Merge xgboost 2.0.1 patch (#9)

* [backport] Support pandas 2.1.0. (dmlc#9557) (dmlc#9655)

* [backport] Add support for cgroupv2. (dmlc#9651) (dmlc#9656)

* Bump version to 2.0.1. (dmlc#9660)

* [backport] [CI] Pull CentOS 7 images from NGC (dmlc#9666) (dmlc#9668)

* Fix build for GCC 8.x (dmlc#9670)

* [backport][pyspark] Support stage-level scheduling (dmlc#9519) (dmlc#9686)

Co-authored-by: Bobby Wang <wbo4958@gmail.com>

* Fix build for AppleClang 11 (dmlc#9684)

* Fix libpath logic for Windows (dmlc#9687)

* [CI] Build libxgboost4j.dylib for Intel Mac (dmlc#9704)

* [jvm-packages] Remove hard dependency on libjvm (dmlc#9698) (dmlc#9705)

* Use sys.base_prefix instead of sys.prefix (dmlc#9711)

* Use sys.base_prefix instead of sys.prefix

* Update libpath.py too

---------

Co-authored-by: Jiaming Yuan <jm.yuan@outlook.com>
Co-authored-by: Philip Hyunsu Cho <chohyu01@cs.washington.edu>
Co-authored-by: Bobby Wang <wbo4958@gmail.com>

.github/workflows/jvm_tests.yml

@@ -51,21 +51,34 @@ jobs:
       id: extract_branch
       if: |
         (github.ref == 'refs/heads/master' || contains(github.ref, 'refs/heads/release_')) &&
-        matrix.os == 'windows-latest'
+        (matrix.os == 'windows-latest' || matrix.os == 'macos-11')
 
     - name: Publish artifact xgboost4j.dll to S3
       run: |
         cd lib/
         Rename-Item -Path xgboost4j.dll -NewName xgboost4j_${{ github.sha }}.dll
         dir
-        python -m awscli s3 cp xgboost4j_${{ github.sha }}.dll s3://xgboost-nightly-builds/${{ steps.extract_branch.outputs.branch }}/ --acl public-read
+        python -m awscli s3 cp xgboost4j_${{ github.sha }}.dll s3://xgboost-nightly-builds/${{ steps.extract_branch.outputs.branch }}/libxgboost4j/ --acl public-read
       if: |
         (github.ref == 'refs/heads/master' || contains(github.ref, 'refs/heads/release_')) &&
         matrix.os == 'windows-latest'
       env:
         AWS_ACCESS_KEY_ID: ${{ secrets.AWS_ACCESS_KEY_ID_IAM_S3_UPLOADER }}
         AWS_SECRET_ACCESS_KEY: ${{ secrets.AWS_SECRET_ACCESS_KEY_IAM_S3_UPLOADER }}
 
+    - name: Publish artifact libxgboost4j.dylib to S3
+      run: |
+        cd lib/
+        mv -v libxgboost4j.dylib libxgboost4j_${{ github.sha }}.dylib
+        ls
+        python -m awscli s3 cp libxgboost4j_${{ github.sha }}.dylib s3://xgboost-nightly-builds/${{ steps.extract_branch.outputs.branch }}/libxgboost4j/ --acl public-read
+      if: |
+        (github.ref == 'refs/heads/master' || contains(github.ref, 'refs/heads/release_')) &&
+        matrix.os == 'macos-11'
+      env:
+        AWS_ACCESS_KEY_ID: ${{ secrets.AWS_ACCESS_KEY_ID_IAM_S3_UPLOADER }}
+        AWS_SECRET_ACCESS_KEY: ${{ secrets.AWS_SECRET_ACCESS_KEY_IAM_S3_UPLOADER }}
+
 
