Preparation for release 2.0.0

jdiedrichsen · jdiedrichsen · commit 4cf95db40063 · 2025-10-26T11:28:00.000-04:00
diff --git a/.readthedocs.yaml b/.readthedocs.yaml
@@ -9,7 +9,7 @@ version: 2
 build:
   os: ubuntu-20.04
   tools:
-    python: "3.9"
+    python: "3.10"
 
 # Build documentation in the docs/ directory with Sphinx
 sphinx:
diff --git a/AUTHORS.rst b/AUTHORS.rst
@@ -8,20 +8,22 @@ the diedrichsenlab lab at `Western University <http://www.diedrichsenlab.org//>`
 
 .. _core_devs:
 
-Core developers
-...............
+Developers
+..........
 
-The SUITPy core developers are:
+Contributors to SUITPy include:
 
-*Joern Diedrichsen
+*Jörn Diedrichsen
 *Maedbh King
 *Da Zhi
-
-Other contributors:
-
+*Ladan Shahshahani
+*Yao Li
 *Carlos Hernandez-Castillo
 *Suzanne Witt
-*Ladan Shahshahani
+*Bassel Arafat
+*Caroline Nettekoven
+*Yaping Wang
+
 
 .. _citing:
 
diff --git a/CITATION.cff b/CITATION.cff
@@ -11,6 +11,6 @@ authors:
   given-names: "Da"
   orcid: "https://orcid.org/0000-0001-6023-6523"
 title: "SUIT: A Python-based toolbox for cerebellar imaging analysis"
-version: 1.3.0
-date-released: 2023-10-08
+version: 2.0.0
+date-released: 2025-10-26
 url: "https://github.com/DiedrichsenLab/SUITPy"
diff --git a/README.rst b/README.rst
@@ -16,14 +16,17 @@ Dependencies
 
 The required dependencies to use the software are:
 
-* python >= 3.6
+* python >= 3.10,
 * setuptools
-* numpy >= 1.16
-* nibabel >= 2.5
-* pandas >= 0.24
-* matplotlib >= 1.5.1
-* scipy >=1.0
+* numpy >= 1.22.0
+* nibabel >= 3.2.1
+* pandas >= 2.0.0
+* matplotlib >= 3.5.0
+* plotly >= 5.10.0
+* scipy >= 1.9.0
 * neuroimagingtools >= 1.1.1
+* antspyx >= 0.6.1
+* torch >= 2.0.0
 
 Install
 -------
diff --git a/SUITPy/__init__.py b/SUITPy/__init__.py
@@ -3,7 +3,7 @@
 """
 import gzip
 
-__version__ = '1.3.2'
+__version__ = '2.0.0'
 
 from .atlas import (fetch_atlas)
 
diff --git a/SUITPy/templates/tpl-MNI152NLin2009cSymC_T1w.nii b/SUITPy/templates/tpl-MNI152NLin2009cSymC_T1w.nii
diff --git a/SUITPy/templates/tpl-MNI152NLin6AsymC_T1w.nii b/SUITPy/templates/tpl-MNI152NLin6AsymC_T1w.nii
diff --git a/docs/source/index.rst b/docs/source/index.rst
@@ -1,12 +1,9 @@
-.. SUITPy documentation master file, created by
-   sphinx-quickstart on Tue Aug 11 12:46:22 2020.
-   You can adapt this file completely to your liking, but it should at least
-   contain the root `toctree` directive.
+.. SUITPy documentation master file
 
 SUITPy Documentation
 ====================
-SUITPy is a Python toolbox dedicated to the analysis of imaging data of the human cerebellum. It provides a subset of the SUIT toolbox for Matlab (https://github.com/jdiedrichsen/suit).
-Currently, only mapping of volume data to the flatmap and display of the flatmap are implemented.
+SUITPy is a Python toolbox for the analysis of imaging data from the human cerebellum. With the new version 2 release it will have most of the functionality of the SUIT toolbox for Matlab (https://github.com/jdiedrichsen/suit).
+The newest developments will be implemented in the Python version.
 
 .. toctree::
    :maxdepth: 1
@@ -30,19 +27,19 @@ Important links
 
 Acknowledgements
 ----------------
-SUITPy is developed by the Diedrichsenlab and collaborators, Carlos Hernandez-Castillo, Yao Li
-
+SUITPy is developed by the Diedrichsenlab and collaborators, including
+Carlos Hernandez-Castillo, Yao Li, Yaping Wang, Bassel Arafat, Caroline Nettekoven, Ladan Shahshahani, Da Zhi, Maedbh King, Jorn Diedrichsen, and many others.
 
