Merge pull request #2 from MEDomics-UdeS/dev

Links and Git Actions update

README.md

@@ -1,14 +1,13 @@
 <div align="center">
 
-<img src="https://raw.githubusercontent.com/MahdiAll99/MEDimage/dev/docs/figures/MEDimageLogo.png" style="width:150px;"/>
+<img src="https://raw.githubusercontent.com/MEDomics-UdeS/MEDimage/dev/docs/figures/MEDimageLogo.png" style="width:150px;"/>
 
 [![PyPI - Python Version](https://img.shields.io/badge/python-3.8%20|%203.9%20|%203.10-blue)](https://www.python.org/downloads/release/python-380/)
 [![TestPyPI - version](https://img.shields.io/badge/pypi-v0.2.0-blue)](https://test.pypi.org/project/medimage-pkg/0.2.0/)
-[![Continuous Integration](https://github.com/MahdiAll99/MEDimage/actions/workflows/python-app.yml/badge.svg)](https://github.com/MahdiAll99/MEDimage/actions/workflows/python-app.yml)
-[![Upload Python Package](https://github.com/MahdiAll99/MEDimage/actions/workflows/python-publish.yml/badge.svg)](https://github.com/MahdiAll99/MEDimage/actions/workflows/python-publish.yml)
+[![Continuous Integration](https://github.com/MEDomics-UdeS/MEDimage/actions/workflows/python-app.yml/badge.svg)](https://github.com/MEDomics-UdeS/MEDimage/actions/workflows/python-app.yml)
 [![Documentation Status](https://readthedocs.org/projects/medimage/badge/?version=latest)](https://medimage.readthedocs.io/en/latest/?badge=latest)
 [![License: GPL-3](https://img.shields.io/badge/license-GPLv3-blue)](LICENSE)
-[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/MahdiAll99/MEDimage/blob/main/notebooks/tutorial/DataManager-Tutorial.ipynb)
+[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/MEDomics-UdeS/MEDimage/blob/main/notebooks/tutorial/DataManager-Tutorial.ipynb)
 
 </div>
 
@@ -28,18 +27,18 @@
 ## 1. Introduction
 MEDimage is an open-source Python package that can be used for processing multi-modal medical images (MRI, CT or PET) and for extracting their radiomic features. This package is meant to facilitate the processing of medical images and the subsequent computation of all types of radiomic features while maintaining the reproducibility of analyses. This package has been standardized with the [IBSI](https://theibsi.github.io/) norms.
 
-![MEDimage overview](https://raw.githubusercontent.com/MahdiAll99/MEDimage/main/docs/figures/pakcage-overview.png)
+![MEDimage overview](https://raw.githubusercontent.com/MEDomics-UdeS/MEDimage/main/docs/figures/pakcage-overview.png)
 
 
 ## 2. Installation
 
 ### Python installation
-The MEDimage package requires *Python 3.8* or more. If you don't have it installed on your machine, follow the instructions [here](https://github.com/MahdiAll99/MEDimage/blob/main/python.md) to install it.
+The MEDimage package requires *Python 3.8* or more. If you don't have it installed on your machine, follow the instructions [here](https://github.com/MEDomics-UdeS/MEDimage/blob/main/python.md) to install it.
 
 ### Package installation
 You can easily install the ``MEDimage`` package from PyPI using:
 ```
-pip install MEDimage
+pip install medimage-pkg
 ```
 
 For more installation options (Conda, Poetry...) check out the [installation documentation](https://medimage.readthedocs.io/en/latest/Installation.html).
@@ -100,22 +99,22 @@ med_obj.save_radiomics(
 
 ## 5. Tutorials
 
-We have created many [tutorial notebooks](https://github.com/MahdiAll99/MEDimage/tree/main/notebooks) to assist you in learning how to use the different parts of the package. More details can be found in the [documentation](https://medimage.readthedocs.io/en/latest/tutorials.html).
+We have created many [tutorial notebooks](https://github.com/MEDomics-UdeS/MEDimage/tree/main/notebooks) to assist you in learning how to use the different parts of the package. More details can be found in the [documentation](https://medimage.readthedocs.io/en/latest/tutorials.html).
 
