tree output #37
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--- | |
name: docker build | |
on: | |
push: | |
branches: [main] | |
pull_request: | |
concurrency: | |
group: ${{ github.workflow }}-${{ github.ref }} | |
cancel-in-progress: true | |
env: | |
USER_NAME: bids | |
REPO_NAME: cat12 | |
IMAGE: /home/runner/work/Remi-Gau/cat12-container/docker | |
jobs: | |
docker-build: | |
runs-on: ubuntu-latest | |
steps: | |
- uses: actions/checkout@v4 | |
with: | |
fetch-depth: 0 | |
- name: Build the Docker image | |
run: | | |
docker build . --tag ${{env.USER_NAME}}/${{env.REPO_NAME}} | |
docker images | |
- name: Check image size and version | |
run: | | |
docker images | |
docker run --rm ${{env.USER_NAME}}/${{env.REPO_NAME}} --version | |
- name: Run simple commands | |
run: | | |
docker run --rm ${{env.USER_NAME}}/${{env.REPO_NAME}} --help | |
docker run --rm ${{env.USER_NAME}}/${{env.REPO_NAME}} . /foo participant view tfce --verbose 3 | |
docker run --rm ${{env.USER_NAME}}/${{env.REPO_NAME}} . /foo participant copy tfce --verbose 3 | |
docker run --rm ${{env.USER_NAME}}/${{env.REPO_NAME}} . /foo participant segment --help | |
- name: Save docker image | |
run: | | |
mkdir -p ${{ env.IMAGE }} | |
docker save "${{env.USER_NAME}}/${{env.REPO_NAME}}" > "${{ env.IMAGE }}/image.tar" | |
- name: Upload docker artifacts | |
uses: actions/upload-artifact@v4 | |
with: | |
name: docker | |
path: ${{ env.IMAGE }} | |
one-session: | |
runs-on: ubuntu-latest | |
strategy: | |
matrix: | |
type: [default, simple, enigma] | |
fail-fast: false | |
needs: docker-build | |
steps: | |
- name: Install dependencies | |
run: | | |
sudo apt-get -y -qq update | |
sudo apt-get -y install tree | |
- uses: actions/checkout@v4 | |
with: | |
fetch-depth: 0 | |
- name: Restore docker image | |
uses: actions/download-artifact@v4 | |
with: | |
name: docker | |
path: ${{ env.IMAGE }} | |
- name: Load image | |
run: docker load -i ${{ env.IMAGE }}/image.tar | |
- name: Get data | |
run: make tests/data/MoAEpilot | |
- name: Segment | |
run: | | |
docker run --rm \ | |
-v ${PWD}/tests/data/MoAEpilot:/data \ | |
${{env.USER_NAME}}/${{env.REPO_NAME}} \ | |
/data /data/derivatives participant \ | |
segment --verbose 3 --type ${{ matrix.type }} | |
tree ${PWD}/tests/data/ | |
tree /home/runner/work/Remi-Gau/cat12-container/tests/data/ | |
- name: Upload output artifact | |
uses: actions/upload-artifact@v4 | |
with: | |
name: output_${{ matrix.type }} | |
path: /home/runner/work/Remi-Gau/cat12-container/tests/data/MoAEpilot/derivatives | |
two-sessions: | |
runs-on: ubuntu-latest | |
strategy: | |
matrix: | |
type: [long_0, long_2] | |
fail-fast: false | |
needs: docker-build | |
steps: | |
- name: Install python | |
uses: actions/setup-python@v5 | |
with: | |
python-version: '3.11' | |
- name: Install dependencies | |
run: | | |
sudo apt-get -y -qq update | |
sudo apt-get -y install git-annex tree | |
pip install datalad | |
- uses: actions/checkout@v4 | |
with: | |
fetch-depth: 0 | |
- name: Restore docker image | |
uses: actions/download-artifact@v4 | |
with: | |
name: docker | |
path: ${{ env.IMAGE }} | |
- name: Load image | |
run: docker load -i ${{ env.IMAGE }}/image.tar | |
- name: Get data | |
run: make data_ds002799 | |
- name: Segment | |
run: | | |
docker run --rm \ | |
-v ${PWD}/tests/data/ds002799:/data \ | |
${{env.USER_NAME}}/${{env.REPO_NAME}} \ | |
/data /data/derivatives participant \ | |
segment --verbose 3 --type ${{ matrix.type }} \ | |
--skip_validation | |
tree ${PWD}/tests/data/ | |
tree /home/runner/work/Remi-Gau/cat12-container/tests/data/ | |
- name: Upload output artifact | |
uses: actions/upload-artifact@v4 | |
with: | |
name: output_${{ matrix.type }} | |
path: /home/runner/work/Remi-Gau/cat12-container/tests/data/ds002799/derivatives |