Merge branch 'master' into sovrn-inplace-predict-java

sovrn · Aug 22, 2023 · 30ed3ca · 30ed3ca
2 parents 8b4885d + 8c10af4
commit 30ed3ca
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diff --git a/.github/dependabot.yml b/.github/dependabot.yml
@@ -9,85 +9,23 @@ updates:
     directory: "/jvm-packages"
     schedule:
       interval: "daily"
-    ignore:
-      # Pin Scala version to 2.12.x
-      - dependency-name: "org.scala-lang:scala-compiler"
-        versions: [">= 2.13.0"]
-      - dependency-name: "org.scala-lang:scala-reflect"
-        versions: [">= 2.13.0"]
-      - dependency-name: "org.scala-lang:scala-library"
-        versions: [">= 2.13.0"]
   - package-ecosystem: "maven"
     directory: "/jvm-packages/xgboost4j"
     schedule:
       interval: "daily"
-    ignore:
-      # Pin Scala version to 2.12.x
-      - dependency-name: "org.scala-lang:scala-compiler"
-        versions: [">= 2.13.0"]
-      - dependency-name: "org.scala-lang:scala-reflect"
-        versions: [">= 2.13.0"]
-      - dependency-name: "org.scala-lang:scala-library"
-        versions: [">= 2.13.0"]
   - package-ecosystem: "maven"
     directory: "/jvm-packages/xgboost4j-gpu"
     schedule:
       interval: "daily"
-    ignore:
-      # Pin Scala version to 2.12.x
-      - dependency-name: "org.scala-lang:scala-compiler"
-        versions: [">= 2.13.0"]
-      - dependency-name: "org.scala-lang:scala-reflect"
-        versions: [">= 2.13.0"]
-      - dependency-name: "org.scala-lang:scala-library"
-        versions: [">= 2.13.0"]
   - package-ecosystem: "maven"
     directory: "/jvm-packages/xgboost4j-example"
     schedule:
       interval: "daily"
-    ignore:
-      # Pin Scala version to 2.12.x
-      - dependency-name: "org.scala-lang:scala-compiler"
-        versions: [">= 2.13.0"]
-      - dependency-name: "org.scala-lang:scala-reflect"
-        versions: [">= 2.13.0"]
-      - dependency-name: "org.scala-lang:scala-library"
-        versions: [">= 2.13.0"]
   - package-ecosystem: "maven"
     directory: "/jvm-packages/xgboost4j-spark"
     schedule:
       interval: "daily"
-    ignore:
-      # Pin Scala version to 2.12.x
-      - dependency-name: "org.scala-lang:scala-compiler"
-        versions: [">= 2.13.0"]
-      - dependency-name: "org.scala-lang:scala-reflect"
-        versions: [">= 2.13.0"]
-      - dependency-name: "org.scala-lang:scala-library"
-        versions: [">= 2.13.0"]
-      # Pin Spark version to 3.0.x
-      - dependency-name: "org.apache.spark:spark-core_2.12"
-        versions: [">= 3.1.0"]
-      - dependency-name: "org.apache.spark:spark-sql_2.12"
-        versions: [">= 3.1.0"]
-      - dependency-name: "org.apache.spark:spark-mllib_2.12"
-        versions: [">= 3.1.0"]
   - package-ecosystem: "maven"
     directory: "/jvm-packages/xgboost4j-spark-gpu"
     schedule:
       interval: "daily"
-    ignore:
-      # Pin Scala version to 2.12.x
-      - dependency-name: "org.scala-lang:scala-compiler"
-        versions: [">= 2.13.0"]
-      - dependency-name: "org.scala-lang:scala-reflect"
-        versions: [">= 2.13.0"]
-      - dependency-name: "org.scala-lang:scala-library"
-        versions: [">= 2.13.0"]
-      # Pin Spark version to 3.0.x
-      - dependency-name: "org.apache.spark:spark-core_2.12"
-        versions: [">= 3.1.0"]
-      - dependency-name: "org.apache.spark:spark-sql_2.12"
-        versions: [">= 3.1.0"]
-      - dependency-name: "org.apache.spark:spark-mllib_2.12"
-        versions: [">= 3.1.0"]
diff --git a/.github/workflows/jvm_tests.yml b/.github/workflows/jvm_tests.yml
@@ -75,3 +75,13 @@ jobs:
       if: matrix.os == 'ubuntu-latest'  # Distributed training doesn't work on Windows
       env:
         RABIT_MOCK: ON
+
+
+    - name: Build and Test XGBoost4J with scala 2.13
+      run: |
+        rm -rfv build/
+        cd jvm-packages
+        mvn -B clean install test -Pdefault,scala-2.13
+      if: matrix.os == 'ubuntu-latest'  # Distributed training doesn't work on Windows
+      env:
+        RABIT_MOCK: ON
diff --git a/.github/workflows/main.yml b/.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: |

