Merge remote-tracking branch 'upstream/master' into 2.0-news

.github/workflows/main.yml

@@ -29,7 +29,7 @@ jobs:
       run: |
         mkdir build
         cd build
-        cmake .. -DGOOGLE_TEST=ON -DUSE_OPENMP=ON -DUSE_DMLC_GTEST=ON -DPLUGIN_DENSE_PARSER=ON -GNinja
+        cmake .. -DGOOGLE_TEST=ON -DUSE_OPENMP=ON -DUSE_DMLC_GTEST=ON -DPLUGIN_DENSE_PARSER=ON -GNinja -DBUILD_DEPRECATED_CLI=ON
         ninja -v
     - name: Run gtest binary
       run: |
@@ -56,7 +56,7 @@ jobs:
       run: |
         mkdir build
         cd build
-        cmake .. -GNinja -DGOOGLE_TEST=ON  -DUSE_DMLC_GTEST=ON -DUSE_OPENMP=OFF
+        cmake .. -GNinja -DGOOGLE_TEST=ON  -DUSE_DMLC_GTEST=ON -DUSE_OPENMP=OFF -DBUILD_DEPRECATED_CLI=ON
         ninja -v
     - name: Run gtest binary
       run: |

.github/workflows/python_tests.yml

@@ -143,7 +143,7 @@ jobs:
         # Set prefix, to use OpenMP library from Conda env
         # See https://github.com/dmlc/xgboost/issues/7039#issuecomment-1025038228
         # to learn why we don't use libomp from Homebrew.
-        cmake .. -GNinja -DCMAKE_PREFIX_PATH=$CONDA_PREFIX
+        cmake .. -GNinja -DCMAKE_PREFIX_PATH=$CONDA_PREFIX -DBUILD_DEPRECATED_CLI=ON
         ninja
 
     - name: Install Python package
@@ -190,7 +190,7 @@ jobs:
       run: |
         mkdir build_msvc
         cd build_msvc
-        cmake .. -G"Visual Studio 17 2022" -DCMAKE_CONFIGURATION_TYPES="Release" -A x64 -DGOOGLE_TEST=ON  -DUSE_DMLC_GTEST=ON
+        cmake .. -G"Visual Studio 17 2022" -DCMAKE_CONFIGURATION_TYPES="Release" -A x64 -DGOOGLE_TEST=ON  -DUSE_DMLC_GTEST=ON -DBUILD_DEPRECATED_CLI=ON
         cmake --build . --config Release --parallel $(nproc)
 
     - name: Install Python package
@@ -234,7 +234,7 @@ jobs:
       run: |
         mkdir build
         cd build
-        cmake .. -GNinja -DCMAKE_PREFIX_PATH=$CONDA_PREFIX
+        cmake .. -GNinja -DCMAKE_PREFIX_PATH=$CONDA_PREFIX -DBUILD_DEPRECATED_CLI=ON
         ninja
 
     - name: Install Python package

.github/workflows/r_tests.yml

@@ -25,7 +25,7 @@ jobs:
       with:
         submodules: 'true'
 
-    - uses: r-lib/actions/setup-r@50d1eae9b8da0bb3f8582c59a5b82225fa2fe7f2 # v2.3.1
+    - uses: r-lib/actions/setup-r@11a22a908006c25fe054c4ef0ac0436b1de3edbe # v2.6.4
       with:
         r-version: ${{ matrix.config.r }}
 
@@ -64,7 +64,7 @@ jobs:
       with:
         submodules: 'true'
 
-    - uses: r-lib/actions/setup-r@50d1eae9b8da0bb3f8582c59a5b82225fa2fe7f2 # v2.3.1
+    - uses: r-lib/actions/setup-r@11a22a908006c25fe054c4ef0ac0436b1de3edbe # v2.6.4
       with:
         r-version: ${{ matrix.config.r }}
 

.gitignore

@@ -146,6 +146,8 @@ __MACOSX/
 model*.json
 
 # R tests
+*.htm
+*.html
 *.libsvm
 *.rds
 Rplots.pdf

.readthedocs.yaml

@@ -32,4 +32,3 @@ formats:
 python:
   install:
    - requirements: doc/requirements.txt
-  system_packages: true

