docker.yml

---
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
        # # cache tarred docker image to speed up build on follow up runs
        # -   uses: actions/cache@v4
        #     id: cache
        #     with:
        #         path: ${{ env.IMAGE }}/image.tar
        #         key: data
        # -   if: ${{ steps.cache.outputs.cache-hit != 'true' }}
        #     name: Load image
        #     run: docker load -i ${{ env.IMAGE }}/image.tar
        -   name: Build the Docker image
            run: |
                docker build . --tag ${{env.USER_NAME}}/${{env.REPO_NAME}}
        -   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 segment --verbose 3
                docker run --rm ${{env.USER_NAME}}/${{env.REPO_NAME}} . /foo participant copy segment --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 ${PWD}/tests/data/
        -   name: Upload output artifact
            uses: actions/upload-artifact@v4
            with:
                name: output_${{ matrix.type }}
                path: /home/runner/work/cat12-container/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 }} \
                        --participant_label 292 294 \
                        --skip_validation
                tree ${PWD}/tests/data/
        -   name: Upload output artifact
            uses: actions/upload-artifact@v4
            with:
                name: output_${{ matrix.type }}
                path: /home/runner/work/cat12-container/cat12-container/tests/data/ds002799/derivatives