tests.yml

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']
        # 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]
        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_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
          - DEPENDENCIES_NUMBA_DEV: true
            # Install dev version from numba/label/dev channel using mamba
            LABEL: -dependencies_numba_dev
            HYPERSPY_VERSION: 'RnMinor'
            RSIO_VERSION: 'dev'
            EXTENSION_VERSION: 'dev'
            DEPENDENCIES: numba
            USE_MAMBA: true

    env:
      EXTENSION: hyperspy-gui-ipywidgets hyperspy-gui-traitsui kikuchipy lumispy pyxem exspy holospy etspy
      TEST_DEPS: pytest pytest-xdist pytest-rerunfailures pytest-mpl filelock
      PYTHON_VERSION: '3.12'
    defaults:
      run:
        shell: bash -l {0}

    steps:
      - uses: actions/checkout@v4

      - uses: conda-incubator/setup-miniconda@v3
        with:
          miniforge-version: latest
          python-version: ${{ env.PYTHON_VERSION }}
          # use base environment, so that when using pip, this is from the
          # miniforge distribution
          # auto-activate-base: true
          activate-environment: "test"

      - name: Install pip, pyqt and Test dependencies
        run: |
          # astra-toolbox from pypi.org only works with gpu
          # ffmpeg is a missing dependencies from etspy, see https://github.com/usnistgov/etspy/issues/25
          mamba install pip pyqt astra-toolbox ffmpeg ${{ env.TEST_DEPS }}

      - name: Install dask 2024.11.2
        run: |
          # remove when tests failure with dask >=2024.12.0 are sorted
          # https://github.com/hyperspy/rosettasciio/issues/345
          mamba install dask-core=2024.8.0

      - 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: |
          mamba install rosettasciio

      - name: Install RosettaSciIO dev
        if: contains(matrix.RSIO_VERSION, 'dev')
        run: |
          pip install "rosettasciio[all] @ git+https://github.com/hyperspy/rosettasciio.git"

      - 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] @ git+https://github.com/hyperspy/hyperspy.git@RELEASE_next_patch"

      - name: Install HyperSpy RnMinor
        if: contains(matrix.HYPERSPY_VERSION, 'RnMinor')
        run: |
          pip install "hyperspy[all] @ git+https://github.com/hyperspy/hyperspy.git@RELEASE_next_minor"

      - name: Install HyperSpy RnMajor
        if: contains(matrix.HYPERSPY_VERSION, 'RnMajor')
        run: |
          pip install "hyperspy[all] @ git+https://github.com/hyperspy/hyperspy.git@RELEASE_next_major"

      - 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 git+https://github.com/hyperspy/exspy.git
          pip install git+https://github.com/hyperspy/holospy.git
          pip install git+https://github.com/lumispy/lumispy.git
          pip install git+https://github.com/pyxem/kikuchipy.git
          pip install git+https://github.com/pyxem/pyxem.git
          pip install git+https://github.com/hyperspy/hyperspy_gui_ipywidgets.git
          pip install git+https://github.com/hyperspy/hyperspy_gui_traitsui.git
          pip install git+https://github.com/usnistgov/etspy.git

      - name: Clear conda and pip cache
        run: |
          conda clean --all
          pip cache purge

      - name: Conda list
        run: |
          conda list

      - name: Run HyperSpy Test Suite
        if: ${{ always() }}
        run: |
          python -m pytest --pyargs hyperspy --reruns 3 -n 2

      - name: Run RosettaScio Test Suite
        if: ${{ always() }}
        run: |
          # mrcz and pyusid doesn't support numpy 2
          python -m pytest --pyargs rsciio -n 1 -k "not test_mrcz.py and not test_usid.py and not TestOperate"

      - name: Run hyperspy_gui_ipywidgets Test Suite
        if: ${{ always() }}
        run: |
          python -m pytest --pyargs hyperspy_gui_ipywidgets

      - 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 exspy Test Suite
        if: ${{ always() }}
        run: |
          python -m pytest --pyargs exspy

      - name: Run holospy Test Suite
        if: ${{ always() }}
        run: |
          python -m pytest --pyargs holospy

      - name: Run kikuchipy Test Suite
        if: ${{ always() }}
        # Run the tests headlessly (pyvista)
        # Unskip test when https://github.com/pyxem/kikuchipy/issues/707 is fixed and
        # released.
        run: |
          xvfb-run python -m pytest --pyargs kikuchipy -k "not test_not_allow_download_raises"

      - 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: |
          python -m pytest --pyargs pyxem

      - name: Run ETSpy Test Suite
        if: ${{ always() }}
        # Test needs to be fixed, see https://github.com/usnistgov/etspy/issues/24
        run: |
          python -m pytest --pyargs etspy -n 2 -k "not test_version"