Merge pull request #62 from neurodatascience/create-pull-request/patch #52
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| --- | |
| 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 inputs/datasets.tsv \ | |
| -p inputs/participants.tsv \ | |
| -o outputs \ | |
| --dataset_types raw mriqc fmriprep \ | |
| --verbosity 3 | |
| - name: get data | |
| run: | | |
| cohort_creator get \ | |
| -d inputs/datasets.tsv \ | |
| -p inputs/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 inputs/datasets.tsv \ | |
| -p inputs/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 |