DOC: URLs link to original numpy and pandas docs #3692
Workflow file for this run
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| name: Python CI | |
| on: | |
| push: | |
| branches: | |
| - '*' | |
| pull_request: | |
| types: ['opened', 'reopened', 'synchronize'] | |
| concurrency: | |
| group: ${{ github.workflow }}-${{ github.ref }} | |
| cancel-in-progress: true | |
| jobs: | |
| lint: | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: [ "ubuntu-latest" ] | |
| python-version: [ "3.10" ] | |
| steps: | |
| - name: Check out code | |
| uses: actions/checkout@v3 | |
| with: | |
| fetch-depth: 0 | |
| submodules: recursive | |
| - name: Set up Python environment | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: "3.10" | |
| - name: flake8 Lint | |
| uses: py-actions/flake8@v2 | |
| with: | |
| path: "python/xorbits" | |
| args: "--config python/setup.cfg" | |
| - name: black | |
| uses: psf/black@stable | |
| with: | |
| src: "python/xorbits" | |
| options: "--check" | |
| version: "23.12.0" | |
| - uses: isort/isort-action@master | |
| with: | |
| sortPaths: "python/xorbits" | |
| configuration: "--check-only --diff --sp python/setup.cfg" | |
| - name: mypy | |
| run: pip install mypy==1.11.2 && cd python && mypy xorbits | |
| - name: codespell | |
| run: pip install codespell==2.2.6 && cd python && codespell xorbits | |
| - name: Set up Node.js | |
| uses: actions/setup-node@v1 | |
| with: | |
| node-version: 16 | |
| # ESLint and Prettier must be in `package.json` | |
| - name: Install Node.js dependencies | |
| run: cd python/xorbits/web/ui && npm ci | |
| - name: ESLint Check | |
| run: cd python/xorbits/web/ui && npx eslint . | |
| - name: Prettier Check | |
| run: cd python/xorbits/web/ui && ./node_modules/.bin/prettier --check . | |
| build_test_job: | |
| if: github.repository == 'xorbitsai/xorbits' | |
| runs-on: ${{ matrix.os }} | |
| needs: lint | |
| env: | |
| CONDA_ENV: xorbits-test | |
| SELF_HOST_PYTHON: /root/miniconda3/envs/xorbits-test/bin/python | |
| SELF_HOST_CONDA: /root/miniconda3/condabin/conda | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: ["ubuntu-latest", "macos-13", "windows-latest"] | |
| python-version: ["3.9", "3.10", "3.11"] | |
| module: ["xorbits", "xorbits/numpy", "xorbits/pandas"] | |
| exclude: | |
| - { os: macos-13, python-version: 3.10} | |
| - { os: macos-13, python-version: 3.9} | |
| - { os: windows-latest, python-version: 3.10} | |
| - { os: windows-latest, python-version: 3.9} | |
| - { os: windows-latest, module: kubernetes} | |
| - { os: macos-13, module: kubernetes} | |
| include: | |
| - { os: ubuntu-latest, module: _mars/dataframe, python-version: 3.9 } | |
| - { os: ubuntu-latest, module: learn, python-version: 3.9 } | |
| - { os: ubuntu-latest, module: mars-core, python-version: 3.9 } | |
| - { os: ubuntu-20.04, module: hadoop, python-version: 3.9 } | |
| - { os: ubuntu-latest, module: vineyard, python-version: 3.11 } | |
| - { os: ubuntu-latest, module: external-storage, python-version: 3.11 } | |
