build-test-publish.yml

name: CI

on:
  push:
  pull_request:
  schedule:
    - cron: 0 0 * * 0
  # Allow job to be triggered manually from GitHub interface
  workflow_dispatch:

# Force pytest to use color
env:
  FORCE_COLOR: true

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

permissions:
  contents: read

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

jobs:
  build-package:
    name: Build & inspect package
    runs-on: ubuntu-latest
    permissions:
      attestations: write
      id-token: write

    steps:
      - uses: actions/checkout@v4
        with:
          fetch-depth: 0
      - uses: hynek/build-and-inspect-python-package@v2

  test:
    if: "!contains(github.event.head_commit.message, '[skip ci]' && (github.event_name == 'push' || github.event.pull_request.head.repo.full_name != 'nipreps/sdcflows'))"
    runs-on: ubuntu-latest
    env:
      TEST_DATA_HOME: /home/runner/sdcflows-tests
      FSLOUTPUTTYPE: NIFTI_GZ
      FSLMULTIFILEQUIT: TRUE
      AFNI_HOME: /opt/afni
      AFNI_MODELPATH: /opt/afni/models
      AFNI_IMSAVE_WARNINGS: NO
      AFNI_TTATLAS_DATASET: /opt/afni/atlases
      AFNI_PLUGINPATH: /opt/afni/plugins
    strategy:
      max-parallel: 6
      matrix:
        python-version: ["3.9", "3.10", "3.11", "3.12"]
        marks: ["not slow"]
        include:
          - python-version: "3.9"
            marks: "slow and not veryslow"
          - python-version: "3.12"
            marks: "veryslow"

    steps:
    - uses: actions/cache@v4
      with:
        path: /var/lib/apt
        key: apt-cache-v3
        restore-keys: |
          apt-cache-v3
    - name: Install dependencies
      run: |
        sudo apt-get update
        sudo apt-get install -y --no-install-recommends \
                        curl bzip2 ca-certificates        \
                        tcsh gsl-bin netpbm               \
                        libjpeg62 xvfb xterm              \
                        libglu1-mesa-dev libglw1-mesa     \
                        libxm4 build-essential

    - uses: actions/cache@v4
      with:
        path: /opt/afni
        key: afni-v1
        restore-keys: |
          afni-v1
    - name: Install AFNI
      run: |
        if [[ ! -d "${AFNI_HOME}" ]]; then
          curl -O https://afni.nimh.nih.gov/pub/dist/bin/misc/@update.afni.binaries && \
          tcsh @update.afni.binaries -package linux_ubuntu_16_64 -bindir ${AFNI_HOME}
        fi

    - name: Git settings (pacify DataLad)
      run: |
        git config --global user.name 'NiPreps Bot'
        git config --global user.email 'nipreps@gmail.com'
    - name: Set up Python ${{ matrix.python-version }}
      uses: conda-incubator/setup-miniconda@v3
      with:
        auto-update-conda: true
        auto-activate-base: true
        python-version: ${{ matrix.python-version }}
        channels: https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/public/,conda-forge
    - uses: actions/cache@v4
      id: conda
      env:
        CACHE_NUM: v5
      with:
        path: |
          ~/conda_pkgs_dir
          /home/runner/.cache/pip
        key: python-${{ matrix.python-version }}-${{ env.CACHE_NUM }}
        restore-keys: |
          python-${{ matrix.python-version }}-${{ env.CACHE_NUM }}
    - name: Install DataLad
      run: |
        conda install git-annex=*=alldep* pip
        pip install datalad datalad-osf
    - name: Install fsl and ANTs
      run: |
        conda install fsl-fugue fsl-topup ants
    - uses: actions/checkout@v4
    - name: Install dependencies
      timeout-minutes: 5
      run: |
        pip install .[tests]


    - uses: actions/cache@v4
      with:
        path: ~/.cache/templateflow
        key: tf-cache-v1
        restore-keys: |
          tf-cache-
    - name: Get TemplateFlow's required objects
      run: |
        python tools/cache_templateflow.py

