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[R] Fix warning about mismatched names when joining #10479

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[R] Fix warning about mismatched names when joining

[R] Fix warning about mismatched names when joining #10479

Workflow file for this run

.github/workflows/python_tests.yml at 02e9ca8
name: XGBoost-Python-Tests
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
jobs:
python-mypy-lint:
runs-on: ubuntu-latest
name: Type and format checks for the Python package
strategy:
matrix:
os: [ubuntu-latest]
steps:
- uses: actions/checkout@a5ac7e51b41094c92402da3b24376905380afc29 # v4.1.6
with:
submodules: 'true'
- uses: conda-incubator/setup-miniconda@a4260408e20b96e80095f42ff7f1a15b27dd94ca # v3.0.4
with:
miniforge-variant: Mambaforge
miniforge-version: latest
activate-environment: python_lint
environment-file: tests/ci_build/conda_env/python_lint.yml
use-mamba: true
- name: Display Conda env
run: |
conda info
conda list
- name: Run mypy
run: |
python tests/ci_build/lint_python.py --format=0 --type-check=1 --pylint=0
- name: Run formatter
run: |
python tests/ci_build/lint_python.py --format=1 --type-check=0 --pylint=0
- name: Run pylint
run: |
python tests/ci_build/lint_python.py --format=0 --type-check=0 --pylint=1
python-sdist-test-on-Linux:
# Mismatched glibcxx version between system and conda forge.
runs-on: ${{ matrix.os }}
name: Test installing XGBoost Python source package on ${{ matrix.os }}
strategy:
matrix:
os: [ubuntu-latest]
steps:
- uses: actions/checkout@a5ac7e51b41094c92402da3b24376905380afc29 # v4.1.6
with:
submodules: 'true'
- uses: conda-incubator/setup-miniconda@a4260408e20b96e80095f42ff7f1a15b27dd94ca # v3.0.4
with:
miniforge-variant: Mambaforge
miniforge-version: latest
activate-environment: sdist_test
environment-file: tests/ci_build/conda_env/sdist_test.yml
use-mamba: true
- name: Display Conda env
run: |
conda info
conda list
- name: Build and install XGBoost
run: |
cd python-package
python --version
python -m build --sdist
pip install -v ./dist/xgboost-*.tar.gz --config-settings use_openmp=False
cd ..
python -c 'import xgboost'
python-sdist-test:
# Use system toolchain instead of conda toolchain for macos and windows.
# MacOS has linker error if clang++ from conda-forge is used
runs-on: ${{ matrix.os }}
name: Test installing XGBoost Python source package on ${{ matrix.os }}
strategy:
matrix:
os: [macos-13, windows-latest]
python-version: ["3.10"]
steps:
- uses: actions/checkout@a5ac7e51b41094c92402da3b24376905380afc29 # v4.1.6
with:
submodules: 'true'
- name: Install osx system dependencies
if: matrix.os == 'macos-13'
run: |
brew install ninja libomp
- uses: conda-incubator/setup-miniconda@a4260408e20b96e80095f42ff7f1a15b27dd94ca # v3.0.4
with:
auto-update-conda: true
python-version: ${{ matrix.python-version }}
activate-environment: test
- name: Install build
run: |
conda install -c conda-forge python-build
- name: Display Conda env
run: |
conda info
conda list
- name: Build and install XGBoost
run: |
cd python-package
python --version
python -m build --sdist
pip install -v ./dist/xgboost-*.tar.gz
cd ..
python -c 'import xgboost'
python-tests-on-macos:
name: Test XGBoost Python package on ${{ matrix.config.os }}
runs-on: ${{ matrix.config.os }}
timeout-minutes: 60
strategy:
matrix:
config:
- {os: macos-13}
steps:
- uses: actions/checkout@a5ac7e51b41094c92402da3b24376905380afc29 # v4.1.6
with:
submodules: 'true'
- uses: conda-incubator/setup-miniconda@a4260408e20b96e80095f42ff7f1a15b27dd94ca # v3.0.4
with:
miniforge-variant: Mambaforge
miniforge-version: latest
activate-environment: macos_cpu_test
environment-file: tests/ci_build/conda_env/macos_cpu_test.yml
use-mamba: true
- name: Display Conda env
run: |
conda info
conda list
- name: Build XGBoost on macos
run: |
brew install ninja
mkdir build
cd build
# Set prefix, to use OpenMP library from Conda env
# See https://github.com/dmlc/xgboost/issues/7039#issuecomment-1025038228
# to learn why we don't use libomp from Homebrew.
cmake .. -GNinja -DCMAKE_PREFIX_PATH=$CONDA_PREFIX -DBUILD_DEPRECATED_CLI=ON
ninja
- name: Install Python package
run: |
cd python-package
python --version