| # always test compatibility with the latest version | |
| # - { os: ubuntu-latest, module: compatibility, python-version: 3.9 } | |
| - { os: ubuntu-latest, module: doc-build, python-version: 3.9 } | |
| - { os: self-hosted, module: gpu, python-version: 3.11} | |
| - { os: ubuntu-latest, module: jax, python-version: 3.9 } | |
| # a self-hosted runner which needs computing resources, activate when necessary | |
| # - { os: juicefs-ci, module: kubernetes-juicefs, python-version: 3.9 } | |
| - { os: ubuntu-latest, module: slurm, python-version: 3.9 } | |
| - { os: ubuntu-latest, module: datasets, python-version: 3.9 } | |
| - { os: ubuntu-latest, module: kubernetes, python-version: 3.11 } | |
| steps: | |
| - name: Check out code | |
| uses: actions/checkout@v3 | |
| with: | |
| fetch-depth: 0 | |
| submodules: recursive | |
| - name: Add msbuild to PATH | |
| if: ${{ matrix.os == 'windows-latest'}} | |
| uses: microsoft/setup-msbuild@v1.1 | |
| - name: Set up conda ${{ matrix.python-version }} | |
| uses: conda-incubator/setup-miniconda@v3 | |
| if: ${{ matrix.module != 'gpu' && matrix.module != 'kubernetes-juicefs' }} | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| activate-environment: ${{ env.CONDA_ENV }} | |
| - name: Start minikube | |
| uses: medyagh/setup-minikube@master | |
| if: ${{ matrix.module == 'kubernetes' }} | |
| with: | |
| driver: none | |
| kubernetes-version: v1.23.12 | |
| minikube-version: 1.31.2 | |
| - name: Install ucx dependencies | |
| if: ${{ (matrix.module != 'gpu') && (matrix.os == 'ubuntu-latest') && (matrix.module != 'doc-build') }} | |
| run: | | |
| # ucx-py move to ucxx and ucxx-cu12 can be run on CPU | |
| # conda install -c conda-forge -c rapidsai ucx-proc=*=cpu ucx ucx-py | |
| pip install ucxx-cu12 | |
| - name: Install libomp (macOS) | |
| if: ${{ matrix.os == 'macos-latest' || matrix.os == 'macos-13' }} | |
| run: brew install libomp | |
| - name: Install dependencies | |
| env: | |
| MODULE: ${{ matrix.module }} | |
| PYTHON: ${{ matrix.python-version }} | |
| if: ${{ matrix.module != 'gpu' }} | |
| run: | | |
| if [[ "$MODULE" == "doc-build" ]]; then | |
| pip install --upgrade --no-cache-dir pip setuptools | |
| pip install --upgrade --no-cache-dir sphinx readthedocs-sphinx-ext | |
| pip install --upgrade --upgrade-strategy only-if-needed --no-cache-dir ".[doc]" | |
| else | |
| pip install -e "git+https://github.com/xorbitsai/xoscar.git@main#subdirectory=python&egg=xoscar" | |
| pip install -U numpy scipy cython pyftpdlib coverage flaky numexpr | |
| if [[ "$MODULE" == "xorbits/pandas" ]]; then | |
| pip install openpyxl | |
| fi | |
| if [[ "$MODULE" == "mars-core" ]]; then | |
| pip install oss2 | |
| fi | |
| if [[ "$MODULE" == "kubernetes" ]]; then | |
| pip install kubernetes | |
| fi | |
| if [[ "$MODULE" == "kubernetes-juicefs" ]]; then | |
| pip install kubernetes | |
| if helm version --short >/dev/null 2>&1; then | |
| echo "Helm installed. Skipping installation." | |
| else | |
| curl https://raw.githubusercontent.com/helm/helm/main/scripts/get-helm-3 | bash | |