CMakeLists.txt

@@ -1,5 +1,5 @@
 cmake_minimum_required(VERSION 3.18 FATAL_ERROR)
-project(xgboost LANGUAGES CXX C VERSION 2.0.0)
+project(xgboost LANGUAGES CXX C VERSION 2.1.0)
 include(cmake/Utils.cmake)
 list(APPEND CMAKE_MODULE_PATH "${xgboost_SOURCE_DIR}/cmake/modules")
 cmake_policy(SET CMP0022 NEW)
@@ -45,8 +45,8 @@ set_default_configuration_release()
 option(BUILD_C_DOC "Build documentation for C APIs using Doxygen." OFF)
 option(USE_OPENMP "Build with OpenMP support." ON)
 option(BUILD_STATIC_LIB "Build static library" OFF)
+option(BUILD_DEPRECATED_CLI "Build the deprecated command line interface" OFF)
 option(FORCE_SHARED_CRT "Build with dynamic CRT on Windows (/MD)" OFF)
-option(RABIT_BUILD_MPI "Build MPI" OFF)
 ## Bindings
 option(JVM_BINDINGS "Build JVM bindings" OFF)
 option(R_LIB "Build shared library for R package" OFF)
@@ -71,10 +71,6 @@ option(USE_NCCL  "Build with NCCL to enable distributed GPU support." OFF)
 option(BUILD_WITH_SHARED_NCCL "Build with shared NCCL library." OFF)
 set(GPU_COMPUTE_VER "" CACHE STRING
   "Semicolon separated list of compute versions to be built against, e.g. '35;61'")
-## Copied From dmlc
-option(USE_HDFS "Build with HDFS support" OFF)
-option(USE_AZURE "Build with AZURE support" OFF)
-option(USE_S3 "Build with S3 support" OFF)
 ## Sanitizers
 option(USE_SANITIZER "Use santizer flags" OFF)
 option(SANITIZER_PATH "Path to sanitizes.")
@@ -109,12 +105,6 @@ if (R_LIB AND GOOGLE_TEST)
   message(WARNING "Some C++ unittests will fail with `R_LIB` enabled,
  as R package redirects some functions to R runtime implementation.")
 endif (R_LIB AND GOOGLE_TEST)
-if (USE_AVX)
-  message(SEND_ERROR  "The option 'USE_AVX' is deprecated as experimental AVX features have been removed from XGBoost.")
-endif (USE_AVX)
-if (PLUGIN_LZ4)
-  message(SEND_ERROR  "The option 'PLUGIN_LZ4' is removed from XGBoost.")
-endif (PLUGIN_LZ4)
 if (PLUGIN_RMM AND NOT (USE_CUDA))
   message(SEND_ERROR "`PLUGIN_RMM` must be enabled with `USE_CUDA` flag.")
 endif (PLUGIN_RMM AND NOT (USE_CUDA))
@@ -147,6 +137,26 @@ if (PLUGIN_FEDERATED)
   endif ()
 endif ()
 
+#-- Removed options
+if (USE_AVX)
+  message(SEND_ERROR  "The option `USE_AVX` is deprecated as experimental AVX features have been removed from XGBoost.")
+endif (USE_AVX)
+if (PLUGIN_LZ4)
+  message(SEND_ERROR  "The option `PLUGIN_LZ4` is removed from XGBoost.")
+endif (PLUGIN_LZ4)
+if (RABIT_BUILD_MPI)
+  message(SEND_ERROR "The option `RABIT_BUILD_MPI` has been removed from XGBoost.")
+endif (RABIT_BUILD_MPI)
+if (USE_S3)
+  message(SEND_ERROR "The option `USE_S3` has been removed from XGBoost")
+endif (USE_S3)
+if (USE_AZURE)
+  message(SEND_ERROR "The option `USE_AZURE` has been removed from XGBoost")
+endif (USE_AZURE)
+if (USE_HDFS)
+  message(SEND_ERROR "The option `USE_HDFS` has been removed from XGBoost")
+endif (USE_HDFS)
+
 #-- Sanitizer
 if (USE_SANITIZER)
   include(cmake/Sanitizer.cmake)
@@ -225,9 +235,6 @@ endif (MSVC)
 
 # rabit
 add_subdirectory(rabit)
-if (RABIT_BUILD_MPI)
-  find_package(MPI REQUIRED)
-endif (RABIT_BUILD_MPI)
 
 # core xgboost
 add_subdirectory(${xgboost_SOURCE_DIR}/src)
@@ -273,19 +280,30 @@ target_include_directories(xgboost
 #-- End shared library
 