diff --git a/.github/workflows/python_tests.yml b/.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
@@ -255,3 +255,44 @@ jobs:
       shell: bash -l {0}
       run: |
         pytest -s -v -rxXs --durations=0 ./tests/test_distributed/test_with_spark
+
+  python-system-installation-on-ubuntu:
+    name: Test XGBoost Python package System Installation on ${{ matrix.os }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ubuntu-latest]
+
+    steps:
+      - uses: actions/checkout@v2
+        with:
+          submodules: 'true'
+
+      - name: Set up Python 3.8
+        uses: actions/setup-python@v4
+        with:
+          python-version: 3.8
+
+      - name: Install ninja
+        run: |
+          sudo apt-get update && sudo apt-get install -y ninja-build
+
+      - name: Build XGBoost on Ubuntu
+        run: |
+          mkdir build
+          cd build
+          cmake .. -GNinja
+          ninja
+
+      - name: Copy lib to system lib
+        run: |
+          cp lib/* "$(python -c 'import sys; print(sys.base_prefix)')/lib"
+
+      - name: Install XGBoost in Virtual Environment
+        run: |
+          cd python-package
+          pip install virtualenv
+          virtualenv venv
+          source venv/bin/activate && \
+            pip install -v . --config-settings use_system_libxgboost=True && \
+            python -c 'import xgboost'
diff --git a/.github/workflows/scorecards.yml b/.github/workflows/scorecards.yml
@@ -27,28 +27,28 @@ jobs:
           persist-credentials: false
 
       - name: "Run analysis"
-        uses: ossf/scorecard-action@99c53751e09b9529366343771cc321ec74e9bd3d # tag=v2.0.6
+        uses: ossf/scorecard-action@08b4669551908b1024bb425080c797723083c031 # tag=v2.2.0
         with:
           results_file: results.sarif
           results_format: sarif
 
           # Publish the results for public repositories to enable scorecard badges. For more details, see
-          # https://github.com/ossf/scorecard-action#publishing-results. 
-          # For private repositories, `publish_results` will automatically be set to `false`, regardless 
+          # https://github.com/ossf/scorecard-action#publishing-results.
+          # For private repositories, `publish_results` will automatically be set to `false`, regardless
           # of the value entered here.
           publish_results: true
 
       # 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@6673cd052c4cd6fcf4b4e6e60ea986c889389535 # tag=v3.0.0
+        uses: actions/upload-artifact@0b7f8abb1508181956e8e162db84b466c27e18ce # tag=v3.1.2
         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@5f532563584d71fdef14ee64d17bafb34f751ce5 # tag=v1.0.26
+        uses: github/codeql-action/upload-sarif@7b6664fa89524ee6e3c3e9749402d5afd69b3cd8 # tag=v2.14.1
         with:
           sarif_file: results.sarif
diff --git a/.github/workflows/update_rapids.yml b/.github/workflows/update_rapids.yml
@@ -0,0 +1,44 @@
+name: update-rapids
+
+on:
+  workflow_dispatch:
+  schedule:
+    - cron: "0 20 * * *"  # Run once daily
+
+permissions:
+  pull-requests: write
+  contents: write
+
+defaults:
+  run:
+    shell: bash -l {0}
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
+  cancel-in-progress: true
+
+env:
+  GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}  # To use GitHub CLI
+
+jobs:
+  update-rapids:
+    name: Check latest RAPIDS
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v2
+      with:
+        submodules: 'true'
+    - name: Check latest RAPIDS and update conftest.sh
+      run: |
+        bash tests/buildkite/update-rapids.sh
+    - name: Create Pull Request
+      uses: peter-evans/create-pull-request@v5
+      if: github.ref == 'refs/heads/master'
+      with:
+        add-paths: |
+          tests/buildkite
+        branch: create-pull-request/update-rapids
+        base: master
+        title: "[CI] Update RAPIDS to latest stable"
+        commit-message: "[CI] Update RAPIDS to latest stable"
+
diff --git a/.gitignore b/.gitignore
@@ -48,6 +48,7 @@ Debug
 *.Rproj
 ./xgboost.mpi
 ./xgboost.mock
+*.bak
 #.Rbuildignore
 R-package.Rproj
 *.cache*

diff --git a/CITATION b/CITATION
@@ -15,4 +15,3 @@
  address = {New York, NY, USA},
  keywords = {large-scale machine learning},
 }
-