[ci] [python-package] [R-package] adapt to scikit-learn...

[ci] [python-package] [R-package] adapt to scikit-learn check_sample_weight_equivalence changes, stop testing against R 3.6 on Linux (#6733)

.ci/install-old-r-packages.R

-# [description]
-#
-#    Installs a pinned set of packages that worked together
-#    as of the last R 3.6 release.
-#
-
-.install_packages <- function(packages) {
-    install.packages(  # nolint: undesirable_function
-        pkgs = paste(  # nolint: paste
-            "https://cran.r-project.org/src/contrib/Archive"
-            , packages
-            , sep = "/"
-        )
-        , dependencies = FALSE
-        , lib = Sys.getenv("R_LIBS")
-        , repos = NULL
-    )
-}
-
-# when confronted with a bunch of URLs like this, install.packages() sometimes
-# struggles to determine install order... so install packages in batches here,
-# starting from the root of the dependency graph and working up
-
-# there was only a single release of {praise}, so there is no contrib/Archive URL for it
-install.packages(  # nolint: undesirable_function
-    pkgs = "https://cran.r-project.org/src/contrib/praise_1.0.0.tar.gz"
-    , dependencies = FALSE
-    , lib = Sys.getenv("R_LIBS")
-    , repos = NULL
-)
-
-.install_packages(c(
-    "brio/brio_1.1.4.tar.gz"              # nolint: non_portable_path
-    , "cli/cli_3.6.2.tar.gz"              # nolint: non_portable_path
-    , "crayon/crayon_1.5.2.tar.gz"        # nolint: non_portable_path
-    , "digest/digest_0.6.36.tar.gz"       # nolint: non_portable_path
-    , "evaluate/evaluate_0.23.tar.gz"     # nolint: non_portable_path
-    , "fansi/fansi_1.0.5.tar.gz"          # nolint: non_portable_path
-    , "fs/fs_1.6.4.tar.gz"                # nolint: non_portable_path
-    , "glue/glue_1.7.0.tar.gz"            # nolint: non_portable_path
-    , "jsonlite/jsonlite_1.8.8.tar.gz"    # nolint: non_portable_path
-    , "lattice/lattice_0.20-41.tar.gz"    # nolint: non_portable_path
-    , "magrittr/magrittr_2.0.2.tar.gz"    # nolint: non_portable_path
-    , "pkgconfig/pkgconfig_2.0.2.tar.gz"  # nolint: non_portable_path
-    , "ps/ps_1.8.0.tar.gz"                # nolint: non_portable_path
-    , "R6/R6_2.5.0.tar.gz"                # nolint: non_portable_path
-    , "rlang/rlang_1.1.3.tar.gz"          # nolint: non_portable_path
-    , "rprojroot/rprojroot_2.0.3.tar.gz"  # nolint: non_portable_path
-    , "utf8/utf8_1.2.3.tar.gz"            # nolint: non_portable_path
-    , "withr/withr_3.0.1.tar.gz"          # nolint: non_portable_path
-))
-
-.install_packages(c(
-    "desc/desc_1.4.2.tar.gz"              # nolint: non_portable_path
-    , "diffobj/diffobj_0.3.4.tar.gz"      # nolint: non_portable_path
-    , "lifecycle/lifecycle_1.0.3.tar.gz"  # nolint: non_portable_path
-    , "processx/processx_3.8.3.tar.gz"    # nolint: non_portable_path
-))
-
-.install_packages(c(
-    "callr/callr_3.7.5.tar.gz"    # nolint: non_portable_path
-    , "vctrs/vctrs_0.6.4.tar.gz"  # nolint: non_portable_path
-))
-
-.install_packages(c(
-    "pillar/pillar_1.8.1.tar.gz"    # nolint: non_portable_path
-    , "tibble/tibble_3.2.0.tar.gz"  # nolint: non_portable_path
-))
-
-.install_packages(c(
-    "pkgbuild/pkgbuild_1.4.4.tar.gz"    # nolint: non_portable_path
-    , "rematch2/rematch2_2.1.1.tar.gz"  # nolint: non_portable_path
-    , "waldo/waldo_0.5.3.tar.gz"        # nolint: non_portable_path
-))
-
-.install_packages(c(
-    "pkgload/pkgload_1.3.4.tar.gz"      # nolint: non_portable_path
-    , "testthat/testthat_3.2.1.tar.gz"  # nolint: non_portable_path
-))

.ci/test-r-package.sh

@@ -20,12 +20,7 @@ fi
 
 # Get details needed for installing R components
 R_MAJOR_VERSION="${R_VERSION%.*}"
-if [[ "${R_MAJOR_VERSION}" == "3" ]]; then
-    export R_MAC_VERSION=3.6.3
-    export R_MAC_PKG_URL=${CRAN_MIRROR}/bin/macosx/R-${R_MAC_VERSION}.nn.pkg
-    export R_LINUX_VERSION="3.6.3-1bionic"
-    export R_APT_REPO="bionic-cran35/"
-elif [[ "${R_MAJOR_VERSION}" == "4" ]]; then
+if [[ "${R_MAJOR_VERSION}" == "4" ]]; then
     export R_MAC_VERSION=4.3.1
     export R_MAC_PKG_URL=${CRAN_MIRROR}/bin/macosx/big-sur-${ARCH}/base/R-${R_MAC_VERSION}-${ARCH}.pkg
     export R_LINUX_VERSION="4.3.1-1.2204.0"
@@ -108,16 +103,10 @@ if [[ $OS_NAME == "macos" ]]; then
     export R_TIDYCMD=/usr/local/bin/tidy
 fi
 
