tests.yml

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: '3.9'
            # Set pillow and scikit-image version to be compatible with imageio and scipy
            # align matplotlib dependency with hyperspy
            DEPENDENCIES: matplotlib==3.6 numpy==1.20.0 tifffile==2022.7.28 dask[array]==2021.5.1 distributed==2021.5.1 numba==0.53 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: '3.10'
            LABEL: '-minimum'
          - os: ubuntu
            os_version: latest
            PYTHON_VERSION: '3.12'
            LABEL: '-hyperspy-dev'
          - os: ubuntu
            os_version: latest
            PYTHON_VERSION: '3.10'
            LABEL: '-without-hyperspy'
          - os: ubuntu
            os_version: latest
            PYTHON_VERSION: '3.9'
          - os: ubuntu
            os_version: latest
            PYTHON_VERSION: '3.12'
          - os: ubuntu
            os_version: latest
            PYTHON_VERSION: '3.13'
            # can remove minimum dependencies when numba supports 3.13
            LABEL: '-minimum'
          - os: macos
            os_version: latest
            PYTHON_VERSION: '3.13'
            # can remove minimum dependencies when numba supports 3.13
            LABEL: '-minimum'
          - os: windows
            os_version: latest
            PYTHON_VERSION: '3.13'
            # can remove minimum dependencies when numba supports 3.13
            LABEL: '-minimum'
          - os: macos
            os_version: '13'
            PYTHON_VERSION: '3.12'

    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 }}
          cache: 'pip'
        
      - 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 traits dev for python 3.13
        if: ${{ matrix.PYTHON_VERSION == '3.13' }}
        run: |
          # traits release with python 3.13 pending
          pip install git+https://github.com/enthought/traits.git

      - name: Install hyperspy and exspy
        if: ${{ ! contains(matrix.LABEL, 'without-hyperspy') && matrix.PYTHON_VERSION != '3.13'}}
        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 hyperspy (python 3.13) and exspy (dev)
        if: ${{ matrix.PYTHON_VERSION == '3.13' }}
        run: |
          # speed up installing scikit-image using pre-release with python 3.13 wheels
          pip install scikit-image --pre 
          pip install git+https://github.com/ericpre/hyperspy.git@python313
          pip install git+https://github.com/hyperspy/exspy.git

      - name: Install python-mrcz dev
        # for numpy 2.0 support for python >= 3.9
        # https://github.com/em-MRCZ/python-mrcz/pull/15
        if: ${{ ! contains(matrix.LABEL, 'oldest') && ! contains(matrix.LABEL, 'minimum') }}
        run: |
          pip install git+https://github.com/ericpre/python-mrcz.git@numpy2.0_and_deprecation_fixes

      - 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@v5
        env:
          CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}