Merge branch 'master' into cv_w_dmatrix

.clang-format

@@ -17,7 +17,7 @@ AllowShortEnumsOnASingleLine: true
 AllowShortBlocksOnASingleLine: Never
 AllowShortCaseLabelsOnASingleLine: false
 AllowShortFunctionsOnASingleLine: All
-AllowShortLambdasOnASingleLine: All
+AllowShortLambdasOnASingleLine: Inline
 AllowShortIfStatementsOnASingleLine: WithoutElse
 AllowShortLoopsOnASingleLine: true
 AlwaysBreakAfterDefinitionReturnType: None

.github/workflows/i386.yml

@@ -5,6 +5,10 @@ on: [push, pull_request]
 permissions:
   contents: read # to fetch code (actions/checkout)
 
+concurrency:
+  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
+  cancel-in-progress: true
+
 jobs:
   build-32bit:
     name: Build 32-bit

.github/workflows/jvm_tests.yml

@@ -5,6 +5,10 @@ on: [push, pull_request]
 permissions:
   contents: read # to fetch code (actions/checkout)
 
+concurrency:
+  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
+  cancel-in-progress: true
+
 jobs:
   test-with-jvm:
     name: Test JVM on OS ${{ matrix.os }}
@@ -15,39 +19,45 @@ jobs:
         os: [windows-latest, ubuntu-latest, macos-11]
 
     steps:
-    - uses: actions/checkout@e2f20e631ae6d7dd3b768f56a5d2af784dd54791 # v2.5.0
+    - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4.1.1
       with:
         submodules: 'true'
 
-    - uses: actions/setup-python@7f80679172b057fc5e90d70d197929d454754a5a # v4.3.0
-      with:
-        python-version: '3.8'
-        architecture: 'x64'
-
-    - uses: actions/setup-java@d202f5dbf7256730fb690ec59f6381650114feb2 # v3.6.0
+    - uses: mamba-org/setup-micromamba@422500192359a097648154e8db4e39bdb6c6eed7  # v1.8.1
       with:
-        java-version: 1.8
-
-    - name: Install Python packages
-      run: |
-        python -m pip install wheel setuptools
-        python -m pip install awscli
+        micromamba-version: '1.5.6-0'
+        environment-name: jvm_tests
+        create-args: >-
+          python=3.10
+          awscli
+        cache-downloads: true
+        cache-environment: true
+        init-shell: bash powershell
 
     - name: Cache Maven packages
-      uses: actions/cache@6998d139ddd3e68c71e9e398d8e40b71a2f39812 # v3.2.5
+      uses: actions/cache@13aacd865c20de90d75de3b17ebe84f7a17d57d2  # v4.0.0
       with:
         path: ~/.m2
         key: ${{ runner.os }}-m2-${{ hashFiles('./jvm-packages/pom.xml') }}
         restore-keys: ${{ runner.os }}-m2-${{ hashFiles('./jvm-packages/pom.xml') }}
 
+    - name: Build xgboost4j.dll
+      run: |
+        mkdir build
+        cd build
+        cmake .. -G"Visual Studio 17 2022" -A x64 -DJVM_BINDINGS=ON
+        cmake --build . --config Release
+      if: matrix.os == 'windows-latest'
+
     - name: Test XGBoost4J (Core)
       run: |
         cd jvm-packages
         mvn test -B -pl :xgboost4j_2.12
 
     - name: Extract branch name
       shell: bash
-      run: echo "##[set-output name=branch;]$(echo ${GITHUB_REF#refs/heads/})"
+      run: |
+        echo "branch=${GITHUB_REF#refs/heads/}" >> "$GITHUB_OUTPUT"
       id: extract_branch
       if: |
         (github.ref == 'refs/heads/master' || contains(github.ref, 'refs/heads/release_')) &&
@@ -58,7 +68,7 @@ jobs:
         cd lib/
         Rename-Item -Path xgboost4j.dll -NewName xgboost4j_${{ github.sha }}.dll
         dir
-        python -m awscli s3 cp xgboost4j_${{ github.sha }}.dll s3://xgboost-nightly-builds/${{ steps.extract_branch.outputs.branch }}/libxgboost4j/ --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 --region us-west-2
       if: |
         (github.ref == 'refs/heads/master' || contains(github.ref, 'refs/heads/release_')) &&
         matrix.os == 'windows-latest'
@@ -67,11 +77,12 @@ jobs:
         AWS_SECRET_ACCESS_KEY: ${{ secrets.AWS_SECRET_ACCESS_KEY_IAM_S3_UPLOADER }}
 
     - name: Publish artifact libxgboost4j.dylib to S3
+      shell: bash -l {0}
       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/${{ steps.extract_branch.outputs.branch }}/libxgboost4j/ --acl public-read
+        python -m awscli s3 cp libxgboost4j_${{ github.sha }}.dylib s3://xgboost-nightly-builds/${{ steps.extract_branch.outputs.branch }}/libxgboost4j/ --acl public-read --region us-west-2
       if: |
         (github.ref == 'refs/heads/master' || contains(github.ref, 'refs/heads/release_')) &&
         matrix.os == 'macos-11'

