DOC: URLs link to original numpy and pandas docs (#824) #3694
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| 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/[email protected] | |
| - 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 }} |