 #-- CLI for xgboost
-add_executable(runxgboost ${xgboost_SOURCE_DIR}/src/cli_main.cc)
-target_link_libraries(runxgboost PRIVATE objxgboost)
-target_include_directories(runxgboost
-  PRIVATE
-  ${xgboost_SOURCE_DIR}/include
-  ${xgboost_SOURCE_DIR}/dmlc-core/include
-  ${xgboost_SOURCE_DIR}/rabit/include
-)
-set_target_properties(runxgboost PROPERTIES OUTPUT_NAME xgboost)
+if (BUILD_DEPRECATED_CLI)
+  add_executable(runxgboost ${xgboost_SOURCE_DIR}/src/cli_main.cc)
+  target_link_libraries(runxgboost PRIVATE objxgboost)
+  target_include_directories(runxgboost
+    PRIVATE
+    ${xgboost_SOURCE_DIR}/include
+    ${xgboost_SOURCE_DIR}/dmlc-core/include
+    ${xgboost_SOURCE_DIR}/rabit/include
+  )
+  set_target_properties(runxgboost PROPERTIES OUTPUT_NAME xgboost)
+  xgboost_target_properties(runxgboost)
+  xgboost_target_link_libraries(runxgboost)
+  xgboost_target_defs(runxgboost)
+
+  if (KEEP_BUILD_ARTIFACTS_IN_BINARY_DIR)
+    set_output_directory(runxgboost ${xgboost_BINARY_DIR})
+  else ()
+    set_output_directory(runxgboost ${xgboost_SOURCE_DIR})
+  endif (KEEP_BUILD_ARTIFACTS_IN_BINARY_DIR)
+endif (BUILD_DEPRECATED_CLI)
 #-- End CLI for xgboost
 
 # Common setup for all targets
-foreach(target xgboost objxgboost dmlc runxgboost)
+foreach(target xgboost objxgboost dmlc)
   xgboost_target_properties(${target})
   xgboost_target_link_libraries(${target})
   xgboost_target_defs(${target})
@@ -298,14 +316,15 @@ if (JVM_BINDINGS)
 endif (JVM_BINDINGS)
 
 if (KEEP_BUILD_ARTIFACTS_IN_BINARY_DIR)
-  set_output_directory(runxgboost ${xgboost_BINARY_DIR})
   set_output_directory(xgboost ${xgboost_BINARY_DIR}/lib)
 else ()
-  set_output_directory(runxgboost ${xgboost_SOURCE_DIR})
   set_output_directory(xgboost ${xgboost_SOURCE_DIR}/lib)
 endif ()
+
 # Ensure these two targets do not build simultaneously, as they produce outputs with conflicting names
-add_dependencies(xgboost runxgboost)
+if (BUILD_DEPRECATED_CLI)
+  add_dependencies(xgboost runxgboost)
+endif (BUILD_DEPRECATED_CLI)
 
 #-- Installing XGBoost
 if (R_LIB)
@@ -341,9 +360,17 @@ install(DIRECTORY ${xgboost_SOURCE_DIR}/include/xgboost
 #
 # https://github.com/dmlc/xgboost/issues/6085
 if (BUILD_STATIC_LIB)
-  set(INSTALL_TARGETS xgboost runxgboost objxgboost dmlc)
+  if (BUILD_DEPRECATED_CLI)
+    set(INSTALL_TARGETS xgboost runxgboost objxgboost dmlc)
+  else()
+    set(INSTALL_TARGETS xgboost objxgboost dmlc)
+  endif (BUILD_DEPRECATED_CLI)
 else (BUILD_STATIC_LIB)
-  set(INSTALL_TARGETS xgboost runxgboost)
+  if (BUILD_DEPRECATED_CLI)
+    set(INSTALL_TARGETS xgboost runxgboost)
+  else(BUILD_DEPRECATED_CLI)
+    set(INSTALL_TARGETS xgboost)
+  endif (BUILD_DEPRECATED_CLI)
 endif (BUILD_STATIC_LIB)
 
 install(TARGETS ${INSTALL_TARGETS}
@@ -393,13 +420,15 @@ if (GOOGLE_TEST)
     ${xgboost_SOURCE_DIR}/tests/cli/machine.conf.in
     ${xgboost_BINARY_DIR}/tests/cli/machine.conf
     @ONLY)
-  add_test(
-    NAME TestXGBoostCLI
-    COMMAND runxgboost ${xgboost_BINARY_DIR}/tests/cli/machine.conf
-    WORKING_DIRECTORY ${xgboost_BINARY_DIR})
-  set_tests_properties(TestXGBoostCLI
-    PROPERTIES
-    PASS_REGULAR_EXPRESSION ".*test-rmse:0.087.*")
+  if (BUILD_DEPRECATED_CLI)
+    add_test(
+      NAME TestXGBoostCLI
+      COMMAND runxgboost ${xgboost_BINARY_DIR}/tests/cli/machine.conf
+      WORKING_DIRECTORY ${xgboost_BINARY_DIR})
+    set_tests_properties(TestXGBoostCLI
+      PROPERTIES
+      PASS_REGULAR_EXPRESSION ".*test-rmse:0.087.*")
+  endif (BUILD_DEPRECATED_CLI)
 endif (GOOGLE_TEST)
 
