From d329bf60658342a5deefa9fd86a1659ace71e1e6 Mon Sep 17 00:00:00 2001
From: Marc Becker <33069354+be-marc@users.noreply.github.com>
Date: Mon, 30 Mar 2020 17:31:52 +0200
Subject: [PATCH] Add Parameter test and missing parameters (#3)

---
 .github/workflows/paramtest.yml               | 97 +++++++++++++++++++
 R/LearnerClassifGAMBoost.R                    | 16 +--
 R/LearnerClassifGLMBoost.R                    |  6 +-
 R/LearnerRegrGAMBoost.R                       |  5 +-
 R/LearnerRegrGLMBoost.R                       |  6 +-
 README.md                                     |  1 +
 inst/paramtest/helper.R                       |  3 +
 .../test_paramtest_classif_gamboost.R         | 29 ++++++
 .../test_paramtest_classif_glmboost.R         | 29 ++++++
 inst/paramtest/test_paramtest_regr_gamboost.R | 29 ++++++
 inst/paramtest/test_paramtest_regr_glmboost.R | 29 ++++++
 11 files changed, 241 insertions(+), 9 deletions(-)
 create mode 100644 .github/workflows/paramtest.yml
 create mode 100644 inst/paramtest/helper.R
 create mode 100644 inst/paramtest/test_paramtest_classif_gamboost.R
 create mode 100644 inst/paramtest/test_paramtest_classif_glmboost.R
 create mode 100644 inst/paramtest/test_paramtest_regr_gamboost.R
 create mode 100644 inst/paramtest/test_paramtest_regr_glmboost.R

diff --git a/.github/workflows/paramtest.yml b/.github/workflows/paramtest.yml
new file mode 100644
index 0000000..9de368b
--- /dev/null
+++ b/.github/workflows/paramtest.yml
@@ -0,0 +1,97 @@
+on:
+  push:
+  pull_request:
+  # for now, CRON jobs only run on the default branch of the repo (i.e. usually on master)
+  schedule:
+    # * is a special character in YAML so you have to quote this string
+    - cron: "0 4 * * *"
+
+name: Parameter Check
+
+jobs:
+  R-CMD-check:
+    runs-on: ${{ matrix.config.os }}
+
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - { os: ubuntu-latest, r: "release" }
+
+    env:
+      # otherwise remotes::fun() errors cause the build to fail. Example: Unavailability of binaries
+      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
+      CRAN: ${{ matrix.config.cran }}
+      # we are not allowed to write to ~/.ccache on GH Actions
+      # setting some ccache options
+      CCACHE_BASEDIR: ${{ GITHUB.WORKSPACE }}
+      CCACHE_DIR: ${{ GITHUB.WORKSPACE }}/.ccache
+      CCACHE_NOHASHDIR: true
+      CCACHE_SLOPPINESS: include_file_ctime
+      # make sure to run `tic::use_ghactions_deploy()` to set up deployment
+      id_rsa: ${{ secrets.id_rsa }}
+      # prevent rgl issues because no X11 display is available
+      RGL_USE_NULL: true
+
+    steps:
+      - uses: actions/checkout@v2
+
+      - uses: r-lib/actions/setup-r@master
+        with:
+          r-version: ${{ matrix.config.r }}
+          Ncpus: 4
+
+      # set date/week for use in cache creation
+      # https://github.community/t5/GitHub-Actions/How-to-set-and-access-a-Workflow-variable/m-p/42970
+      # - cache R packages daily
+      # - cache ccache weekly -> 'ccache' helps rebuilding the package cache faster
+      - name: "[Cache] Prepare daily timestamp for cache"
+        if: runner.os != 'Windows'
+        id: date
+        run: echo "::set-output name=date::$(date '+%d-%m')"
+
+      - name: "[Cache] Prepare weekly timestamp for cache"
