Initial check in

.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
+    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

.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="Spleen data downloader" \
+      org.opencontainers.image.description="A ChRIS FS plugin to download a set of spleen data"
+
+ARG SRCDIR=/usr/local/src/pl-spleendata
+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 ["spleendata"]

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.

README.md

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+# Spleen data downloader
+
+[![Version](https://img.shields.io/docker/v/fnndsc/pl-spleendatads?sort=semver)](https://hub.docker.com/r/fnndsc/pl-spleendatadsds)
+[![MIT License](https://img.shields.io/github/license/fnndsc/pl-spleendatads)](https://github.com/FNNDSC/pl-spleendatads/blob/main/LICENSE)
+[![ci](https://github.com/FNNDSC/pl-spleendatads/actions/workflows/ci.yml/badge.svg)](https://github.com/FNNDSC/pl-spleendatads/actions/workflows/ci.yml)
+
+`pl-spleendatads` is a [_ChRIS_](https://chrisproject.org/) _DS_ plugin which downloads an exemplar spleen dataset useful for training and inference experiments.
+
+## Abstract
+
+This is a simple _DS_ plugin suitable for training and inference on 3D spleen NiFTI volumes, as part of the [MONAI spleen segmentation exemplar notebook](https://github.com/Project-MONAI/tutorials/blob/main/3d_segmentation/spleen_segmentation_3d.ipynb). _DS_ plugins are suitable as non-root nodes of ChRIS compute trees, i.e. nodes that have a parent node. If you need a _root node_ spleen data origin, use the [companion _FS_ spleen data node](https://github.com/FNNDSC/pl-spleendata).
+
+By default, the download is pretty big -- 1.2Gb, so make sure you have time and space. It is possible to post-download prune this. For example, if you are only interested in _training_, you can use a `--trainingOnly` flag which will prune out the 43Mb of testing NiFTI volumes. Conversely, if you are just interested in _inference_, the `--testingOnly` will remove the post download 1.2Gb of training data, saving lots of space.
+
+You still need to download the whole set, however, before you can prune.
+
+## Installation
+
+`pl-spleendatads` is a _[ChRIS](https://chrisproject.org/) plugin_, meaning it can run from either within _ChRIS_ or the command-line.
+
+## Local Usage
+
+### On the metal
+
+If you have checked out the repo, you can simply run `spleendatads` using
+
+```shell
+source venv/bin/activate
+pip install -U ./
+spleendatads input/ output/
+```
+
+### PyPI
+
+Alternatively, you can just do a
+
+```shell
+pip install spleendatads
+```
+
+to get directly from PyPI.
+
+### apptainer
+
+The recommended way is to use [Apptainer](https://apptainer.org/) (a.k.a. Singularity) to run `pl-spleendatads` as a container:
+
+```shell
+apptainer exec docker://fnndsc/pl-spleendatads spleendatads [--args values...] input/ output/
+```
+
+To print its available options, run:
+
+```shell
+apptainer exec docker://fnndsc/pl-spleendatads spleendatads --help
+```
+
+## Examples
+
+`spleendatads`, being a ChRIS _DS_ plugin, requires two positional arguments: an input directory from the upstream parent, and a directory that will contain the output data. Simply create an empty `input` and `output`.
+
+```shell
+mkdir output
+apptainer exec docker://fnndsc/pl-spleendatads:latest spleendatads [--args] input/ output/
+```
+
+## Development
+
+Instructions for developers.
+
+### Building
+
+Build a local container image:
+
+```shell
+docker build -t localhost/fnndsc/pl-spleendatads .
+```
+
+### Running
+
+Mount the source code `spleendatads.py` into a container to try out changes without rebuild.
+
+```shell
+docker run --rm -it --userns=host -u $(id -u):$(id -g) \
+    -v $PWD/spleendatads.py:/usr/local/lib/python3.12/site-packages/spleendatads.py:ro \
+    -v $PWD/in:/incoming:ro -v $PWD/out:/outgoing:rw -w /outgoing \
+    localhost/fnndsc/pl-spleendatads spleendatads /incoming /outgoing
+```
+
+### Testing
+
+Run unit tests using `pytest`. It's recommended to rebuild the image to ensure that sources are up-to-date. Use the option `--build-arg extras_require=dev` to install extra dependencies for testing.
+
+```shell
+docker build -t localhost/fnndsc/pl-spleendatads:dev --build-arg extras_require=dev .
+docker run --rm -it localhost/fnndsc/pl-spleendatads:dev pytest
+```
+
+## Release
+
+Steps for release can be automated by [Github Actions](.github/workflows/ci.yml).
+This section is about how to do those steps manually.
+
+### Increase Version Number
+
+Increase the version number in `setup.py` and commit this file.
+
+### Push Container Image
+
+Build and push an image tagged by the version. For example, for version `1.2.3`:
+
+```
+docker build -t docker.io/fnndsc/pl-spleendatads:1.2.3 .
+docker push docker.io/fnndsc/pl-spleendatads:1.2.3
+```
+
+### Get JSON Representation
+
+Run [`chris_plugin_info`](https://github.com/FNNDSC/chris_plugin#usage)
+to produce a JSON description of this plugin, which can be uploaded to _ChRIS_.
+
+```shell
+docker run --rm docker.io/fnndsc/pl-spleendatads:1.2.3 chris_plugin_info -d docker.io/fnndsc/pl-spleendatads:1.2.3 > chris_plugin_info.json
+```
+
+Intructions on how to upload the plugin to _ChRIS_ can be found here:
+https://chrisproject.org/docs/tutorials/upload_plugin
+
+_-30-_