.github/workflows/main.yml

@@ -9,6 +9,10 @@ on: [push, pull_request]
 permissions:
   contents: read # to fetch code (actions/checkout)
 
+concurrency:
+  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
+  cancel-in-progress: true
+
 # A workflow run is made up of one or more jobs that can run sequentially or in parallel
 jobs:
   gtest-cpu:
@@ -174,7 +178,7 @@ jobs:
     - uses: actions/checkout@e2f20e631ae6d7dd3b768f56a5d2af784dd54791 # v2.5.0
       with:
         submodules: 'true'
-    - uses: actions/setup-python@7f80679172b057fc5e90d70d197929d454754a5a # v4.3.0
+    - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5.0.0
       with:
         python-version: "3.8"
         architecture: 'x64'

.github/workflows/python_tests.yml

@@ -9,6 +9,10 @@ defaults:
   run:
     shell: bash -l {0}
 
+concurrency:
+  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
+  cancel-in-progress: true
+
 jobs:
   python-mypy-lint:
     runs-on: ubuntu-latest
@@ -310,7 +314,7 @@ jobs:
           submodules: 'true'
 
       - name: Set up Python 3.8
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5.0.0
         with:
           python-version: 3.8
 

.github/workflows/python_wheels.yml

@@ -5,6 +5,10 @@ on: [push, pull_request]
 permissions:
   contents: read # to fetch code (actions/checkout)
 
+concurrency:
+  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
+  cancel-in-progress: true
+
 jobs:
   python-wheels:
     name: Build wheel for ${{ matrix.platform_id }}
@@ -17,11 +21,11 @@ jobs:
         - os: macos-latest
           platform_id: macosx_arm64
     steps:
-    - uses: actions/checkout@e2f20e631ae6d7dd3b768f56a5d2af784dd54791 # v2.5.0
+    - uses: actions/checkout@a12a3943b4bdde767164f792f33f40b04645d846 # v3.0.0
       with:
         submodules: 'true'
     - name: Setup Python
-      uses: actions/setup-python@7f80679172b057fc5e90d70d197929d454754a5a # v4.3.0
+      uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5.0.0
       with:
         python-version: "3.8"
     - name: Build wheels

.github/workflows/r_nold.yml

@@ -10,6 +10,10 @@ on:
 permissions:
   contents: read # to fetch code (actions/checkout)
 
+concurrency:
+  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
+  cancel-in-progress: true
+
 jobs:
   test-R-noLD:
     if: github.event.comment.body == '/gha run r-nold-test' && contains('OWNER,MEMBER,COLLABORATOR', github.event.comment.author_association)

.github/workflows/r_tests.yml

@@ -8,6 +8,10 @@ env:
 permissions:
   contents: read # to fetch code (actions/checkout)
 
+concurrency:
+  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
+  cancel-in-progress: true
+
 jobs:
   lintr:
     runs-on: ${{ matrix.config.os }}
@@ -46,19 +50,25 @@ jobs:
         MAKEFLAGS="-j$(nproc)" R CMD INSTALL R-package/
         Rscript tests/ci_build/lint_r.R $(pwd)
 
-  test-R-on-Windows:
+  test-Rpkg:
     runs-on: ${{ matrix.config.os }}
     name: Test R on OS ${{ matrix.config.os }}, R ${{ matrix.config.r }}, Compiler ${{ matrix.config.compiler }}, Build ${{ matrix.config.build }}
     strategy:
       fail-fast: false
       matrix:
         config:
           - {os: windows-latest, r: 'release', compiler: 'mingw', build: 'autotools'}
+          - {os: ubuntu-latest, r: 'release', compiler: 'none', build: 'cmake'}
     env:
       R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
       RSPM: ${{ matrix.config.rspm }}
 
     steps:
+    - name: Install system dependencies
+      run: |
+        sudo apt update
+        sudo apt install libcurl4-openssl-dev libssl-dev libssh2-1-dev libgit2-dev libglpk-dev libxml2-dev libharfbuzz-dev libfribidi-dev
+      if: matrix.config.os == 'ubuntu-latest'
     - uses: actions/checkout@e2f20e631ae6d7dd3b768f56a5d2af784dd54791 # v2.5.0
       with:
         submodules: 'true'
@@ -74,7 +84,7 @@ jobs:
         key: ${{ runner.os }}-r-${{ matrix.config.r }}-6-${{ hashFiles('R-package/DESCRIPTION') }}
         restore-keys: ${{ runner.os }}-r-${{ matrix.config.r }}-6-${{ hashFiles('R-package/DESCRIPTION') }}
 