 # For MSVC: Call msvc_use_static_runtime() once again to completely

R-package/CMakeLists.txt

@@ -1,41 +1,54 @@
 find_package(LibR REQUIRED)
 message(STATUS "LIBR_CORE_LIBRARY " ${LIBR_CORE_LIBRARY})
 
-file(GLOB_RECURSE R_SOURCES
+file(
+  GLOB_RECURSE R_SOURCES
   ${CMAKE_CURRENT_LIST_DIR}/src/*.cc
-  ${CMAKE_CURRENT_LIST_DIR}/src/*.c)
+  ${CMAKE_CURRENT_LIST_DIR}/src/*.c
+)
+
 # Use object library to expose symbols
 add_library(xgboost-r OBJECT ${R_SOURCES})
-if (ENABLE_ALL_WARNINGS)
+
+if(ENABLE_ALL_WARNINGS)
   target_compile_options(xgboost-r PRIVATE -Wall -Wextra)
-endif (ENABLE_ALL_WARNINGS)
-target_compile_definitions(xgboost-r
-  PUBLIC
+endif()
+
+target_compile_definitions(
+  xgboost-r PUBLIC
   -DXGBOOST_STRICT_R_MODE=1
   -DXGBOOST_CUSTOMIZE_GLOBAL_PRNG=1
   -DDMLC_LOG_BEFORE_THROW=0
   -DDMLC_DISABLE_STDIN=1
   -DDMLC_LOG_CUSTOMIZE=1
-  -DRABIT_STRICT_CXX98_)
-target_include_directories(xgboost-r
-  PRIVATE
+  -DRABIT_STRICT_CXX98_
+)
+
+target_include_directories(
+  xgboost-r PRIVATE
   ${LIBR_INCLUDE_DIRS}
   ${PROJECT_SOURCE_DIR}/include
   ${PROJECT_SOURCE_DIR}/dmlc-core/include
-  ${PROJECT_SOURCE_DIR}/rabit/include)
+  ${PROJECT_SOURCE_DIR}/rabit/include
+)
+
 target_link_libraries(xgboost-r PUBLIC ${LIBR_CORE_LIBRARY})
-if (USE_OPENMP)
+
+if(USE_OPENMP)
   find_package(OpenMP REQUIRED)
   target_link_libraries(xgboost-r PUBLIC OpenMP::OpenMP_CXX OpenMP::OpenMP_C)
-endif (USE_OPENMP)
+endif()
+
 set_target_properties(
   xgboost-r PROPERTIES
   CXX_STANDARD 17
   CXX_STANDARD_REQUIRED ON
-  POSITION_INDEPENDENT_CODE ON)
+  POSITION_INDEPENDENT_CODE ON
+)
 
 # Get compilation and link flags of xgboost-r and propagate to objxgboost
 target_link_libraries(objxgboost PUBLIC xgboost-r)
+
 # Add all objects of xgboost-r to objxgboost
 target_sources(objxgboost INTERFACE $<TARGET_OBJECTS:xgboost-r>)
 

R-package/DESCRIPTION

@@ -1,8 +1,8 @@
 Package: xgboost
 Type: Package
 Title: Extreme Gradient Boosting
-Version: 2.0.0.1
-Date: 2022-10-18
+Version: 2.1.0.0
+Date: 2023-08-19
 Authors@R: c(
   person("Tianqi", "Chen", role = c("aut"),
          email = "[email protected]"),

R-package/R/callbacks.R

@@ -70,7 +70,7 @@ cb.print.evaluation <- function(period = 1, showsd = TRUE) {
         i == env$begin_iteration ||
         i == env$end_iteration) {
       stdev <- if (showsd) env$bst_evaluation_err else NULL
-      msg <- format.eval.string(i, env$bst_evaluation, stdev)
+      msg <- .format_eval_string(i, env$bst_evaluation, stdev)
       cat(msg, '\n')
     }
   }
@@ -380,7 +380,9 @@ cb.early.stop <- function(stopping_rounds, maximize = FALSE,
     if ((maximize && score > best_score) ||
         (!maximize && score < best_score)) {
 
-      best_msg <<- format.eval.string(i, env$bst_evaluation, env$bst_evaluation_err)
+      best_msg <<- .format_eval_string(
+        i, env$bst_evaluation, env$bst_evaluation_err
+      )
       best_score <<- score
       best_iteration <<- i
       best_ntreelimit <<- best_iteration * env$num_parallel_tree
@@ -754,7 +756,7 @@ xgb.gblinear.history <- function(model, class_index = NULL) {
 #
 
 # Format the evaluation metric string
-format.eval.string <- function(iter, eval_res, eval_err = NULL) {
+.format_eval_string <- function(iter, eval_res, eval_err = NULL) {
   if (length(eval_res) == 0)
     stop('no evaluation results')
   enames <- names(eval_res)