Cleanup

.github/workflows/gpu.yml

@@ -33,12 +33,10 @@
 #       run: |
 #         pip install torch==1.11.0+cu115 torchvision==0.12.0+cu115 -f https://download.pytorch.org/whl/torch_stable.html
 #
-#     - name: Install package and test dependencies
+#     - name: Install dependencies
 #       run: |
-#         python -m pip install --upgrade "pip<24.0"
-#         pip install -r requirements.txt
-#         pip install pytest pytest-cov
-#         python setup.py develop
+#         python -m pip install --upgrade pip
+#         pip install -e .
 #
 #     - name: Setup test data
 #       run: |

.github/workflows/main.yml

@@ -48,12 +48,10 @@ jobs:
       run: |
         pip install torch torchvision --index-url https://download.pytorch.org/whl/cpu
 
-    - name: Install package and test dependencies
+    - name: Install dependencies
       run: |
-        python -m pip install --upgrade "pip<24.0"
-        pip install -r requirements.txt
-        pip install pytest pytest-cov
-        python setup.py develop
+        python -m pip install --upgrade pip
+        pip install .
 
     - name: Setup test data
       run: |

README.md

@@ -22,9 +22,19 @@ learning research into action detection:
 ## Installation
 For full installation instructions, see [this readme file](docs/installation.md).
 
-In brief:
-* [Install PyTorch](https://pytorch.org/)
-* `pip install deepethogram`
+### Quick Install (Recommended)
+We recommend using [UV](https://docs.astral.sh/uv/) for fast, reliable Python package management:
+
+1. Install UV:
+   ```bash
+   curl -LsSf https://astral.sh/uv/install.sh | sh
+   ```
+   For troubleshooting or Windows, see [other installation methods](https://docs.astral.sh/uv/getting-started/installation/)
+
+2. Install DeepEthogram:
+   ```bash
+   uv pip install deepethogram
+   ```
 
 ## Data
 **NEW!** All datasets collected and annotated by the DeepEthogram authors are now available from this DropBox link:
@@ -65,7 +75,7 @@ The major dependencies for DeepEthogram are as follows:
 * pytorch, torchvision: all the neural networks, training, and inference pipelines were written in PyTorch
 * pytorch-lightning: for nice model training base classes
 * kornia: for GPU-based image augmentations
-* pyside2: for the GUI
+* PySide6: for the GUI (upgraded from PySide2 in v0.3.0)
 * opencv: for video and image reading and writing
 * opencv_transforms: for fast image augmentation
 * scikit-learn, scipy: for binary classification metrics

deepethogram/gui/custom_widgets.py

@@ -7,8 +7,8 @@
 from typing import Union
 
 import numpy as np
-from PySide2 import QtCore, QtGui, QtWidgets
-from PySide2.QtCore import Signal, Slot
+from PySide6 import QtCore, QtGui, QtWidgets
+from PySide6.QtCore import Signal, Slot
 
 from deepethogram.file_io import VideoReader
 
@@ -19,7 +19,7 @@
 
 
 def numpy_to_qpixmap(image: np.ndarray) -> QtGui.QPixmap:
-    if image.dtype == np.float:
+    if image.dtype == np.float64 or image.dtype == np.float32:
         image = float_to_uint8(image)
     H, W, C = int(image.shape[0]), int(image.shape[1]), int(image.shape[2])
     if C == 4:
@@ -33,7 +33,7 @@ def numpy_to_qpixmap(image: np.ndarray) -> QtGui.QPixmap:
 
 
 def float_to_uint8(image: np.ndarray) -> np.ndarray:
-    if image.dtype == np.float:
+    if image.dtype == np.float64 or image.dtype == np.float32:
         image = (image * 255).clip(min=0, max=255).astype(np.uint8)
     return image
 
@@ -650,7 +650,7 @@ def initialize(
             button = self._make_button(behavior, i)
             self.buttons.append(button)
             layout.addWidget(button, 0, alignment=QtCore.Qt.AlignTop)
-        layout.setMargin(0)
+        layout.setContentsMargins(0, 0, 0, 0)
         layout.setSpacing(0)
         self.layout = layout
         self.setLayout(self.layout)
@@ -788,7 +788,7 @@ def add_behavior(self, behavior: str):
 
         self.label._add_row()
         if i < 10:
-            self.toggle_shortcuts.append(QtWidgets.QShortcut(QtGui.QKeySequence(str(i)), self))
+            self.toggle_shortcuts.append(QtGui.QShortcut(QtGui.QKeySequence(str(i)), self))
         self.toggle_shortcuts[i].activated.connect(self.buttons.buttons[i].click)
 
 
@@ -875,10 +875,10 @@ def __init__(self):
             fixed=False,
         )
 
