Initial commit

.dockerignore

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

.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:3.10.2-slim-buster
+
+LABEL org.opencontainers.image.authors="FNNDSC <[email protected]>" \
+      org.opencontainers.image.title="ChRIS Plugin Title" \
+      org.opencontainers.image.description="A ChRIS ds plugin that..."
+
+WORKDIR /usr/local/src/app
+
+COPY requirements.txt .
+RUN pip install -r requirements.txt
+
+COPY . .
+RUN pip install .
+
+CMD ["commandname", "--help"]

LICENSE

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+MIT License
+
+Copyright (c) 2022 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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+# _ChRIS_ ds Plugin Template
+
+<!--
+[![Version](https://img.shields.io/docker/v/fnndsc/pl-appname?sort=semver)](https://hub.docker.com/r/fnndsc/pl-appname)
+[![MIT License](https://img.shields.io/github/license/fnndsc/pl-appname)](https://github.com/FNNDSC/pl-appname/blob/main/LICENSE)
+[![Build](https://github.com/FNNDSC/pl-appname/actions/workflows/ci.yml/badge.svg)](https://github.com/FNNDSC/pl-appname/actions)
+-->
+
+
+This is a minimal template repository for _ChRIS_ _ds_ plugin applications.
+For a more comprehensive boilerplate, use
+
+https://github.com/fnndsc/cookiecutter-chrisapp
+
+## How to Use This Template
+
+1. Click "Use this template"
+2. Clone the newly created repository
+3. Replace placeholder text
+
+```shell
+function replace () {
+  find . -type f -not -path '*/\.*/*' -not -path '*/\venv/*' -exec sed -i -e "s/$1/$2/g" '{}' \;
+}
+
+replace commandname my_command_name
+replace pl-appname pl-my-plugin-name
+replace fnndsc my_username
+```
+
+### Template Examples
+
+Here are some good, complete examples of _ChRIS_ plugins created from this template.
+
+- https://github.com/FNNDSC/pl-nums2mask
+- https://github.com/FNNDSC/pl-nii2mnc-u8
+
+Advanced users can `cp -rv .github/workflows` into their own repositories to enable
+automatic builds.
+
+## Abstract
+
+PROGRAMNAME is a [_ChRIS_](https://chrisproject.org/)
+_ds_ plugin which takes in ...  as input files and
+creates ... as output files.
+
+## Usage
+
+```shell
+singularity exec docker://fnndsc/pl-appname commandname [--args values...] input/ output/
+```
+
+## Examples
+
+```shell
+mkdir incoming/ outgoing/
+mv some.dat other.dat incoming/
+singularity exec docker://fnndsc/pl-appname:latest commandname [--args] incoming/ outgoing/
+```
+
+## Development
+
+### Building
+
+```shell
+docker build -t localhost/fnndsc/pl-appname .
+```
+
+### Get JSON Representation
+
+```shell
+docker run --rm localhost/fnndsc/pl-appname chris_plugin_info > MyProgram.json
+```
+
+### Local Test Run
+
+```shell
+docker run --rm -it --userns=host -u $(id -u):$(id -g) \
+    -v $PWD/app.py:/usr/local/lib/python3.10/site-packages/app.py:ro \
+    -v $PWD/in:/incoming:ro -v $PWD/out:/outgoing:rw -w /outgoing \
+    localhost/fnndsc/pl-appname commandname /incoming /outgoing
+```

app.py

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+#!/usr/bin/env python
+
+from pathlib import Path
+from argparse import ArgumentParser, Namespace
+from chris_plugin import chris_plugin
+
+parser = ArgumentParser(description='cli description')
+parser.add_argument('-e', '--example', default='jelly',
+                    help='argument which does not do anything')
+
+
+# documentation: https://fnndsc.github.io/chris_plugin/
+@chris_plugin(
+    parser=parser,
+    title='My ChRIS plugin',
+    category='',                 # ref. https://chrisstore.co/plugins
+    min_memory_limit='100Mi',    # supported units: Mi, Gi
+    min_cpu_limit='1000m',       # millicores, e.g. "1000m" = 1 CPU core
+    min_gpu_limit=0              # set min_gpu_limit=1 to enable GPU
+)
+def main(options: Namespace, inputdir: Path, outputdir: Path):
+    print(f'Option: {options.example}')
+
+
+if __name__ == '__main__':
+    main()

requirements.txt

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+chris_plugin~=0.0.12

setup.py

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+from setuptools import setup
+
+setup(
+    name             = 'chris-plugin-template',
+    version          = '1.0.0',
+    description      = 'A ChRIS DS plugin template',
+    author           = 'FNNDSC',
+    author_email     = '[email protected]',
+    url              = 'https://github.com/FNNDSC/python-chrisapp-template',
+    py_modules       = ['app'],
+    install_requires = ['chris_plugin'],
+    license          = 'MIT',
+    python_requires  = '>=3.8.2',
+    entry_points     = {
+        'console_scripts': [
+            'commandname = app:main'
+            ]
+        },
+    classifiers      = [
+        'License :: OSI Approved :: MIT License',
+        'Programming Language :: Python :: 3.10',
+        'Topic :: Scientific/Engineering',
+        'Topic :: Scientific/Engineering :: Bio-Informatics',
+        'Topic :: Scientific/Engineering :: Medical Science Apps.'
+    ]
+)