---

# 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: Lint and test workflow

on:

  push:

  workflow_dispatch:

jobs:

  quality:

    runs-on: ubuntu-latest

    steps:

      - name: Install non-python dependencies

        run: |

          sudo apt-get install -y graphviz-dev

      - name: Setup Python environment

        uses: khanlab/actions/.github/actions/action-setup_task-installPyProject@v0.3.2

        with:

          python-version: "3.9"

      - name: isort

        run: poetry run isort hippunfold/*.py -c

      - name: Black

        run: poetry run black hippunfold --check

      - name: snakefmt

        run: poetry run snakefmt hippunfold --check

  test:

    runs-on: ubuntu-latest

    needs: ["quality"]

    strategy:

      matrix:

        python-version: ["3.8", "3.9"]

    steps:

      - name: Install non-python dependencies

        run: |

          sudo apt-get install -y graphviz-dev

      - name: Set up Python ${{ matrix.python-version }}

        uses: actions/setup-python@v3

        with:

          python-version: ${{ matrix.python-version }}

      - name: Setup Python environments

        uses: khanlab/actions/.github/actions/action-setup_task-installPyProject@v0.3.2

        with:

          python-version: ${{ matrix.python-version }}

          install-library: true

      - name: Setup env for hippunfold

        run: |

          echo "HIPPUNFOLD_CACHE_DIR=`pwd`/test_data/hippunfold_cache_dir" >> $GITHUB_ENV

      - name: Test single T2w bids

        run: |

          poetry run hippunfold test_data/bids_singleT2w test_out participant -np --modality T2w

      - name: Test running on existing folder

        run: |

          mkdir test_newout

          poetry run hippunfold test_data/bids_singleT2w test_newout participant -np --modality T2w

      - name: Test single T2w bids, right hemi

        run: |

          poetry run hippunfold test_data/bids_singleT2w test_out participant -np --modality T2w --hemi R

      - name: Test single T2w bids, left hemi

        run: |

          poetry run hippunfold test_data/bids_singleT2w test_out participant -np --modality T2w --hemi L

      - name: Test multiple T2w bids

        run: |

          poetry run hippunfold test_data/bids_multiT2w test_out participant -np --modality T2w

      - name: Test T1w bids

        run: |

          poetry run hippunfold test_data/bids_T1w test_out participant -np --modality T1w

      - name: Test hipp b500 bids

        run: |

          poetry run hippunfold test_data/bids_hippb500 test_out participant -np --modality hippb500

      - name: Test T1w multi-session/longitudinal bids

        run: |

          poetry run hippunfold test_data/bids_T1w_longitudinal test_out participant -np --modality T1w

      - name: Test single T2w multi-session/longitudinal bids

        run: |

          poetry run hippunfold test_data/bids_singleT2w_longitudinal test_out participant -np --modality T2w

      - name: Test manual seg T2w bids

        run: |

          poetry run hippunfold test_data/bids_segT2w test_out participant -np --modality segT2w

      - name: Test cropseg bids, with path override

        run: |

          poetry run hippunfold . test_out participant -np --modality cropseg --path_cropseg test_data/data_cropseg/sub-{subject}_hemi-{hemi}_dseg.nii.gz

      - name: Test cropseg bids, with path override, left hemi

        run: |

          poetry run hippunfold . test_out participant -np --modality cropseg --path_cropseg test_data/data_cropseg_1hemi/sub-{subject}_hemi-{hemi}_dseg.nii.gz --hemi L

      - name: Test T2w with T1w template registration

        run: |

          poetry run hippunfold test_data/bids_singleT2w test_out participant -np --modality T2w --t1_reg_template

      - name: Test T2w with T1w output space

        run: |

          poetry run hippunfold test_data/bids_singleT2w test_out participant -np --modality T2w --output_space T1w

      - name: Test modality T2w with myelin map

        run: |

          poetry run hippunfold test_data/bids_singleT2w test_out participant -np --modality T2w --generate-myelin-map

      - name: Test modality T1w with myelin map

        run: |

          poetry run hippunfold test_data/bids_singleT2w test_out participant -np --modality T1w --generate-myelin-map

      - name: Test modality T1w with magdeburg atlas

        run: |

          poetry run hippunfold test_data/bids_T1w test_out participant -np --modality T1w --atlas magdeburg

      - name: Test modality T1w with freesurfer atlas

        run: |

          poetry run hippunfold test_data/bids_T1w test_out participant -np --modality T1w --atlas freesurfer

      - name: Test modality T1w with bigbrain and freesurfer atlas

        run: |

          poetry run hippunfold test_data/bids_T1w test_out participant -np --modality T1w --atlas bigbrain freesurfer