Integration tests #978
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| name: Integration tests | |
| on: | |
| workflow_dispatch: | |
| schedule: | |
| - cron: '10 0 * * *' | |
| push: | |
| branches: | |
| - '*' | |
| pull_request: | |
| branches: | |
| - '*' | |
| jobs: | |
| integration_test: | |
| name: rs_${{ matrix.RSIO_VERSION }}-hs_${{ matrix.HYPERSPY_VERSION }}-ext_${{ matrix.EXTENSION_VERSION }}${{ matrix.LABEL }} | |
| runs-on: ubuntu-latest | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| HYPERSPY_VERSION: ['release', 'RnPatch', 'RnMinor', 'RnMajor'] | |
| # When RostteSciIO is released, extent build matrix with released version | |
| RSIO_VERSION: ['release'] | |
| EXTENSION_VERSION: ['release', 'dev'] | |
| DEPENDENCIES_DEV: [false] | |
| DEPENDENCIES_PRE_RELEASE: [false] | |
| DEPENDENCIES_NUMBA_DEV: [false] | |
| USE_MAMBA: [true] | |
| PYTHON_VERSION: ['3.10'] | |
| include: | |
| # test against upstream dev | |
| - DEPENDENCIES_DEV: true | |
| # Install dev version from https://anaconda.org/scientific-python-nightly-wheels/ | |
| LABEL: -dependencies_dev | |
| HYPERSPY_VERSION: 'RnMinor' | |
| RSIO_VERSION: 'dev' | |
| EXTENSION_VERSION: 'dev' | |
| # numba dev version is installed separately from numba/label/dev channel | |
| # others are installed as wheels from | |
| # https://anaconda.org/scientific-python-nightly-wheels/ | |
| # see https://scientific-python.org/specs/spec-0004/ | |
| DEPENDENCIES: matplotlib scipy scikit-image scikit-learn | |
| USE_MAMBA: false | |
| - DEPENDENCIES_DEV: true | |
| # Install dev version from https://anaconda.org/scientific-python-nightly-wheels/ | |
| LABEL: -dependencies_dev | |
| HYPERSPY_VERSION: 'RnMajor' | |
| RSIO_VERSION: 'dev' | |
| EXTENSION_VERSION: 'dev' | |
| DEPENDENCIES: matplotlib scipy scikit-image scikit-learn | |
| USE_MAMBA: false | |
| - DEPENDENCIES_PRE_RELEASE: true | |
| # Install RC version available on pypi | |
| LABEL: -dependencies_pre_release | |
| HYPERSPY_VERSION: 'RnMinor' | |
| RSIO_VERSION: 'dev' | |
| EXTENSION_VERSION: 'dev' | |
| DEPENDENCIES: matplotlib scipy scikit-learn sympy h5py scikit-image numba | |
| USE_MAMBA: false | |
| PYTHON_VERSION: '3.11' | |
| - DEPENDENCIES_NUMBA_DEV: true | |
| # Install dev version from numba/label/dev channel using mamba | |
| LABEL: -dependencies_numba_dev | |
| RSIO_VERSION: 'dev' | |
| HYPERSPY_VERSION: 'RnMajor' | |
| EXTENSION_VERSION: 'dev' | |
| DEPENDENCIES: numba | |
| USE_MAMBA: true | |
| PYTHON_VERSION: '3.11' | |
| exclude: | |
| # Don't test RELEASE_next_major with released version of extension as | |
| # they don't support the hyperspy 2.0 API changes | |
| - HYPERSPY_VERSION: 'RnMajor' | |
| EXTENSION_VERSION: 'release' | |
| env: | |
| EXTENSION: hyperspy-gui-ipywidgets hyperspy-gui-traitsui kikuchipy lumispy pyxem | |
| TEST_DEPS: pytest pytest-xdist pytest-rerunfailures pytest-mpl | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: conda-incubator/setup-miniconda@main | |
| with: | |
| miniforge-variant: Mambaforge | |
| miniforge-version: latest | |
| python-version: ${{ matrix.PYTHON_VERSION }} | |
| # use base environment, so that when using pip, this is from the | |
| # mambaforge distribution | |
| # auto-activate-base: true | |
| activate-environment: "test" | |
| - name: Install pip pyqt and Test dependencies | |
| run: | | |
| mamba install pip pyqt ${{ env.TEST_DEPS }} | |
| - name: Conda info | |
| run: | | |
| conda info | |
| conda list | |
| - name: Install numba development version | |
| if: ${{ matrix.DEPENDENCIES_NUMBA_DEV }} | |
| run: | | |
| # Install numba dev version | |
| mamba install -c numba/label/dev ${{ matrix.DEPENDENCIES }} | |
| - name: Install dependencies development version | |
| if: ${{ matrix.DEPENDENCIES_DEV }} | |
| run: | | |
| pip install --upgrade --pre --extra-index-url \ | |
