Handle .txt and add test #3
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| # Continuous integration testing for ChRIS Plugin. | |
| # https://github.com/FNNDSC/python-chrisapp-template/wiki/Continuous-Integration | |
| # | |
| # - on push and PR: run pytest | |
| # - on push to main: build and push container images as ":latest" | |
| # - on push to semver tag: build and push container image with tag and | |
| # upload plugin description to https://chrisstore.co | |
| name: build | |
| on: | |
| push: | |
| branches: [ main ] | |
| tags: | |
| - "v?[0-9]+.[0-9]+.[0-9]+*" | |
| pull_request: | |
| branches: [ main ] | |
| jobs: | |
| build: | |
| name: Build | |
| if: github.event_name == 'push' || github.event_name == 'release' | |
| # needs: [ test ] # uncomment to require passing tests | |
| runs-on: ubuntu-22.04 | |
| steps: | |
| - name: Decide image tags | |
| id: info | |
| shell: python | |
| run: | | |
| import os | |
| import itertools | |
| def join_tag(t): | |
| registry, repo, tag = t | |
| return f'{registry}/{repo}:{tag}'.lower() | |
| registries = ['docker.io', 'ghcr.io'] | |
| repos = ['${{ github.repository }}'] | |
| if '${{ github.ref_type }}' == 'branch': | |
| tags = ['latest'] | |
| elif '${{ github.ref_type }}' == 'tag': | |
| tag = '${{ github.ref_name }}' | |
| version = tag[1:] if tag.startswith('v') else tag | |
| tags = ['latest', version] | |
| else: | |
| tags = [] | |
| if '${{ github.ref_type }}' == 'tag': | |
| local_tag = join_tag(('ghcr.io', '${{ github.repository }}', version)) | |
| else: | |
| local_tag = join_tag(('localhost', '${{ github.repository }}', 'latest')) | |
| product = itertools.product(registries, repos, tags) | |
| tags_csv = ','.join(map(join_tag, product)) | |
| outputs = { | |
| 'tags_csv' : tags_csv, | |
| 'push' : 'true' if tags_csv else 'false', | |
| 'local_tag': local_tag | |
| } | |
| with open(os.environ['GITHUB_OUTPUT'], 'a') as out: | |
| for k, v in outputs.items(): | |
| out.write(f'{k}={v}\n') | |
| - uses: actions/checkout@v3 | |
| # QEMU is used for non-x86_64 builds | |
| - uses: docker/setup-qemu-action@v3 | |
| # buildx adds additional features to docker build | |
| - uses: docker/setup-buildx-action@v3 | |
| with: | |
| driver-opts: network=host | |
| # Here, we want to do the docker build twice: | |
| # The first build pushes to our local registry for testing. | |
| # The second build pushes to Docker Hub and ghcr.io | |
| - name: Build (local only) | |
| uses: docker/build-push-action@v3 | |
| id: docker_build | |
| with: | |
| context: . | |
| file: ./Dockerfile | |
| tags: ${{ steps.info.outputs.local_tag }} | |
| load: true | |
| cache-from: type=gha | |
| - name: Download example data | |
| run: examples/download.sh | |
| - name: Run examples | |
| id: run_examples | |
| run: | | |
| mkdir /tmp/outgoing | |
| docker run --rm -u "$(id -u):$(id -g)" \ | |
| -v "${{ github.workspace }}/examples/incoming:/incoming:ro" \ | |
| -v "/tmp/outgoing:/outgoing:rw" \ | |
| ${{ steps.info.outputs.local_tag }} | |
| mni2common /incoming /outgoing | |
| - name: Assert example outputs are found | |
| run: | | |
| expected_outputs=( | |
| outgoing/colin27_t1_tal_lin.mnc2nii.log | |
| outgoing/colin27_t1_tal_lin.nii | |
| outgoing/colin27_t1_tal_lin_headmask.mnc2nii.log | |
| outgoing/colin27_t1_tal_lin_headmask.nii | |
| outgoing/colin27_t1_tal_lin_mask.mnc2nii.log | |
| outgoing/colin27_t1_tal_lin_mask.nii | |
| outgoing/colin_white_mc_left.mz3 | |
| outgoing/colin_white_mc_mask_left.mz3 | |
| outgoing/colin_white_mc_mask_right.mz3 | |
| outgoing/colin_white_mc_right.mz3 | |
| ) | |
| for expected_output in "${expected_outputs[@]}"; do | |
| if ! [ -f "$1" ]; then | |
| echo "expected $1 to be a file, but it does not." | |
| parent_dir="$(dirname "$1")" | |
| set -ex | |
| ls -lh "$parent_dir" | |
| exit 1 | |
| fi | |
| done | |
| - name: Login to DockerHub | |
| if: (github.event_name == 'push' || github.event_name == 'release') && contains(steps.info.outputs.tags_csv, 'docker.io') | |
| uses: docker/login-action@v3 | |
| with: | |
| username: ${{ secrets.DOCKERHUB_USERNAME }} | |
| password: ${{ secrets.DOCKERHUB_PASSWORD }} | |
| - name: Login to GitHub Container Registry | |
| if: (github.event_name == 'push' || github.event_name == 'release') && contains(steps.info.outputs.tags_csv, 'ghcr.io') | |
| uses: docker/login-action@v3 | |
| with: | |
| registry: ghcr.io | |
| username: ${{ github.repository_owner }} | |
| password: ${{ secrets.GITHUB_TOKEN }} | |
| - name: Build and push | |
| uses: docker/build-push-action@v3 | |
| if: (github.event_name == 'push' || github.event_name == 'release') | |
| with: | |
| context: . | |
| file: ./Dockerfile | |
| tags: ${{ steps.info.outputs.tags_csv }} | |
| # if non-x86_84 architectures are supported, add them here | |
| platforms: linux/amd64 #,linux/arm64,linux/ppc64le | |
| push: ${{ steps.info.outputs.push }} | |
| cache-to: type=gha,mode=max | |
| - name: Upload ChRIS Plugin | |
| id: upload | |
| if: github.ref_type == 'tag' | |
| uses: FNNDSC/upload-chris-plugin@v1 | |
| with: | |
| dock_image: ${{ steps.info.outputs.local_tag }} | |
| username: ${{ secrets.CHRISPROJECT_USERNAME }} | |
| password: ${{ secrets.CHRISPROJECT_PASSWORD }} | |
| chris_url: https://cube.chrisproject.org/api/v1/ | |
| compute_names: host,galena | |
| - name: Update DockerHub description | |
| if: steps.upload.outcome == 'success' | |
| uses: peter-evans/dockerhub-description@v3 | |
| continue-on-error: true # it is not crucial that this works | |
| with: | |
| username: ${{ secrets.DOCKERHUB_USERNAME }} | |
| password: ${{ secrets.DOCKERHUB_PASSWORD }} | |
| short-description: ${{ steps.upload.outputs.title }} | |
| readme-filepath: ./README.md |