Run keras model once for a series #28
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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 | |
| if: false # delete this line to enable automatic testing | |
| runs-on: ubuntu-22.04 | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - uses: docker/setup-buildx-action@v2 | |
| - name: Cache Docker layers | |
| uses: actions/cache@v3 | |
| with: | |
| path: /tmp/.buildx-cache | |
| key: ${{ runner.os }}-buildx-${{ github.sha }} | |
| restore-keys: | | |
| ${{ runner.os }}-buildx- | |
| - name: Build | |
| uses: docker/build-push-action@v3 | |
| with: | |
| build-args: extras_require=dev | |
| context: . | |
| load: true | |
| push: false | |
| tags: "localhost/local/app:dev" | |
| cache-from: type=local,src=/tmp/.buildx-cache | |
| cache-to: type=local,dest=/tmp/.buildx-cache | |
| - name: Run pytest | |
| run: | | |
| docker run -v "$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: Get git tag | |
| id: git_info | |
| if: startsWith(github.ref, 'refs/tags/') | |
| run: echo "tag=${GITHUB_REF##*/}" >> $GITHUB_OUTPUT | |
| - name: Get project info | |
| id: determine | |
| env: | |
| git_tag: ${{ steps.git_info.outputs.tag }} | |
| run: | | |
| repo="${GITHUB_REPOSITORY,,}" # to lower case | |
| # if build triggered by tag, use tag name | |
| tag="${git_tag:-latest}" | |
| # if tag is a version number prefixed by 'v', remove the 'v' | |
| if [[ "$tag" =~ ^v[0-9].* ]]; then | |
| tag="${tag:1}" | |
| fi | |
| dock_image=$repo:$tag | |
| echo $dock_image | |
| echo "dock_image=$dock_image" >> $GITHUB_OUTPUT | |
| echo "repo=$repo" >> $GITHUB_OUTPUT | |
| - uses: actions/checkout@v3 | |
| # QEMU is used for non-x86_64 builds | |
| - uses: docker/setup-qemu-action@v2 | |
| # buildx adds additional features to docker build | |
| - uses: docker/setup-buildx-action@v2 | |
| with: | |
| driver-opts: network=host | |
| # cache slightly improves rebuild time | |
| - name: Cache Docker layers | |
| uses: actions/cache@v3 | |
| with: | |
| path: /tmp/.buildx-cache | |
| key: ${{ runner.os }}-buildx-${{ github.sha }} | |
| restore-keys: | | |
| ${{ runner.os }}-buildx- | |
| # Here, we want to do the docker build twice: | |
| # The first build pushes to our local registry for testing. | |
| # The second build pushes to Docker Hub and ghcr.io | |
| - name: Build (local only) | |
| uses: docker/build-push-action@v3 | |
| id: docker_build | |
| with: | |
| context: . | |
| file: ./Dockerfile | |
| tags: localhost/${{ steps.determine.outputs.dock_image }} | |
| load: true | |
| cache-from: type=local,src=/tmp/.buildx-cache | |
| cache-to: type=local,dest=/tmp/.buildx-cache | |
| # If you have a directory called examples/incoming/ and examples/outgoing/, then | |
| # run your ChRIS plugin with no parameters, and asser 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=localhost/${{ steps.determine.outputs.dock_image }} | |
| output_dir=$(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 | |
| id: dockerhub_login | |
| uses: docker/login-action@v2 | |
| with: | |
| username: ${{ secrets.DOCKERHUB_USERNAME }} | |
| password: ${{ secrets.DOCKERHUB_PASSWORD }} | |
| - name: Login to GitHub Container Registry | |
| uses: docker/login-action@v2 | |
| with: | |
| registry: ghcr.io | |
| username: ${{ github.repository_owner }} | |
| password: ${{ secrets.GITHUB_TOKEN }} | |
| - name: Build and push | |
| uses: docker/build-push-action@v3 | |
| if: github.event_name == 'push' || github.event_name == 'release' | |
| with: | |
| context: . | |
| file: ./Dockerfile | |
| tags: | | |
| docker.io/${{ steps.determine.outputs.dock_image }} | |
| ghcr.io/${{ steps.determine.outputs.dock_image }} | |
| # if non-x86_84 architectures are supported, add them here | |
| platforms: linux/amd64 #,linux/arm64,linux/ppc64le | |
| push: true | |
| cache-from: type=local,src=/tmp/.buildx-cache | |
| cache-to: type=local,dest=/tmp/.buildx-cache | |
| - name: Get plugin meta | |
| id: pluginmeta | |
| run: | | |
| repo=${{ steps.determine.outputs.repo }} | |
| dock_image=${{ steps.determine.outputs.dock_image }} | |
| docker run --rm localhost/$dock_image chris_plugin_info > /tmp/description.json | |
| jq < /tmp/description.json # pretty print in log | |
| echo "title=$(jq -r '.title' < /tmp/description.json)" >> $GITHUB_OUTPUT | |
| - name: Update DockerHub description | |
| 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.pluginmeta.outputs.title }} | |
| readme-filepath: ./README.md | |
| repository: ${{ steps.determine.outputs.repo }} | |
| - name: Upload to ChRIS Store | |
| # only upload to ChRIS Store if this is a tagged release | |
| if: steps.git_info.outcome != 'skipped' | |
| uses: FNNDSC/chrisstore-action@master | |
| with: | |
| descriptor_file: /tmp/description.json | |
| auth: ${{ secrets.CHRIS_STORE_USER }} | |
| ## Optional ChRIS backend admin information | |
| # chris_admin_auth: ${{ secrets.CUBE_CHRISPROJECT_ORG_ADMIN_USER }} | |
| # chris_admin_url: https://cube.chrisproject.org/chris-admin/api/v1/ | |
| # compute_resources: host,moc # comma-separated list of names |