-        next_shortcut = QtWidgets.QShortcut(QtGui.QKeySequence("Right"), self)
+        next_shortcut = QtGui.QShortcut(QtGui.QKeySequence("Right"), self)
         next_shortcut.activated.connect(partial(self.label.label.change_view_dx, 1))
         # next_shortcut.activated.connect(partial(self.label.change_view_dx, 1))
-        back_shortcut = QtWidgets.QShortcut(QtGui.QKeySequence("Left"), self)
+        back_shortcut = QtGui.QShortcut(QtGui.QKeySequence("Left"), self)
         back_shortcut.activated.connect(partial(self.label.label.change_view_dx, -1))
 
         self.setCentralWidget(self.label)
@@ -897,4 +897,4 @@ def sizeHint(self):
     testing.initialize(behaviors=["background", "a", "b", "c", "d", "e"], n_timepoints=15000, debug=True)
     testing.update()
     testing.show()
-    app.exec_()
+    app.exec()

deepethogram/gui/main.py

@@ -9,9 +9,9 @@
 import numpy as np
 import pandas as pd
 from omegaconf import DictConfig, OmegaConf
-from PySide2 import QtCore, QtGui, QtWidgets
-from PySide2.QtCore import Slot
-from PySide2.QtWidgets import QFileDialog, QInputDialog, QMainWindow
+from PySide6 import QtCore, QtGui, QtWidgets
+from PySide6.QtCore import Slot
+from PySide6.QtWidgets import QFileDialog, QInputDialog, QMainWindow
 
 from deepethogram import configuration, projects, utils
 from deepethogram.file_io import VideoReader
@@ -63,37 +63,37 @@ def __init__(self, cfg: DictConfig):
 
         # scroll down to Standard Shorcuts to find what the keys are called:
         # https://doc.qt.io/qt-5/qkeysequence.html
-        next_shortcut = QtWidgets.QShortcut(QtGui.QKeySequence("Right"), self)
+        next_shortcut = QtGui.QShortcut(QtGui.QKeySequence("Right"), self)
         # partial functions create a new, separate function with certain default arguments
         next_shortcut.activated.connect(partial(self.move_n_frames, 1))
         next_shortcut.activated.connect(self.user_did_something)
 
-        up_shortcut = QtWidgets.QShortcut(QtGui.QKeySequence("Up"), self)
+        up_shortcut = QtGui.QShortcut(QtGui.QKeySequence("Up"), self)
         up_shortcut.activated.connect(partial(self.move_n_frames, -cfg.vertical_arrow_jump))
         up_shortcut.activated.connect(self.user_did_something)
 
-        down_shortcut = QtWidgets.QShortcut(QtGui.QKeySequence("Down"), self)
+        down_shortcut = QtGui.QShortcut(QtGui.QKeySequence("Down"), self)
         down_shortcut.activated.connect(partial(self.move_n_frames, cfg.vertical_arrow_jump))
         down_shortcut.activated.connect(self.user_did_something)
 
-        back_shortcut = QtWidgets.QShortcut(QtGui.QKeySequence("Left"), self)
+        back_shortcut = QtGui.QShortcut(QtGui.QKeySequence("Left"), self)
         back_shortcut.activated.connect(partial(self.move_n_frames, -1))
         back_shortcut.activated.connect(self.user_did_something)
 
-        jumpleft_shortcut = QtWidgets.QShortcut(QtGui.QKeySequence("Ctrl+Left"), self)
+        jumpleft_shortcut = QtGui.QShortcut(QtGui.QKeySequence("Ctrl+Left"), self)
         jumpleft_shortcut.activated.connect(partial(self.move_n_frames, -cfg.control_arrow_jump))
         jumpleft_shortcut.activated.connect(self.user_did_something)
 
-        jumpright_shortcut = QtWidgets.QShortcut(QtGui.QKeySequence("Ctrl+Right"), self)
+        jumpright_shortcut = QtGui.QShortcut(QtGui.QKeySequence("Ctrl+Right"), self)
         jumpright_shortcut.activated.connect(partial(self.move_n_frames, cfg.control_arrow_jump))
         jumpright_shortcut.activated.connect(self.user_did_something)
 