+        if: runner.os != 'Windows'
+        id: datew
+        run: echo "::set-output name=datew::$(date '+%Y-%V')"
+
+      - name: "[Cache] Cache R packages"
+        if: runner.os != 'Windows'
+        uses: pat-s/always-upload-cache@v1.1.4
+        with:
+          path: ${{ env.R_LIBS_USER }}
+          key: ${{ runner.os }}-r-${{ matrix.config.r }}-${{steps.date.outputs.date}}-1
+          restore-keys: ${{ runner.os }}-r-${{ matrix.config.r }}-${{steps.date.outputs.date}}-1
+
+      - name: "[Cache] Cache ccache"
+        if: runner.os != 'Windows'
+        uses: pat-s/always-upload-cache@v1.1.4
+        with:
+          path: ${{ env.CCACHE_DIR}}
+          key: ${{ runner.os }}-r-${{ matrix.config.r }}-ccache-${{steps.datew.outputs.datew}}
+          restore-keys: ${{ runner.os }}-r-${{ matrix.config.r }}-ccache-${{steps.datew.outputs.datew}}
+
+      # install ccache and write config file
+      - name: "[Linux] ccache"
+        if: runner.os == 'Linux'
+        run: |
+          sudo apt install ccache libcurl4-openssl-dev
+          mkdir -p ~/.R && echo -e 'CXX_STD = CXX14\n\nCC=ccache gcc -std=gnu99\nCXX=ccache g++\nCXX11=ccache g++ -std=gnu99\nCXX14=ccache g++ -std=gnu99\nC11=ccache g++\nC14=ccache g++\nFC=ccache gfortran\nF77=ccache gfortran' > $HOME/.R/Makevars
+
+      # for some strange Windows reason this step and the next one need to be decoupled
+      - name: "[Stage] Prepare"
+        run: |
+          Rscript -e "if (!requireNamespace('remotes')) install.packages('remotes', type = 'source')"
+          Rscript -e "if (getRversion() < '3.2' && !requireNamespace('curl')) install.packages('curl', type = 'source')"
+
+      - name: "[Stage] Install"
+        if: matrix.config.os != 'macOS-latest' || matrix.config.r != 'devel'
+        run: Rscript -e "remotes::install_github('ropensci/tic')" -e "print(tic::dsl_load())" -e "tic::prepare_all_stages()" -e "tic::before_install()" -e "tic::install()"
+
+      - name: "[Stage] Parameter test"
+        run: |
+          R CMD INSTALL .
+          Rscript -e "remotes::install_github('mlr-org/mlr3@paramtest')"
+          Rscript -e "testthat::test_dir(system.file('paramtest', package = 'mlr3learners.mboost'))"
diff --git a/R/LearnerClassifGAMBoost.R b/R/LearnerClassifGAMBoost.R
index abb7614..0155981 100644
--- a/R/LearnerClassifGAMBoost.R
+++ b/R/LearnerClassifGAMBoost.R
@@ -39,7 +39,10 @@ LearnerClassifGAMBoost = R6Class("LearnerClassifGAMBoost",
           ParamDbl$new(id = "nu", default = 0.1, tags = "train"),
           ParamFct$new(id = "risk", default = "inbag",
             levels = c("inbag", "oobag", "none"), tags = "train"),
-          ParamUty$new(id = "oobweights", default = NULL, tags = "train")
+          ParamUty$new(id = "oobweights", default = NULL, tags = "train"),
+          ParamLgl$new(id = "trace", default = FALSE, tags = "train"),
+          ParamUty$new(id = "stopintern", default = FALSE, tags = "train"),
+          ParamUty$new(id = "na.action", default = na.omit, tags = "train")
         )
       )
       ps$add_dep("type", "family", CondEqual$new("Binomial"))
@@ -84,7 +87,7 @@ LearnerClassifGAMBoost = R6Class("LearnerClassifGAMBoost",
       }
 
       pars_gamboost$family = switch(pars_gamboost$family,
