Merge branch 'master' into unify-model-output

.appveyor.yml

@@ -1,4 +1,4 @@
-version: 4.0.0.99.{build}
+version: 4.1.0.99.{build}
 
 image: Visual Studio 2015
 platform: x64

.ci/lint_r_code.R

@@ -33,29 +33,37 @@ LINTERS_TO_USE <- list(
  , "any_duplicated" = lintr::any_duplicated_linter()
  , "any_is_na" = lintr::any_is_na_linter()
  , "assignment" = lintr::assignment_linter()
+ , "boolean_arithmetic" = lintr::boolean_arithmetic_linter()
  , "braces" = lintr::brace_linter()
  , "class_equals" = lintr::class_equals_linter()
  , "commas" = lintr::commas_linter()
  , "duplicate_argument" = lintr::duplicate_argument_linter()
+ , "empty_assignment" = lintr::empty_assignment_linter()
  , "equals_na" = lintr::equals_na_linter()
+ , "for_loop_index" = lintr::for_loop_index_linter()
  , "function_left" = lintr::function_left_parentheses_linter()
  , "implicit_integers" = lintr::implicit_integer_linter()
  , "infix_spaces" = lintr::infix_spaces_linter()
  , "inner_combine" = lintr::inner_combine_linter()
+ , "is_numeric" = lintr::is_numeric_linter()
  , "fixed_regex" = lintr::fixed_regex_linter()
+ , "function_return" = lintr::function_return_linter()
+ , "lengths" = lintr::lengths_linter()
  , "literal_coercion" = lintr::literal_coercion_linter()
  , "long_lines" = lintr::line_length_linter(length = 120L)
+ , "matrix" = lintr::matrix_apply_linter()
  , "missing_argument" = lintr::missing_argument_linter()
- , "no_tabs" = lintr::no_tab_linter()
  , "non_portable_path" = lintr::nonportable_path_linter()
  , "numeric_leading_zero" = lintr::numeric_leading_zero_linter()
  , "outer_negation" = lintr::outer_negation_linter()
  , "package_hooks" = lintr::package_hooks_linter()
  , "paste" = lintr::paste_linter()
+ , "quotes" = lintr::quotes_linter()
+ , "redundant_equals" = lintr::redundant_equals_linter()
  , "regex_subset" = lintr::regex_subset_linter()
+ , "routine_registration" = lintr::routine_registration_linter()
  , "semicolon" = lintr::semicolon_linter()
  , "seq" = lintr::seq_linter()
- , "single_quotes" = lintr::single_quotes_linter()
  , "spaces_inside" = lintr::spaces_inside_linter()
  , "spaces_left_parens" = lintr::spaces_left_parentheses_linter()
  , "sprintf" = lintr::sprintf_linter()
@@ -96,9 +104,11 @@ LINTERS_TO_USE <- list(
  , "??" = interactive_text
  )
  )
- , "unneeded_concatenation" = lintr::unneeded_concatenation_linter()
- , "unreachable_code" = lintr::unreachable_code_linter()
- , "vector_logic" = lintr::vector_logic_linter()
+ , "unnecessary_concatenation" = lintr::unnecessary_concatenation_linter()
+ , "unnecessary_lambda" = lintr::unnecessary_lambda_linter()
+ , "unreachable_code" = lintr::unreachable_code_linter()
+ , "vector_logic" = lintr::vector_logic_linter()
+ , "whitespace" = lintr::whitespace_linter()
 )
 
 noquote(paste0(length(FILES_TO_LINT), " R files need linting"))

.ci/test-python-oldest.sh

@@ -7,6 +7,7 @@
 #
 echo "installing lightgbm's dependencies"
 pip install \
+ 'dataclasses' \
  'numpy==1.12.0' \
  'pandas==0.24.0' \
  'scikit-learn==0.18.2' \

.ci/test.sh

@@ -73,7 +73,7 @@ if [[ $TASK == "lint" ]]; then
  cpplint \
  isort \
  mypy \
- 'r-lintr>=3.0' \
+ 'r-lintr>=3.1' \
  ruff
  source activate $CONDA_ENV
  echo "Linting Python code"
@@ -119,15 +119,21 @@ if [[ $TASK == "check-docs" ]] || [[ $TASK == "check-links" ]]; then
  exit 0
 fi
 
