Python package #105
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| name: Python package | |
| on: | |
| push: | |
| branches: | |
| - master | |
| pull_request: | |
| branches: | |
| - master | |
| - docs | |
| schedule: | |
| - cron: "0 2 * * 1-5" | |
| # to make bash use ~/.bashrc, see https://github.com/marketplace/actions/setup-miniconda#example-5-custom-installer | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| concurrency: | |
| group: ${{ github.ref }} | |
| cancel-in-progress: true | |
| jobs: | |
| main: | |
| env: | |
| CACHE_NUMBER_COMPILE: 6 | |
| MAMBA_ROOT_PREFIX: /dev/shm/mambaroot | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| fail-fast: false | |
| max-parallel: 12 | |
| matrix: | |
| os: [ubuntu-latest, windows-latest, macOS-11] | |
| python-version: [3.6, 3.7, 3.8, 3.9] | |
| steps: | |
| - name: disk space | |
| if: ${{ (github.event.pull_request.head.repo.full_name == 'vaexio/vaex') && (matrix.os == 'ubuntu-latest') }} | |
| run: | | |
| df -h | |
| - uses: maxim-lobanov/setup-xcode@v1 | |
| # alternative would be to upgrade tapi to 1100.0.11, we can possibly remove this in the future | |
| if: matrix.os == 'macOS-11' | |
| with: | |
| xcode-version: "11.7.0" | |
| - uses: actions/checkout@v2 | |
| with: | |
| submodules: true | |
| - uses: actions/checkout@v2 | |
| if: ${{ (github.event.pull_request.head.repo.full_name == 'vaexio/vaex') && (matrix.os == 'ubuntu-latest') }} | |
| with: | |
| repository: vaexio/vaex-enterprise | |
| token: ${{ secrets.PAT_PULL_ENTERPRISE }} | |
| path: vaex-enterprise | |
| - name: install micromamba | |
| uses: mamba-org/provision-with-micromamba@main | |
| with: | |
| environment-name: vaex-dev | |
| environment-file: ci/conda-env.yml | |
| extra-specs: | | |
| python=${{ matrix.python-version }} | |
| - name: Extra non-windows installs | |
| if: matrix.os != 'windows-latest' | |
| run: | | |
| echo "not needed for now" | |
| # - name: Extra windows installs | |
| # if: matrix.os == 'windows-latest' | |
| # run: | | |
| # # not sure why, but the conda env is strange (old dask) if we put this constraint in the conda solver | |
| # # also might solve scipy issues | |
| # micromamba update scipy ipython dask | |
| # micromamba install scipy=1.7.1 | |
| # - name: free disk space | |
| # if: matrix.os == 'ubuntu-latest' | |
| # run: | | |
| # sudo swapoff -a | |
| # sudo rm -f /swapfile | |
| # sudo apt clean | |
| # docker rmi $(docker image ls -aq) | |
| # df -h | |
| - name: Install OpenMP runtime (Mac-only) | |
| if: matrix.os == 'macOS-11' | |
| run: | | |
| brew install libomp | |
| - name: Cache compiled binaries | |
| # this fails for this combination, leading to binaries filled with 0's | |
| if: matrix.python-version != '3.6' || matrix.os != 'macOS-11' | |
| id: cache-compiled-binaries | |
| uses: actions/cache@v2 | |
| with: | |
| path: | | |
| packages/vaex-core/build/lib*/vaex/vaexfast* | |
| packages/vaex-core/build/lib*/vaex/super* | |
| key: ${{ runner.OS }}-${{ matrix.python-version }}-${{ hashFiles('packages/vaex-core/src/*') }}-${{ env.CACHE_NUMBER_COMPILE }} | |
| - name: Fix cache timestamp | |
| run: | | |
| touch packages/vaex-core/build/lib*/vaex/vaexfast* || echo "ok to fail" | |
| touch packages/vaex-core/build/lib*/vaex/super* || echo "ok to fail" | |
| ls -alh packages/vaex-core/build/lib*/vaex/ || echo "ok to fail" | |
