Initial commit

.dockerignore

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+.git/
+.github/
+.dockerignore
+Dockerfile
+
+*~
+*.DS_Store
+*.egg-info/
+__pycache__/
+
+.docker
+
+.idea/
+.vscode/
+
+examples/
+
+venv/

.github/workflows/ci.yml

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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: false  # delete this line and uncomment the line below to enable automatic builds
+    # 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

.gitignore

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+*~
+*.DS_Store
+*.egg-info/
+__pycache__/
+
+.docker
+
+.idea/
+.vscode/
+
+venv/

Dockerfile

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+# Python version can be changed, e.g.
+# FROM python:3.8
+# FROM docker.io/fnndsc/conda:python3.10.2-cuda11.6.0
+FROM docker.io/python:3.11.3-slim-bullseye
+
+LABEL org.opencontainers.image.authors="FNNDSC <[email protected]>" \
+      org.opencontainers.image.title="ChRIS Plugin Title" \
+      org.opencontainers.image.description="A ChRIS plugin that..."
+
+ARG SRCDIR=/usr/local/src/app
+WORKDIR ${SRCDIR}
+
+COPY requirements.txt .
+RUN pip install -r requirements.txt
+
+COPY . .
+ARG extras_require=none
+RUN pip install ".[${extras_require}]" \
+    && cd / && rm -rf ${SRCDIR}
+WORKDIR /
+
+CMD ["commandname"]

LICENSE

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+MIT License
+
+Copyright (c) 2023 FNNDSC / BCH
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.