updated docs

FNNDSC · Oct 24, 2023 · 8ff2faf · 8ff2faf
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diff --git a/README.md b/README.md
@@ -1,115 +1,47 @@
-# _ChRIS_ Plugin Template
+# pl-dicom_filter
 
-[![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)
+[![Version](https://img.shields.io/docker/v/fnndsc/pl-dicom_filter?sort=semver)](https://hub.docker.com/r/fnndsc/pl-dicom_filter)
+[![MIT License](https://img.shields.io/github/license/fnndsc/pl-dicom_filter)](https://github.com/FNNDSC/pl-dicom_filter/blob/main/LICENSE)
+[![ci](https://github.com/FNNDSC/pl-dicom_filter/actions/workflows/ci.yml/badge.svg)](https://github.com/FNNDSC/pl-dicom_filter/actions/workflows/ci.yml)
 
-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.
+`pl-dicom_filter` is a [_ChRIS_](https://chrisproject.org/)
+_ds_ plugin which takes in DICOM files in its input directory and filters DICOMs that 
+matches a specified criteria into its output directory.
 
 ## Abstract
 
-...
+A ChRIS plugin to filter dicoms using filters on dicom tags.
 
 ## Installation
 
-`pl-appname` is a _[ChRIS](https://chrisproject.org/) plugin_, meaning it can
+`pl-dicom_filter` is a _[ChRIS](https://chrisproject.org/) plugin_, meaning it can
 run from either within _ChRIS_ or the command-line.
 
-[![Get it from chrisstore.co](https://raw.githubusercontent.com/FNNDSC/ChRIS_store_ui/963938c241636e4c3dc4753ee1327f56cb82d8b5/src/assets/public/badges/light.svg)](https://chrisstore.co/plugin/pl-appname)
-
 ## 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:
+(a.k.a. Singularity) to run `pl-dicom_filter` as a container:
 
 ```shell
-apptainer exec docker://fnndsc/pl-appname commandname [--args values...] input/ output/
+apptainer exec docker://fnndsc/pl-dicom_filter dicom_filter [--args values...] input/ output/
 ```
 
 To print its available options, run:
 
 ```shell
-apptainer exec docker://fnndsc/pl-appname commandname --help
+apptainer exec docker://fnndsc/pl-dicom_filter dicom_filter --help
 ```
 
 ## Examples
 
-`commandname` requires two positional arguments: a directory containing
+`dicom_unpack` 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/
+apptainer exec docker://fnndsc/pl-dicom_filter:latest dicom_filter [--args] incoming/ outgoing/
 ```
 
 ## Development
@@ -121,18 +53,18 @@ Instructions for developers.
 Build a local container image:
 
 ```shell
-docker build -t localhost/fnndsc/pl-appname .
+docker build -t localhost/fnndsc/pl-dicom_unpack .
 ```
 
 ### Running
 
-Mount the source code `dicom_filter.py` into a container to try out changes without rebuild.
+Mount the source code `dicom_unpack.py` into a container to try out changes without rebuild.
 
 ```shell
 docker run --rm -it --userns=host -u $(id -u):$(id -g) \
     -v $PWD/dicom_filter.py:/usr/local/lib/python3.11/site-packages/dicom_filter.py:ro \
     -v $PWD/in:/incoming:ro -v $PWD/out:/outgoing:rw -w /outgoing \
-    localhost/fnndsc/pl-appname commandname /incoming /outgoing
+    localhost/fnndsc/pl-dicom_filter dicom_filter /incoming /outgoing
 ```
 
 ### Testing
@@ -142,8 +74,8 @@ 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
+docker build -t localhost/fnndsc/pl-dicom_filter:dev --build-arg extras_require=dev .
+docker run --rm -it localhost/fnndsc/pl-dicom_filter:dev pytest
 ```
 
 ## Release
@@ -160,17 +92,19 @@ Increase the version number in `setup.py` and commit this file.
 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
+docker build -t docker.io/fnndsc/pl-dicom_filter:1.2.3 .
+docker push docker.io/fnndsc/pl-dicom_filter: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 a _ChRIS Store_.
+to produce a JSON description of this plugin, which can be uploaded to _ChRIS_.
 
 ```shell
-docker run --rm localhost/fnndsc/pl-appname:dev chris_plugin_info > chris_plugin_info.json
+docker run --rm docker.io/fnndsc/pl-dicom_filter:1.2.3 chris_plugin_info -d docker.io/fnndsc/pl-dicom_filter:1.2.3 > chris_plugin_info.json
 ```
 
-END README TEMPLATE -->
+Instructions on how to upload the plugin to _ChRIS_ can be found here:
+https://chrisproject.org/docs/tutorials/upload_plugin
+