Various fixes

.github/dependabot.yml

@@ -0,0 +1,35 @@
+# To get started with Dependabot version updates, you'll need to specify which
+# package ecosystems to update and where the package manifests are located.
+# Please see the documentation for all configuration options:
+# https://docs.github.com/github/administering-a-repository/configuration-options-for-dependency-updates
+
+version: 2
+updates:
+  - package-ecosystem: "maven"
+    directory: "/jvm-packages"
+    schedule:
+      interval: "monthly"
+  - package-ecosystem: "maven"
+    directory: "/jvm-packages/xgboost4j"
+    schedule:
+      interval: "monthly"
+  - package-ecosystem: "maven"
+    directory: "/jvm-packages/xgboost4j-gpu"
+    schedule:
+      interval: "monthly"
+  - package-ecosystem: "maven"
+    directory: "/jvm-packages/xgboost4j-example"
+    schedule:
+      interval: "monthly"
+  - package-ecosystem: "maven"
+    directory: "/jvm-packages/xgboost4j-spark"
+    schedule:
+      interval: "monthly"
+  - package-ecosystem: "maven"
+    directory: "/jvm-packages/xgboost4j-spark-gpu"
+    schedule:
+      interval: "monthly"
+  - package-ecosystem: "github-actions"
+    directory: /
+    schedule:
+      interval: "monthly"

.github/lock.yml

@@ -0,0 +1,32 @@
+# Configuration for lock-threads - https://github.com/dessant/lock-threads
+
+# Number of days of inactivity before a closed issue or pull request is locked
+daysUntilLock: 90
+
+# Issues and pull requests with these labels will not be locked. Set to `[]` to disable
+exemptLabels:
+  - feature-request
+
+# Label to add before locking, such as `outdated`. Set to `false` to disable
+lockLabel: false
+
+# Comment to post before locking. Set to `false` to disable
+lockComment: false
+
+# Assign `resolved` as the reason for locking. Set to `false` to disable
+setLockReason: true
+
+# Limit to only `issues` or `pulls`
+# only: issues
+
+# Optionally, specify configuration settings just for `issues` or `pulls`
+# issues:
+#   exemptLabels:
+#     - help-wanted
+#   lockLabel: outdated
+
+# pulls:
+#   daysUntilLock: 30
+
+# Repository to extend settings from
+# _extends: repo

.github/workflows/freebsd.yml

@@ -0,0 +1,34 @@
+name: FreeBSD
+
+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:
+    runs-on: ubuntu-latest
+    timeout-minutes: 20
+    name: A job to run test in FreeBSD
+    steps:
+    - uses: actions/checkout@v4
+      with:
+        submodules: 'true'
+    - name: Test in FreeBSD
+      id: test
+      uses: vmactions/freebsd-vm@v1
+      with:
+        usesh: true
+        prepare: |
+          pkg install -y cmake git ninja googletest
+
+        run: |
+          mkdir build
+          cd build
+          cmake .. -GNinja -DGOOGLE_TEST=ON
+          ninja -v
+          ./testxgboost

.github/workflows/r_nold.yml

@@ -0,0 +1,44 @@
+# Run expensive R tests with the help of rhub. Only triggered by a pull request review
+# See discussion at https://github.com/dmlc/xgboost/pull/6378
+
+name: XGBoost-R-noLD
+
+on:
+  pull_request_review_comment:
+    types: [created]
+
+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)
+    timeout-minutes: 120
+    runs-on: ubuntu-latest
+    container:
+      image: rhub/debian-gcc-devel-nold
+    steps:
+    - name: Install git and system packages
+      shell: bash
+      run: |
+        apt update && apt install libcurl4-openssl-dev libssl-dev libssh2-1-dev libgit2-dev libglpk-dev libxml2-dev libharfbuzz-dev libfribidi-dev git -y
+
+    - uses: actions/checkout@a5ac7e51b41094c92402da3b24376905380afc29 # v4.1.6
+      with:
+        submodules: 'true'
+
+    - name: Install dependencies
+      shell: bash -l {0}
+      run: |
+        /tmp/R-devel/bin/Rscript -e "source('./R-package/tests/helper_scripts/install_deps.R')"
+
+    - name: Run R tests
+      shell: bash
+      run: |
+        cd R-package && \
+        /tmp/R-devel/bin/R CMD INSTALL . && \
+        /tmp/R-devel/bin/R -q -e "library(testthat); setwd('tests'); source('testthat.R')"