+Funding for this work was provided by:
 
 .. image::
-   images/CIHR.png
+   images/RCP.png
    :width: 200 px
 
 .. image::
-   images/RCP.png
+   images/CIHR.png
    :width: 200 px
 
-
 Indices and tables
 ------------------
 
diff --git a/docs/source/install.rst b/docs/source/install.rst
@@ -12,12 +12,11 @@ The required dependencies to use the software are:
 * nibabel >= 3.2.1
 * pandas >= 2.0.0
 * matplotlib >= 3.5.0
+* plotly >= 5.10.0
 * scipy >= 1.9.0
 * neuroimagingtools >= 1.1.1
 * antspyx >= 0.6.1
-* torch >= 2.5.0
-
-(It is highly recommended to use the latest version of PyTorch as new generations of GPU (50 series, etc.) use the sm_120 CUDA architecture which is not compatible with older versions.)
+* torch >= 2.0.0
 
 Install over pip
 ----------------
diff --git a/docs/source/isolate.rst b/docs/source/isolate.rst
@@ -28,10 +28,11 @@ The optional input parameters are
 
     --T1: T1w- image
     --T2: Additional (or standalone T2w image)
-    --result_folder dir:
-    --brain_mask Mask_image: Binary mask image from skull stripping step to improve affine normalization
-    --template template: Templa] [--params PARAMS] [--save_cropped_files] [--save_transform]
-
+    --result_folder: Folder to save the results (default: current folder)
+    --brain_mask: Binary mask image from skull stripping step to improve affine normalization (optional)
+    --template: Template for affine normalization
+    --save_cropped_files: Save the images cropped and resampled to the UNet window
+    --save_transform: Save the affine transformation matrix
 
 
 Architecture
diff --git a/docs/source/normalize.rst b/docs/source/normalize.rst
@@ -1,5 +1,5 @@
 Normalization Module
 ====================
 
-The normalization module of the SUIT toolbox calculates a deformation field that maps the cerebellum of an individual subject to the SUIT template, using the mask generated by the isolation module. The Pysthon-version uses the ANTSPy package to perform the normalization. The deformation field can then be used to reslice functional and anatomical data into SUIT space.
+The normalization module of the SUIT toolbox calculates a deformation field that maps the cerebellum of an individual subject to the SUIT template, using the mask generated by the isolation module. The Python-version uses the ANTSPy package to perform the normalization and will be released with version 2.1. The deformation field can then be used to reslice functional and anatomical data into SUIT space.
 
diff --git a/setup.py b/setup.py
@@ -14,7 +14,7 @@
     'https://suitpy.readthedocs.io/en/latest/install.html#installation')
 
 REQUIRED_MODULE_METADATA = ['numpy>=1.22.0',
-                            'nibabel>=3.5.0',
+                            'nibabel>=3.2.1',
                             'neuroimagingtools>=1.1.1',
                             'requests>=2',
                             'scipy>=1.9.0',
@@ -24,7 +24,7 @@
                             'joblib>=1.2.0',
                             'scipy>=1.9.0',
                             'antspyx>=0.6.1',
-                            'torch>=2.5.0',]
+                            'torch>=2.2.0',]
 
 def is_installing():
     # Allow command-lines such as "python setup.py build install"
@@ -34,11 +34,11 @@ def is_installing():
 # Make sources available using relative paths from this file's directory.
 os.chdir(os.path.dirname(os.path.abspath(__file__)))
 
-DESCRIPTION = 'Mapping and plotting cerebellar fMRI data in Python'
+DESCRIPTION = 'Analysis toolbox for cerebellar fMRI data in Python'
 with open('README.rst') as fp:
     LONG_DESCRIPTION = fp.read()
-DOWNLOAD_URL = 'https://github.com/DiedrichsenLab/SUITPy/archive/refs/tags/v.1.3.3.tar.gz'
-VERSION = '1.3.3'
+DOWNLOAD_URL = 'https://github.com/DiedrichsenLab/SUITPy/archive/refs/tags/v.2.0.0.tar.gz'
+VERSION = '2.0.0'
 
 if __name__ == "__main__":
 
@@ -63,11 +63,9 @@ def is_installing():
               'Operating System :: POSIX',
               'Operating System :: Unix',
               'Operating System :: MacOS',
-              'Programming Language :: Python :: 3.6',
-              'Programming Language :: Python :: 3.7',
-              'Programming Language :: Python :: 3.8',
-              'Programming Language :: Python :: 3.9',
               'Programming Language :: Python :: 3.10',
+              'Programming Language :: Python :: 3.11',
+              'Programming Language :: Python :: 3.12'
           ],
           packages=find_packages(),
           package_data={
