**BREAKING** pygmt.grdcut: Refactor to store output in virtualfiles for grids #15749
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| # Test PyGMT on Linux/macOS/Windows | |
| # | |
| # This workflow runs regular PyGMT tests and uploads test coverage reports stored in | |
| # `.coverage.xml` to https://app.codecov.io/gh/GenericMappingTools/pygmt via the | |
| # [Codecov GitHub Action](https://github.com/codecov/codecov-action). More codecov | |
| # related configurations are stored in `.github/codecov.yml`. If any tests fail, it also | |
| # uploads the diff images as workflow artifacts. | |
| # | |
| # It is run: | |
| # 1. on every commit to the main branch | |
| # 2. on every commit to the pull request branches, unless the pull requests only contain | |
| # non-code changes. | |
| # 3. when a new release is published | |
| # | |
| # It is also scheduled to run daily on the main branch. | |
| # | |
| # In draft pull request, only jobs on Linux are triggered to save on Continuous | |
| # Integration resources: | |
| # | |
| # - Minimum supported Python + core packages (minimum supported versions) | |
| # + optional packages (minimum supported versions if any) | |
| # - Latest Python + core packages (latest versions) + optional packages | |
| # - Last release before the latest Python + core packages | |
| # | |
| name: Tests | |
| on: | |
| push: | |
| branches: [ main ] | |
| paths: | |
| - 'pygmt/**' | |
| - '.github/workflows/ci_tests.yaml' | |
| pull_request: | |
| types: [opened, reopened, synchronize, ready_for_review] | |
| paths: | |
| - 'pygmt/**' | |
| - '.github/workflows/ci_tests.yaml' | |
| workflow_dispatch: | |
| release: | |
| types: | |
| - published | |
| # Schedule daily tests | |
| schedule: | |
| - cron: '0 0 * * *' | |
| concurrency: | |
| group: ${{ github.workflow }}-${{ github.ref }} | |
| cancel-in-progress: ${{ github.ref != 'refs/heads/main' }} | |
| jobs: | |
| test: | |
| name: ${{ matrix.os }} - Python ${{ matrix.python-version }} / NumPy ${{ matrix.numpy-version }} | |
| runs-on: ${{ matrix.os }} | |
| permissions: | |
| id-token: write # This is required for requesting OIDC token for codecov | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| python-version: ['3.10', '3.12'] | |
| os: [ubuntu-latest, macos-latest, windows-latest] | |
| # Is it a draft Pull Request (true or false)? | |
| isDraft: | |
| - ${{ github.event.pull_request.draft }} | |
| # Only run three jobs on Ubuntu for draft PRs | |
| exclude: | |
| - os: macos-latest | |
| isDraft: true | |
| - os: windows-latest | |
| isDraft: true | |
| include: | |
| # Python 3.10 + core packages (minimum supported versions) + optional packages (minimum supported versions if any) | |
| - python-version: '3.10' | |
| numpy-version: '1.24' | |
| pandas-version: '=2.0' | |
| xarray-version: '=2023.04' | |
| optional-packages: ' contextily geopandas<1 ipython pyarrow rioxarray sphinx-gallery' | |
| # Python 3.12 + core packages (latest versions) + optional packages | |
| - python-version: '3.12' | |
| numpy-version: '2.2' | |
| pandas-version: '' | |
| xarray-version: '' | |
| optional-packages: ' contextily geopandas>=1.0 ipython pyarrow rioxarray sphinx-gallery' | |
| # Python 3.11 + core packages (Linux only) | |
| - os: 'ubuntu-latest' | |
| python-version: '3.11' | |
| numpy-version: '' | |
| pandas-version: '' | |
| xarray-version: '' | |
| optional-packages: '' | |
| timeout-minutes: 30 | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| # Environment variables used by codecov | |
| env: | |
| OS: ${{ matrix.os }} | |
| PYTHON: ${{ matrix.python-version }} | |
| NUMPY: ${{ matrix.numpy-version }} | |
| steps: | |
| # Checkout current git repository | |
| - name: Checkout | |
| uses: actions/[email protected] | |
| with: | |
| # fetch all history so that setuptools-scm works | |
| fetch-depth: 0 | |
| - name: Get current week number of year | |
| id: date | |
| run: echo "date=$(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=${{ matrix.python-version }}${{ matrix.optional-packages }} | |
| gmt=6.5.0 | |
| ghostscript=10.04.0 | |
| numpy=${{ matrix.numpy-version }} | |
| pandas${{ matrix.pandas-version }} | |
| xarray${{ matrix.xarray-version }} | |
| netCDF4 | |
| packaging | |
| dvc | |
| make | |
| pip | |
| python-build | |
| pytest | |
| pytest-cov | |
| pytest-doctestplus | |
| pytest-mpl | |
| pytest-rerunfailures | |
| # Download cached remote files (artifacts) from GitHub | |
| - name: Download remote data from GitHub | |
| run: | | |
| # Download 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: ${{ github.token }} | |
| # Pull baseline image data from dvc remote (DAGsHub) | |
| - name: Pull baseline image data from dvc remote | |
| run: dvc pull --no-run-cache --verbose && ls -lhR pygmt/tests/baseline/ | |
| # Install the package that we want to test | |
| - name: Install the package | |
| run: make install | |
| # Run the regular tests | |
| - name: Run tests | |
| run: make test PYTEST_EXTRA="-r P --reruns 2" | |
| # Upload diff images on test failure | |
| - name: Upload diff images if any test fails | |
| uses: actions/[email protected] | |
| if: failure() | |
| with: | |
| name: artifact-${{ runner.os }}-${{ matrix.python-version }} | |
| path: tmp-test-dir-with-unique-name | |
| # Upload coverage to Codecov | |
| - name: Upload coverage to Codecov | |
| uses: codecov/[email protected] | |
| if: success() || failure() | |
| with: | |
| use_oidc: true | |
| files: ./coverage.xml # optional | |
| env_vars: OS,PYTHON,NUMPY | |
| fail_ci_if_error: false |