[ENH] No participant listing required #77
Workflow file for this run
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| --- | |
| name: system_test | |
| concurrency: | |
| group: ${{ github.workflow }}-${{ github.ref }} | |
| cancel-in-progress: true | |
| on: | |
| push: | |
| branches: [main] | |
| pull_request: | |
| branches: ['*'] | |
| jobs: | |
| system_test: | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| python-version: ['3.11'] | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v3 | |
| with: | |
| fetch-depth: 0 | |
| submodules: recursive | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Install dependencies | |
| run: | | |
| sudo apt-get update | |
| sudo apt-get install -y git-annex tree | |
| python -m pip install --upgrade pip | |
| - name: Install | |
| run: pip install .[test] | |
| - name: Post-install | |
| run: | | |
| git config --global --add user.name "Ford Escort" | |
| git config --global --add user.email [email protected] | |
| - name: Check set up | |
| run: | | |
| datalad wtf | |
| cohort_creator --version | |
| - name: install datasets | |
| run: | | |
| cohort_creator install \ | |
| -d tests/data/datasets.tsv \ | |
| -p tests/data/participants.tsv \ | |
| -o outputs \ | |
| --dataset_types raw mriqc fmriprep \ | |
| --verbosity 3 | |
| - name: get data | |
| run: | | |
| cohort_creator get \ | |
| -d tests/data/datasets.tsv \ | |
| -p tests/data/participants.tsv \ | |
| -o outputs \ | |
| --dataset_types raw mriqc fmriprep \ | |
| --datatype anat func \ | |
| --space T1w MNI152NLin2009cAsym \ | |
| --jobs 6 \ | |
| --verbosity 3 | |
| - name: copy data | |
| run: | | |
| cohort_creator copy \ | |
| -d tests/data/datasets.tsv \ | |
| -p tests/data/participants.tsv \ | |
| -o outputs \ | |
| --dataset_types raw mriqc fmriprep \ | |
| --datatype anat func \ | |
| --space T1w MNI152NLin2009cAsym \ | |
| --verbosity 3 | |
| - name: Check outputs | |
| run: | | |
| cat outputs/logs/docker.log | |
| tree -L 2 --dirsfirst outputs | |
| tree --dirsfirst outputs/study-ds000002 |