Updated project files

.dockerignore

@@ -16,3 +16,4 @@ __pycache__/
 examples/
 
 venv/
+data/

.gitignore

@@ -9,3 +9,4 @@ __pycache__/
 .vscode/
 
 venv/
+data

Dockerfile

@@ -4,8 +4,8 @@
 FROM docker.io/python:3.12.1-slim-bookworm
 
 LABEL org.opencontainers.image.authors="FNNDSC <[email protected]>" \
-      org.opencontainers.image.title="Multiple image registration" \
-      org.opencontainers.image.description="A ChRIS plugin to do multiple image registration"
+      org.opencontainers.image.title="Images registration" \
+      org.opencontainers.image.description="A ChRIS plugin to do image registration"
 
 ARG SRCDIR=/usr/local/src/pl-images-register
 WORKDIR ${SRCDIR}

archives/Trash/README.md

@@ -0,0 +1,177 @@
+# _ChRIS_ Plugin Template
+
+[![test status](https://github.com/FNNDSC/python-chrisapp-template/actions/workflows/src.yml/badge.svg)](https://github.com/FNNDSC/python-chrisapp-template/actions/workflows/src.yml)
+[![MIT License](https://img.shields.io/github/license/FNNDSC/python-chrisapp-template)](LICENSE)
+
+This is a minimal template repository for _ChRIS_ plugin applications in Python.
+
+## About _ChRIS_ Plugins
+
+A _ChRIS_ plugin is a scientific data-processing software which can run anywhere all-the-same:
+in the cloud via a [web app](https://github.com/FNNDSC/ChRIS_ui/), or on your own laptop
+from the terminal. They are easy to build and easy to understand: most simply, a
+_ChRIS_ plugin is a command-line program which processes data from an input directory
+and creates data to an output directory with the usage
+`commandname [options...] inputdir/ outputdir/`.
+
+For more information, visit our website https://chrisproject.org
+
+## How to Use This Template
+
+Go to https://github.com/FNNDSC/python-chrisapp-template and click "Use this template".
+The newly created repository is ready to use right away.
+
+A script `bootstrap.sh` is provided to help fill in and rename values for your new project.
+It is optional to use.
+
+1. Edit the variables in `bootstrap.sh`
+2. Run `./bootstrap.sh`
+3. Follow the instructions it will print out
+
+## Example Plugins
+
+Here are some good, complete examples of _ChRIS_ plugins created from this template.
+
+- https://github.com/FNNDSC/pl-dcm2niix (basic command wrapper example)
+- <https://github.com/FNNDSC/pl-adapt_object_mesh> (parallelizes a command)
+- https://github.com/FNNDSC/pl-mri-preview (uses [NiBabel](https://nipy.org/nibabel/))
+- https://github.com/FNNDSC/pl-pyvista-volume (example using Python package project structure and pytest)
+- https://github.com/FNNDSC/pl-fetal-cp-surface-extract (has a good README.md)
+
+## What's Inside
+
+| Path                       | Purpose                                                                                                                                                                                                  |
+|----------------------------|----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
+| `app.py`                   | Main script: start editing here!                                                                                                                                                                         |
+| `tests/`                   | Unit tests                                                                                                                                                                                               |
+| `setup.py`                 | [Python project metadata and installation script](https://packaging.python.org/en/latest/guides/distributing-packages-using-setuptools/#setup-py)                                                        |
+| `requirements.txt`         | List of Python dependencies                                                                                                                                                                              |
+| `Dockerfile`               | [Container image build recipe](https://docs.docker.com/engine/reference/builder/)                                                                                                                        |
+| `.github/workflows/ci.yml` | "continuous integration" using [Github Actions](https://docs.github.com/en/actions/learn-github-actions/understanding-github-actions): automatic testing, building, and uploads to https://chrisstore.co |
+
+## Contributing
+
+The source code for the `main` branch of this repository is on the
+[src](https://github.com/fnndsc/python-chrisapp-template/tree/src)
+branch, which has an additional file
+[`.github/workflows/src.yml`](https://github.com/FNNDSC/python-chrisapp-template/blob/src/.github/workflows/src.yml)
+When tests pass, changes are automatically merged into `main`.
+Developers should commit to or make pull requests targeting `src`.
+Do not push directly to `main`.
+
+This is a workaround in order to do automatic testing of this template
+without including the `.github/workflows/src.yml` file in the template itself.
+
+<!-- BEGIN README TEMPLATE
+
+# ChRIS Plugin Title
+
+[![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)
+[![ci](https://github.com/FNNDSC/pl-appname/actions/workflows/ci.yml/badge.svg)](https://github.com/FNNDSC/pl-appname/actions/workflows/ci.yml)
+
+`pl-appname` is a [_ChRIS_](https://chrisproject.org/)
+_ds_ plugin which takes in ...  as input files and
+creates ... as output files.
+
+## Abstract
+
+...
+
+## Installation
+
+`pl-appname` is a _[ChRIS](https://chrisproject.org/) plugin_, meaning it can
+run from either within _ChRIS_ or the command-line.
+
+## Local Usage
+
+To get started with local command-line usage, use [Apptainer](https://apptainer.org/)
+(a.k.a. Singularity) to run `pl-appname` as a container:
+
+```shell
+apptainer exec docker://fnndsc/pl-appname commandname [--args values...] input/ output/
+```
+
+To print its available options, run:
+
+```shell
+apptainer exec docker://fnndsc/pl-appname commandname --help
+```
+
+## Examples
+
+`commandname` requires two positional arguments: a directory containing
+input data, and a directory where to create output data.
+First, create the input directory and move input data into it.
+
+```shell
+mkdir incoming/ outgoing/
+mv some.dat other.dat incoming/
+apptainer exec docker://fnndsc/pl-appname:latest commandname [--args] incoming/ outgoing/
+```
+
+## Development
+
+Instructions for developers.
+
+### Building
+
+Build a local container image:
+
+```shell
+docker build -t localhost/fnndsc/pl-appname .
+```
+
+### Running
+
+Mount the source code `app.py` into a container to try out changes without rebuild.
+
+```shell
+docker run --rm -it --userns=host -u $(id -u):$(id -g) \
+    -v $PWD/app.py:/usr/local/lib/python3.12/site-packages/app.py:ro \
+    -v $PWD/in:/incoming:ro -v $PWD/out:/outgoing:rw -w /outgoing \
+    localhost/fnndsc/pl-appname commandname /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-appname:dev --build-arg extras_require=dev .
+docker run --rm -it localhost/fnndsc/pl-appname: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-appname:1.2.3 .
+docker push docker.io/fnndsc/pl-appname: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-appname:1.2.3 chris_plugin_info -d docker.io/fnndsc/pl-appname: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
+
+END README TEMPLATE -->

