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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,41 +1,61 @@ | ||
| name: Tests | ||
|
|
||
| on: [push, pull_request, workflow_dispatch] | ||
| on: | ||
| pull_request: | ||
| push: | ||
| branches-ignore: | ||
| - 'dependabot/**' | ||
| - 'pre-commit-ci-update-config' | ||
| workflow_dispatch: | ||
|
|
||
| jobs: | ||
| run_test_site: | ||
| name: ${{ matrix.os }}-py${{ matrix.PYTHON_VERSION }}${{ matrix.LABEL }} | ||
| runs-on: ${{ matrix.os }}-latest | ||
| 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 imagecodecs==2020.1.31 tifffile==2020.2.16 dask[array]==2021.3.1 numba==0.52 imageio==2.16 pillow==8.3.2 scikit-image==0.18.0 | ||
| 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: | ||
|
|
@@ -59,7 +79,19 @@ jobs: | |
| 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 | ||
|
|
@@ -76,35 +108,57 @@ jobs: | |
| python --version | ||
| pip --version | ||
| - name: Install oldest supported version | ||
| if: contains(matrix.LABEL, 'oldest') | ||
| run: | | ||
| pip install ${{ matrix.DEPENDENCIES }} | ||
| - name: Install (HyperSpy dev) | ||
| - name: Install hyperspy and exspy | ||
| if: ${{ ! contains(matrix.LABEL, 'without-hyperspy') }} | ||
| # Need to install hyperspy dev until hyperspy 2.0 is released | ||
| run: | | ||
| pip install git+https://github.com/hyperspy/hyperspy.git@RELEASE_next_major | ||
| pip install hyperspy exspy | ||
| - name: Install (exspy) | ||
| if: ${{ ! contains(matrix.LABEL, '-minimum') && ! contains(matrix.LABEL, 'without-hyperspy') }} | ||
| - 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 2 --cov=. --cov-report=xml | ||
| 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@v3 | ||
| uses: codecov/codecov-action@v4 | ||
| env: | ||
| CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }} | ||
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