Jordandekraker patch 1 (#317) #1046
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| # 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/[email protected] | |
| 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/[email protected] | |
| 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 |