Update library requirements.txt

README.md

@@ -1,11 +1,12 @@
 # JAX Animal Behavior System (JABS)
 
 ## ReadTheDocs Tutorial
+
 https://jabs-tutorial.readthedocs.io/en/latest/index.html
 
 ## Copyright
 
-Copyright 2021 The Jackson Laboratory -- All rights reserved.
+Copyright 2023 The Jackson Laboratory -- All rights reserved.
 
 ## Contact
 
@@ -24,10 +25,10 @@ training data and prediction output, are forthcoming.
 ## Pose Files
 
 JABS requires pose files generated from the Kumar Lab's mouse pose 
-estimation neural network. Contact us for more information.
+estimation neural networks. Single mouse pose files are generated from [this repository](https://github.com/KumarLabJax/deep-hrnet-mouse). Multi-mouse is still under development. Contact us for more information.
 
 ## Requirements
-Developed and tested on Python 3.7, 3.8, and 3.9. See the `requirements.txt` 
+Developed and tested on Python 3.10. See the `requirements.txt` 
 for a list of required Python packages. These packages are available from the 
 Python Package Index (PyPI)
 
@@ -66,17 +67,6 @@ The virtual environment can be deactivated if you no longer need it:
 deactivate
 ```
 
-### Installing on Apple M1/M2 Silicone
-
-To install the app on Apple's newer M1/M2 macbooks, the user needs to install via [anaconda](https://www.anaconda.com/download#macos)
-using the following instructions:
-
-```commandline
-conda env create -n jabs -f environment_jabs.yml
-conda activate jabs 
-python app.py 
-```
-
 #### Enabling XGBoost Classifier
 
 The XGBoost Classifier has a dependency on the OpenMP library. This does
@@ -87,7 +77,7 @@ can't use Homebrew, but this is beyond the scope of this Readme.
 
 ### Windows
 
-Make sure that a compatible version of Python is installed (3.7, 3.8, or 3.9).
+Make sure that a compatible version of Python is installed (3.10).
 
 #### Windows Scripts
 
@@ -123,3 +113,8 @@ directory and run the following commands:
 jabs.venv\Scripts\activate.bat
 python app.py
 ```
+
+### Singularity/Linux
+
+We supply a tested pair of singularity definition files. The [first vm](vm/behavior-classifier-vm.def) is indended for command-line use on compute clusters when scaling inferences. The [second vm](vm/behavior-classifier-gui-vm.def) is designed for interacting with the GUI in a portable environment. Please inspect the definition files for related linux packages to run the software.
+

app.py

@@ -6,12 +6,7 @@
 import argparse
 import sys
 
-#### For Mac M1 compatibility ######
-import os
-os.environ['QT_MAC_WANTS_LAYER'] = '1'
-####################################
-
-from PySide2 import QtWidgets
+from PySide6 import QtWidgets
 
 from src import APP_NAME, APP_NAME_LONG
 from src.ui import MainWindow
@@ -36,7 +31,7 @@ def main():
     main_window.show()
     if main_window.show_license_dialog() == QtWidgets.QDialog.Accepted:
         # user accepted license terms, run the main application loop
-        sys.exit(app.exec_())
+        sys.exit(app.exec())
 
     # user rejected license terms
     sys.exit(1)

requirements.txt

@@ -1,18 +1,18 @@
-h5py==3.1.0
-joblib==1.0.1
-markdown2==2.4.2
-numpy==1.21
-opencv-python-headless==4.5.1.48
-pip-licenses==3.3.1
+h5py==3.9.0
+joblib==1.3.1
+markdown2==2.4.9
+numpy==1.25
+opencv-python-headless==4.8.0.74
+pip-licenses==4.3.2
 PTable==0.9.2
-PySide2==5.15.2
+PySide6==6.2.4
 PyYAML==6.0
-scikit-learn==0.24.1
-scipy==1.6.1
-Shapely==1.7.1
-shiboken2==5.15.2
-six==1.14.0
-tabulate==0.8.8
-threadpoolctl==2.1.0
-unittest-xml-reporting==3.0.2
-xgboost==1.2.1
+scikit-learn==1.3.0
+scipy==1.11.1
+Shapely==2.0.1
+shiboken6==6.2.4
+six==1.16.0
+tabulate==0.9.0
+threadpoolctl==3.2.0
+unittest-xml-reporting==3.2.0
+xgboost==1.7.6

src/classifier/classifier.py

@@ -20,7 +20,7 @@
 from src.project import TrackLabels
 from src.project import ProjectDistanceUnit
 
-_VERSION = 3
+_VERSION = 4
 
 
 class ClassifierType(IntEnum):

src/feature_extraction/features.py

@@ -13,7 +13,7 @@
 from .landmark_features import LandmarkFeatureGroup
 
 
-FEATURE_VERSION = 4
+FEATURE_VERSION = 5
 
 _FEATURE_MODULES = [
     BaseFeatureGroup,

src/project/project.py

@@ -158,7 +158,7 @@ def __init__(self, project_path, use_cache=True, enable_video_check=True):
             pose_versions.append(get_pose_file_major_version(pose_path))
             static_object_sets.append(set(get_static_objects_in_file(pose_path)))
         self._min_pose_version = min(pose_versions) if len(pose_versions) else 0
-        self._supported_static_objects = set.intersection(*static_object_sets)
+        self._supported_static_objects = set.intersection(*static_object_sets) if len(static_object_sets) else []
 
