clib.conversion._to_numpy: Add tests for pandas.Series with pyarrow numeric dtypes #5134
Workflow file for this run
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| # Test PyGMT with GMT dev version on Linux/macOS/Windows | |
| # | |
| # This workflow runs regular PyGMT tests with the GMT dev version, and also pre-release | |
| # versions of several dependencies like NumPy, pandas, Xarray, etc. If any tests fail, | |
| # it also uploads the diff images as workflow artifacts. The GMT dev version is | |
| # installed by fetching the latest source codes from the GMT master branch and | |
| # compiling. | |
| # | |
| # It is triggered in a pull request if labeled with 'run/test-gmt-dev'. | |
| # It is also scheduled to run on Monday, Wednesday, and Friday on the main branch. | |
| # | |
| name: GMT Dev Tests | |
| on: | |
| # push: | |
| # branches: [ main ] | |
| pull_request: | |
| types: [ opened, reopened, labeled, synchronize ] | |
| paths: | |
| - 'pygmt/**' | |
| - '.github/workflows/ci_tests_dev.yaml' | |
| workflow_dispatch: | |
| # Schedule tests on Monday/Wednesday/Friday | |
| schedule: | |
| - cron: '0 0 * * 1,3,5' | |
| concurrency: | |
| group: ${{ github.workflow }}-${{ github.ref }} | |
| cancel-in-progress: ${{ github.ref != 'refs/heads/main' }} | |
| jobs: | |
| test_gmt_dev: | |
| name: ${{ matrix.os }} - GMT ${{ matrix.gmt_git_ref }} | |
| runs-on: ${{ matrix.os }} | |
| if: github.event_name != 'pull_request' || contains(github.event.pull_request.labels.*.name, 'run/test-gmt-dev') | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: [ubuntu-24.04, macos-15, windows-2022] | |
| gmt_git_ref: [master] | |
| timeout-minutes: 30 | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| steps: | |
| # Checkout current git repository | |
| - name: Checkout | |
| uses: actions/[email protected] | |
| with: | |
| # fetch all history so that setuptools-scm works | |
| fetch-depth: 0 | |
| - name: Get current week number of year | |
| id: date | |
| run: echo "date=$(date +%Y-W%W)" >> $GITHUB_OUTPUT # e.g., 2024-W19 | |
| # Install Micromamba with conda-forge dependencies | |
| - name: Setup Micromamba | |
| uses: mamba-org/[email protected] | |
| with: | |
| environment-name: pygmt | |
| condarc: | | |
| channels: | |
| - conda-forge | |
| - nodefaults | |
| cache-downloads: false | |
| cache-environment: true | |
| # environment cache is persistent for one week. | |
| cache-environment-key: micromamba-environment-${{ steps.date.outputs.date }} | |
| create-args: >- | |
| python=3.12 | |
| cmake | |
| make | |
| ninja | |
| curl | |
| fftw | |
| ghostscript=10.04.0 | |
| glib | |
| hdf5 | |
| libblas | |
| libcblas | |
| libgdal | |
| liblapack | |
| libnetcdf | |
| pcre | |
| zlib | |
| # Install the GSHHG and DCW datasets on Linux/macOS to avoid corrupted files | |
| # during GMT auto-downloading. Currently, we can't install them on Windows CI, | |
| # because the Windows CI fails to compile "gshhg_version.c" due to unknown reasons | |
| # (likely missing DLLs). | |
| - name: Install GMT GSHHG and DCW datasets (Linux/macOS) | |
| run: micromamba install dcw-gmt gshhg-gmt | |
| if: runner.os != 'Windows' | |
| # Checkout current GMT repository | |
| - name: Checkout the GMT source from ${{ matrix.gmt_git_ref }} branch | |