archives/Trash/app.py

@@ -0,0 +1,70 @@
+#!/usr/bin/env python
+
+from pathlib import Path
+from argparse import ArgumentParser, Namespace, ArgumentDefaultsHelpFormatter
+
+from chris_plugin import chris_plugin, PathMapper
+
+__version__ = '1.0.0'
+
+DISPLAY_TITLE = r"""
+ChRIS Plugin Template Title
+"""
+
+
+parser = ArgumentParser(description='!!!CHANGE ME!!! An example ChRIS plugin which '
+                                    'counts the number of occurrences of a given '
+                                    'word in text files.',
+                        formatter_class=ArgumentDefaultsHelpFormatter)
+parser.add_argument('-w', '--word', required=True, type=str,
+                    help='word to count')
+parser.add_argument('-p', '--pattern', default='**/*.txt', type=str,
+                    help='input file filter glob')
+parser.add_argument('-V', '--version', action='version',
+                    version=f'%(prog)s {__version__}')
+
+
+# The main function of this *ChRIS* plugin is denoted by this ``@chris_plugin`` "decorator."
+# Some metadata about the plugin is specified here. There is more metadata specified in setup.py.
+#
+# documentation: https://fnndsc.github.io/chris_plugin/chris_plugin.html#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):
+    """
+    *ChRIS* plugins usually have two positional arguments: an **input directory** containing
+    input files and an **output directory** where to write output files. Command-line arguments
+    are passed to this main method implicitly when ``main()`` is called below without parameters.
+
+    :param options: non-positional arguments parsed by the parser given to @chris_plugin
+    :param inputdir: directory containing (read-only) input files
+    :param outputdir: directory where to write output files
+    """
+
+    print(DISPLAY_TITLE)
+
+    # Typically it's easier to think of programs as operating on individual files
+    # rather than directories. The helper functions provided by a ``PathMapper``
+    # object make it easy to discover input files and write to output files inside
+    # the given paths.
+    #
+    # Refer to the documentation for more options, examples, and advanced uses e.g.
+    # adding a progress bar and parallelism.
+    mapper = PathMapper.file_mapper(inputdir, outputdir, glob=options.pattern, suffix='.count.txt')
+    for input_file, output_file in mapper:
+        # The code block below is a small and easy example of how to use a ``PathMapper``.
+        # It is recommended that you put your functionality in a helper function, so that
+        # it is more legible and can be unit tested.
+        data = input_file.read_text()
+        frequency = data.count(options.word)
+        output_file.write_text(str(frequency))
+
+
+if __name__ == '__main__':
+    main()