+# older versions of Dask are incompatible with pandas>=2.0, but not all conda packages' metadata accurately reflects that
+#
+# ref: https://github.com/microsoft/LightGBM/issues/6030
+CONSTRAINED_DEPENDENCIES="'dask-core>=2023.5.0' 'distributed>=2023.5.0' 'pandas>=2.0'"
+if [[ $PYTHON_VERSION == "3.7" ]]; then
+ CONSTRAINED_DEPENDENCIES="'dask-core' 'distributed' 'pandas<2.0'"
+fi
+
 # including python=version[build=*cpython] to ensure that conda doesn't fall back to pypy
 conda create -q -y -n $CONDA_ENV \
+ ${CONSTRAINED_DEPENDENCIES} \
  cloudpickle \
- dask-core \
- distributed \
  joblib \
  matplotlib \
  numpy \
- pandas \
  psutil \
  pytest \
  ${CONDA_PYTHON_REQUIREMENT} \

.ci/test_r_package.sh

@@ -21,9 +21,9 @@ if [[ "${R_MAJOR_VERSION}" == "3" ]]; then
  export R_LINUX_VERSION="3.6.3-1bionic"
  export R_APT_REPO="bionic-cran35/"
 elif [[ "${R_MAJOR_VERSION}" == "4" ]]; then
- export R_MAC_VERSION=4.2.2
- export R_MAC_PKG_URL=${CRAN_MIRROR}/bin/macosx/base/R-${R_MAC_VERSION}.pkg
- export R_LINUX_VERSION="4.2.2-1.2204.0"
+ export R_MAC_VERSION=4.3.1
+ export R_MAC_PKG_URL=${CRAN_MIRROR}/bin/macosx/big-sur-x86_64/base/R-${R_MAC_VERSION}-x86_64.pkg
+ export R_LINUX_VERSION="4.3.1-1.2204.0"
  export R_APT_REPO="jammy-cran40/"
 else
  echo "Unrecognized R version: ${R_VERSION}"
@@ -36,7 +36,10 @@ fi
 #
 # `devscripts` is required for 'checkbashisms' (https://github.com/r-lib/actions/issues/111)
 if [[ $OS_NAME == "linux" ]]; then
+ mkdir -p ~/.gnupg
+ echo "disable-ipv6" >> ~/.gnupg/dirmngr.conf
  sudo apt-key adv \
+ --homedir ~/.gnupg \
  --keyserver keyserver.ubuntu.com \
  --recv-keys E298A3A825C0D65DFD57CBB651716619E084DAB9 || exit -1
  sudo add-apt-repository \
@@ -53,6 +56,7 @@ if [[ $OS_NAME == "linux" ]]; then
  texlive-latex-recommended \
  texlive-fonts-recommended \
  texlive-fonts-extra \
+ tidy \
  qpdf \
  || exit -1
 

.ci/test_r_package_windows.ps1

@@ -203,6 +203,19 @@ if ($env:COMPILER -ne "MSVC") {
  }
 }
 
+# Checking that the correct R version was used
+if ($env:TOOLCHAIN -ne "MSVC") {
+ $checks = Select-String -Path "${LOG_FILE_NAME}" -Pattern "using R version $env:R_WINDOWS_VERSION"
+ $checks_cnt = $checks.Matches.length
+} else {
+ $checks = Select-String -Path "${INSTALL_LOG_FILE_NAME}" -Pattern "R version passed into FindLibR.* $env:R_WINDOWS_VERSION"
+ $checks_cnt = $checks.Matches.length
+}
+if ($checks_cnt -eq 0) {
+ Write-Output "Wrong R version was found (expected '$env:R_WINDOWS_VERSION'). Check the build logs."
+ Check-Output $False
+}
+
 # Checking that we actually got the expected compiler. The R package has some logic
 # to fail back to MinGW if MSVC fails, but for CI builds we need to check that the correct
 # compiler was used.

.ci/test_windows.ps1

@@ -124,7 +124,7 @@ if (($env:TASK -eq "regular") -or (($env:APPVEYOR -eq "true") -and ($env:TASK -e
  cd $env:BUILD_SOURCESDIRECTORY/examples/python-guide
  @("import matplotlib", "matplotlib.use('Agg')") + (Get-Content "plot_example.py") | Set-Content "plot_example.py"
  (Get-Content "plot_example.py").replace('graph.render(view=True)', 'graph.render(view=False)') | Set-Content "plot_example.py" # prevent interactive window mode
- conda install -q -y -n $env:CONDA_ENV h5py ipywidgets notebook
+ conda install -q -y -n $env:CONDA_ENV "h5py>3.0" ipywidgets notebook
  foreach ($file in @(Get-ChildItem *.py)) {
  @("import sys, warnings", "warnings.showwarning = lambda message, category, filename, lineno, file=None, line=None: sys.stdout.write(warnings.formatwarning(message, category, filename, lineno, line))") + (Get-Content $file) | Set-Content $file
  python $file ; Check-Output $?