-        Binomial = invoke(mboost::Binomial, .args = pars_binomial),
+        Binomial = mlr3misc::invoke(mboost::Binomial, .args = pars_binomial),
         AdaExp = mboost::AdaExp(),
         AUC = mboost::AUC())
 
@@ -94,12 +97,12 @@ LearnerClassifGAMBoost = R6Class("LearnerClassifGAMBoost",
         data[[task$target_names]] = factor(data[[task$target_names]], levs)
       }
 
-      ctrl = invoke(mboost::boost_control, .args = pars_boost)
+      ctrl = mlr3misc::invoke(mboost::boost_control, .args = pars_boost)
 
       # baselearner argument requires attached mboost package
       withr::with_package("mboost", {
-        invoke(mboost::gamboost, formula = f, data = data, control = ctrl,
-          .args = pars_gamboost)
+        mlr3misc::invoke(mboost::gamboost, formula = f, data = data,
+          control = ctrl, .args = pars_gamboost)
       })
     },
 
@@ -116,7 +119,8 @@ LearnerClassifGAMBoost = R6Class("LearnerClassifGAMBoost",
         p = invoke(predict, self$model, newdata = newdata, type = "class")
         PredictionClassif$new(task = task, response = p)
       } else {
-        p = invoke(predict, self$model, newdata = newdata, type = "response")
+        p = mlr3misc::invoke(predict, self$model, newdata = newdata,
+          type = "response")
         p = matrix(c(p, 1 - p), ncol = 2L, nrow = length(p))
         colnames(p) = task$class_names
         PredictionClassif$new(task = task, prob = p)
diff --git a/R/LearnerClassifGLMBoost.R b/R/LearnerClassifGLMBoost.R
index b584cea..ba40ce3 100644
--- a/R/LearnerClassifGLMBoost.R
+++ b/R/LearnerClassifGLMBoost.R
@@ -37,7 +37,11 @@ LearnerClassifGLMBoost = R6Class("LearnerClassifGLMBoost",
           ParamDbl$new(id = "nu", default = 0.1, tags = "train"),
           ParamFct$new(id = "risk", default = "inbag",
             levels = c("inbag", "oobag", "none"), tags = "train"),
-          ParamUty$new(id = "oobweights", default = NULL, tags = "train")
+          ParamUty$new(id = "oobweights", default = NULL, tags = "train"),
+          ParamLgl$new(id = "trace", default = FALSE, tags = "train"),
+          ParamUty$new(id = "stopintern", default = FALSE, tags = "train"),
+          ParamUty$new(id = "na.action", default = na.omit, tags = "train"),
+          ParamUty$new(id = "contrasts.arg", tags = "train")
         )
       )
       ps$add_dep("link", "family", CondEqual$new("Binomial"))
diff --git a/R/LearnerRegrGAMBoost.R b/R/LearnerRegrGAMBoost.R
index 8b9070c..e35805e 100644
--- a/R/LearnerRegrGAMBoost.R
+++ b/R/LearnerRegrGAMBoost.R
@@ -38,7 +38,10 @@ LearnerRegrGAMBoost = R6Class("LearnerRegrGAMBoost", inherit = LearnerRegr,
           ParamDbl$new(id = "nu", default = 0.1, tags = "train"),
           ParamFct$new(id = "risk", default = "inbag",
             levels = c("inbag", "oobag", "none"), tags = "train"),
-          ParamUty$new(id = "oobweights", default = NULL, tags = "train")
+          ParamUty$new(id = "oobweights", default = NULL, tags = "train"),
+          ParamLgl$new(id = "trace", default = FALSE, tags = "train"),
+          ParamUty$new(id = "stopintern", default = FALSE, tags = "train"),
+          ParamUty$new(id = "na.action", default = na.omit, tags = "train")
         )
       )