     - name: Test XGBoost4J (Core, Spark, Examples)
       run: |

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 2.0.1)
 include(cmake/Utils.cmake)
 list(APPEND CMAKE_MODULE_PATH "${xgboost_SOURCE_DIR}/cmake/modules")
 cmake_policy(SET CMP0022 NEW)
@@ -237,6 +237,11 @@ endif (RABIT_BUILD_MPI)
 add_subdirectory(${xgboost_SOURCE_DIR}/src)
 target_link_libraries(objxgboost PUBLIC dmlc)
 
+# Link -lstdc++fs for GCC 8.x
+if(CMAKE_CXX_COMPILER_ID STREQUAL "GNU" AND CMAKE_CXX_COMPILER_VERSION VERSION_LESS "9.0")
+  target_link_libraries(objxgboost PUBLIC stdc++fs)
+endif()
+
 # Exports some R specific definitions and objects
 if (R_LIB)
   add_subdirectory(${xgboost_SOURCE_DIR}/R-package)

R-package/DESCRIPTION

@@ -1,8 +1,8 @@
 Package: xgboost
 Type: Package
 Title: Extreme Gradient Boosting
-Version: 2.0.0.1
-Date: 2023-09-11
+Version: 2.0.1.1
+Date: 2023-10-12
 Authors@R: c(
   person("Tianqi", "Chen", role = c("aut"),
          email = "tianqi.tchen@gmail.com"),

R-package/configure

@@ -1,6 +1,6 @@
 #! /bin/sh
 # Guess values for system-dependent variables and create Makefiles.
-# Generated by GNU Autoconf 2.71 for xgboost 2.0.0.
+# Generated by GNU Autoconf 2.71 for xgboost 2.0.1.
 #
 #
 # Copyright (C) 1992-1996, 1998-2017, 2020-2021 Free Software Foundation,
@@ -607,8 +607,8 @@ MAKEFLAGS=
 # Identity of this package.
 PACKAGE_NAME='xgboost'
 PACKAGE_TARNAME='xgboost'
-PACKAGE_VERSION='2.0.0'
-PACKAGE_STRING='xgboost 2.0.0'
+PACKAGE_VERSION='2.0.1'
+PACKAGE_STRING='xgboost 2.0.1'
 PACKAGE_BUGREPORT=''
 PACKAGE_URL=''
 
@@ -1225,7 +1225,7 @@ if test "$ac_init_help" = "long"; then
   # Omit some internal or obsolete options to make the list less imposing.
   # This message is too long to be a string in the A/UX 3.1 sh.
   cat <<_ACEOF
-\`configure' configures xgboost 2.0.0 to adapt to many kinds of systems.
+\`configure' configures xgboost 2.0.1 to adapt to many kinds of systems.
 
 Usage: $0 [OPTION]... [VAR=VALUE]...
 
@@ -1287,7 +1287,7 @@ fi
 
 if test -n "$ac_init_help"; then
   case $ac_init_help in
-     short | recursive ) echo "Configuration of xgboost 2.0.0:";;
+     short | recursive ) echo "Configuration of xgboost 2.0.1:";;
    esac
   cat <<\_ACEOF
 
@@ -1367,7 +1367,7 @@ fi
 test -n "$ac_init_help" && exit $ac_status
 if $ac_init_version; then
   cat <<\_ACEOF
-xgboost configure 2.0.0
+xgboost configure 2.0.1
 generated by GNU Autoconf 2.71
 
 Copyright (C) 2021 Free Software Foundation, Inc.
@@ -1533,7 +1533,7 @@ cat >config.log <<_ACEOF
 This file contains any messages produced by compilers while
 running configure, to aid debugging if configure makes a mistake.
 
