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test latest image

test latest image #17

Workflow file for this run

---
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 }}