pythonpackage.yml

#This workflow will install Python dependencies, run tests and lint with a variety of Python versions
# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions

name: Python package

# Set once
env:
  SUBPACKAGE: nipype1
  FSLCONDA: https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/public/
  NO_ET: 1  # etelemetry causes order-of-magnitude slowdowns

on:
  push:
    branches: [main]
  pull_request:
    branches: [main]
  release:
    types:
      - published

concurrency:
  group: ${{ github.workflow }}-${{ github.ref }}
  cancel-in-progress: true

defaults:
  run:
    shell: bash -el {0}

jobs:
  devcheck:
    runs-on: ubuntu-latest
    strategy:
      matrix:
        python-version: ["3.8", "3.12"] # Check oldest and newest versions
        pip-flags: ["", "--editable"]
        pydra:
          - "pydra"
          - "--editable git+https://github.com/nipype/pydra.git#egg=pydra"

    steps:
      - uses: actions/checkout@v4
      - name: Set up Python ${{ matrix.python-version }}
        uses: actions/setup-python@v5
        with:
          python-version: ${{ matrix.python-version }}
      - name: Install build dependencies
        run: |
          python -m pip install --upgrade pip
      - name: Install Pydra
        run: |
          pip install ${{ matrix.pydra }}
          python -c "import pydra as m; print(f'{m.__name__} {m.__version__} @ {m.__file__}')"
      - name: Install task package
        run: |
          pip install ${{ matrix.pip-flags }} ".[dev]"
          python -c "import pydra.tasks.$SUBPACKAGE as m; print(f'{m.__name__} {m.__version__} @ {m.__file__}')"
          python -c "import pydra as m; print(f'{m.__name__} {m.__version__} @ {m.__file__}')"

  test:
    runs-on: ubuntu-latest
    strategy:
      matrix:
        python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"]

    steps:
      - uses: actions/checkout@v4
      - name: Set up Python ${{ matrix.python-version }}
        uses: conda-incubator/setup-miniconda@v3
        with:
          python-version: ${{ matrix.python-version }}
          mamba-version: "*"
          channels: ${{ env.FSLCONDA }},conda-forge,defaults
          channel-priority: true
      - name: Install FSL
        run: |
          mamba install fsl-avwutils
          mamba env config vars set FSLDIR="$CONDA_PREFIX" FSLOUTPUTTYPE="NIFTI_GZ"
          # Hack because we're not doing a full FSL install
          echo "6.0.7.9" > $CONDA_PREFIX/etc/fslversion
      - name: Upgrade pip
        run: |
          python -m pip install --upgrade pip
      - name: Install task package
        run: |
          pip install ".[test]"
          python -c "import pydra.tasks.$SUBPACKAGE as m; print(f'{m.__name__} {m.__version__} @ {m.__file__}')"
          python -c "import pydra as m; print(f'{m.__name__} {m.__version__} @ {m.__file__}')"
      - name: Test with pytest
        run: |
          pytest -sv --doctest-modules --pyargs pydra.tasks.$SUBPACKAGE \
              --cov pydra.tasks.$SUBPACKAGE --cov-report xml --cov-report term-missing
      - uses: codecov/codecov-action@v4
        if: ${{ always() }}
        with:
          token: ${{ secrets.CODECOV_TOKEN }}

  build:
    runs-on: ubuntu-latest
    steps:
      - uses: actions/checkout@v4
        with:
          submodules: recursive
          fetch-depth: 0
      - uses: hynek/build-and-inspect-python-package@v2

  deploy:
    needs: [build, devcheck, test]
    runs-on: ubuntu-latest
    permissions:
      id-token: write
    if: github.repository_owner == 'nipype' && github.event.action == 'published'
    environment: Publish
    steps:
      - uses: actions/download-artifact@v4
        with:
          name: Packages
          path: dist
      - uses: pypa/gh-action-pypi-publish@release/v1