archives/Trash/qodana.yaml

@@ -0,0 +1,29 @@
+#-------------------------------------------------------------------------------#
+#               Qodana analysis is configured by qodana.yaml file               #
+#             https://www.jetbrains.com/help/qodana/qodana-yaml.html            #
+#-------------------------------------------------------------------------------#
+version: "1.0"
+
+#Specify inspection profile for code analysis
+profile:
+  name: qodana.starter
+
+#Enable inspections
+#include:
+#  - name: <SomeEnabledInspectionId>
+
+#Disable inspections
+#exclude:
+#  - name: <SomeDisabledInspectionId>
+#    paths:
+#      - <path/where/not/run/inspection>
+
+#Execute shell command before Qodana execution (Applied in CI/CD pipeline)
+#bootstrap: sh ./prepare-qodana.sh
+
+#Install IDE plugins before Qodana execution (Applied in CI/CD pipeline)
+#plugins:
+#  - id: <plugin.id> #(plugin id can be found at https://plugins.jetbrains.com)
+
+#Specify Qodana linter for analysis (Applied in CI/CD pipeline)
+linter: jetbrains/qodana-python:latest

archives/Trash/requirements.txt

@@ -0,0 +1 @@
+chris_plugin==0.4.0

archives/Trash/setup.py

@@ -0,0 +1,48 @@
+from setuptools import setup
+import re
+
+_version_re = re.compile(r"(?<=^__version__ = (\"|'))(.+)(?=\"|')")
+
+def get_version(rel_path: str) -> str:
+    """
+    Searches for the ``__version__ = `` line in a source code file.
+
+    https://packaging.python.org/en/latest/guides/single-sourcing-package-version/
+    """
+    with open(rel_path, 'r') as f:
+        matches = map(_version_re.search, f)
+        filtered = filter(lambda m: m is not None, matches)
+        version = next(filtered, None)
+        if version is None:
+            raise RuntimeError(f'Could not find __version__ in {rel_path}')
+        return version.group(0)
+
+
+setup(
+    name='chris-plugin-template',
+    version=get_version('archives/Trash/app.py'),
+    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',
+    entry_points={
+        'console_scripts': [
+            'commandname = app:main'
+        ]
+    },
+    classifiers=[
+        'License :: OSI Approved :: MIT License',
+        'Topic :: Scientific/Engineering',
+        'Topic :: Scientific/Engineering :: Bio-Informatics',
+        'Topic :: Scientific/Engineering :: Medical Science Apps.'
+    ],
+    extras_require={
+        'none': [],
+        'dev': [
+            'pytest~=7.1'
+        ]
+    }
+)

archives/Trash/tests/test_example.py

@@ -0,0 +1,21 @@
+from pathlib import Path
+
+from archives.Trash.app import parser, main
+
+
+def test_main(tmp_path: Path):
+    # setup example data
+    inputdir = tmp_path / 'incoming'
+    outputdir = tmp_path / 'outgoing'
+    inputdir.mkdir()
+    outputdir.mkdir()
+    (inputdir / 'plaintext.txt').write_text('hello ChRIS, I am a ChRIS plugin')
+
+    # simulate run of main function
+    options = parser.parse_args(['--word', 'ChRIS', '--pattern', '*.txt'])
+    main(options, inputdir, outputdir)
+
+    # assert behavior is expected
+    expected_output_file = outputdir / 'plaintext.count.txt'
+    assert expected_output_file.exists()
+    assert expected_output_file.read_text() == '2'