.github/CODEOWNERS

@@ -7,56 +7,4 @@
 # offer a reasonable automatic best-guess
 
 # catch-all rule (this only gets matched if no rules below match)
-* @guolinke @StrikerRUS @jameslamb @shiyu1994
-
-# other catch-alls that will get matched if specific rules below are not matched
-*.R @jameslamb @jmoralez
-*.py @StrikerRUS @jmoralez @jameslamb @shiyu1994
-*.cpp @guolinke @shiyu1994
-*.h @guolinke @shiyu1994
-
-# main C++ code
-include/ @guolinke @shiyu1994
-src/ @guolinke @shiyu1994
-CMakeLists.txt @guolinke @jameslamb @StrikerRUS @shiyu1994
-tests/c_api_test/ @guolinke @shiyu1994
-tests/cpp_tests/ @guolinke @shiyu1994
-tests/data/ @guolinke @shiyu1994
-windows/ @guolinke @StrikerRUS @shiyu1994
-
-# R code
-build_r.R @jameslamb @StrikerRUS @jmoralez
-build-cran-package.sh @jameslamb @StrikerRUS @jmoralez
-R-package/ @jameslamb @jmoralez
-
-# Python code
-python-package/ @StrikerRUS @shiyu1994 @jameslamb @jmoralez
-
-# Dask integration
-python-package/lightgbm/dask.py @jameslamb @jmoralez
-tests/python_package_test/test_dask.py @jameslamb @jmoralez
-
-# helpers
-helpers/ @StrikerRUS @guolinke
-
-# CI administrative stuff
-.ci/ @StrikerRUS @jameslamb
-docs/ @StrikerRUS @jameslamb
-examples/ @StrikerRUS @jameslamb @guolinke @jmoralez
-*.yml @StrikerRUS @jameslamb
-.vsts-ci.yml @StrikerRUS @jameslamb
-
-# docker setup
-docker/ @StrikerRUS @jameslamb
-docker/dockerfile-cli @guolinke @shiyu1994 @StrikerRUS @jameslamb
-docker/gpu/ @StrikerRUS @jameslamb
-docker/dockerfile-python @StrikerRUS @shiyu1994 @jameslamb @jmoralez
-docker/dockerfile-r @jameslamb @jmoralez
-
-# GPU code
-docs/GPU-*.rst @shiyu1994 @guolinke
-src/treelearner/gpu_tree_learner.cpp @guolinke @shiyu1994
-src/treelearner/tree_learner.cpp @guolinke @shiyu1994
-
-# JAVA code
-swig/ @guolinke @shiyu1994
+* @guolinke @jameslamb @shiyu1994 @jmoralez

.github/workflows/lock.yml

@@ -0,0 +1,44 @@
+name: 'Lock Inactive Threads'
+
+on:
+ schedule:
+ # midnight UTC, every Wednesday
+ - cron: '0 0 * * 3'
+ # allow manual triggering from GitHub UI
+ workflow_dispatch:
+
+permissions:
+ issues: write
+ pull-requests: write
+
+concurrency:
+ group: lock
+
+jobs:
+ action:
+ runs-on: ubuntu-latest
+ steps:
+ - uses: dessant/lock-threads@v4
+ with:
+ github-token: ${{ github.token }}
+ # after how many days of inactivity should a closed issue/PR be locked?
+ issue-inactive-days: '90'
+ pr-inactive-days: '90'
+ # do not close feature request issues...
+ # we close those but track them in https://github.com/microsoft/LightGBM/issues/2302
+ exclude-any-issue-labels: '"feature request"'
+ # what labels should be removed prior to locking?
+ remove-issue-labels: 'awaiting response,awaiting review,blocking,in progress'
+ remove-pr-labels: 'awaiting response,awaiting review,blocking,in progress'
+ # what message should be posted prior to locking?
+ issue-comment: >
+ This issue has been automatically locked since there has not been any recent activity since it was closed.
+ To start a new related discussion, open a new issue at https://github.com/microsoft/LightGBM/issues
+ including a reference to this.
+ pr-comment: >
+ This pull request has been automatically locked since there has not been any recent activity since it was closed.
+ To start a new related discussion, open a new issue at https://github.com/microsoft/LightGBM/issues
+ including a reference to this.
+ # what shoulld the locking status be?
+ issue-lock-reason: 'resolved'
+ pr-lock-reason: 'resolved'