       ps$add_dep("oobweights", "risk", CondEqual$new("oobag"))
diff --git a/R/LearnerRegrGLMBoost.R b/R/LearnerRegrGLMBoost.R
index 2fe1731..5e3128b 100644
--- a/R/LearnerRegrGLMBoost.R
+++ b/R/LearnerRegrGLMBoost.R
@@ -36,7 +36,11 @@ LearnerRegrGLMBoost = R6Class("LearnerRegrGLMBoost", inherit = LearnerRegr,
           ParamDbl$new(id = "nu", default = 0.1, tags = "train"),
           ParamFct$new(id = "risk", default = "inbag",
             levels = c("inbag", "oobag", "none"), tags = "train"),
-          ParamUty$new(id = "oobweights", default = NULL, tags = "train")
+          ParamUty$new(id = "oobweights", default = NULL, tags = "train"),
+          ParamLgl$new(id = "trace", default = FALSE, tags = "train"),
+          ParamUty$new(id = "stopintern", default = FALSE, tags = "train"),
+          ParamUty$new(id = "na.action", default = na.omit, tags = "train"),
+          ParamUty$new(id = "contrasts.arg", tags = "train")
         )
       )
       ps$add_dep("oobweights", "risk", CondEqual$new("oobag"))
diff --git a/README.md b/README.md
index 69c8be5..2c21cd5 100644
--- a/README.md
+++ b/README.md
@@ -2,6 +2,7 @@
 
 <!-- badges: start -->
 [![R CMD Check via {tic}](https://github.com/mlr3learners/mlr3learners.mboost/workflows/R%20CMD%20Check%20via%20{tic}/badge.svg?branch=master)](https://github.com/mlr3learners/mlr3learners.mboost/actions)
+![Parameter Check](https://github.com/mlr3learners/mlr3learners.mboost/workflows/Parameter%20Check/badge.svg?branch=master)
 [![codecov](https://codecov.io/gh/mlr3learners/mlr3learners.mboost/branch/master/graph/badge.svg)](https://codecov.io/gh/mlr3learners/mlr3learners.mboost)
 [![StackOverflow](https://img.shields.io/badge/stackoverflow-mlr3-orange.svg)](https://stackoverflow.com/questions/tagged/mlr3)
 <!-- badges: end -->
diff --git a/inst/paramtest/helper.R b/inst/paramtest/helper.R
new file mode 100644
index 0000000..c45e08b
--- /dev/null
+++ b/inst/paramtest/helper.R
@@ -0,0 +1,3 @@
+library(mlr3)
+lapply(list.files(system.file("testthat", package = "mlr3"),
+  pattern = "helper_autotest", full.names = TRUE), source)
diff --git a/inst/paramtest/test_paramtest_classif_gamboost.R b/inst/paramtest/test_paramtest_classif_gamboost.R
new file mode 100644
index 0000000..bcfb9f8
--- /dev/null
+++ b/inst/paramtest/test_paramtest_classif_gamboost.R
@@ -0,0 +1,29 @@
+library(mlr3learners.mboost)
+
+test_that("classif.gamboost", {
+  learner = lrn("classif.gamboost")
+  fun = mboost::gamboost
+  exclude = c(
+    "formula", # handled via mlr3
+    "data", # handled via mlr3
+    "weights", # handled via mlr3
+    "control", # handled to mboost::boost_control
+    "..." # not used
+  )
+
+  ParamTest = run_paramtest(learner, fun, exclude)
+  expect_true(ParamTest, info = paste0("\nMissing parameters:\n",
+    paste0("- '", ParamTestresult$missing,"'", collapse = "\n")))
+})
+
+test_that("classif.gamboost_boost_control", {
+  learner = lrn("classif.gamboost")
+  fun = mboost::boost_control
+  exclude = c(
+    "center" # deprecated
+  )
+
+  ParamTest = run_paramtest(learner, fun, exclude)
+  expect_true(ParamTest, info = paste0("\nMissing parameters:\n",
+    paste0("- '", ParamTest$missing,"'", collapse = "\n")))
+})
