autogaita 0.0.6__tar.gz → 0.2.0__tar.gz

{autogaita-0.0.6 → autogaita-0.2.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: autogaita
-Version: 0.0.6
+Version: 0.2.0
 Summary: Automatic Gait Analysis in Python
 Home-page: https://github.com/mahan-hosseini/AutoGaitA/
 Author: Mahan Hosseini

{autogaita-0.0.6 → autogaita-0.2.0}/README.md

@@ -1,8 +1,11 @@
 ![AutoGaitA](https://github.com/mahan-hosseini/AutoGaitA/blob/main/res/autogaita_logo.png?raw=true)
-[![PyPI version](https://badge.fury.io/py/autogaita.svg)](https://badge.fury.io/py/autogaita)
+![Repository Active](https://www.repostatus.org/badges/latest/active.svg)
 [![Test AutoGaitA](https://github.com/mahan-hosseini/AutoGaitA/actions/workflows/auto_test_gaita.yml/badge.svg)](https://github.com/mahan-hosseini/AutoGaitA/actions/workflows/auto_test_gaita.yml)
 ![Python](https://img.shields.io/badge/python-v3.10+-blue.svg)
-![License: GPL v3](https://img.shields.io/badge/License-GPLv3-blue.svg)
+[![PyPI - Version](https://img.shields.io/pypi/v/autogaita)](https://pypi.org/project/autogaita/)
+![license: GPL v3](https://img.shields.io/badge/license-GPLv3-blue.svg)
+[![paper: biorxiv](https://img.shields.io/badge/paper-biorxiv-blue)](https://doi.org/10.1101/2024.04.14.589409) 
+
 ![Black](https://img.shields.io/badge/code%20style-black-000000.svg)
 # Automated Gait Analysis in Python 🐸
 
@@ -13,7 +16,7 @@
 
 ## Getting Started
 
-***Note!** Our documentation provides step-by-step walkthroughs of how to install autogaita for **[Windows](https://docs.google.com/document/d/1Y4wrrsjs0ybLDKPzE2LAatqPDq9jtwjIuk4M0jRZ3wE/edit#heading=h.28j6wu2vamre)** and **[Mac](https://docs.google.com/document/d/1Y4wrrsjs0ybLDKPzE2LAatqPDq9jtwjIuk4M0jRZ3wE/edit)***
+***Note!** [Our documentation](https://docs.google.com/document/d/1Y4wrrsjs0ybLDKPzE2LAatqPDq9jtwjIuk4M0jRZ3wE/edit?usp=sharing) provides step-by-step walkthroughs of how to install autogaita for **[Windows](https://docs.google.com/document/d/1Y4wrrsjs0ybLDKPzE2LAatqPDq9jtwjIuk4M0jRZ3wE/edit#heading=h.28j6wu2vamre)** and **[Mac](https://docs.google.com/document/d/1Y4wrrsjs0ybLDKPzE2LAatqPDq9jtwjIuk4M0jRZ3wE/edit)***
 
 It is strongly recommended that a separate virtual environment for AutoGaitA is created (note that the approach below creates the virtual environment to your current directory):
 
@@ -28,19 +31,23 @@ It is strongly recommended that a separate virtual environment for AutoGaitA is
 
 - Access the main user interface via `python -m autogaita`.
 
+- To update to the latest release (see the *Releases* panel on the right for the current version) activate your virtual environment & enter `pip install autogaita -U`. 
+
 ## Tutorials and Examples
 
 ### Video Walkthrough Tutorials
 
 **[The AutoGaitA YouTube Channel](https://youtube.com/playlist?list=PLCn5T7K_H8K56NIcEsfDK664OP7cN_Bad&si=mV5p2--nYvbofkPh) provides tutorials for file preparation and instructions on how to use AutoGaitA**
 
+*Please note that tutorial videos might not always reflect the most up-to-date version of our toolbox, especially in the beginning when things are regularly changing. We will make sure to record new videos whenever there are major changes, though.*
+
 ### Example Data
 We provide an example dataset in the **example data** folder of this repository, with a set of mice walking over differently wide beams and both the beam as well as body coordinates being tracked with DLC. Note that this dataset was used in our tutorial videos introducing *AutoGaitA_DLC*, *AutoGaitA_Group* and in our video explaining file preparation for *AutoGaitA_DLC*.  We further provide a **group** folder there that can be used alongside the *AutoGaitA_Group* tutorial to confirm that users generate the same set of results following our instructions.
 
 ### Annotation Table Examples and Templates
 Annotation Table example and template files for *AutoGaitA_DLC* and *AutoGaitA_Simi* can be found in the [**annotation tables**](https://github.com/mahan-hosseini/AutoGaitA/tree/main/annotation%20tables) folder of this repository.
 
-Users are advised to read the ***important note*** of that folder, use the template to enter their data's timestamp information and to then compare the resulting table with our example to check formatting.
+Users are advised to read the ***important note*** of that folder, use the template to enter their data's timestamp information and to then compare the resulting table with our example to check formatting. Users working with ImageJ/FIJI are encouraged to check out the [AnnotationTable-Plugin](https://github.com/luca-flemming/AnnotationTable-Plugin) developed by our contributor Luca Flemming.
 
 ## Documentation
 
@@ -57,6 +64,9 @@ By default, *AutoGaitA DLC* and *AutoGaitA Simi* implement standard values for m
 - [Documentation - AutoGaitA DLC](https://docs.google.com/document/d/1Y4wrrsjs0ybLDKPzE2LAatqPDq9jtwjIuk4M0jRZ3wE/edit#heading=h.20bg7b7ymt0b)
 - [Documentation - AutoGaitA Simi](https://docs.google.com/document/d/1Y4wrrsjs0ybLDKPzE2LAatqPDq9jtwjIuk4M0jRZ3wE/edit#heading=h.uz61bpmua7qz)
 
+## Analysing other behaviours - AutoCyclA 🚴
+Even though AutoGaitA's main focus is to automate and standardise gait analyses, our toolbox can be used to automate the analyses of any rhythmic behaviour of interest. For a proof-of-principle demonstration and an introduction of the general workflow of such analyses, see **[AutoCyclA - Automated Cycling Analysis with AutoGaitA.](https://github.com/mahan-hosseini/AutoGaitA/tree/main/autocycla)**
+
 ## Reference
 If you use this code or data please [cite our preprint](https://www.biorxiv.org/content/10.1101/2024.04.14.589409v1).
 
@@ -66,4 +76,14 @@ AutoGaitA is licensed under [GPL v3.0](https://github.com/mahan-hosseini/AutoGai
 The AutoGaitA software is provided without warranty of any kind, express or implied, including, but not limited to, the implied warranty of fitness for a particular purpose.
 
 ## Authors
-Mahan Hosseini
+[Mahan Hosseini](https://github.com/mahan-hosseini)
+
+## Contributors
+[Luca Flemming](https://github.com/luca-flemming) - Undergraduate Student
+
+[Nicholas del Grosso](https://github.com/nickdelgrosso) - RSE Advisor
+
+## Contributing
+If you would like to contribute to the AutoGaitA toolbox, feel free to open a pull request or contact us at autogaita@fz-juelich.de! 
+
+We are looking forward to your input and ideas 😊

{autogaita-0.0.6 → autogaita-0.2.0}/autogaita/autogaita.py

@@ -6,7 +6,6 @@ from PIL import Image, ImageTk
 from importlib import resources
 import platform
 
-
 # %% global constants
 TXT_COLOR = "#ffffff"  # white
 FONT_SIZE = 20