| fi | |
| if helm repo list | grep "juicefs" >/dev/null 2>&1; then | |
| echo "Repo juicefs existed. Skipping adding to helm repos." | |
| else | |
| helm repo add juicefs https://juicedata.github.io/charts/ | |
| helm repo update | |
| helm fetch --untar juicefs/juicefs-csi-driver | |
| fi | |
| if kubectl get pods -n kube-system | grep "juicefs-csi" >/dev/null 2>&1; then | |
| echo "Juicefs-csi-driver installed. Skipping installation." | |
| else | |
| helm install juicefs-csi-driver juicefs/juicefs-csi-driver -n kube-system -f xorbits/deploy/kubernetes/external_storage/juicefs/tests/values.yaml | |
| fi | |
| sleep 60 | |
| kubectl apply -f xorbits/deploy/kubernetes/external_storage/juicefs/tests/example-redis-config.yaml | |
| sleep 60 | |
| fi | |
| if [[ "$MODULE" == "hadoop" ]]; then | |
| ../CI/install-hadoop.sh | |
| echo "import coverage; coverage.process_startup()" > \ | |
| $(python -c "import site; print(site.getsitepackages()[-1])")/coverage.pth | |
| conda install --quiet --yes conda-forge::libffi==3.4.2 conda-forge::skein==0.8.1 conda-forge::conda-pack==0.8.0 conda-forge::protobuf==3.20.1 conda-forge::grpcio==1.42.0 | |
| fi | |
| if [[ "$MODULE" == "vineyard" ]]; then | |
| pip install vineyard | |
| mkdir -p /tmp/etcd-download-test | |
| export ETCD_VER=v3.4.13 | |
| export ETCD_DOWNLOAD_URL=https://github.com/etcd-io/etcd/releases/download | |
| curl -L $ETCD_DOWNLOAD_URL/$ETCD_VER/etcd-$ETCD_VER-linux-amd64.tar.gz -o /tmp/etcd-$ETCD_VER-linux-amd64.tar.gz | |
| tar xzvf /tmp/etcd-$ETCD_VER-linux-amd64.tar.gz -C /tmp/etcd-download-test --strip-components=1 | |
| sudo mv /tmp/etcd-download-test/etcd /usr/local/bin/ | |
| sudo mv /tmp/etcd-download-test/etcdctl /usr/local/bin/ | |
| rm -fr /tmp/etcd-$ETCD_VER-linux-amd64.tar.gz /tmp/etcd-download-test | |
| fi | |
| if [[ "$MODULE" == "external-storage" ]]; then | |
| export CUR_DIR=$(pwd) | |
| mkdir -p /tmp/alluxio-download-test | |
| cd /tmp/alluxio-download-test | |
| wget -q https://downloads.alluxio.io/downloads/files/2.9.3/alluxio-2.9.3-bin.tar.gz | |
| tar -xzf alluxio-2.9.3-bin.tar.gz | |
| cd alluxio-2.9.3 | |
| cp conf/alluxio-env.sh.template conf/alluxio-env.sh | |
| cp conf/alluxio-site.properties.template conf/alluxio-site.properties | |
| echo "alluxio.master.hostname=localhost" >> conf/alluxio-site.properties | |
| cd $CUR_DIR | |
| sudo mv /tmp/alluxio-download-test/alluxio-2.9.3 /usr/local/bin/ | |
| rm -R /tmp/alluxio-download-test | |
| unset CUR_DIR | |
| export ALLUXIO_HOME="/usr/local/bin/alluxio-2.9.3" | |
| ${ALLUXIO_HOME}/bin/alluxio format | |
| ${ALLUXIO_HOME}/bin/alluxio-start.sh local SudoMount | |
| curl -sSL https://d.juicefs.com/install | sh - | |
| curl -fsSL https://packages.redis.io/gpg | sudo gpg --dearmor -o /usr/share/keyrings/redis-archive-keyring.gpg | |
| echo "deb [signed-by=/usr/share/keyrings/redis-archive-keyring.gpg] https://packages.redis.io/deb $(lsb_release -cs) main" | sudo tee /etc/apt/sources.list.d/redis.list | |
| sudo apt-get update | |
| sudo apt-get install redis | |
