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[pre-commit.ci] pre-commit autoupdate #63

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[pre-commit.ci] pre-commit autoupdate

[pre-commit.ci] pre-commit autoupdate #63

Workflow file for this run

.github/workflows/docker.yml at 5504d6f
---
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}}
- 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
docker-push:
runs-on: ubuntu-latest
needs: [one-session]
defaults:
run:
shell: bash -el {0}
if: ${{ github.ref == 'refs/heads/main' || github.ref_type == 'tag' }}
steps:
- uses: actions/checkout@v4
with:
fetch-depth: 0
- name: Restore docker image
uses: actions/download-artifact@v4
with:
name: docker
path: ${{ env.IMAGE }}
- name: Log in to Docker Hub
uses: docker/login-action@9780b0c442fbb1117ed29e0efdff1e18412f7567
with:
username: ${{ secrets.DOCKERHUB_USERNAME }}
password: ${{ secrets.DOCKERHUB_TOKEN }}
- name: Load image
run: docker load -i ${{ env.IMAGE }}/image.tar
- name: Push unstable to dockerhub on tags or on main
run: |
echo "Pushing unstable versions to DockerHub"
unstable="${{env.USER_NAME}}/${{env.REPO_NAME}}:unstable"
docker tag "${{env.USER_NAME}}/${{env.REPO_NAME}}" "${unstable}"
docker push "${unstable}"
- name: Push stable release to dockerhub on tags only
if: ${{ github.ref_type == 'tag' }}
run: |
echo "Pushing stable and latest versions to DockerHub for latest and ${{ github.ref_name }}"
unstable="${{env.USER_NAME}}/${{env.REPO_NAME}}:unstable"
latest="${{env.USER_NAME}}/${{env.REPO_NAME}}:latest"
docker tag "${unstable}" "${latest}"
docker push "${latest}"
tagged_release="${{env.USER_NAME}}/${{env.REPO_NAME}}:${{ github.ref_name }}"
docker tag "${unstable}" "${tagged_release}"
docker push "${tagged_release}"