test latest image #16
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| --- | |
| name: test latest image | |
| on: | |
| schedule: | |
| - cron: 0 0 1 * * | |
| workflow_dispatch: | |
| concurrency: | |
| group: ${{ github.workflow }}-${{ github.ref }} | |
| cancel-in-progress: true | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| jobs: | |
| test_latest_image: | |
| strategy: | |
| matrix: | |
| dataset: ['1', '2'] | |
| fail-fast: false | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Install dependencies | |
| run: | | |
| sudo apt-get update | |
| sudo apt-get install -y tree | |
| - name: Clone repo | |
| uses: actions/checkout@v3 | |
| - name: pull docker image | |
| run: docker pull bids/afni_proc:latest | |
| - name: print version | |
| run: | | |
| docker run -t --rm --read-only \ | |
| -v /tmp:/tmp \ | |
| -v /var/tmp:/var/tmp \ | |
| bids/afni_proc:latest -v | |
| docker run -t --rm --read-only \ | |
| -v /tmp:/tmp \ | |
| -v /var/tmp:/var/tmp \ | |
| bids/afni_proc:latest -h | |
| - name: get data | |
| run: | | |
| wget https://raw.githubusercontent.com/bids-apps/maintenance-tools/main/utils/get_data_from_osf.sh | |
| bash get_data_from_osf.sh ds114_test${{ matrix.dataset }} | |
| - name: prepare output dir | |
| run: mkdir -p ${HOME}/outputs${{ matrix.dataset }} | |
| - name: participant level tests | |
| run: | | |
| docker run -t --rm --read-only \ | |
| -v ${HOME}/data/ds114_test${{ matrix.dataset }}:/bids_dataset \ | |
| -v ${HOME}/outputs${{ matrix.dataset }}:/outputs \ | |
| -v /tmp:/tmp \ | |
| -v /var/tmp:/var/tmp \ | |
| bids/afni_proc \ | |
| /bids_dataset /outputs participant \ | |
| --participant_label 01 \ | |
| --afni_proc \ | |
| '-subj_id {subj_id} -script proc.bids -scr_overwrite -out_dir {out_dir} -blocks tshift volreg blur scale -copy_anat {anat_path} -tcat_remove_first_trs 0 -dsets {epi_paths} -volreg_align_to MIN_OUTLIER -blur_size 4.0 -bash' | |
| docker run -t --rm --read-only \ | |
| -v ${HOME}/data/ds114_test${{ matrix.dataset }}:/bids_dataset \ | |
| -v ${HOME}/outputs${{ matrix.dataset }}:/outputs \ | |
| -v /tmp:/tmp \ | |
| -v /var/tmp:/var/tmp \ | |
| bids/afni_proc \ | |
| /bids_dataset /outputs participant \ | |
| --participant_label 02 \ | |
| --afni_proc \ | |
| '-subj_id {subj_id} -script proc.bids -scr_overwrite -out_dir {out_dir} -blocks tshift volreg blur scale -copy_anat {anat_path} -tcat_remove_first_trs 0 -dsets {epi_paths} -volreg_align_to MIN_OUTLIER -blur_size 4.0 -bash' | |
| - name: check output | |
| run: tree ${HOME}/outputs${{ matrix.dataset }} |