| export JUICEFS_HOME="/usr/local/bin/juicefs" | |
| fi | |
| if [[ "$PYTHON" == '3.9' ]]; then | |
| pip install h5py zarr matplotlib fastparquet | |
| conda install -n test --quiet --yes -c conda-forge python=$PYTHON \ | |
| "tiledb-py>=0.4.3,<0.6.0" "tiledb<2.0.0" || true | |
| fi | |
| if [[ "$MODULE" == "_mars/learn" ]]; then | |
| pip install scikit-learn | |
| pip install xgboost lightgbm keras tensorflow faiss-cpu\<1.7.3 torch torchvision \ | |
| statsmodels tsfresh dask[complete] mimesis\<9.0.0 | |
| fi | |
| if [[ "$MODULE" == "learn" ]]; then | |
| pip install xgboost lightgbm | |
| fi | |
| if [[ "$MODULE" == "compatibility" ]]; then | |
| # test if compatible with older versions | |
| pip install "pandas==1.5.3" "scipy<=1.10.1" "numpy<=1.24.1" "matplotlib<=3.7.0" "pyarrow<12.0.0" "sqlalchemy<2" | |
| fi | |
| if [[ "$MODULE" == "jax" ]]; then | |
| # test jax | |
| pip install "jax>=0.4.0" "jaxlib>=0.4.0" | |
| fi | |
| if [[ "$MODULE" == "datasets" ]]; then | |
| # test huggingface datasets | |
| pip install datasets torch | |
| fi | |
| pip install -e ".[dev,extra,aws]" | |
| fi | |
| working-directory: ./python | |
| - name: Install on JuiceFsCI | |
| if: ${{ matrix.module == 'kubernetes-juicefs' }} | |
| run: | | |
| pip install -U xoscar | |
| python setup.py build_ext -i | |
| working-directory: ./python | |
| - name: Slurm Setup Job queuing system | |
| if: ${{ matrix.module == 'slurm' }} | |
| run: | | |
| source CI/slurm/${{ matrix.module }}.sh | |
| jobqueue_before_install | |
| - name: Slurm Install xorbits | |
| if: ${{ matrix.module == 'slurm' }} | |
| run: | | |
| source CI/slurm/${{ matrix.module }}.sh | |
| jobqueue_install | |
| - name: Install on GPU | |
| if: ${{ matrix.module == 'gpu' }} | |
| run: | | |
| source activate ${{ env.CONDA_ENV }} | |
| pip install --extra-index-url=https://pypi.nvidia.com cudf-cu12==24.8.* | |
| pip install ucxx-cu12 cython "numpy>=1.14.0,<2.0.0" cloudpickle scikit-learn \ | |
| pyyaml psutil tornado sqlalchemy defusedxml tqdm uvloop coverage \ | |
| pytest pytest-cov pytest-timeout pytest-forked pytest-asyncio pytest-mock | |
| pip install -U xoscar | |
| pip install -e ".[dev,extra,aws]" | |
| working-directory: ./python | |
| - name: Build doc | |
| if: ${{ matrix.module == 'doc-build' }} | |
| run: | | |
| make html | |
| make html_zh_cn | |
| working-directory: ./doc | |
| - name: Test with pytest | |
| if: ${{ matrix.module != 'doc-build' && matrix.module != 'gpu' }} | |
| env: | |
| MODULE: ${{ matrix.module }} | |
| run: | | |
| if [[ "$MODULE" == "xorbits" ]]; then | |
| pytest --ignore xorbits/_mars/ --ignore xorbits/pandas --ignore xorbits/numpy \ | |
| --ignore xorbits/xgboost --ignore xorbits/lightgbm --ignore xorbits/sklearn \ | |
| --ignore xorbits/datasets \ | |
| --ignore xorbits/core/tests/test_execution_exit.py \ | |
| --timeout=1500 \ | |
| -W ignore::PendingDeprecationWarning \ | |
| --cov-config=setup.cfg --cov-report=xml --cov=xorbits \ | |
| -k "not test_execution_with_process_exit_message" \ | |
| xorbits | |