| - name: Install vaex | |
| run: | | |
| pip install myst_parser | |
| pip install -e . -v | |
| # ./ci/03-install-vaex.sh micromamba | |
| # - name: Install vaex-enterprise | |
| # if: ${{ (github.event.pull_request.head.repo.full_name == 'vaexio/vaex') && (matrix.os == 'ubuntu-latest') }} | |
| # run: | | |
| # cd vaex-enterprise | |
| # micromamba install -c conda-forge distributed | |
| # pip install ray | |
| # pip install -e . | |
| - name: Copy dll | |
| if: (matrix.os == 'windows-latest') | |
| uses: ./ci/actions/windll | |
| - name: Build Python packages | |
| run: | | |
| mkdir dist | |
| (cd packages/vaex-core && python setup.py bdist_wheel); cp packages/vaex-core/dist/* dist | |
| (cd packages/vaex-graphql && python setup.py bdist_wheel); cp packages/vaex-graphql/dist/* dist | |
| (cd packages/vaex-jupyter && python setup.py bdist_wheel); cp packages/vaex-jupyter/dist/* dist | |
| (cd packages/vaex-ml && python setup.py bdist_wheel); cp packages/vaex-ml/dist/* dist | |
| (cd packages/vaex-viz && python setup.py bdist_wheel); cp packages/vaex-viz/dist/* dist | |
| (cd packages/vaex-astro && python setup.py bdist_wheel); cp packages/vaex-astro/dist/* dist | |
| (cd packages/vaex-hdf5 && python setup.py bdist_wheel); cp packages/vaex-hdf5/dist/* dist | |
| (cd packages/vaex-server && python setup.py bdist_wheel); cp packages/vaex-server/dist/* dist | |
| (cd packages/vaex-meta && python setup.py bdist_wheel); cp packages/vaex-server/dist/* dist | |
| - name: Upload builds | |
| uses: actions/upload-artifact@v2 | |
| with: | |
| name: dist-${{ github.run_number }}-${{ matrix.python-version }}-${{ matrix.os }} | |
| path: ./dist | |
| # - name: Lint with flake8 | |
| # run: | | |
| # echo "soon" | |
| # # pip install flake8 | |
| # # stop the build if there are Python syntax errors or undefined names | |
| # # flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics | |
| # # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide | |
| # # flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics | |
| - name: Install fixes for Python 3.6 | |
| if: matrix.python-version == '3.6' | |
| run: | | |
| # by default on 3.6 we get an old version, so manually upgrade | |
| pip install gcsfs==0.8.0 | |
| - name: Install pytest-asyncio correct version | |
| if: matrix.python-version != '3.10' | |
| run: | | |
| # 3.10 doesn't seem to work | |
| pip install "pytest-asyncio<0.14" | |
| - name: Test with pytest | |
| run: | | |
| ./ci/04-run-test-suite.sh | |
| - name: Test with pytest (with cache on) | |
| if: matrix.python-version == '3.9' && matrix.os == 'ubuntu-latest' | |
| run: | | |
| VAEX_CACHE_RESULTS=1 ./ci/04-run-test-suite.sh | |
| - name: Check ml spec | |
| # no catboost for py39 and py37 | |
| if: matrix.python-version != '3.9' && matrix.os != 'windows-latest' && matrix.python-version != '3.7' | |
| run: | | |
| python -m vaex.ml.spec packages/vaex-ml/vaex/ml/spec_new.json | |
| diff packages/vaex-ml/vaex/ml/spec_new.json packages/vaex-ml/vaex/ml/spec.json | |
| # - name: Test with pytest (vaex-enterprise) | |
| # if: ${{ (github.event.pull_request.head.repo.full_name == 'vaexio/vaex') && (matrix.os == 'ubuntu-latest') }} | |
| # run: | | |
| # py.test vaex-enterprise/tests --timeout=1000 | |
| - name: Test notebooks | |
| if: matrix.os != 'windows-latest' && matrix.python-version != '3.6' | |