-# fix for issue where CRAN was not returning {evaluate}, {lattice}, or {waldo} when using R 3.6
-# "Warning: dependency ‘lattice’ is not available"
-if [[ "${R_MAJOR_VERSION}" == "3" ]]; then
-    Rscript --vanilla ./.ci/install-old-r-packages.R
-else
-    # {Matrix} needs {lattice}, so this needs to run before manually installing {Matrix}.
-    # This should be unnecessary on R >=4.4.0
-    # ref: https://github.com/microsoft/LightGBM/issues/6433
-    Rscript --vanilla -e "install.packages('lattice', repos = '${CRAN_MIRROR}', lib = '${R_LIB_PATH}')"
-fi
+# {Matrix} needs {lattice}, so this needs to run before manually installing {Matrix}.
+# This should be unnecessary on R >=4.4.0
+# ref: https://github.com/microsoft/LightGBM/issues/6433
+Rscript --vanilla -e "install.packages('lattice', repos = '${CRAN_MIRROR}', lib = '${R_LIB_PATH}')"
 
 # manually install {Matrix}, as {Matrix}=1.7-0 raised its R floor all the way to R 4.4.0
 # ref: https://github.com/microsoft/LightGBM/issues/6433

.github/workflows/r_package.yml

@@ -14,10 +14,6 @@ concurrency:
   cancel-in-progress: true
 
 env:
-  # https://github.com/actions/checkout/issues/1590#issuecomment-2207052044
-  #
-  # this could be removed (hopefully) when R 3.6 support is removed
-  ACTIONS_ALLOW_USE_UNSECURE_NODE_VERSION: true
   # in CMake-driven builds, parallelize compilation
   CMAKE_BUILD_PARALLEL_LEVEL: 4
   # on Debian-based images, avoid interactive prompts
@@ -48,12 +44,6 @@ jobs:
           ################
           # CMake builds #
           ################
-          - os: ubuntu-latest
-            task: r-package
-            compiler: gcc
-            r_version: 3.6
-            build_type: cmake
-            container: 'ubuntu:18.04'
           - os: ubuntu-latest
             task: r-package
             compiler: gcc
@@ -174,19 +164,12 @@ jobs:
         run: |
           git config --global --add safe.directory "${GITHUB_WORKSPACE}"
       - name: Checkout repository
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           fetch-depth: 5
           submodules: true
       - name: Install pandoc
         uses: r-lib/actions/setup-pandoc@v2
-        if: matrix.container != 'ubuntu:18.04'
-      # R 3.6 binary isn't easily available on Ubuntu 18.04,
-      # but setup-pandoc>=2.7.1 is uses a too-new glibc for it.
-      # ref: https://github.com/microsoft/LightGBM/issues/6298
-      - name: Install pandoc
-        uses: r-lib/actions/setup-pandoc@v2.6.0
-        if: matrix.container == 'ubuntu:18.04'
       - name: Install tinytex
         if: startsWith(matrix.os, 'windows')
         uses: r-lib/actions/setup-tinytex@v2

python-package/lightgbm/sklearn.py

@@ -673,6 +673,15 @@ class LGBMModel(_LGBMModelBase):
     # is >=1.6.
     # ref: https://github.com/microsoft/LightGBM/pull/6651
     def _more_tags(self) -> Dict[str, Any]:
+        check_sample_weight_str = (
+            "In LightGBM, setting a sample's weight to 0 can produce a different result than omitting the sample. "
+            "Such samples intentionally still affect count-based measures like 'min_data_in_leaf' "
+            "(https://github.com/microsoft/LightGBM/issues/5626#issuecomment-1712706678) and the estimated distribution "
+            "of features for Dataset construction (see https://github.com/microsoft/LightGBM/issues/5553)."
+        )
+        # "check_sample_weight_equivalence" can be removed when lightgbm's
+        # minimum supported scikit-learn version is at least 1.6
+        # ref: https://github.com/scikit-learn/scikit-learn/pull/30137
         return {
             "allow_nan": True,
             "X_types": ["2darray", "sparse", "1dlabels"],
@@ -680,12 +689,9 @@ class LGBMModel(_LGBMModelBase):
                 "check_no_attributes_set_in_init": "scikit-learn incorrectly asserts that private attributes "
                 "cannot be set in __init__: "
                 "(see https://github.com/microsoft/LightGBM/issues/2628)",
-                "check_sample_weight_equivalence": (
-                    "In LightGBM, setting a sample's weight to 0 can produce a different result than omitting the sample. "
-                    "Such samples intentionally still affect count-based measures like 'min_data_in_leaf' "
-                    "(https://github.com/microsoft/LightGBM/issues/5626#issuecomment-1712706678) and the estimated distribution "
-                    "of features for Dataset construction (see https://github.com/microsoft/LightGBM/issues/5553)."
-                ),
+                "check_sample_weight_equivalence": check_sample_weight_str,
+                "check_sample_weight_equivalence_on_dense_data": check_sample_weight_str,
+                "check_sample_weight_equivalence_on_sparse_data": check_sample_weight_str,
             },
         }