.github/workflows/r_package.yml

@@ -48,7 +48,7 @@ jobs:
  - os: ubuntu-latest
  task: r-package
  compiler: gcc
- r_version: 4.2
+ r_version: 4.3
  build_type: cmake
  container: 'ubuntu:22.04'
  - os: ubuntu-latest
@@ -60,19 +60,19 @@ jobs:
  - os: ubuntu-latest
  task: r-package
  compiler: clang
- r_version: 4.2
+ r_version: 4.3
  build_type: cmake
  container: 'ubuntu:22.04'
  - os: macOS-latest
  task: r-package
  compiler: gcc
- r_version: 4.2
+ r_version: 4.3
  build_type: cmake
  container: null
  - os: macOS-latest
  task: r-package
  compiler: clang
- r_version: 4.2
+ r_version: 4.3
  build_type: cmake
  container: null
  - os: windows-latest
@@ -125,13 +125,13 @@ jobs:
  - os: ubuntu-latest
  task: r-package
  compiler: gcc
- r_version: 4.2
+ r_version: 4.3
  build_type: cran
  container: 'ubuntu:22.04'
  - os: macOS-latest
  task: r-package
  compiler: clang
- r_version: 4.2
+ r_version: 4.3
  build_type: cran
  container: null
  ################
@@ -140,7 +140,7 @@ jobs:
  - os: ubuntu-latest
  task: r-rchk
  compiler: gcc
- r_version: 4.2
+ r_version: 4.3
  build_type: cran
  container: 'ubuntu:22.04'
  steps:

.gitignore

@@ -139,8 +139,6 @@ publish/
 # Publish Web Output
 *.[Pp]ublish.xml
 *.azurePubxml
-# TODO: Comment the next line if you want to checkin your web deploy settings 
-# but database connection strings (with potential passwords) will be unencrypted
 *.pubxml
 *.publishproj
 

CMakeLists.txt

@@ -326,6 +326,13 @@ if(UNIX OR MINGW OR CYGWIN)
  CMAKE_CXX_FLAGS
  "${CMAKE_CXX_FLAGS} -std=c++11 -pthread -Wextra -Wall -Wno-ignored-attributes -Wno-unknown-pragmas -Wno-return-type"
  )
+ if(MINGW)
+ # ignore this warning: https://gcc.gnu.org/bugzilla/show_bug.cgi?id=95353
+ set(
+ CMAKE_CXX_FLAGS
+ "${CMAKE_CXX_FLAGS} -Wno-stringop-overflow"
+ )
+ endif()
  if(USE_DEBUG)
  set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -g -O0")
  else()

R-package/R/callback.R

@@ -24,7 +24,7 @@ CB_ENV <- R6::R6Class(
 )
 
 # Format the evaluation metric string
-format.eval.string <- function(eval_res, eval_err) {
+.format_eval_string <- function(eval_res, eval_err) {
 
  # Check for empty evaluation string
  if (is.null(eval_res) || length(eval_res) == 0L) {
@@ -40,7 +40,7 @@ format.eval.string <- function(eval_res, eval_err) {
 
 }
 
-merge.eval.string <- function(env) {
+.merge_eval_string <- function(env) {
 
  # Check length of evaluation list
  if (length(env$eval_list) <= 0L) {
@@ -63,7 +63,7 @@ merge.eval.string <- function(env) {
  }
 
  # Set error message
- msg <- c(msg, format.eval.string(eval_res = env$eval_list[[j]], eval_err = eval_err))
+ msg <- c(msg, .format_eval_string(eval_res = env$eval_list[[j]], eval_err = eval_err))
 
  }
 
@@ -86,11 +86,11 @@ cb_print_evaluation <- function(period) {
  if ((i - 1L) %% period == 0L || is.element(i, c(env$begin_iteration, env$end_iteration))) {
 
  # Merge evaluation string
- msg <- merge.eval.string(env = env)
+ msg <- .merge_eval_string(env = env)
 
  # Check if message is existing
  if (nchar(msg) > 0L) {
- print(merge.eval.string(env = env))
+ print(.merge_eval_string(env = env))
  }
 
  }
@@ -270,7 +270,7 @@ cb_early_stop <- function(stopping_rounds, first_metric_only, verbose) {
 
  # Prepare to print if verbose
  if (verbose) {
- best_msg[[i]] <<- as.character(merge.eval.string(env = env))
+ best_msg[[i]] <<- as.character(.merge_eval_string(env = env))
  }
 
  } else {