diff --git a/inst/paramtest/test_paramtest_classif_glmboost.R b/inst/paramtest/test_paramtest_classif_glmboost.R
new file mode 100644
index 0000000..dbb3c65
--- /dev/null
+++ b/inst/paramtest/test_paramtest_classif_glmboost.R
@@ -0,0 +1,29 @@
+library(mlr3learners.mboost)
+
+test_that("classif.glmboost", {
+  learner = lrn("classif.glmboost")
+  fun = mboost:::glmboost.formula
+  exclude = c(
+    "formula", # handled via mlr3
+    "data", # handled via mlr3
+    "weights", # handled via mlr3
+    "control", # handled to mboost::boost_control
+    "..." # not used
+  )
+
+  ParamTest = run_paramtest(learner, fun, exclude)
+  expect_true(ParamTest, info = paste0("\nMissing parameters:\n",
+    paste0("- '", ParamTest$missing, "'", collapse = "\n")))
+})
+
+test_that("classif.glmboost_boost_control", {
+  learner = lrn("classif.glmboost")
+  fun = mboost::boost_control
+  exclude = c(
+    "center" # deprecated
+  )
+
+  ParamTest = run_paramtest(learner, fun, exclude)
+  expect_true(ParamTest, info = paste0("\nMissing parameters:\n",
+    paste0("- '", ParamTest$missing, "'", collapse = "\n")))
+})
diff --git a/inst/paramtest/test_paramtest_regr_gamboost.R b/inst/paramtest/test_paramtest_regr_gamboost.R
new file mode 100644
index 0000000..e391c3a
--- /dev/null
+++ b/inst/paramtest/test_paramtest_regr_gamboost.R
@@ -0,0 +1,29 @@
+library(mlr3learners.mboost)
+
+test_that("regr.gamboost", {
+  learner = lrn("regr.gamboost")
+  fun = mboost::gamboost
+  exclude = c(
+    "formula", # handled via mlr3
+    "data", # handled via mlr3
+    "weights", # handled via mlr3
+    "control", # handled to mboost::boost_control
+    "..." # not used
+  )
+
+  ParamTest = run_paramtest(learner, fun, exclude)
+  expect_true(ParamTest, info = paste0("\nMissing parameters:\n",
+    paste0("- '", ParamTest$missing, "'", collapse = "\n")))
+})
+
+test_that("regr.gamboost_boost_control", {
+  learner = lrn("regr.gamboost")
+  fun = mboost::boost_control
+  exclude = c(
+    "center" # deprecated
+  )
+
+  ParamTest = run_paramtest(learner, fun, exclude)
+  expect_true(ParamTest, info = paste0("\nMissing parameters:\n",
+    paste0("- '", ParamTest$missing, "'", collapse = "\n")))
+})
diff --git a/inst/paramtest/test_paramtest_regr_glmboost.R b/inst/paramtest/test_paramtest_regr_glmboost.R
new file mode 100644
index 0000000..02af01a
--- /dev/null
+++ b/inst/paramtest/test_paramtest_regr_glmboost.R
@@ -0,0 +1,29 @@
+library(mlr3learners.mboost)
+
+test_that("regr.glmboost", {
+  learner = lrn("regr.glmboost")
+  fun = mboost:::glmboost.formula
+  exclude = c(
+    "formula", # handled via mlr3
+    "data", # handled via mlr3
+    "weights", # handled via mlr3
+    "control", # handled to mboost::boost_control
+    "..." # not used
+  )
+
+  ParamTest = run_paramtest(learner, fun, exclude)
+  expect_true(ParamTest, info = paste0("\nMissing parameters:\n",
+    paste0("- '", ParamTest$missing, "'", collapse = "\n")))
+})
+
+test_that("regr.glmboost_boost_control", {
+  learner = lrn("regr.glmboost")
+  fun = mboost::boost_control
+  exclude = c(
+    "center" # deprecated
+  )
+
+  ParamTest = run_paramtest(learner, fun, exclude)
+  expect_true(ParamTest, info = paste0("\nMissing parameters:\n",
+    paste0("- '", ParamTest$missing, "'", collapse = "\n")))
+})