectionmatrix
-GLM.dispersion(::RobustLinearModel, ::Bool)
-StatsBase.response
-StatsBase.residuals
+dispersion(::RobustLinearModel, ::Bool)
+StatsAPI.response
+StatsAPI.residuals
+StatsModels.hasintercept
+hasformula
+formula
 scale
 tauscale
 RobustModels.location_variance
 Estimator
+GLM.linpred!
+RobustModels.pirls!
+RobustModels.pirls_Sestimate!
+RobustModels.pirls_τestimate!
 ```
 
 ## Estimators
@@ -78,18 +92,23 @@ RobustModels.QuantileEstimator
 
 ## Loss functions
 ```@docs
+BoundedLossFunction
 L2Loss
 L1Loss
 HuberLoss
 L1L2Loss
 FairLoss
 LogcoshLoss
 ArctanLoss
+CatoniWideLoss
+CatoniNarrowLoss
 CauchyLoss
 GemanLoss
 WelschLoss
 TukeyLoss
 YohaiZamarLoss
+HardThresholdLoss
+HampelLoss
 ```
 
 ## Estimator and Loss functions methods
@@ -98,7 +117,7 @@ RobustModels.rho
 RobustModels.psi
 RobustModels.psider
 RobustModels.weight
-RobustModels.values
+RobustModels.estimator_values
 RobustModels.estimator_norm
 RobustModels.estimator_bound
 tuning_constant
@@ -121,5 +140,3 @@ RobustModels.update_weight!
 RobustModels.tau_scale_estimate
 RobustModels.quantile_weight
 ```
-
-
diff --git a/docs/src/examples.md b/docs/src/examples.md
@@ -37,12 +37,12 @@ X            2.02857      0.200679  10.11    0.0005    1.4714     2.58575
 ─────────────────────────────────────────────────────────────────────────
 
 julia> round.(stderror(ols), digits=5)
-2-element Array{Float64,1}:
+2-element Vector{Float64}:
  0.78153
  0.20068
 
 julia> round.(predict(ols), digits=5)
-6-element Array{Float64,1}:
+6-element Vector{Float64}:
   2.09524
   4.12381
   6.15238
@@ -61,7 +61,7 @@ julia> data[5, :Y] = 1; data
    4 │     4      8
    5 │     5      1
    6 │     6     13
- 
+
 julia> rob = rlm(@formula(Y ~ X), data, MMEstimator{TukeyLoss}(); σ0=:mad)
 Robust regression with MM-Estimator(TukeyLoss(1.5476), TukeyLoss(4.685))
 
@@ -76,4 +76,3 @@ X             2.18005     0.14112   15.45    0.0001    1.78824    2.57186
 ─────────────────────────────────────────────────────────────────────────
 
 ```
-