pip install -v .
- name: Test Python package
run: |
pytest -s -v -rxXs --durations=0 ./tests/python
- name: Test Dask Interface
run: |
pytest -s -v -rxXs --durations=0 ./tests/test_distributed/test_with_dask
python-tests-on-win:
name: Test XGBoost Python package on ${{ matrix.config.os }}
runs-on: ${{ matrix.config.os }}
timeout-minutes: 60
strategy:
matrix:
config:
- {os: windows-latest, python-version: '3.10'}
steps:
- uses: actions/checkout@a5ac7e51b41094c92402da3b24376905380afc29 # v4.1.6
with:
submodules: 'true'
- uses: conda-incubator/setup-miniconda@a4260408e20b96e80095f42ff7f1a15b27dd94ca # v3.0.4
with:
auto-update-conda: true
python-version: ${{ matrix.config.python-version }}
activate-environment: win64_env
environment-file: tests/ci_build/conda_env/win64_cpu_test.yml
- name: Display Conda env
run: |
conda info
conda list
- name: Build XGBoost on Windows
run: |
mkdir build_msvc
cd build_msvc
cmake .. -G"Visual Studio 17 2022" -DCMAKE_CONFIGURATION_TYPES="Release" -A x64 -DBUILD_DEPRECATED_CLI=ON
cmake --build . --config Release --parallel $(nproc)
- name: Install Python package
run: |
cd python-package
python --version
pip wheel -v . --wheel-dir dist/
pip install ./dist/*.whl
- name: Test Python package
run: |
pytest -s -v -rxXs --durations=0 ./tests/python
python-tests-on-ubuntu:
name: Test XGBoost Python package on ${{ matrix.config.os }}
runs-on: ${{ matrix.config.os }}
timeout-minutes: 90
strategy:
matrix:
config:
- {os: ubuntu-latest, python-version: "3.10"}
steps:
- uses: actions/checkout@a5ac7e51b41094c92402da3b24376905380afc29 # v4.1.6
with:
submodules: 'true'
- uses: conda-incubator/setup-miniconda@a4260408e20b96e80095f42ff7f1a15b27dd94ca # v3.0.4
with:
miniforge-variant: Mambaforge
miniforge-version: latest
activate-environment: linux_cpu_test
environment-file: tests/ci_build/conda_env/linux_cpu_test.yml
use-mamba: true
- name: Display Conda env
run: |
conda info
conda list
- name: Build XGBoost on Ubuntu
run: |
mkdir build
cd build
cmake .. -GNinja -DCMAKE_PREFIX_PATH=$CONDA_PREFIX -DBUILD_DEPRECATED_CLI=ON
ninja
- name: Install Python package
run: |
cd python-package
python --version
pip install -v .
- name: Test Python package
run: |
pytest -s -v -rxXs --durations=0 ./tests/python
- name: Test Dask Interface
run: |
pytest -s -v -rxXs --durations=0 ./tests/test_distributed/test_with_dask
- name: Test PySpark Interface
shell: bash -l {0}
run: |
pytest -s -v -rxXs --durations=0 ./tests/test_distributed/test_with_spark
python-sycl-tests-on-ubuntu:
name: Test XGBoost Python package with SYCL on ${{ matrix.config.os }}
runs-on: ${{ matrix.config.os }}
timeout-minutes: 90
strategy:
matrix:
config:
- {os: ubuntu-latest, python-version: "3.10"}
steps:
- uses: actions/checkout@a5ac7e51b41094c92402da3b24376905380afc29 # v4.1.6
with:
submodules: 'true'
- uses: conda-incubator/setup-miniconda@a4260408e20b96e80095f42ff7f1a15b27dd94ca # v3.0.4
with:
miniforge-variant: Mambaforge
miniforge-version: latest
activate-environment: linux_sycl_test
environment-file: tests/ci_build/conda_env/linux_sycl_test.yml
use-mamba: true
- name: Display Conda env
run: |
conda info
conda list
- name: Build XGBoost on Ubuntu
run: |
mkdir build
cd build
cmake .. -DPLUGIN_SYCL=ON -DCMAKE_CXX_COMPILER=g++ -DCMAKE_C_COMPILER=gcc -DCMAKE_PREFIX_PATH=$CONDA_PREFIX
make -j$(nproc)
- name: Install Python package
run: |
cd python-package
python --version
pip install -v .
- name: Test Python package
run: |
pytest -s -v -rxXs --durations=0 ./tests/python-sycl/
python-system-installation-on-ubuntu:
name: Test XGBoost Python package System Installation on ${{ matrix.os }}
runs-on: ${{ matrix.os }}
strategy:
matrix:
os: [ubuntu-latest]
steps:
- uses: actions/checkout@a5ac7e51b41094c92402da3b24376905380afc29 # v4.1.6
with:
submodules: 'true'
- name: Set up Python 3.10
uses: actions/setup-python@f677139bbe7f9c59b41e40162b753c062f5d49a3 # v5.2.0
with:
python-version: "3.10"
- name: Install ninja
run: |
sudo apt-get update && sudo apt-get install -y ninja-build
- name: Build XGBoost on Ubuntu
run: |
mkdir build
cd build
cmake .. -GNinja
ninja
- name: Copy lib to system lib
run: |
cp lib/* "$(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'