         # determine if this project can use social features or not
         # if all pose files are V3 or greater, enable social features for this

src/ui/about_dialog.py

@@ -1,5 +1,5 @@
-from PySide2.QtWidgets import QVBoxLayout, QDialog, QLabel, QPushButton
-from PySide2.QtCore import Qt
+from PySide6.QtWidgets import QVBoxLayout, QDialog, QLabel, QPushButton
+from PySide6.QtCore import Qt
 
 from src.version import version_str
 

src/ui/archive_behavior_dialog.py

@@ -1,5 +1,5 @@
-from PySide2.QtWidgets import QVBoxLayout, QHBoxLayout, QDialog, QCheckBox, QPushButton, QComboBox
-from PySide2 import QtCore
+from PySide6.QtWidgets import QVBoxLayout, QHBoxLayout, QDialog, QCheckBox, QPushButton, QComboBox
+from PySide6 import QtCore
 
 
 class ArchiveBehaviorDialog(QDialog):

src/ui/central_widget.py

@@ -1,7 +1,7 @@
 import sys
 
 import numpy as np
-from PySide2 import QtWidgets, QtCore, QtGui
+from PySide6 import QtWidgets, QtCore, QtGui
 from shapely.geometry import Point
 
 from src.classifier.classifier import Classifier

src/ui/classification_thread.py

@@ -1,5 +1,5 @@
 import numpy as np
-from PySide2 import QtCore
+from PySide6 import QtCore
 
 from src.project import ProjectDistanceUnit
 from src.feature_extraction import IdentityFeatures

src/ui/frame_labels_widget.py

@@ -1,6 +1,6 @@
-from PySide2.QtCore import QSize, Qt
-from PySide2.QtGui import QPainter, QFont, QFontMetrics
-from PySide2.QtWidgets import QWidget, QSizePolicy, QApplication
+from PySide6.QtCore import QSize, Qt
+from PySide6.QtGui import QPainter, QFont, QFontMetrics
+from PySide6.QtWidgets import QWidget, QSizePolicy, QApplication
 
 
 class FrameLabelsWidget(QWidget):
@@ -90,7 +90,7 @@ def _draw_ticks(self, painter, start, end):
                 painter.drawRect(offset, 0, 2, 8)
 
                 label_text = f"{i}"
-                label_width = self._font_metrics.width(label_text)
+                label_width = self._font_metrics.horizontalAdvance(label_text)
                 painter.setPen(QApplication.palette().text().color())
                 painter.drawText(offset - label_width/2 + 1,
                                  self._font_height + 8, label_text)

src/ui/global_inference_widget.py

@@ -1,6 +1,6 @@
 import numpy as np
-from PySide2.QtCore import Qt
-from PySide2.QtGui import QPainter, QPixmap, QColor
+from PySide6.QtCore import Qt
+from PySide6.QtGui import QPainter, QPixmap, QColor
 
 from src.project import TrackLabels
 from .timeline_label_widget import TimelineLabelWidget

src/ui/identity_combo_box.py

@@ -1,4 +1,4 @@
-from PySide2 import QtWidgets, QtCore
+from PySide6 import QtWidgets, QtCore
 
 
 class IdentityComboBox(QtWidgets.QComboBox):

src/ui/k_fold_slider_widget.py

@@ -1,5 +1,5 @@
-from PySide2 import QtWidgets, QtCore
-from PySide2.QtCore import Qt, Signal
+from PySide6 import QtWidgets, QtCore
+from PySide6.QtCore import Qt, Signal
 
 
 class KFoldSliderWidget(QtWidgets.QWidget):

src/ui/label_count_widget.py

@@ -1,8 +1,8 @@
 import sys
 
 
-from PySide2 import QtWidgets, QtGui
-from PySide2.QtCore import Qt
+from PySide6 import QtWidgets, QtGui
+from PySide6.QtCore import Qt
 
 
 class FrameLabelCountWidget(QtWidgets.QWidget):

src/ui/license_dialog.py

@@ -1,5 +1,5 @@
-from PySide2.QtCore import Qt
-from PySide2.QtWidgets import (QDialog, QVBoxLayout, QHBoxLayout, QLabel,
+from PySide6.QtCore import Qt
+from PySide6.QtWidgets import (QDialog, QVBoxLayout, QHBoxLayout, QLabel,
                                QPushButton)
 
 from src import APP_NAME, APP_NAME_LONG

src/ui/main_control_widget.py

@@ -1,6 +1,6 @@
 import sys
 
-from PySide2 import QtWidgets, QtCore
+from PySide6 import QtWidgets, QtCore
 
 from src.classifier import Classifier