Merge pull request #13 from MEDomicsLab/dev

Changed documentation links

Author: MahdiAll99

README.md

@@ -5,7 +5,7 @@
 [![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/)
 [![PyPI - version](https://img.shields.io/badge/pypi-v0.9.8-blue)](https://pypi.org/project/medimage-pkg/)
 [![Continuous Integration](https://github.com/MEDomicsLab/MEDiml/actions/workflows/python-app.yml/badge.svg)](https://github.com/MEDomicsLab/MEDiml/actions/workflows/python-app.yml)
-[![Documentation Status](https://readthedocs.org/projects/medimage/badge/?version=latest)](https://medimage.readthedocs.io/en/latest/?badge=latest)
+[![Documentation Status](https://readthedocs.org/projects/medimage/badge/?version=latest)](https://mediml.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)
 
@@ -41,10 +41,10 @@ You can easily install the ``MEDiml`` package from PyPI using:
 pip install MEDiml
 ```
 
-For more installation options (Conda, Poetry...) check out the [installation documentation](https://medimage.readthedocs.io/en/latest/Installation.html).
+For more installation options (Conda, Poetry...) check out the [installation documentation](https://mediml.readthedocs.io/en/latest/Installation.html).
 
 ## 3. Generating the documentation locally
-The [documentation](https://medimage.readthedocs.io/en/latest/) of the MEDiml package was created using Sphinx. However, you can generate and host it locally by compiling the documentation source code using :
+The [documentation](https://mediml.readthedocs.io/en/latest/) of the MEDiml package was created using Sphinx. However, you can generate and host it locally by compiling the documentation source code using :
 
 ```
 cd docs
@@ -99,7 +99,7 @@ med_obj.save_radiomics(
 
 ## 5. Tutorials
 
-We have created many [tutorial notebooks](https://github.com/MEDomicsLab/MEDiml/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/MEDomicsLab/MEDiml/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://mediml.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:

notebooks/demo/Glioma-Demo.ipynb

@@ -30,7 +30,7 @@
    "source": [
     "## Introduction\n",
     "\n",
-    "We assume that you now understand the usage of most parts of the package. If that's not the case, we invite you to take a look at the available tutorials [here](https://medimage.readthedocs.io/en/latest/tutorials.html).\n",
+    "We assume that you now understand the usage of most parts of the package. If that's not the case, we invite you to take a look at the available tutorials [here](https://mediml.readthedocs.io/en/latest/tutorials.html).\n",
     "\n",
     "This is a final notebook that demonstrates the usage of the ``MEDimage`` package for one scan. It is a final demo that shows in a brief way the flexibility and the versatility of the code in radiomics analysis. We will use a **[glioma TCGA](https://www.cancer.gov/about-nci/organization/ccg/research/structural-genomics/tcga)** cancer scan.\n",
     "\n",

notebooks/tutorial/BatchExtractor-Tutorial.ipynb

@@ -35,7 +35,7 @@
     "This notebook is a tutorial of radiomics batch extraction using the *MEDimage* package and specifically the ``BatchExtractor`` class. For this task, the ``BatchExtractor`` class is the main object used to order scans and prepare batches and run processing and features extraction. The class extracts all type of family features and organizes the results in json files and csv tables.\n",
     "\n",
     "\n",
-    "In a nutshell, This tutorial will help you learn everything you need about batch extraction in the *MEDimage package*. We also advise you to read the [class documentation](https://medimage.readthedocs.io/en/documentation/biomarkers.html#module-MEDimage.biomarkers.BatchExtractor) before starting to test it."
+    "In a nutshell, This tutorial will help you learn everything you need about batch extraction in the *MEDimage package*. We also advise you to read the [class documentation](https://mediml.readthedocs.io/en/documentation/biomarkers.html#module-MEDimage.biomarkers.BatchExtractor) before starting to test it."
    ]
   },
   {

notebooks/tutorial/DataManager-Tutorial.ipynb

@@ -566,7 +566,7 @@
     "\n",
     "<img src=\"images/DataManagerClassDiagram.png\"/>\n",
     "\n",
-    "We will go through all the functionalities of the ``DataManager`` class. For more details about the class please refer to the [DataManager documentation](https://medimage.readthedocs.io/en/documentation/wrangling.html#module-MEDimage.wrangling.DataManager)"
+    "We will go through all the functionalities of the ``DataManager`` class. For more details about the class please refer to the [DataManager documentation](https://mediml.readthedocs.io/en/documentation/wrangling.html#module-MEDimage.wrangling.DataManager)"
    ]
   },
   {

notebooks/tutorial/Learning-Tutorial.ipynb

@@ -137,7 +137,7 @@
    "source": [
     "### Setting up and running the experiment\n",
     "\n",
-    "The learning module also uses multiple JSON configuration files to set the parameters of the learning process. Details about the configuration files, are available here: https://medimage.readthedocs.io/en/learning/configurations_file.html#learning."
+    "The learning module also uses multiple JSON configuration files to set the parameters of the learning process. Details about the configuration files, are available here: https://mediml.readthedocs.io/en/learning/configurations_file.html#learning."
    ]
   },
   {

notebooks/tutorial/MEDscan-Tutorial.ipynb

@@ -417,7 +417,7 @@
     "\n",
     "<img src=\"images/MEDimageClassDiagram.png\"/>\n",
     "\n",
-    "For more details about the class please refer to the [*MEDimage* documentation](https://medimage.readthedocs.io/en/latest/)"
+    "For more details about the class please refer to the [*MEDimage* documentation](https://mediml.readthedocs.io/en/latest/)"
    ]
   },
   {
@@ -942,7 +942,7 @@
    "id": "93d9e8da",
    "metadata": {},
    "source": [
-    "You can update every class attribute value using the right class methods for that (check the class diagram above or the [*MEDimage* documentation](https://medimage.readthedocs.io/en/latest/))"
+    "You can update every class attribute value using the right class methods for that (check the class diagram above or the [*MEDimage* documentation](https://mediml.readthedocs.io/en/latest/))"
    ]
   }
  ],

pyproject.toml

@@ -7,12 +7,16 @@ license = "GPL-3.0"
 readme = "README.md"
 homepage = "https://mediml.app/"
 repository = "https://github.com/MEDomicsLab/MEDiml/"
+documentation = "https://mediml.readthedocs.io/"
 keywords = ["python", "ibsi", "medical-imaging", 
             "cancer-imaging-research", "radiomics", 
             "medical-image-analysis", "features-extraction", 
             "radiomics-extraction", "radiomics-features", "radiomics-analysis"]
 packages = [ {include = "MEDiml"} ]
 
+[tool.poetry.urls]
+"Bug Tracker" = "https://github.com/MEDomicsLab/MEDiml/issues"
+
 [tool.poetry.dependencies]
 python = ">=3.8.0,<=3.10"
 numpy = "*"

setup.py

@@ -22,7 +22,7 @@
     long_description_content_type="text/markdown",
     url="https://github.com/MEDomicsLab/MEDiml",
     project_urls={
-        'Documentation': 'https://medimage.readthedocs.io/en/latest/index.html',
+        'Documentation': 'https://mediml.readthedocs.io/en/latest/index.html',
         'Github': 'https://github.com/MEDomicsLab/MEDiml'
     },
     classifiers=[