| # workaround: this case will hang, run it separately. | |
| pytest --timeout=1500 \ | |
| -W ignore::PendingDeprecationWarning \ | |
| --cov-config=setup.cfg --cov-report=xml --cov=xorbits \ | |
| -k "test_execution_with_process_exit_message" \ | |
| xorbits/core/tests/test_execution.py | |
| elif [[ "$MODULE" == "xorbits/pandas" ]]; then | |
| pytest --timeout=1500 \ | |
| -W ignore::PendingDeprecationWarning \ | |
| --cov-config=setup.cfg --cov-report=xml \ | |
| --cov=xorbits xorbits/pandas | |
| elif [[ "$MODULE" == "xorbits/numpy" ]]; then | |
| pytest --timeout=1500 \ | |
| -W ignore::PendingDeprecationWarning \ | |
| --cov-config=setup.cfg --cov-report=xml --cov=xorbits \ | |
| -k "not test_numpy_fallback" \ | |
| xorbits/numpy | |
| # workaround: this case will hang, run it separately. | |
| pytest --timeout=1500 \ | |
| -W ignore::PendingDeprecationWarning \ | |
| --cov-config=setup.cfg --cov-report=xml \ | |
| --cov=xorbits \ | |
| -k "test_numpy_fallback" \ | |
| xorbits/numpy/numpy_adapters/tests/test_numpy_adapters.py | |
| elif [[ "$MODULE" == "mars-core" ]]; then | |
| pytest --forked --log-level=DEBUG --ignore xorbits/_mars/dataframe --ignore xorbits/_mars/tensor \ | |
| --ignore xorbits/_mars/learn --ignore xorbits/_mars/remote \ | |
| --timeout=1500 \ | |
| -W ignore::PendingDeprecationWarning \ | |
| --cov-config=setup.cfg --cov-report=xml --cov=xorbits xorbits/_mars | |
| elif [[ "$MODULE" == "kubernetes" ]]; then | |
| pytest --ignore xorbits/_mars/ --timeout=1500 \ | |
| -W ignore::PendingDeprecationWarning \ | |
| --cov-config=setup.cfg --cov-report=xml --cov=xorbits xorbits/deploy/kubernetes | |
| elif [[ "$MODULE" == "kubernetes-juicefs" ]]; then | |
| pytest --ignore xorbits/_mars/ --timeout=1500 \ | |
| -W ignore::PendingDeprecationWarning \ | |
| --cov-config=setup.cfg --cov-report=xml --cov=xorbits xorbits/deploy/kubernetes/external_storage/juicefs | |
| elif [[ "$MODULE" == "slurm" ]]; then | |
| docker exec c1 /bin/bash -c "pip install xorbits" | |
| docker exec c2 /bin/bash -c "pip install xorbits" | |
| docker exec slurmctld /bin/bash -c \ | |
| "pytest /xorbits/python/xorbits/deploy/slurm/tests/test_slurm.py " | |
| elif [[ "$MODULE" == "hadoop" ]]; then | |
| export WITH_HADOOP="1" | |
| export HADOOP_HOME="/usr/local/hadoop" | |
| export CLASSPATH=`$HADOOP_HOME/bin/hadoop classpath --glob` | |
| export HADOOP_INSTALL=$HADOOP_HOME | |
| export HADOOP_MAPRED_HOME=$HADOOP_HOME | |
| export HADOOP_COMMON_HOME=$HADOOP_HOME | |
| export HADOOP_HDFS_HOME=$HADOOP_HOME | |
| export YARN_HOME=$HADOOP_HOME | |
| export HADOOP_COMMON_LIB_NATIVE_DIR="$HADOOP_HOME/lib/native" | |
| export PATH="$PATH:$HADOOP_HOME/sbin:$HADOOP_HOME/bin" | |
| pytest --ignore xorbits/_mars/learn --timeout=1500 -W ignore::PendingDeprecationWarning xorbits/_mars -m hadoop | |
| elif [[ "$MODULE" == "vineyard" ]]; then | |
| pytest --timeout=1500 -W ignore::PendingDeprecationWarning \ | |
| --cov-config=setup.cfg --cov-report=xml --cov=xorbits xorbits/_mars/storage/tests/test_libs.py | |