| https://pypi.anaconda.org/scientific-python-nightly-wheels/simple \ | |
| ${{ matrix.DEPENDENCIES }} | |
| - name: Install dependencies pre release version | |
| if: ${{ matrix.DEPENDENCIES_PRE_RELEASE }} | |
| run: | | |
| pip install --upgrade --pre ${{ matrix.DEPENDENCIES }} | |
| - name: Conda list | |
| run: | | |
| conda list | |
| - name: Install RosettaSciIO release | |
| if: contains(matrix.RSIO_VERSION, 'release') | |
| run: | | |
| # Use mamba when package is available on conda-forge | |
| pip install rosettasciio[all] | |
| - name: Install RosettaSciIO dev | |
| if: contains(matrix.RSIO_VERSION, 'dev') | |
| run: | | |
| pip install "rosettasciio[all] @ https://github.com/hyperspy/rosettasciio/archive/main.zip" | |
| - name: Install HyperSpy release | |
| if: contains(matrix.HYPERSPY_VERSION, 'release') | |
| run: | | |
| mamba install hyperspy-base | |
| - name: Install HyperSpy RnPatch | |
| if: contains(matrix.HYPERSPY_VERSION, 'RnPatch') | |
| run: | | |
| pip install "hyperspy[all] @ https://github.com/hyperspy/hyperspy/archive/RELEASE_next_patch.zip" | |
| - name: Install HyperSpy RnMinor | |
| if: contains(matrix.HYPERSPY_VERSION, 'RnMinor') | |
| run: | | |
| pip install "hyperspy[all] @ https://github.com/hyperspy/hyperspy/archive/RELEASE_next_minor.zip" | |
| - name: Install HyperSpy RnMajor | |
| if: contains(matrix.HYPERSPY_VERSION, 'RnMajor') | |
| run: | | |
| pip install "hyperspy[all] @ https://github.com/hyperspy/hyperspy/archive/RELEASE_next_major.zip" | |
| - name: Install Extension Release | |
| if: contains(matrix.EXTENSION_VERSION, 'release') | |
| run: | | |
| mamba install ${{ env.EXTENSION }} | |
| - name: Install Extension Dev | |
| if: contains(matrix.EXTENSION_VERSION, 'dev') | |
| run: | | |
| pip install https://github.com/lumispy/lumispy/archive/main.zip | |
| pip install https://github.com/pyxem/kikuchipy/archive/develop.zip | |
| pip install https://github.com/pyxem/pyxem/archive/main.zip | |
| pip install https://github.com/hyperspy/hyperspy_gui_ipywidgets/archive/main.zip | |
| pip install https://github.com/hyperspy/hyperspy_gui_traitsui/archive/main.zip | |
| - name: Clear conda and pip cache | |
| run: | | |
| conda clean --all | |
| pip cache purge | |
| - name: Conda list | |
| run: | | |
| conda list | |
| - name: Run HyperSpy Test Suite | |
| run: | | |
| # Need to fix packaging to remove skipping the | |
| python -m pytest --pyargs hyperspy --reruns 3 -n 2 -k "not test_model_backcompatibility" | |
| - name: Run RosettaScio Test Suite | |
| if: contains(matrix.HYPERSPY_VERSION, 'RnMajor') | |
| run: | | |
| # Not possible to use "-n 2" because downloading test files will be ignored | |
| # Test fixed in dev branch but not release yet | |
| python -m pytest --pyargs rsciio -k "not (TestSpec and test_metadata)" | |
| - name: Run hyperspy_gui_ipywidgets Test Suite | |
| if: ${{ always() }} | |
| run: | | |
| python -m pytest --pyargs hyperspy_gui_ipywidgets -k "not test_spikes_removal_tool and not test_eels_table_tool" | |
| - name: Run hyperspy_gui_traitsui Test Suite | |
| if: ${{ always() }} | |
| # run the tests headlessly | |
| run: | | |
| xvfb-run python -m pytest --pyargs hyperspy_gui_traitsui | |
| # - name: Run kikuchipy Test Suite | |
| # if: ${{ contains(matrix.HYPERSPY_VERSION, 'RnMajor') == false }} | |
| # run: | | |
| # python -m pytest --pyargs kikuchipy | |
| - name: Run LumiSpy Test Suite | |
| if: ${{ always() }} | |
| #if: contains(matrix.EXTENSION_VERSION, 'dev') # Tests only against development version, if a fix is not released yet. | |
| run: | | |
| python -m pytest --pyargs lumispy | |
| - name: Run Pyxem Test Suite | |
| if: ${{ always() }} | |
| run: | | |
| # Failure most likely related to numpy 1.25 | |
| python -m pytest --pyargs pyxem -k "not (TestMake4dPeakArrayTestData and test_rotation)" |