-It was created by xgboost $as_me 2.0.0, which was
+It was created by xgboost $as_me 2.0.1, which was
 generated by GNU Autoconf 2.71.  Invocation command line was
 
   $ $0$ac_configure_args_raw
@@ -3412,7 +3412,7 @@ cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
 # report actual input values of CONFIG_FILES etc. instead of their
 # values after options handling.
 ac_log="
-This file was extended by xgboost $as_me 2.0.0, which was
+This file was extended by xgboost $as_me 2.0.1, which was
 generated by GNU Autoconf 2.71.  Invocation command line was
 
   CONFIG_FILES    = $CONFIG_FILES
@@ -3467,7 +3467,7 @@ ac_cs_config_escaped=`printf "%s\n" "$ac_cs_config" | sed "s/^ //; s/'/'\\\\\\\\
 cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
 ac_cs_config='$ac_cs_config_escaped'
 ac_cs_version="\\
-xgboost config.status 2.0.0
+xgboost config.status 2.0.1
 configured by $0, generated by GNU Autoconf 2.71,
   with options \\"\$ac_cs_config\\"
 

R-package/configure.ac

@@ -2,7 +2,7 @@
 
 AC_PREREQ(2.69)
 
-AC_INIT([xgboost],[2.0.0],[],[xgboost],[])
+AC_INIT([xgboost],[2.0.1],[],[xgboost],[])
 
 : ${R_HOME=`R RHOME`}
 if test -z "${R_HOME}"; then

include/xgboost/version_config.h

@@ -6,6 +6,6 @@
 
 #define XGBOOST_VER_MAJOR 2  /* NOLINT */
 #define XGBOOST_VER_MINOR 0  /* NOLINT */
-#define XGBOOST_VER_PATCH 0  /* NOLINT */
+#define XGBOOST_VER_PATCH 1  /* NOLINT */
 
 #endif  // XGBOOST_VERSION_CONFIG_H_

jvm-packages/CMakeLists.txt

@@ -25,4 +25,3 @@ target_include_directories(xgboost4j
   ${PROJECT_SOURCE_DIR}/rabit/include)
 
 set_output_directory(xgboost4j ${PROJECT_SOURCE_DIR}/lib)
-target_link_libraries(xgboost4j PRIVATE ${JAVA_JVM_LIBRARY})

jvm-packages/pom.xml

@@ -6,7 +6,7 @@
 
     <groupId>ml.dmlc</groupId>
     <artifactId>xgboost-jvm</artifactId>
-    <version>2.0.0</version>
+    <version>2.0.1</version>
     <packaging>pom</packaging>
     <name>XGBoost JVM Package</name>
     <description>JVM Package for XGBoost</description>

jvm-packages/xgboost4j-example/pom.xml

@@ -6,11 +6,11 @@
     <parent>
         <groupId>ml.dmlc</groupId>
         <artifactId>xgboost-jvm</artifactId>
-        <version>2.0.0</version>
+        <version>2.0.1</version>
     </parent>
     <name>xgboost4j-example</name>
     <artifactId>xgboost4j-example_${scala.binary.version}</artifactId>
-    <version>2.0.0</version>
+    <version>2.0.1</version>
     <packaging>jar</packaging>
     <build>
         <plugins>

jvm-packages/xgboost4j-flink/pom.xml

@@ -6,12 +6,12 @@
     <parent>
         <groupId>ml.dmlc</groupId>
         <artifactId>xgboost-jvm</artifactId>
-        <version>2.0.0</version>
+        <version>2.0.1</version>
     </parent>
 
     <name>xgboost4j-flink</name>
     <artifactId>xgboost4j-flink_${scala.binary.version}</artifactId>
-    <version>2.0.0</version>
+    <version>2.0.1</version>
     <properties>
       <flink-ml.version>2.2.0</flink-ml.version>
     </properties>

jvm-packages/xgboost4j-gpu/pom.xml

@@ -6,11 +6,11 @@
     <parent>
         <groupId>ml.dmlc</groupId>
         <artifactId>xgboost-jvm</artifactId>
-        <version>2.0.0</version>
+        <version>2.0.1</version>
     </parent>
     <artifactId>xgboost4j-gpu_${scala.binary.version}</artifactId>
     <name>xgboost4j-gpu</name>
-    <version>2.0.0</version>
+    <version>2.0.1</version>
     <packaging>jar</packaging>
 
