update

.github/workflows/python-publish.yml

@@ -0,0 +1,39 @@
+# This workflow will upload a Python Package using Twine when a release is created
+# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python#publishing-to-package-registries
+
+# This workflow uses actions that are not certified by GitHub.
+# They are provided by a third-party and are governed by
+# separate terms of service, privacy policy, and support
+# documentation.
+
+name: Upload Python Package
+
+on:
+  release:
+    types: [published]
+
+permissions:
+  contents: read
+
+jobs:
+  deploy:
+
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v3
+    - name: Set up Python
+      uses: actions/setup-python@v3
+      with:
+        python-version: '3.x'
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install build
+    - name: Build package
+      run: python -m build
+    - name: Publish package
+      uses: pypa/gh-action-pypi-publish@27b31702a0e7fc50959f5ad993c78deac1bdfc29
+      with:
+        user: __token__
+        password: ${{ secrets.PYPI_API_TOKEN }}

.readthedocs.yaml

@@ -0,0 +1,24 @@
+# Required
+version: 2
+
+# Set the OS, Python version and other tools you might need
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.12"
+  jobs:
+    pre_create_environment:
+      - asdf plugin add poetry
+      - asdf install poetry latest
+      - asdf global poetry latest
+      - poetry config virtualenvs.create false
+    post_install:
+      - poetry install --with dev
+
+# Build documentation in the "docs/" directory with Sphinx
+sphinx:
+  configuration: docs/conf.py
+
+submodules:
+  include: all  # Include all submodules, if any
+  recursive: true

README.md

@@ -1,52 +1,35 @@
 # ElikoPy
 
+[![Documentation Status](https://readthedocs.org/projects/elikopy/badge/?version=latest)](https://elikopy.readthedocs.io/en/latest/?badge=latest) [![PyPI](https://img.shields.io/pypi/v/elikopy?label=pypi%20package)](https://pypi.org/project/elikopy//) ![GitHub repo size](https://img.shields.io/github/repo-size/Hyedryn/elikopy) [![DOI](https://zenodo.org/badge/296056994.svg)](https://zenodo.org/doi/10.5281/zenodo.10514465)
 
-ElikoPy is Python library aiming at easing the processing of diffusion imaging for microstructural analysis. 
-This Python library is based on
-  - DIPY, a python library for the analysis of MR diffusion imaging.
-  - Microstructure fingerprinting, a python library doing estimation of white matter microstructural properties from a dictionary of Monte Carlo diffusion MRI fingerprints.
-  - FSL, a comprehensive library of analysis tools for FMRI, MRI and DTI brain imaging data.
-  - DIAMOND, a c software that is characterizing brain tissue by assessment of the distribution of anisotropic microstructural environments in diffusion‐compartment imaging.
+ElikoPy is a Python library designed to simplify the processing of diffusion imaging for microstructural analysis.
 
-### Installation
+## Installation
 
-ElikoPy requires [Python](https://www.python.org/) v3.8+ to run.
+### Prerequistes
 
-After cloning the repo, you can either firstly install all the python dependencies including optionnal dependency used to speed up the code:
+ElikoPy requires [Python](https://www.python.org/) v3.8+.
 
-```sh
-$ pip install -r requirements.txt --user
-```
-Or you can install directly the library with only the mandatory dependencies (if you performed the previous step, you still need to perform this step):
-
-```sh
-$ python3 -m pip install .
-```
+### Installation Steps
 
-Microstructure Fingerprinting is currently not avaible in the standard python repo, you can clone and install this library manually.
+Clone the repository and install the dependencies:
 
 ```sh
-$ git clone git@github.com:rensonnetg/microstructure_fingerprinting.git
-$ cd microstructure_fingerprinting
-$ python setup.py install
+git clone https://github.com/Hyedryn/elikopy.git
+cd elikopy
+python -m pip install .
 ```
 
-FSL also needs to be installed and availabe in our path if you want to perform mouvement correction or tbss.
-
-Unfortunatly, the DIAMOND code is not publically available. If you do not have it in your possesion, you will not be able to use this algorithm. If you have it, simply add the executable to your path. 
-
-### Usage
-
-Todo
+If you wish to use movement correction or TBSS, ensure FSL is installed and available in your path.
 
-### Development
+**Note:** The DIAMOND microstructural model is not publicly available. If you have it, add the executable to your path. Otherwise, you won't be able to use this algorithm.
 
-Want to contribute? Great!
+## Development
 
-Do not hesitate to open issue or pull request!
-### Todos
+Interested in contributing? Wonderful!
 
- - Release a complete and accurate documentation for the library
+Feel free to open issues or pull requests. Your contributions are welcome!
 
+## Publications & Citations
 
-**Free Software, Hell Yeah!**
+If you use ElikoPy in your research, please cite it using the package DOI [![DOI](https://zenodo.org/badge/296056994.svg)](https://zenodo.org/doi/10.5281/zenodo.10514465).

docs/conf.py

@@ -13,9 +13,8 @@
 autodoc_mock_imports = ['torch']
 import os
 import sys
-sys.path.insert(0, os.path.abspath('..'))
+sys.path.insert(0, os.path.abspath('../elikopy'))
 
-import elikopy
 import sphinx_rtd_theme
 
 
@@ -36,8 +35,10 @@
 extensions = [
     'sphinx_rtd_theme',
     'sphinx.ext.autodoc',
+    'sphinx_autodoc_typehints',
 ]
 
+
 # Add any paths that contain templates here, relative to this directory.
 templates_path = ['_templates']
 

elikopy/__init__.py

@@ -3,11 +3,6 @@
 import elikopy.utils
 import elikopy.utilsSynb0Disco
 import elikopy.registration
-try:
-    import elikopy.mouse
-except ImportError as e:
-    elikopy.mouse = None
-    print("Mouse module not available: {}".format(e))
 
 
 try: