Initialize src

.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@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 "$GITHUB_WORKSPACE:/app:ro" -w /app localhost/local/app:dev \
+            pytest -o cache_dir=/tmp/pytest
+
+  build:
+    name: Build
+    if: false  # delete this line and uncomment the line below to enable automatic builds
+    # if: github.event_name == 'push' || github.event_name == 'release'
+    # needs: [ test ]  # uncomment to require passing tests
+    runs-on: ubuntu-22.04
+
+    steps:
+      - name: Decide image tags
+        id: info
+        shell: python
+        run: |
+          import os
+          import itertools
+
+          def join_tag(t):
+            registry, repo, tag = t
+            return f'{registry}/{repo}:{tag}'.lower()
+
+          registries = ['docker.io', 'ghcr.io']
+          repos = ['${{ 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

.github/workflows/src.yml

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+name: Source
+
+on:
+  push:
+    branches:
+      - src
+  pull_request:
+    branches:
+      - src
+
+jobs:
+  local:
+    name: Local test
+    runs-on: ubuntu-20.04
+    strategy:
+      matrix:
+        python-version: [ '3.8.2', '3.9', '3.10', '3.11', '3.12' ]
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Configure git
+        run: |
+          git config --global user.email "[email protected]"
+          git config --global user.name "FNNDSC in Github Actions"
+      - name: Run ./bootstrap.sh
+        run: |
+          sed -i -e 's/#READY=yes/READY=yes/' bootstrap.sh
+          ./bootstrap.sh
+      - name: Generated unit tests
+        run: |
+          source venv/bin/activate
+          pytest
+      - name: Run program
+        run: |
+          source venv/bin/activate
+          mkdir /tmp/incoming
+          echo 'on-the-metal test is very testy test test' > /tmp/incoming/ghaction.txt
+          commandname --word 'test' /tmp/incoming /tmp/outgoing
+
+          if ! [ -e '/tmp/outgoing/ghaction.count.txt' ]; then
+            echo "Contents of /tmp/outgoing: " /tmp/outgoing/*
+            echo "::error ::File outgoing/ghaction.count.txt was not created."
+          fi
+
+          rm -rvf /tmp/incoming /tmp/outgoing
+
+  integration:
+    name: Integration tests
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - name: Edit code
+        run: |
+          git config --global user.email "[email protected]"
+          git config --global user.name "FNNDSC in Github Actions"
+
+          temp_file=$(mktemp)
+          sed 's/#READY=yes/READY=yes/' bootstrap.sh \
+            | sed 's/^PLUGIN_NAME=.*/PLUGIN_NAME=pl-ghactions-testtemplate/' \
+            | sed 's/^SCRIPT_NAME=.*/SCRIPT_NAME=ghtest_template/' \
+            | sed 's/^PLUGIN_TITLE=.*/PLUGIN_TITLE="A test in GH Actions"/' \
+            > $temp_file
+          mv $temp_file ./bootstrap.sh
+
+          chmod +x bootstrap.sh
+          ./bootstrap.sh
+
+          if ! [ -f ghtest_template.py ]; then
+            echo "::error ::File ghtest_template.py was not created."
+            exit 1
+          fi
+
+          # change the version of this ChRIS plugin
+          sed -i -e 's/^__version__ = .*/__version__ = "1.2.3"/' ghtest_template.py
+      - name: Build image
+        run: docker build -t localhost/fnndsc/pl-ghactions-testtemplate:1.2.3 .
+      - name: Spin up ChRIS
+        uses: FNNDSC/miniChRIS-docker@master
+        with:
+          plugins: localhost/fnndsc/pl-ghactions-testtemplate:1.2.3
+      - name: Assert plugin registered
+        run: |
+          qs='name_exact=pl-ghactions-testtemplate&version=1.2.3'
+          res="$(
+            curl -u 'chris:chris1234' \
+              -H 'Accept: application/json' \
+              "http://localhost:8000/api/v1/plugins/search/?$qs"
+          )"
+          
+          count="$(jq -r '.count' <<< "$res")"
+          if [ "$count" != '1' ]; then
+            echo "::error ::expected count=1"
+            echo "$res"
+            exit 1
+          fi
+
+  push:
+    name: Push to main
+    if: github.event_name == 'push'
+    runs-on: ubuntu-latest
+    needs: [ local, integration ]
+    steps:
+    - name: Git checkout
+      uses: actions/checkout@v4
+      with:
+        persist-credentials: false
+        fetch-depth: 0
+    - name: Configure git
+      run: |
+        git config --local user.email "github-actions[bot]@users.noreply.github.com"
+        git config --local user.name "github-actions[bot]"
+    - name: Merge ref into main
+      run: |
+        git switch main
+
+        set +e
+        output="$(git merge --no-ff --no-commit ${{ github.ref }})"
+        set -e
+        echo "$output"
+
+        # ignore merge conflicts to this file
+        filtered="$(sed '/CONFLICT (modify\/delete): \.github\/workflows\/src\.yml/d' <<< "$output")"
+        if ( echo "$filtered" | grep -Fq CONFLICT ); then
+          echo "::error ::Unacceptable merge conflict. Someone changed main, please merge manually."
+          exit 1
+        fi
+
+        # Important! Deletes this Github workflow file
+        if [ -e .github/workflows/src.yml ]; then
+          git rm --force .github/workflows/src.yml
+        fi
+
+        git commit --no-edit
+    - name: Push to main
+      uses: ad-m/github-push-action@552c074ed701137ebd2bf098e70c394ca293e87f
+      with:
+        github_token: ${{ secrets.GITHUB_TOKEN }}
+        branch: main

.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 ghcr.io/mamba-org/micromamba:1.5.1-focal-cuda-11.3.1
+FROM docker.io/python:3.12.1-slim-bookworm
+
+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 ${SRCDIR}
+
+COPY requirements.txt .
+RUN --mount=type=cache,sharing=private,target=/root/.cache/pip pip install -r requirements.txt
+
+COPY . .
+ARG extras_require=none
+RUN pip install ".[${extras_require}]" \
+    && cd / && rm -rf ${SRCDIR}
+WORKDIR /
+
+CMD ["commandname"]