-    - uses: actions/setup-python@7f80679172b057fc5e90d70d197929d454754a5a # v4.3.0
+    - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5.0.0
       with:
         python-version: "3.8"
         architecture: 'x64'
@@ -89,6 +99,12 @@ jobs:
     - name: Test R
       run: |
         python tests/ci_build/test_r_package.py --compiler='${{ matrix.config.compiler }}' --build-tool="${{ matrix.config.build }}" --task=check
+      if: matrix.config.compiler != 'none'
+
+    - name: Test R
+      run: |
+        python tests/ci_build/test_r_package.py --build-tool="${{ matrix.config.build }}" --task=check
+      if: matrix.config.compiler == 'none'
 
   test-R-on-Debian:
     name: Test R package on Debian

.github/workflows/scorecards.yml

@@ -22,12 +22,12 @@ jobs:
 
     steps:
       - name: "Checkout code"
-        uses: actions/checkout@a12a3943b4bdde767164f792f33f40b04645d846 # tag=v3.0.0
+        uses: actions/checkout@a12a3943b4bdde767164f792f33f40b04645d846 # v3.0.0
         with:
           persist-credentials: false
 
       - name: "Run analysis"
-        uses: ossf/scorecard-action@08b4669551908b1024bb425080c797723083c031 # tag=v2.2.0
+        uses: ossf/scorecard-action@0864cf19026789058feabb7e87baa5f140aac736 # v2.3.1
         with:
           results_file: results.sarif
           results_format: sarif
@@ -41,14 +41,14 @@ jobs:
       # Upload the results as artifacts (optional). Commenting out will disable uploads of run results in SARIF
       # format to the repository Actions tab.
       - name: "Upload artifact"
-        uses: actions/upload-artifact@0b7f8abb1508181956e8e162db84b466c27e18ce # tag=v3.1.2
+        uses: actions/upload-artifact@5d5d22a31266ced268874388b861e4b58bb5c2f3 # v4.3.1
         with:
           name: SARIF file
           path: results.sarif
           retention-days: 5
 
       # Upload the results to GitHub's code scanning dashboard.
       - name: "Upload to code-scanning"
-        uses: github/codeql-action/upload-sarif@7b6664fa89524ee6e3c3e9749402d5afd69b3cd8 # tag=v2.14.1
+        uses: github/codeql-action/upload-sarif@83a02f7883b12e0e4e1a146174f5e2292a01e601 # v2.16.4
         with:
           sarif_file: results.sarif

R-package/CMakeLists.txt

@@ -26,7 +26,6 @@ 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

R-package/DESCRIPTION

@@ -56,7 +56,8 @@ Suggests:
     testthat,
     igraph (>= 1.0.1),
     float,
-    titanic
+    titanic,
+    RhpcBLASctl
 Depends:
     R (>= 4.3.0)
 Imports:

R-package/NAMESPACE

@@ -20,15 +20,9 @@ export("xgb.attr<-")
 export("xgb.attributes<-")
 export("xgb.config<-")
 export("xgb.parameters<-")
-export(cb.cv.predict)
-export(cb.early.stop)
-export(cb.evaluation.log)
-export(cb.gblinear.history)
-export(cb.print.evaluation)
-export(cb.reset.parameters)
-export(cb.save.model)
 export(getinfo)
 export(setinfo)
+export(xgb.Callback)
 export(xgb.DMatrix)
 export(xgb.DMatrix.hasinfo)
 export(xgb.DMatrix.save)
@@ -39,6 +33,13 @@ export(xgb.QuantileDMatrix)
 export(xgb.QuantileDMatrix.from_iterator)
 export(xgb.attr)
 export(xgb.attributes)
+export(xgb.cb.cv.predict)
+export(xgb.cb.early.stop)
+export(xgb.cb.evaluation.log)
+export(xgb.cb.gblinear.history)
+export(xgb.cb.print.evaluation)
+export(xgb.cb.reset.parameters)
+export(xgb.cb.save.model)
 export(xgb.config)
 export(xgb.copy.Booster)
 export(xgb.create.features)
@@ -72,14 +73,10 @@ export(xgb.slice.DMatrix)
 export(xgb.train)
 export(xgboost)
 import(methods)
+importClassesFrom(Matrix,CsparseMatrix)
 importClassesFrom(Matrix,dgCMatrix)
 importClassesFrom(Matrix,dgRMatrix)
-importClassesFrom(Matrix,dgeMatrix)
-importFrom(Matrix,colSums)
 importFrom(Matrix,sparse.model.matrix)
-importFrom(Matrix,sparseMatrix)
-importFrom(Matrix,sparseVector)
-importFrom(Matrix,t)
 importFrom(data.table,":=")
 importFrom(data.table,as.data.table)
 importFrom(data.table,data.table)
@@ -101,6 +98,7 @@ importFrom(methods,new)
 importFrom(stats,coef)
 importFrom(stats,median)
 importFrom(stats,predict)
+importFrom(stats,sd)
 importFrom(stats,variable.names)
 importFrom(utils,head)
 importFrom(utils,object.size)