Bump for pypi versioning (#124)

* Bump for pypi versioning

* Change authors

* Update abstract readme and authorship

* Update badge to general DOI

CITATION.cff

@@ -3,31 +3,13 @@
 
 cff-version: 1.2.0
 title: >-
-  Paradigma: Toolbox for Digital Biomarkers in Parkinson's
-  Disease
+  ParaDigMa: Parkinson's Disease Digital Markers Toolbox
 message: >-
   If you use this software, please cite it using the
   metadata from this file.
 type: software
 authors:
-  - given-names: Peter
-    family-names: Kok
-    email: p.kok@esciencecenter.nl
-    affiliation: Netherlands eScience Center
-    orcid: 'https://orcid.org/0000-0002-6630-7326'
-  - given-names: Vedran
-    family-names: Kasalica
-    email: v.kasalica@esciencecenter.nl
-    affiliation: Netherlands eScience Center
-    orcid: 'https://orcid.org/0000-0002-0097-1056'
-  - given-names: Luc J.W.
-    family-names: Evers
-    email: luc.evers@radboudumc.nl
-    affiliation: >-
-      Radboud University, Nijmegen, Netherlands; Radboud
-      University Medical Center, Nijmegen, Netherlands
-    orcid: 'https://orcid.org/0000-0002-8241-5087'
-  - given-names: Erik
+- given-names: Erik
     family-names: Post
     email: erik.post@radboudumc.nl
     affiliation: >-
@@ -53,26 +35,41 @@ authors:
       Center for Engineering, Modeling and Applied Social
       Sciences (CECS), Federal University of ABC (UFABC),
       Brazil
+  - given-names: Vedran
+    family-names: Kasalica
+    email: v.kasalica@esciencecenter.nl
+    affiliation: Netherlands eScience Center
+    orcid: 'https://orcid.org/0000-0002-0097-1056'
+  - given-names: Peter
+    family-names: Kok
+    email: p.kok@esciencecenter.nl
+    affiliation: Netherlands eScience Center
+    orcid: 'https://orcid.org/0000-0002-6630-7326'
+  - given-names: Luc J.W.
+    family-names: Evers
+    email: luc.evers@radboudumc.nl
+    affiliation: >-
+      Radboud University, Nijmegen, Netherlands; Radboud
+      University Medical Center, Nijmegen, Netherlands
+    orcid: 'https://orcid.org/0000-0002-8241-5087'
 repository-code: 'https://github.com/biomarkersParkinson/paradigma'
 url: 'https://biomarkersparkinson.github.io/paradigma/'
 abstract: >-
-  Paradigma: Digital Biomarkers for Parkinson's Disease
-  Toolbox is a Python software package designed for
-  processing wearable sensor data to identify digital
-  biomarkers associated with Parkinson’s disease (PD). The
-  toolbox facilitates the detection and analysis of sensor
-  data, focusing on key gait and photoplethysmography (PPG)
-  features that are critical for PD research. By leveraging
-  the Time Series Data Format (TSDF), a unified and
-  user-friendly format for handling both numerical data and
-  metadata, Paradigma simplifies the process of working with
-  raw binary sensor measurements alongside JSON-based
-  metadata. The toolbox enables researchers to efficiently
-  extract PD biomarkers, aiding in early diagnosis and
-  monitoring. Future updates will introduce tremor detection
-  and expanded feature extraction capabilities, further
-  enhancing its utility for PD research and clinical
-  applications.
+  The Parkinsons Disease Digital Markers (ParaDigMa) toolbox is a Python
+  software package designed for processing passively collected wrist 
+  sensor data to extract digital measures of motor and non-motor signs
+  of Parkinson's disease (PD).  
+  
+  Specifically, the toolbox contains three data processing pipelines: 
+  (1) arm swing during gait, (2) tremor, and (3) heart rate analysis.
+  Furthermore, the toolbox contains general functionalities for signal
+  processing and feature extraction, such as filtering, peak detection,
+  and spectral analysis. The toolbox is designed to be user-friendly and
+  modular, enabling researchers to easily extend the toolbox with new
+  algorithms and functionalities. The toolbox is accompanied by a set of
+  example scripts and notebooks for each domain that demonstrate how to use
+  the toolbox for processing sensor data and extracting digital measures.
+
 keywords:
   - parkinson's disease
   - digital biomarkers

