EMD Velox: update error msg for missing sparse module #1245
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| name: Tests | |
| on: | |
| pull_request: | |
| push: | |
| branches-ignore: | |
| - 'dependabot/**' | |
| - 'pre-commit-ci-update-config' | |
| workflow_dispatch: | |
| jobs: | |
| run_test_site: | |
| name: ${{ matrix.os }}-${{ matrix.os_version }}-py${{ matrix.PYTHON_VERSION }}${{ matrix.LABEL }} | |
| runs-on: ${{ matrix.os }}-${{ matrix.os_version }} | |
| timeout-minutes: 30 | |
| env: | |
| MPLBACKEND: agg | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: [ubuntu, windows, macos] | |
| os_version: [latest] | |
| PYTHON_VERSION: ['3.9', '3.10'] | |
| LABEL: [''] | |
| include: | |
| # test oldest supported version of main dependencies on python 3.8 | |
| - os: ubuntu | |
| os_version: latest | |
| PYTHON_VERSION: '3.8' | |
| # Set pillow and scikit-image version to be compatible with imageio and scipy | |
| # matplotlib needs 3.5 to support markers in hyperspy 2.0 (requires `collection.set_offset_transform`) | |
| DEPENDENCIES: matplotlib==3.5 numpy==1.20.0 tifffile==2022.7.28 dask[array]==2021.5.1 distributed==2021.5.1 numba==0.52 imageio==2.16 pillow==8.3.2 scikit-image==0.18.0 python-box==6.0.0 | |
| LABEL: '-oldest' | |
| # test minimum requirement | |
| - os: ubuntu | |
| os_version: latest | |
| PYTHON_VERSION: '3.9' | |
| LABEL: '-minimum' | |
| - os: ubuntu | |
| os_version: latest | |
| PYTHON_VERSION: '3.12' | |
| LABEL: '-minimum-without-hyperspy' | |
| - os: ubuntu | |
| os_version: latest | |
| PYTHON_VERSION: '3.11' | |
| LABEL: '-hyperspy-dev' | |
| - os: ubuntu | |
| os_version: latest | |
| PYTHON_VERSION: '3.9' | |
| LABEL: '-without-hyperspy' | |
| - os: ubuntu | |
| os_version: latest | |
| PYTHON_VERSION: '3.8' | |
| - os: ubuntu | |
| os_version: latest | |
| PYTHON_VERSION: '3.11' | |
| - os: macos | |
| os_version: '13' | |
| PYTHON_VERSION: '3.11' | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 0 | |
| - name: get repository name | |
| shell: bash | |
| run: echo "REPOSITORY_NAME=${GITHUB_REPOSITORY#*/}" >> $GITHUB_ENV | |
| - name: Fetch tags upstream | |
| if: ${{ github.repository_owner != 'hyperspy' }} | |
| # Needs to fetch the tags from upstream to get the | |
| # correct version with setuptools_scm | |
| run: | | |
| git remote add upstream https://github.com/hyperspy/${{ env.REPOSITORY_NAME }}.git | |
| git fetch upstream --tags | |
| - uses: actions/setup-python@v5 | |
| name: Install Python | |
| with: | |
| python-version: ${{ matrix.PYTHON_VERSION }} | |
| - name: Get the number of CPUs | |
| id: cpus | |
| run: | | |
| import os, platform | |
| num_cpus = os.cpu_count() | |
| print(f"Number of CPU: {num_cpus}") | |
| print(f"Architecture: {platform.machine()}") | |
| output_file = os.environ["GITHUB_OUTPUT"] | |
| with open(output_file, "a", encoding="utf-8") as output_stream: | |
| output_stream.write(f"count={num_cpus}\n") | |
| shell: python | |
| - name: Set Environment Variable | |
| shell: bash | |
| # Set PIP_SELECTOR environment variable according to matrix.LABEL | |
| run: | | |
| if [[ -n "${{ matrix.LABEL }}" && "${{ matrix.LABEL }}" == *"minimum"* ]]; then | |
| PIP_SELECTOR="[tests]" | |
| else | |
| PIP_SELECTOR="[all, tests]" | |
| fi | |
| echo "PIP_SELECTOR=${PIP_SELECTOR}" >> $GITHUB_ENV | |
| - name: Display version | |
| run: | | |
| python --version | |
| pip --version | |
| - name: Install hyperspy and exspy | |
| if: ${{ ! contains(matrix.LABEL, 'without-hyperspy') }} | |
| run: | | |
| pip install hyperspy exspy | |
| - name: Install hyperspy and exspy (dev) | |
| if: ${{ contains(matrix.LABEL, 'hyperspy-dev') }} | |
| run: | | |
| pip install git+https://github.com/hyperspy/hyperspy.git | |
| pip install git+https://github.com/hyperspy/exspy.git | |
| - name: Install pint and python-mrcz dev | |
| # for numpy 2.0 support for python >= 3.9 | |
| # https://github.com/em-MRCZ/python-mrcz/pull/15 | |
| # https://github.com/hgrecco/pint/issues/1974 | |
| if: ${{ ! contains(matrix.LABEL, 'oldest') && matrix.PYTHON_VERSION != '3.8' }} | |
| run: | | |
| pip install git+https://github.com/ericpre/[email protected]_and_deprecation_fixes | |
| pip install git+https://github.com/hgrecco/pint | |
| - name: Install | |
| shell: bash | |
| run: | | |
| pip install --upgrade -e .'${{ env.PIP_SELECTOR }}' | |
| - name: Uninstall pyUSID | |
| # remove when pyUSID supports numpy 2 | |
| if: ${{ ! contains(matrix.LABEL, 'oldest') && matrix.PYTHON_VERSION != '3.8' }} | |
| run: | | |
| pip uninstall -y pyUSID | |
| - name: Install oldest supported version | |
| if: contains(matrix.LABEL, 'oldest') | |
| run: | | |
| pip install ${{ matrix.DEPENDENCIES }} | |
| - name: Install numpy 2.0 | |
| if: ${{ ! contains(matrix.LABEL, 'oldest') && matrix.PYTHON_VERSION != '3.8' }} | |
| run: | | |
| pip install numpy==2 | |
| - name: Pip list | |
| run: | | |
| pip list | |
| - name: Run test suite | |
| run: | | |
| pytest --pyargs rsciio --reruns 3 -n ${{ steps.cpus.outputs.count }} --cov=. --cov-report=xml | |
| - name: Upload coverage to Codecov | |
| if: ${{ always() }} | |
| uses: codecov/codecov-action@v4 | |
| env: | |
| CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }} |