Update and rename app.py to mdharvester.py #3
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| # 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: | |
| test: | |
| name: Unit tests | |
| runs-on: ubuntu-22.04 | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: docker/setup-buildx-action@v3 | |
| - name: Build | |
| uses: docker/build-push-action@v5 | |
| with: | |
| build-args: extras_require=dev | |
| context: . | |
| load: true | |
| push: false | |
| tags: "localhost/local/app:dev" | |
| cache-from: type=gha | |
| cache-to: type=gha,mode=max | |
| - name: Run pytest | |
| run: | | |
| docker run -v "$GITHUB_WORKSPACE:/app:ro" -w /app localhost/local/app:dev \ | |
| pytest -o cache_dir=/tmp/pytest | |
| build: | |
| name: Build | |
| if: github.event_name == 'push' || github.event_name == 'release' | |
| # needs: [ test ] # uncomment to require passing tests | |
| runs-on: ubuntu-22.04 | |
| steps: | |
| - name: Decide image tags | |
| id: info | |
| shell: python | |
| run: | | |
| import os | |
| import itertools | |
| def join_tag(t): | |
| registry, repo, tag = t | |
| return f'{registry}/{repo}:{tag}'.lower() | |
| registries = ['docker.io', 'ghcr.io'] | |
| repos = ['${{ 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@v4 | |
| # 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: ${{ steps.info.outputs.local_tag }} | |
| load: true | |
| cache-from: type=gha | |
| # If you have a directory called examples/incoming/ and examples/outgoing/, then | |
| # run your ChRIS plugin with no parameters, and assert that it creates all the files | |
| # which are expected. File contents are not compared. | |
| - name: Run examples | |
| id: run_examples | |
| run: | | |
| if ! [ -d 'examples/incoming/' ] || ! [ -d 'examples/outgoing/' ]; then | |
| echo "No examples." | |
| exit 0 | |
| fi | |
| dock_image=${{ steps.info.outputs.local_tag }} | |
| output_dir=$(mktemp -d) | |
| cmd=$(docker image inspect -f '{{ (index .Config.Cmd 0) }}' $dock_image) | |
| docker run --rm -u "$(id -u):$(id -g)" \ | |
| -v "$PWD/examples/incoming:/incoming:ro" \ | |
| -v "$output_dir:/outgoing:rw" \ | |
| $dock_image $cmd /incoming /outgoing | |
| for expected_file in $(find examples/outgoing -type f); do | |
| fname="${expected_file##*/}" | |
| out_path="$output_dir/$fname" | |
| printf "Checking output %s exists..." "$out_path" | |
| if [ -f "$out_path" ]; then | |
| echo "ok" | |
| else | |
| echo "not found" | |
| 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@v5 | |
| 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: NERC | |
| - 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 |