     <dependencies>

jvm-packages/xgboost4j-spark-gpu/pom.xml

@@ -6,7 +6,7 @@
     <parent>
         <groupId>ml.dmlc</groupId>
         <artifactId>xgboost-jvm</artifactId>
-        <version>2.0.0</version>
+        <version>2.0.1</version>
     </parent>
     <name>xgboost4j-spark-gpu</name>
     <artifactId>xgboost4j-spark-gpu_${scala.binary.version}</artifactId>

jvm-packages/xgboost4j-spark/pom.xml

@@ -6,7 +6,7 @@
     <parent>
         <groupId>ml.dmlc</groupId>
         <artifactId>xgboost-jvm</artifactId>
-        <version>2.0.0</version>
+        <version>2.0.1</version>
     </parent>
     <name>xgboost4j-spark</name>
     <artifactId>xgboost4j-spark_${scala.binary.version}</artifactId>

jvm-packages/xgboost4j/pom.xml

@@ -6,11 +6,11 @@
     <parent>
         <groupId>ml.dmlc</groupId>
         <artifactId>xgboost-jvm</artifactId>
-        <version>2.0.0</version>
+        <version>2.0.1</version>
     </parent>
     <name>xgboost4j</name>
     <artifactId>xgboost4j_${scala.binary.version}</artifactId>
-    <version>2.0.0</version>
+    <version>2.0.1</version>
     <packaging>jar</packaging>
 
     <dependencies>

python-package/packager/nativelib.py

@@ -132,16 +132,28 @@ def locate_or_build_libxgboost(
 
     if build_config.use_system_libxgboost:
         # Find libxgboost from system prefix
-        sys_base_prefix = pathlib.Path(sys.base_prefix).absolute().resolve()
-        libxgboost_sys = sys_base_prefix / "lib" / _lib_name()
-        if not libxgboost_sys.exists():
-            raise RuntimeError(
-                f"use_system_libxgboost was specified but {_lib_name()} is "
-                f"not found in {libxgboost_sys.parent}"
-            )
-
-        logger.info("Using system XGBoost: %s", str(libxgboost_sys))
-        return libxgboost_sys
+        sys_prefix = pathlib.Path(sys.base_prefix)
+        sys_prefix_candidates = [
+            sys_prefix / "lib",
+            # Paths possibly used on Windows
+            sys_prefix / "bin",
+            sys_prefix / "Library",
+            sys_prefix / "Library" / "bin",
+            sys_prefix / "Library" / "lib",
+        ]
+        sys_prefix_candidates = [
+            p.expanduser().resolve() for p in sys_prefix_candidates
+        ]
+        for candidate_dir in sys_prefix_candidates:
+            libtreelite_sys = candidate_dir / _lib_name()
+            if libtreelite_sys.exists():
+                logger.info("Using system XGBoost: %s", str(libtreelite_sys))
+                return libtreelite_sys
+        raise RuntimeError(
+            f"use_system_libxgboost was specified but {_lib_name()} is "
+            f"not found. Paths searched (in order): \n"
+            + "\n".join([f"* {str(p)}" for p in sys_prefix_candidates])
+        )
 
     libxgboost = locate_local_libxgboost(toplevel_dir, logger=logger)
     if libxgboost is not None:

python-package/pyproject.toml

@@ -7,7 +7,7 @@ build-backend = "packager.pep517"
 
 [project]
 name = "xgboost"
-version = "2.0.0"
+version = "2.0.1"
 authors = [
     { name = "Hyunsu Cho", email = "chohyu01@cs.washington.edu" },
     { name = "Jiaming Yuan", email = "jm.yuan@outlook.com" }

python-package/xgboost/VERSION

@@ -1 +1 @@
-2.0.0
+2.0.1