| pytest --timeout=1500 -W ignore::PendingDeprecationWarning \ | |
| --cov-config=setup.cfg --cov-report=xml --cov=xorbits xorbits/_mars/deploy/oscar/tests/test_local.py | |
| pytest --timeout=1500 -W ignore::PendingDeprecationWarning \ | |
| --cov-config=setup.cfg --cov-report=xml --cov=xorbits -k "vineyard" \ | |
| xorbits/_mars/tensor/datastore/tests/test_datastore_execution.py \ | |
| xorbits/_mars/dataframe/datastore/tests/test_datastore_execution.py | |
| elif [[ "$MODULE" == "external-storage" ]]; then | |
| export ALLUXIO_HOME="/usr/local/bin/alluxio-2.9.3" | |
| export JUICEFS_HOME="/usr/local/bin/juicefs" | |
| pytest --timeout=1500 -W ignore::PendingDeprecationWarning \ | |
| --cov-config=setup.cfg --cov-report=xml --cov=xorbits xorbits/_mars/storage/tests/test_libs.py | |
| elif [[ "$MODULE" == "_mars/learn" ]]; then | |
| pytest --timeout=1500 \ | |
| -W ignore::PendingDeprecationWarning \ | |
| --cov-config=setup.cfg --cov-report=xml --cov=xorbits \ | |
| xorbits/$MODULE xorbits/_mars/contrib/dask/tests/test_dask.py | |
| elif [[ "$MODULE" == "learn" ]]; then | |
| pytest --timeout=1500 \ | |
| -W ignore::PendingDeprecationWarning \ | |
| --cov-config=setup.cfg --cov-report=xml --cov=xorbits \ | |
| xorbits/xgboost xorbits/lightgbm | |
| elif [ "$MODULE" == "jax" ]; then | |
| pytest --cov-config=setup.cfg --cov-report=xml --cov=xorbits xorbits/_mars/tensor/fuse/tests/test_runtime_fusion.py | |
| pytest --cov-config=setup.cfg --cov-report=xml --cov=xorbits xorbits/_mars/tensor/ | |
| elif [ "$MODULE" == "datasets" ]; then | |
| pytest --cov-config=setup.cfg --cov-report=xml --cov=xorbits xorbits/datasets/backends | |
| pytest --cov-config=setup.cfg --cov-report=xml --cov=xorbits xorbits/datasets/tests | |
| elif [ "$MODULE" == "compatibility" ]; then | |
| pytest --timeout=1500 \ | |
| -W ignore::PendingDeprecationWarning \ | |
| --cov-config=setup.cfg --cov-report=xml --cov=xorbits/deploy --cov=xorbits xorbits/_mars/dataframe | |
| pytest --timeout=1500 \ | |
| -W ignore::PendingDeprecationWarning \ | |
| --cov-config=setup.cfg --cov-report=xml --cov=xorbits/deploy --cov=xorbits xorbits/_mars/services/storage | |
| else | |
| pytest --timeout=1500 \ | |
| -W ignore::PendingDeprecationWarning \ | |
| --cov-config=setup.cfg --cov-report=xml --cov=xorbits/deploy --cov=xorbits xorbits/$MODULE | |
| fi | |
| working-directory: ./python | |
| - name: Test with pytest GPU | |
| if: ${{ matrix.module == 'gpu' }} | |
| run: | | |
| source activate ${{ env.CONDA_ENV }} | |
| pytest -m cuda --gpu --ignore xorbits/datasets \ | |
| --ignore xorbits/sklearn --ignore xorbits/_mars/learn \ | |
| --cov-config=setup.cfg --cov-report=xml --cov=xorbits \ | |
| xorbits | |
| working-directory: ./python | |
| - name: Cleanup on slurm | |
| if: ${{ matrix.module == 'slurm' }} | |
| run: | | |
| source CI/slurm/${{ matrix.module }}.sh | |
| jobqueue_after_script | |
| - name: Report coverage data | |
| uses: codecov/codecov-action@v4 | |
| with: | |
| working-directory: ./python | |
| flags: unittests | |
| token: ${{ secrets.CODECOV_TOKEN }} |