| uses: actions/[email protected] | |
| with: | |
| repository: 'GenericMappingTools/gmt' | |
| ref: ${{ matrix.gmt_git_ref }} | |
| path: 'gmt' | |
| # Build GMT from source on Linux/macOS, script is adapted from | |
| # https://github.com/GenericMappingTools/gmt/blob/6.5.0/ci/build-gmt.sh | |
| - name: Build GMT on Linux/macOS | |
| run: | | |
| cd gmt/ | |
| mkdir build | |
| cd build | |
| cmake -G Ninja .. \ | |
| -DCMAKE_INSTALL_PREFIX=${{ env.GMT_INSTALL_DIR }} \ | |
| -DCMAKE_BUILD_TYPE=Release \ | |
| -DGMT_ENABLE_OPENMP=TRUE \ | |
| -DGMT_USE_THREADS=TRUE | |
| cmake --build . | |
| cmake --build . --target install | |
| cd .. | |
| rm -rf gmt/ | |
| env: | |
| GMT_INSTALL_DIR: ${{ runner.temp }}/gmt-install-dir | |
| if: runner.os != 'Windows' | |
| - name: Build GMT on Windows | |
| shell: cmd | |
| run: | | |
| cd gmt/ | |
| mkdir build | |
| cd build | |
| call "C:\Program Files\Microsoft Visual Studio\2022\Enterprise\VC\Auxiliary\Build\vcvars64.bat" | |
| cmake -G Ninja .. ^ | |
| -DCMAKE_INSTALL_PREFIX=${{ env.GMT_INSTALL_DIR }} ^ | |
| -DCMAKE_BUILD_TYPE=Release ^ | |
| -DCMAKE_PREFIX_PATH=${{ env.MAMBA_ROOT_PREFIX }}\envs\pygmt\Library ^ | |
| -DGMT_ENABLE_OPENMP=TRUE ^ | |
| -DGMT_USE_THREADS=TRUE | |
| cmake --build . | |
| cmake --build . --target install | |
| cd .. | |
| rm -rf gmt/ | |
| env: | |
| GMT_INSTALL_DIR: ${{ runner.temp }}/gmt-install-dir | |
| if: runner.os == 'Windows' | |
| - name: Add GMT's bin to PATH | |
| run: echo '${{ runner.temp }}/gmt-install-dir/bin' >> $GITHUB_PATH | |
| # Install dependencies from PyPI | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install --pre --prefer-binary \ | |
| --extra-index https://pypi.anaconda.org/scientific-python-nightly-wheels/simple \ | |
| numpy pandas xarray netCDF4 packaging \ | |
| build contextily dvc geopandas ipython pyarrow rioxarray \ | |
| pytest pytest-cov pytest-doctestplus pytest-mpl pytest-rerunfailures pytest-xdist\ | |
| sphinx-gallery | |
| # Show installed pkg information for postmortem diagnostic | |
| - name: List installed packages | |
| run: micromamba list | |
| # Pull baseline image data from dvc remote (DAGsHub) | |
| - name: Pull baseline image data from dvc remote | |
| run: dvc pull --no-run-cache --verbose && ls -lhR pygmt/tests/baseline/ | |
| # Download cached remote files (artifacts) from GitHub | |
| - name: Download remote data from GitHub | |
| run: | | |
| # Download cached files to ~/.gmt directory and list them | |
| gh run download --name gmt-cache --dir ~/.gmt/ | |
| # Change modification times of the two files, so GMT won't refresh it | |
| touch ~/.gmt/gmt_data_server.txt ~/.gmt/gmt_hash_server.txt | |
| ls -lhR ~/.gmt | |
| env: | |
| GH_TOKEN: ${{ github.token }} | |
| # Install the package that we want to test | |
| - name: Install the package | |
| run: make install | |
| # Run the tests | |
| - name: Test with pytest | |
| run: make test PYTEST_EXTRA="-r P -n auto --reruns 2" | |
| env: | |
| GMT_LIBRARY_PATH: ${{ runner.temp }}/gmt-install-dir/lib | |
| # Upload diff images on test failure | |
| - name: Upload diff images if any test fails | |
| uses: actions/[email protected] | |
| if: ${{ failure() }} | |
| with: | |
| name: artifact-GMT-${{ matrix.gmt_git_ref }}-${{ runner.os }} | |
| path: tmp-test-dir-with-unique-name |