 ## 6. IBSI Standardization
 The image biomarker standardization initiative ([IBSI](https://theibsi.github.io)) is an independent international collaboration that aims to standardize the extraction of image biomarkers from acquired imaging. The IBSI therefore seeks to provide image biomarker nomenclature and definitions, benchmark datasets, and benchmark values to verify image processing and image biomarker calculations, as well as reporting guidelines, for high-throughput image analysis. We participate in this collaboration with our package to make sure it respects international nomenclatures and definitions. The participation was separated into two chapters:
 
   - ### IBSI Chapter 1
-      [The IBSI chapter 1](https://theibsi.github.io/ibsi1/) is dedicated to the standardization of commonly used radiomic features. It was initiated in September 2016 and reached completion in March 2020. We have created two [jupyter notebooks](https://github.com/MahdiAll99/MEDimage/tree/main/notebooks/ibsi) for each phase of the chapter and made them available for the users to run the IBSI tests for themselves. The tests can also be explored in interactive Colab notebooks that are directly accessible here:
+      [The IBSI chapter 1](https://theibsi.github.io/ibsi1/) is dedicated to the standardization of commonly used radiomic features. It was initiated in September 2016 and reached completion in March 2020. We have created two [jupyter notebooks](https://github.com/MEDomics-UdeS/MEDimage/tree/main/notebooks/ibsi) for each phase of the chapter and made them available for the users to run the IBSI tests for themselves. The tests can also be explored in interactive Colab notebooks that are directly accessible here:
       
-      - **Phase 1**: [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/MahdiAll99/MEDimage/blob/main/notebooks/ibsi/ibsi1p1.ipynb)
-      - **Phase 2**: [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/MahdiAll99/MEDimage/blob/main/notebooks/ibsi/ibsi1p2.ipynb)
+      - **Phase 1**: [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/MEDomics-UdeS/MEDimage/blob/main/notebooks/ibsi/ibsi1p1.ipynb)
+      - **Phase 2**: [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/MEDomics-UdeS/MEDimage/blob/main/notebooks/ibsi/ibsi1p2.ipynb)
 
   - ### IBSI Chapter 2 (In progress)
-      [The IBSI chapter 2](https://theibsi.github.io/ibsi2/) was launched in June 2020 and is still in progress. It is dedicated to the standardization of commonly used imaging filters in radiomic studies. We have created two [jupyter notebooks](https://github.com/MahdiAll99/MEDimage/tree/main/notebooks/ibsi) for each phase of the chapter and made them available for the users to run the IBSI tests for themselves and validate image filtering and image biomarker calculations from filter response maps. The tests can also be explored in interactive Colab notebooks that are directly accessible here: 
+      [The IBSI chapter 2](https://theibsi.github.io/ibsi2/) was launched in June 2020 and is still in progress. It is dedicated to the standardization of commonly used imaging filters in radiomic studies. We have created two [jupyter notebooks](https://github.com/MEDomics-UdeS/MEDimage/tree/main/notebooks/ibsi) for each phase of the chapter and made them available for the users to run the IBSI tests for themselves and validate image filtering and image biomarker calculations from filter response maps. The tests can also be explored in interactive Colab notebooks that are directly accessible here: 
 
-      - **Phase 1**: [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/MahdiAll99/MEDimage/blob/main/notebooks/ibsi/ibsi2p1.ipynb)
-      - **Phase 2**: [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/MahdiAll99/MEDimage/blob/main/notebooks/ibsi/ibsi2p2.ipynb)
+      - **Phase 1**: [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/MEDomics-UdeS/MEDimage/blob/main/notebooks/ibsi/ibsi2p1.ipynb)
+      - **Phase 2**: [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/MEDomics-UdeS/MEDimage/blob/main/notebooks/ibsi/ibsi2p2.ipynb)
 
       Our team at *UdeS* (a.k.a. Université de Sherbrooke) has already submitted the benchmarked values to the [IBSI uploading website](https://ibsi.radiomics.hevs.ch/).
 
@@ -177,4 +176,4 @@ Here's what the license entails:
 9. The software author or license can not be held liable for any damages inflicted by the software.
 ```
 
-More information on about the [LICENSE can be found here](https://github.com/MahdiAll99/MEDimage/blob/main/LICENSE.md)
+More information on about the [LICENSE can be found here](https://github.com/MEDomics-UdeS/MEDimage/blob/main/LICENSE.md)

docs/Installation.rst

@@ -11,7 +11,7 @@ Install via pip
 ---------------
 ``MEDimage`` is available on PyPi for installation via ``pip`` which allows you to install the package in one step ::
 
-    pip install MEDimage
+    pip install medimage-pkg
 
 Install from source
 -------------------