Merge pull request #83 from BrainLesion/82-update-readme-to-new-brain…

…les-standard

82 update readme to new brainles standard

.readthedocs.yaml

@@ -14,7 +14,7 @@ build:
       # https://python-poetry.org/docs/managing-dependencies/#dependency-groups
       # VIRTUAL_ENV needs to be set manually for now.
       # See https://github.com/readthedocs/readthedocs.org/pull/11152/
-      - VIRTUAL_ENV=$READTHEDOCS_VIRTUALENV_PATH poetry install --with docs
+      - VIRTUAL_ENV=$READTHEDOCS_VIRTUALENV_PATH poetry install --with docs --all-extras
 
 sphinx:
   configuration: docs/source/conf.py

README.md

@@ -1,9 +1,13 @@
-[![PyPI version preprocessing](https://badge.fury.io/py/brainles-preprocessing.svg)](https://pypi.python.org/pypi/brainles-preprocessing/)
-[![Documentation Status](https://readthedocs.org/projects/brainles-preprocessing/badge/?version=latest)](http://brainles-preprocessing.readthedocs.io/?badge=latest)
-[![tests](https://github.com/BrainLesion/preprocessing/actions/workflows/tests.yml/badge.svg)](https://github.com/BrainLesion/preprocessing/actions/workflows/tests.yml)
 
 
 # BrainLes-Preprocessing
+[![Python Versions](https://img.shields.io/pypi/pyversions/brainles-preprocessing)](https://pypi.org/project/brainles-preprocessing/)
+[![Stable Version](https://img.shields.io/pypi/v/brainles-preprocessing?label=stable)](https://pypi.python.org/pypi/brainles-preprocessing/)
+[![Documentation Status](https://readthedocs.org/projects/brainles-preprocessing/badge/?version=latest)](http://brainles-preprocessing.readthedocs.io/?badge=latest)
+[![tests](https://github.com/BrainLesion/preprocessing/actions/workflows/tests.yml/badge.svg)](https://github.com/BrainLesion/preprocessing/actions/workflows/tests.yml)
+<!-- [![codecov](https://codecov.io/gh/BrainLesion/brainles-preprocessing/graph/badge.svg?token=A7FWUKO9Y4)](https://codecov.io/gh/BrainLesion/brainles-preprocessing) -->
+<!-- [![License](https://img.shields.io/badge/License-Apache%202.0-blue.svg)](https://opensource.org/licenses/Apache-2.0) -->
+
 `BrainLes preprocessing` is a comprehensive tool for preprocessing tasks in biomedical imaging, with a focus on (but not limited to) multi-modal brain MRI. It can be used to build to build modular preprocessing pipelines:
 
 This includes **normalization**, **co-registration**, **atlas registration** and **skulstripping / brain extraction**.
@@ -25,11 +29,20 @@ pip install brainles-preprocessing
 
 
 ## Usage
-Please have a look at our [Jupyter Notebook tutorials](https://github.com/BrainLesion/tutorials/tree/main/preprocessing) illustrating the usage of BrainLes preprocessing.
+A minimal example can be found following these badges:  
+[![nbviewer](https://raw.githubusercontent.com/jupyter/design/master/logos/Badges/nbviewer_badge.svg)](https://nbviewer.org/github/BrainLesion/tutorials/blob/main/preprocessing/preprocessing_tutorial.ipynb)
+<a target="_blank" href="https://colab.research.google.com/github/BrainLesion/tutorials/blob/main/preprocessing/preprocessing_tutorial.ipynb">
+  <img src="https://colab.research.google.com/assets/colab-badge.svg" alt="Open In Colab"/>
+</a>
+
+
+For further information please have a look at our [Jupyter Notebook tutorials](https://github.com/BrainLesion/tutorials/tree/main/preprocessing) illustrating the usage of BrainLes preprocessing.
 
 
 <!-- TODO citation -->
 
+## Documentation
+We provide a (WIP) documentation. Have a look [here](https://brainles-preprocessing.readthedocs.io/en/latest/?badge=latest)
 
 ## FAQ
 Please credit the authors by citing their work.

docs/source/registration.rst

@@ -8,7 +8,19 @@ registration.registrator
 .. automodule:: brainles_preprocessing.registration.registrator
 
 
+registration.ANTs
+--------------------------------------
+
+.. automodule:: brainles_preprocessing.registration.ANTs.ANTs
+
+
+registration.eReg
+--------------------------------------
+
+.. automodule:: brainles_preprocessing.registration.eReg.eReg
+
+
 registration.niftyreg
 --------------------------------------
 
-.. automodule:: brainles_preprocessing.registration.niftyreg
+.. automodule:: brainles_preprocessing.registration.niftyreg.niftyreg