| run: | | |
| ./ci/05-run-notebooks.sh | |
| - name: Authenticate Google Cloud Platform | |
| if: ${{ (github.event.pull_request.head.repo.full_name == 'vaexio/vaex') && !((matrix.os == 'windows-latest') || (matrix.os == 'macOS-11' && matrix.python-version == '3.6')) }} | |
| uses: google-github-actions/setup-gcloud@v0 | |
| with: | |
| project_id: ${{ secrets.GCP_PROJECT_ID_VAEX }} | |
| service_account_key: ${{ secrets.GCP_SA_KEY_VAEX }} | |
| export_default_credentials: true | |
| - name: Test vaex-contrib | |
| # do not run in a PR from someone else, skip windows, and osx+py36 | |
| if: ${{ (github.event.pull_request.head.repo.full_name == 'vaexio/vaex') && !((matrix.os == 'windows-latest') || (matrix.os == 'macOS-11' && matrix.python-version == '3.6')) }} | |
| env: | |
| PROJECT_ID: ${{ secrets.GCP_PROJECT_ID_VAEX }} | |
| run: | | |
| pip install -e 'packages/vaex-contrib[gcp]' | |
| ./ci/06-run-contrib-tests.sh | |
| install: | |
| runs-on: ${{ matrix.os }} | |
| needs: [main] | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: [ubuntu-latest, windows-latest, macOS-11] | |
| python-version: [3.7, 3.8, 3.9] | |
| # ssl/certifi issues with this combination | |
| exclude: | |
| - os: windows-latest | |
| python-version: 3.7 | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - uses: actions/download-artifact@v2 | |
| with: | |
| name: dist-${{ github.run_number }}-${{ matrix.python-version }}-${{ matrix.os }} | |
| path: ./dist | |
| - name: Install micromamba | |
| uses: mamba-org/provision-with-micromamba@main | |
| with: | |
| environment-name: vaex-test | |
| environment-file: ci/conda-base-minimal.yml | |
| extra-specs: | | |
| python=${{ matrix.python-version }} | |
| pcre | |
| rich | |
| # it shouldn't be needed to use pcre, maybe we should make the wheels similar to how we make distributions | |
| - name: Cache pip | |
| uses: actions/cache@v2 | |
| env: | |
| # Increase this value to reset cache | |
| CACHE_NUMBER: 0 | |
| with: | |
| path: | | |
| ~/.cache/pip | |
| key: | |
| pip-${{ runner.os }}-${{ matrix.python-version }}-${{ env.CACHE_NUMBER }} | |
| - name: Install core packages | |
| run: | | |
| pip install -vv dist/vaex*core* dist/vaex*hdf5* | |
| - name: Test core import | |
| run: | | |
| python -c "import vaex; df = vaex.example()" | |
| - name: Install all packages | |
| run: | | |
| pip install -vv dist/* | |
| - name: Test import | |
| run: | | |
| python -c "import vaex; df = vaex.example()" | |
| - name: Test comand line | |
| run: | | |
| vaex convert ~/.vaex/data/helmi-dezeeuw-2000-FeH-v2-10percent.hdf5 test.parquet | |
| pip install rich | |
| VAEX_PROGRESS_TYPE=rich vaex convert ~/.vaex/data/helmi-dezeeuw-2000-FeH-v2-10percent.hdf5 test.parquet | |
| vaex settings yaml | |
| vaex settings md | |
| - name: Test server | |
| if: matrix.os != 'windows-latest' | |
| run: | | |
| vaex server --add-example --port 9999& | |
| - name: Wait for Vaex server | |
| if: matrix.os != 'windows-latest' | |
| uses: ifaxity/wait-on-action@v1 | |
| with: | |
| resource: http-get://localhost:9999/hello | |
| timeout: 5000 | |
| - name: Use the Vaex server | |
| if: matrix.os != 'windows-latest' | |
| run: | | |
| python -c "import vaex; df = vaex.open('ws://localhost:9999/example'); df.x.sum()" | |
| curl -i http://localhost:9999/histogram/example/x |