Make it possible to set fill value at read #237
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| name: CI | |
| # https://docs.github.com/en/actions/reference/workflow-syntax-for-github-actions#concurrency | |
| # https://docs.github.com/en/developers/webhooks-and-events/events/github-event-types#pullrequestevent | |
| concurrency: | |
| group: ${{ github.workflow }}-${{ github.event.number || github.event.ref }}-${{ github.event.type }} | |
| cancel-in-progress: true | |
| on: [push, pull_request] | |
| env: | |
| CACHE_NUMBER: 0 | |
| jobs: | |
| test: | |
| runs-on: ${{ matrix.os }} | |
| continue-on-error: ${{ matrix.experimental }} | |
| strategy: | |
| fail-fast: true | |
| matrix: | |
| os: ["windows-latest", "ubuntu-latest", "macos-latest"] | |
| python-version: ["3.10", "3.11", "3.12"] | |
| experimental: [false] | |
| include: | |
| - python-version: "3.12" | |
| os: "ubuntu-latest" | |
| experimental: true | |
| env: | |
| PYTHON_VERSION: ${{ matrix.python-version }} | |
| OS: ${{ matrix.os }} | |
| UNSTABLE: ${{ matrix.experimental }} | |
| ACTIONS_ALLOW_UNSECURE_COMMANDS: true | |
| steps: | |
| - name: Checkout source | |
| uses: actions/checkout@v4 | |
| - name: Setup Conda Environment | |
| uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| miniforge-version: latest | |
| python-version: ${{ matrix.python-version }} | |
| activate-environment: test-environment | |
| channels: conda-forge | |
| - name: Set cache environment variables | |
| shell: bash -l {0} | |
| run: | | |
| echo "DATE=$(date +'%Y%m%d')" >> $GITHUB_ENV | |
| CONDA_PREFIX=$(python -c "import sys; print(sys.prefix)") | |
| echo "CONDA_PREFIX=$CONDA_PREFIX" >> $GITHUB_ENV | |
| - uses: actions/cache@v4 | |
| with: | |
| path: ${{ env.CONDA_PREFIX }} | |
| key: ${{ matrix.os }}-${{matrix.python-version}}-conda-${{ hashFiles('continuous_integration/environment.yaml') }}-${{ env.DATE }}-${{matrix.experimental}}-${{ env.CACHE_NUMBER }} | |
| id: cache | |
| - name: Update environment | |
| run: mamba env update -n test-environment -f continuous_integration/environment.yaml | |
| if: steps.cache.outputs.cache-hit != 'true' | |
| - name: Install unstable dependencies | |
| if: matrix.experimental == true | |
| shell: bash -l {0} | |
| # Install pykdtree with --no-build-isolation so it builds with numpy 2.0 | |
| # We must get LD_PRELOAD for stdlibc++ or else the manylinux wheels | |
| # may break the conda-forge libraries trying to use newer glibc versions | |
| # NOTE: Many of the packages removed and then reinstalled below are to avoid | |
| # compatibility issues with numpy 2. When conda-forge has numpy 2 available | |
| # this shouldn't be needed. | |
| run: | | |
| python -m pip install versioneer extension-helpers setuptools-scm configobj pkgconfig hatchling hatch-vcs | |
| python -m pip install \ | |
| --index-url https://pypi.anaconda.org/scientific-python-nightly-wheels/simple/ \ | |
| --trusted-host pypi.anaconda.org \ | |
| --no-deps --pre --upgrade \ | |
| matplotlib \ | |
| numpy \ | |
| pandas \ | |
| scipy | |
| conda remove --force-remove -y pykdtree pyresample python-geotiepoints pyhdf netcdf4 h5py cftime astropy pyerfa || true | |
| python -m pip install --upgrade --no-deps --pre --no-build-isolation \ | |
| pyerfa \ | |
| git+https://github.com/storpipfugl/pykdtree \ | |
| git+https://github.com/pytroll/pyresample \ | |
| git+https://github.com/pytroll/trollimage \ | |
| git+https://github.com/pytroll/python-geotiepoints \ | |
| git+https://github.com/fhs/pyhdf \ | |
| git+https://github.com/h5py/h5py \ | |
| git+https://github.com/h5netcdf/h5netcdf \ | |
| git+https://github.com/Unidata/netcdf4-python \ | |
| git+https://github.com/dask/dask \ | |
| git+https://github.com/dask/distributed \ | |
| git+https://github.com/Unidata/cftime \ | |
| git+https://github.com/rasterio/rasterio \ | |
| git+https://github.com/pydata/bottleneck \ | |
| git+https://github.com/pydata/xarray \ | |
| git+https://github.com/shapely/shapely \ | |
| git+https://github.com/astropy/astropy | |
| LD_PRELOAD=$(python -c "import sys; print(sys.prefix)")/lib/libstdc++.so | |
| echo "LD_PRELOAD=${LD_PRELOAD}" >> $GITHUB_ENV | |
| - name: Install satpy | |
| shell: bash -l {0} | |
| run: | | |
| python -m pip install --no-deps -e . | |
| - name: Run unit tests | |
| shell: bash -l {0} | |
| run: | | |
| export LD_PRELOAD=${{ env.LD_PRELOAD }}; | |
| pytest -n auto --cov=satpy satpy/tests --cov-report=xml --cov-report= | |
| - name: Upload unittest coverage to Codecov | |
| uses: codecov/codecov-action@v4 | |
| with: | |
| flags: unittests | |
| file: ./coverage.xml | |
| env_vars: OS,PYTHON_VERSION,UNSTABLE | |
| - name: Coveralls Parallel | |
| uses: AndreMiras/coveralls-python-action@develop | |
| with: | |
| flag-name: run-${{ matrix.test_number }} | |
| parallel: true | |
| if: runner.os == 'Linux' | |
| - name: Run behaviour tests | |
| shell: bash -l {0} | |
| run: | | |
| export LD_PRELOAD=${{ env.LD_PRELOAD }}; | |
| coverage run --source=satpy -m behave satpy/tests/features --tags=-download | |
| coverage xml | |
| - name: Upload behaviour test coverage to Codecov | |
| uses: codecov/codecov-action@v4 | |
| with: | |
| flags: behaviourtests | |
| file: ./coverage.xml | |
| env_vars: OS,PYTHON_VERSION,UNSTABLE | |
| coveralls: | |
| needs: [test] | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Coveralls Finished | |
| uses: AndreMiras/coveralls-python-action@develop | |
| with: | |
| parallel-finished: true |