diff --git a/README.md b/README.md index fd6599c..09acf8a 100644 --- 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) -- (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. - - +Instructions on how to upload the plugin to _ChRIS_ can be found here: +https://chrisproject.org/docs/tutorials/upload_plugin +