autogaita 0.0.5__tar.gz → 0.1.0__tar.gz

autogaita-0.1.0/PKG-INFO

@@ -0,0 +1,23 @@
+Metadata-Version: 2.1
+Name: autogaita
+Version: 0.1.0
+Summary: Automatic Gait Analysis in Python
+Home-page: https://github.com/mahan-hosseini/AutoGaitA/
+Author: Mahan Hosseini
+License: GPLv3
+Requires-Python: >=3.10
+License-File: LICENSE
+Requires-Dist: customtkinter>=5.2
+Requires-Dist: pandas>=2.0
+Requires-Dist: numpy>=1.24
+Requires-Dist: matplotlib>=3.7
+Requires-Dist: scikit-learn>=1.2
+Requires-Dist: pingouin>=0.5
+Requires-Dist: scipy>=1.11
+Requires-Dist: ffmpeg-python>=0.2
+Requires-Dist: openpyxl>=3.1
+Requires-Dist: pillow>=10.3
+Requires-Dist: pyobjc
+Provides-Extra: dev
+Requires-Dist: pytest; extra == "dev"
+Requires-Dist: hypothesis; extra == "dev"

{autogaita-0.0.5 → autogaita-0.1.0}/README.md

@@ -1,6 +1,11 @@
 ![AutoGaitA](https://github.com/mahan-hosseini/AutoGaitA/blob/main/res/autogaita_logo.png?raw=true)
-![Python](https://img.shields.io/badge/python-v3.6+-blue.svg)
-![License: GPL v3](https://img.shields.io/badge/License-GPLv3-blue.svg)
+![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)
+[![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 🐸
 
@@ -13,17 +18,18 @@
 
 ***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)***
 
-It is strongly recommended that a separate virtual environment for AutoGaitA is created via
-
-`python -m venv env_gaita`
+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):
 
-After creating and activating the virtual environment, AutoGaitA can be installed via pip
+- Create the virtual environment
+    - `python -m venv env_gaita`
 
-`pip install autogaita`
+- After creation, activate the virtual environment via:
+    - *Windows:* `env_gaita\Scripts\activate`
+    - *Mac:* `source env_gaita/bin/activate`
 
-The main user interface can then be accessed via
+- Once activated, install AutoGaitA in the virtual environment via pip: `pip install autogaita`.
 
-`python -m autogaita`
+- Access the main user interface via `python -m autogaita`.
 
 ## Tutorials and Examples
 
@@ -31,6 +37,8 @@ The main user interface can then be accessed via
 
 **[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.
 
@@ -54,9 +62,13 @@ 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)
 
+## Reference
+If you use this code or data please [cite our preprint](https://www.biorxiv.org/content/10.1101/2024.04.14.589409v1).
+
 ## License
+AutoGaitA is licensed under [GPL v3.0](https://github.com/mahan-hosseini/AutoGaitA/blob/main/LICENSE) and Forschungszentrum Jülich GmbH holds all copyrights. 
 
-AutoGaitA is licensed under [GPL v3.0](https://github.com/mahan-hosseini/AutoGaitA/blob/main/LICENSE) and Forschungszentrum Jülich GmbH holds all copyrights.
+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

autogaita-0.1.0/autogaita/__init__.py

@@ -0,0 +1,20 @@
+# main gui
+from .autogaita import gui  # autogaita.gui()
+
+# 3 sub-guis
+from .autogaita_dlc_gui import dlc_gui  # autogaita.dlc_gui()
+from .autogaita_simi_gui import simi_gui  # autogaita.simi_gui()
+from .autogaita_group_gui import group_gui  # autogaita.group_gui()
+
+# 3 main functions
+from .autogaita_dlc import dlc  # autogaita.dlc(info, folderinfo, cfg)
+from .autogaita_simi import simi  # autogaita.simi(info, folderinfo, cfg)
+from .autogaita_group import group  # autogaita.group(folderinfo, cfg)
+
+# 6 batchrun functions - call via e.g. autogaita.dlc_singlerun()
+from .batchrun_scripts.autogaita_dlc_singlerun import dlc_singlerun
+from .batchrun_scripts.autogaita_dlc_multirun import dlc_multirun
+from .batchrun_scripts.autogaita_simi_singlerun import simi_singlerun
+from .batchrun_scripts.autogaita_simi_multirun import simi_multirun
+from .batchrun_scripts.autogaita_group_dlcrun import group_dlcrun
+from .batchrun_scripts.autogaita_group_simirun import group_simirun

{autogaita-0.0.5 → autogaita-0.1.0}/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
@@ -124,7 +123,7 @@ def configure_the_icon(root):
         try:
             from Cocoa import NSApplication, NSImage
         except ImportError:
-            print('Unable to import pyobjc modules')
+            print("Unable to import pyobjc modules")
         else:
             with resources.path("autogaita", "autogaita_icon.icns") as icon_path:
                 ns_application = NSApplication.sharedApplication()