    - uses: actions/cache@v4
      with:
        path: ${{ env.TEST_DATA_HOME }}
        key: data-cache-v2
        restore-keys: |
          data-cache-
    - name: Install test data
      run: |
        mkdir -p ${{ env.TEST_DATA_HOME }}
        cd ${{ env.TEST_DATA_HOME }}

        # ds001600
        datalad install -r https://github.com/nipreps-data/ds001600.git
        datalad update -r --merge -d ds001600/
        datalad get -r -J 2 -d ds001600/ ds001600/sub-1/

        # HCP/sub-101006
        datalad install -r https://github.com/nipreps-data/HCP101006.git
        datalad update -r --merge -d HCP101006/
        datalad get -r -J 2 -d HCP101006 HCP101006/*

        # ds001771
        datalad install -r https://github.com/nipreps-data/ds001771.git
        datalad update -r --merge -d ds001771/
        datalad get -r -J 2 -d ds001771/ ds001771/sub-36/*
        datalad get -r -J 2 -d ds001771/derivatives ds001771/derivatives/openneuro/sub-36/*

        # ds000054
        datalad install -r https://github.com/nipreps-data/ds000054.git
        datalad update --merge -d ds000054/
        datalad get -r -d ds000054/ ds000054/sub-100185/*
        datalad get -r -J 2 -d ds000054/ ds000054/derivatives/smriprep-0.6/sub-100185/anat/

        # ds000206
        datalad install -r https://github.com/nipreps-data/ds000206.git
        datalad update -r --merge -d ds000206/
        datalad get -r -J 2 -d ds000206/ ds000206/sub-05/

        # Brain extraction tests
        datalad install -r https://gin.g-node.org/nipreps-data/brain-extraction-tests
        datalad update --merge -d brain-extraction-tests/
        datalad get -r -J 2 -d brain-extraction-tests brain-extraction-tests/*

        # HCPH pilot
        datalad install -r https://github.com/nipreps-data/hcph-pilot_fieldmaps.git
        datalad update -r --merge -d hcph-pilot_fieldmaps/
        datalad get -r -J 2 -d hcph-pilot_fieldmaps/ hcph-pilot_fieldmaps/*

    - name: Set FreeSurfer variables
      run: |
        echo "FREESURFER_HOME=$HOME/.cache/freesurfer" >> $GITHUB_ENV
        echo "FS_LICENSE=$HOME/.cache/freesurfer/license.txt" >> $GITHUB_ENV

    - name: Install FreeSurfer's mri_robust_template
      env:
        MRI_ROBUST_TEMPLATE: sx2n7/providers/osfstorage/5e825301d0e35400ebb481f2
      run: |
        curl https://files.osf.io/v1/resources/$MRI_ROBUST_TEMPLATE?direct > mri_robust_template
        sudo install mri_robust_template /usr/local/bin
        mkdir -p $( dirname $FS_LICENSE )
        echo "b2VzdGViYW5Ac3RhbmZvcmQuZWR1CjMwNzU2CiAqQ1MzYkJ5VXMxdTVNCiBGU2kvUGJsejJxR1V3Cg==" | base64 -d > $FS_LICENSE

    - name: Run pytest with coverage
      run: |
        export PATH=${AFNI_HOME}:$PATH
        export FSLDIR=${CONDA_PREFIX}
        pytest -v --cov sdcflows --cov-report xml:cov.xml --doctest-modules -n auto sdcflows \
          --durations=20 --durations-min=10 -m "$MARKS"
      env:
        MARKS: ${{ matrix.marks }}

    - uses: codecov/codecov-action@v4
      with:
        file: cov.xml
        token: ${{ secrets.CODECOV_TOKEN }}
      if: ${{ always() }}

  publish:
    name: Publish released package to pypi.org
    environment: release-pypi
    if: github.event.action == 'published'
    runs-on: ubuntu-latest
    needs: [build-package, test]
    permissions:
      attestations: write
      id-token: write

    steps:
      - name: Download packages built by build-and-inspect-python-package
        uses: actions/download-artifact@v4
        with:
          name: Packages
          path: dist

      - name: Upload package to PyPI
        uses: pypa/gh-action-pypi-publish@release/v1