README.md

@@ -5,22 +5,31 @@
 | Badges | |
 |:----:|----|
 | **Packages and Releases** | [![Latest release](https://img.shields.io/github/release/biomarkersparkinson/paradigma.svg)](https://github.com/biomarkersparkinson/paradigma/releases/latest) [![PyPI](https://img.shields.io/pypi/v/paradigma.svg)](https://pypi.python.org/pypi/paradigma/)  [![Static Badge](https://img.shields.io/badge/RSD-paradigma-lib)](https://research-software-directory.org/software/paradigma) |
-| **DOI** | [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.13838393.svg)](https://doi.org/10.5281/zenodo.13838393) |
+| **DOI** | [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.13838392.svg)](https://doi.org/10.5281/zenodo.13838392) |
 | **Build Status** | [![](https://img.shields.io/badge/python-3.10+-blue.svg)](https://www.python.org/downloads/) [![Build and test](https://github.com/biomarkersParkinson/paradigma/actions/workflows/build-and-test.yml/badge.svg)](https://github.com/biomarkersParkinson/paradigma/actions/workflows/build-and-test.yml) [![pages-build-deployment](https://github.com/biomarkersParkinson/paradigma/actions/workflows/pages/pages-build-deployment/badge.svg)](https://github.com/biomarkersParkinson/paradigma/actions/workflows/pages/pages-build-deployment) |
 | **License** |  [![GitHub license](https://img.shields.io/github/license/biomarkersParkinson/paradigma)](https://github.com/biomarkersparkinson/paradigma/blob/main/LICENSE) |
 <!-- | **Fairness** |  [![fair-software.eu](https://img.shields.io/badge/fair--software.eu-%E2%97%8F%20%20%E2%97%8F%20%20%E2%97%8F%20%20%E2%97%8F%20%20%E2%97%8F-green)](https://fair-software.eu) [![OpenSSF Best Practices](https://bestpractices.coreinfrastructure.org/projects/8083/badge)](https://www.bestpractices.dev/projects/8083) | --> 
 
 ## Introduction
-ParaDigMa is a Python package for processing time series data of wrist-worn sensors to quantify signs of Parkinson’s disease (PD). It contains functionalities for processing the following sensor types:
+The Parkinsons Disease Digital Markers (ParaDigMa) toolbox is a Python
+software package designed for processing passively collected wrist 
+sensor data to extract digital measures of motor and non-motor signs
+of Parkinson's disease (PD).  
+
+Specifically, the toolbox contains three data processing pipelines: 
+(1) arm swing during gait, (2) tremor, and (3) heart rate analysis.
+Furthermore, the toolbox contains general functionalities for signal
+processing and feature extraction, such as filtering, peak detection,
+and spectral analysis. The toolbox is designed to be user-friendly and
+modular, enabling researchers to easily extend the toolbox with new
+algorithms and functionalities. The toolbox is accompanied by a set of
+example scripts and notebooks for each domain that demonstrate how to use
+the toolbox for processing sensor data and extracting digital measures.
+
+It contains functionalities for processing the following sensor types:
 
 - Inertial Measurement Units (accelerometer, gyroscope)
--  Photoplethysmogram (PPG)
-
-And analyses of the following motor and non-motor domains:
-
-- Gait
-- Tremor
-- Heart Rate
+- Photoplethysmogram (PPG)
 
 ## More about ParaDigMa
 The components of ParaDigMa are visually shown in the diagram below.
@@ -97,7 +106,8 @@ Interested in contributing? Check out the contributing guidelines. Please note t
 
 ## License
 
-ParaDigMa was created by Peter Kok, Vedran Kasalica, Erik Post, Kars Veldkamp, Nienke Timmermans, Diogo Coutinho Soriano, Luc Evers. It is licensed under the terms of the Apache License 2.0 license.
+The core team of ParaDigMa consists of Erik Post, Kars Veldkamp, Nienke Timmermans, Diogo Coutinho Soriano, Luc Evers, 
+Peter Kok and Vedran Kasalica. Advisors to the project are Max Little, Jordan Raykov, Twan van Laarhoven, Hayriye Cagnan, and Bas Bloem. It is licensed under the terms of the Apache License 2.0 license.
 
 ## Credits
 

docs/conf.py

@@ -7,9 +7,9 @@
 # -- Project information -----------------------------------------------------
 
 project = "paradigma"
-copyright = "2023, Erik Post, Kars Veldkamp, Nienke Timmermans, Peter Kok, Vedran Kasalica, Diogo Coutinho Soriano, Luc Evers"
+copyright = "2025, Erik Post, Kars Veldkamp, Nienke Timmermans, Diogo Coutinho Soriano, Vedran Kasalica, Peter Kok, and Luc Evers"
 author = (
-    "Erik Post, Kars Veldkamp, Nienke Timmermans, Peter Kok, Vedran Kasalica, Diogo Coutinho Soriano, Luc Evers"
+    "Erik Post, Kars Veldkamp, Nienke Timmermans, Diogo Coutinho Soriano, Vedran Kasalica, Peter Kok, and Luc Evers"
 )
 
 # -- General configuration ---------------------------------------------------

pyproject.toml

@@ -1,14 +1,15 @@
 [tool.poetry]
 name = "paradigma"
-version = "0.4.0"
+version = "0.4.1"
 description = "Paradigma - a toolbox for Digital Biomarkers for Parkinson's Disease"
-authors = [ "Peter Kok <p.kok@esciencecenter.nl>",
+authors = [ "Erik Post <erik.post@radboudumc.nl>",
+            "Kars Veldkamp <kars.veldkamp@radboudumc.nl>",
+            "Nienke Timmermans <nienke.timmermans@radboudumc.nl>",
+            "Diogo Soriano",
             "Vedran Kasalica <v.kaslica@esciencecenter.nl>",
-            "Erik Post",
-            "Kars Veldkamp",
-            "Nienke Timmermans",
-            "Diogo Coutinho Soriano",
-            "Luc Evers" ]
+            "Peter Kok <p.kok@esciencecenter.nl>",
+            "Luc Evers <luc.evers@radboudumc.nl>",
+            ]
 license = "Apache License 2.0"
 readme = "README.md"