test_template.yml

name: DIPY  Base Workflow Template

on:
  workflow_call:
    inputs:
      runs-on:
        description: "Select on which environment you want to run the workflow"
        type: string
        required: false
        default: '"ubuntu-latest"'
      python-version:
        description: "Select Python version"
        type: string
        required: false
        default: '["3.10", ]'
      use-pre:
        description: "bal"
        type: boolean
        required: false
      coverage:
        description: "coverage"
        type: boolean
        required: false
      enable-viz-tests:
        description: "Activate viz tests and headless"
        type: boolean
        required: false
      install-type:
        description: ""
        type: string
        required: false
        default: '["pip", ]'
      depends:
        description: ""
        type: string
        required: false
        default: cython!=0.29.29 numpy matplotlib h5py nibabel cvxpy<=1.4.4 tqdm
      extra-depends:
        description: ""
        type: string
        required: false

    secrets:
      codecov-token:
        description: "codecov token to send the report"
        required: false

defaults:
  run:
    shell: bash

jobs:
  build:
    runs-on: ${{ matrix.os }}
    timeout-minutes: 120
    strategy:
      fail-fast: false
      matrix:
        python-version: ${{fromJSON(inputs.python-version) }}
        os: ${{fromJSON(inputs.runs-on) }}
        install-type: ${{fromJSON(inputs.install-type) }}
        exclude:
          - os: macos-14
            python-version: 3.9
    env:
      DEPENDS: ${{ inputs.depends }}
      EXTRA_DEPENDS: ${{ inputs.extra-depends }}
      INSTALL_TYPE: ${{ matrix.install-type }}
      PYTHON_VERSION: ${{ matrix.python-version }}
      VENV_ARGS: "--python=python"
      USE_PRE: ${{ inputs.use-pre }}
      COVERAGE: ${{ inputs.coverage }}
      DIPY_WERRORS: 1
      CODECOV_TOKEN: ${{ secrets.codecov-token }}
      TEST_WITH_XVFB: ${{ inputs.enable-viz-tests }}
      PRE_WHEELS: "https://pypi.anaconda.org/scientific-python-nightly-wheels/simple"  # "https://pypi.anaconda.org/scipy-wheels-nightly/simple"
    steps:
    - uses: actions/checkout@v4
    - name: Set up Python ${{ matrix.python-version }}
      if: ${{ matrix.install-type != 'conda' }}
      uses: actions/setup-python@v5
      with:
        python-version: ${{ matrix.python-version }}
    - name: Set up Virtualenv
      if: ${{ matrix.install-type != 'conda' }}
      run: |
        python -m pip install --upgrade pip virtualenv
        virtualenv $VENV_ARGS venv
    - name: Setup Miniconda
      uses: conda-incubator/setup-miniconda@v3
      if: ${{ matrix.install-type == 'conda' }}
      with:
        auto-update-conda: true
        auto-activate-base: false
        activate-environment: venv
        python-version: ${{ matrix.python-version }}
        channels: defaults, conda-forge
        use-only-tar-bz2: true
    - name: Install HDF5 and pytables on macOS
      if: ${{ (runner.os == 'macOS')  &&  (env.EXTRA_DEPENDS != '')  &&  (env.INSTALL_TYPE == 'pip') }}
      run: |
        pip install cython
        brew install hdf5
        brew install c-blosc
        export HDF5_DIR=/opt/homebrew/opt/hdf5
        export BLOSC_DIR=/opt/homebrew/opt/c-blosc
        pip install tables

    - name: Install Dependencies
      run: |
        if [ "${{ inputs.use-pre }}" == "true" ]; then
          tools/ci/install_dependencies.sh || echo "::warning::Experimental Job so Install Dependencies failure ignored!"
        else
          tools/ci/install_dependencies.sh
        fi
    - name: Install OpenMP on macOS
      if: runner.os == 'macOS'
      run: |
        brew install llvm
        brew install libomp
        echo "CC=clang" >> $GITHUB_ENV
    - name: Install DIPY
      run: |
        if [ "${{ inputs.use-pre }}" == "true" ]; then
          tools/ci/install.sh || echo "::warning::Experimental Job so Install DIPY failure ignored!"
        else
          tools/ci/install.sh
        fi
    - name: Setup Headless
      if: ${{ inputs.enable-viz-tests }}
      run: tools/ci/setup_headless.sh
    - name: Run the Tests
      run: |
        if [ "${{ inputs.use-pre }}" == "true" ]; then
          tools/ci/run_tests.sh || echo "::warning::Experimental Job so failure ignored!"
        else
          tools/ci/run_tests.sh
        fi
    - name: Upload coverage to Codecov
      uses: codecov/codecov-action@v4
      if: ${{ fromJSON(env.COVERAGE) }}
      with:
        token: ${{ secrets.CODECOV_TOKEN }}
        directory: for_testing
        files: coverage.xml
        fail_ci_if_error: true
        flags: unittests
        name: codecov-umbrella
        verbose: true