.github/workflows/sycl_tests.yml

@@ -5,6 +5,10 @@ on: [push, pull_request]
 permissions:
   contents: read  # to fetch code (actions/checkout)
 
+defaults:
+  run:
+    shell: bash -l {0}
+
 concurrency:
   group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
   cancel-in-progress: true
@@ -37,20 +41,16 @@ jobs:
         conda info
         conda list
     - name: Build and install XGBoost
-      shell: bash -l {0}
       run: |
         mkdir build
         cd build
-        cmake .. -DGOOGLE_TEST=ON -DUSE_DMLC_GTEST=ON -DPLUGIN_SYCL=ON -DCMAKE_CXX_COMPILER=g++ -DCMAKE_C_COMPILER=gcc -DCMAKE_INSTALL_PREFIX=$CONDA_PREFIX
-        make -j$(nproc)
-    - name: Run gtest binary for SYCL
-      run: |
-        cd build
-        ./testxgboost --gtest_filter=Sycl*
-    - name: Run gtest binary for non SYCL
+        cmake .. -DGOOGLE_TEST=ON -DUSE_DMLC_GTEST=ON -DPLUGIN_SYCL=ON -DCMAKE_CXX_COMPILER=g++ \
+          -DCMAKE_C_COMPILER=gcc -DCMAKE_INSTALL_PREFIX=$CONDA_PREFIX -GNinja
+        ninja
+    - name: Run gtest
       run: |
         cd build
-        ./testxgboost --gtest_filter=-Sycl*
+        ./testxgboost
 
   python-sycl-tests-on-ubuntu:
     name: Test XGBoost Python package with SYCL on ${{ matrix.os }}
@@ -82,8 +82,9 @@ jobs:
       run: |
         mkdir build
         cd build
-        cmake .. -DPLUGIN_SYCL=ON -DCMAKE_CXX_COMPILER=g++ -DCMAKE_C_COMPILER=gcc -DCMAKE_PREFIX_PATH=$CONDA_PREFIX
-        make -j$(nproc)
+        cmake .. -DPLUGIN_SYCL=ON -DCMAKE_CXX_COMPILER=g++ -DCMAKE_C_COMPILER=gcc \
+          -DCMAKE_PREFIX_PATH=$CONDA_PREFIX -GNinja
+        ninja
     - name: Install Python package
       run: |
         cd python-package

ops/conda_env/linux_sycl_test.yml

@@ -18,6 +18,7 @@ dependencies:
 - pytest-timeout
 - pytest-cov
 - dask
+- ninja
 - dpcpp_linux-64
 - onedpl-devel
 - intel-openmp

ops/docker/dockerfile/Dockerfile.gpu_build_rockylinux8

@@ -76,7 +76,7 @@ RUN set -ex; \
 
 # Default entry-point to use if running locally
 # It will preserve attributes of created files
-COPY entrypoint.sh /scripts/
+COPY docker/entrypoint.sh /scripts/
 
 WORKDIR /workspace
 ENTRYPOINT ["/scripts/entrypoint.sh"]

ops/pipeline/build-jvm-doc-impl.sh

@@ -27,7 +27,7 @@ mvn --no-transfer-progress javadoc:javadoc -Pdocs
 
 # Package JVM docs in a tarball
 mkdir -p tmp/scaladocs
-cp -rv xgboost4j/target/site/apidocs/ ./tmp/javadocs/
+cp -rv xgboost4j/target/reports/apidocs/ ./tmp/javadocs/
 cp -rv xgboost4j/target/site/scaladocs/ ./tmp/scaladocs/xgboost4j/
 cp -rv xgboost4j-spark/target/site/scaladocs/ ./tmp/scaladocs/xgboost4j-spark/
 cp -rv xgboost4j-spark-gpu/target/site/scaladocs/ ./tmp/scaladocs/xgboost4j-spark-gpu/