         self.ui.actionSave_Project.triggered.connect(self.save)
-        save_shortcut = QtWidgets.QShortcut(QtGui.QKeySequence("Ctrl+S"), self)
+        save_shortcut = QtGui.QShortcut(QtGui.QKeySequence("Ctrl+S"), self)
         save_shortcut.activated.connect(self.save)
-        finalize_shortcut = QtWidgets.QShortcut(QtGui.QKeySequence("Ctrl+F"), self)
+        finalize_shortcut = QtGui.QShortcut(QtGui.QKeySequence("Ctrl+F"), self)
         finalize_shortcut.activated.connect(self.finalize)
-        open_shortcut = QtWidgets.QShortcut(QtGui.QKeySequence("Ctrl+O"), self)
+        open_shortcut = QtGui.QShortcut(QtGui.QKeySequence("Ctrl+O"), self)
         open_shortcut.activated.connect(self.load_project)
         self.ui.finalize_labels.clicked.connect(self.finalize)
         self.ui.exportPredictions.clicked.connect(self.export_predictions)
@@ -109,7 +109,7 @@ def __init__(self, cfg: DictConfig):
         self.latent_name = None
         self.thresholds = None
         for i in range(10):
-            self.toggle_shortcuts.append(QtWidgets.QShortcut(QtGui.QKeySequence(str(i)), self))
+            self.toggle_shortcuts.append(QtGui.QShortcut(QtGui.QKeySequence(str(i)), self))
             tmp_func = partial(self.respond_to_keypress, i)
             self.toggle_shortcuts[i].activated.connect(tmp_func)
             self.toggle_shortcuts[i].activated.connect(self.user_did_something)
@@ -394,7 +394,7 @@ def generate_featureextractor_inference_args(self):
             keys.append(key)
             no_outputs.append(record["output"] is None)
         form = ShouldRunInference(keys, no_outputs)
-        ret = form.exec_()
+        ret = form.exec()
         if not ret:
             return
         should_infer = form.get_outputs()
@@ -518,7 +518,7 @@ def generate_sequence_inference_args(self):
             if has_latents[i]:
                 keys_with_features.append(key)
         form = ShouldRunInference(keys_with_features, no_sequence_outputs)
-        ret = form.exec_()
+        ret = form.exec()
         if not ret:
             return
         should_infer = form.get_outputs()
@@ -617,7 +617,7 @@ def run_overnight(self):
 
     def _new_project(self):
         form = CreateProject()
-        ret = form.exec_()
+        ret = form.exec()
         if not ret:
             return
         project_name = form.project_box.text()
@@ -1183,7 +1183,7 @@ def run() -> None:
     window.resize(1024, 768)
     window.show()
 
-    sys.exit(app.exec_())
+    sys.exit(app.exec())
 
 
 def entry() -> None:

deepethogram/gui/mainwindow.py

@@ -8,7 +8,7 @@
 #
 # WARNING! All changes made in this file will be lost!
 
-from PySide2 import QtCore, QtWidgets
+from PySide6 import QtCore, QtGui, QtWidgets
 
 
 class Ui_MainWindow(object):
@@ -186,41 +186,41 @@ def setupUi(self, MainWindow):
         self.statusBar = QtWidgets.QStatusBar(MainWindow)
         self.statusBar.setObjectName("statusBar")
         MainWindow.setStatusBar(self.statusBar)
-        self.actionNew_Project = QtWidgets.QAction(MainWindow)
+        self.actionNew_Project = QtGui.QAction(MainWindow)
         self.actionNew_Project.setObjectName("actionNew_Project")
-        self.actionSave_Project = QtWidgets.QAction(MainWindow)
+        self.actionSave_Project = QtGui.QAction(MainWindow)
         self.actionSave_Project.setEnabled(False)
         self.actionSave_Project.setObjectName("actionSave_Project")
-        self.actionAdd = QtWidgets.QAction(MainWindow)
+        self.actionAdd = QtGui.QAction(MainWindow)
         self.actionAdd.setEnabled(False)
         self.actionAdd.setObjectName("actionAdd")
-        self.actionRemove = QtWidgets.QAction(MainWindow)
+        self.actionRemove = QtGui.QAction(MainWindow)
         self.actionRemove.setEnabled(False)
         self.actionRemove.setObjectName("actionRemove")
-        self.actionStyle = QtWidgets.QAction(MainWindow)
+        self.actionStyle = QtGui.QAction(MainWindow)
         self.actionStyle.setObjectName("actionStyle")
-        self.actionOpen = QtWidgets.QAction(MainWindow)
+        self.actionOpen = QtGui.QAction(MainWindow)
         self.actionOpen.setEnabled(False)
         self.actionOpen.setObjectName("actionOpen")
-        self.actionEdit_list = QtWidgets.QAction(MainWindow)
+        self.actionEdit_list = QtGui.QAction(MainWindow)
         self.actionEdit_list.setObjectName("actionEdit_list")
-        self.actionNext = QtWidgets.QAction(MainWindow)
+        self.actionNext = QtGui.QAction(MainWindow)
         self.actionNext.setObjectName("actionNext")
-        self.actionPrevious = QtWidgets.QAction(MainWindow)
+        self.actionPrevious = QtGui.QAction(MainWindow)
         self.actionPrevious.setObjectName("actionPrevious")
-        self.actionOpen_Project = QtWidgets.QAction(MainWindow)
+        self.actionOpen_Project = QtGui.QAction(MainWindow)
         self.actionOpen_Project.setObjectName("actionOpen_Project")
-        self.importLabels = QtWidgets.QAction(MainWindow)
+        self.importLabels = QtGui.QAction(MainWindow)
         self.importLabels.setObjectName("importLabels")
-        self.actionAdd_videos = QtWidgets.QAction(MainWindow)
+        self.actionAdd_videos = QtGui.QAction(MainWindow)
         self.actionAdd_videos.setObjectName("actionAdd_videos")
-        self.classifierInference = QtWidgets.QAction(MainWindow)
+        self.classifierInference = QtGui.QAction(MainWindow)
         self.classifierInference.setCheckable(True)
         self.classifierInference.setObjectName("classifierInference")
-        self.actionOvernight = QtWidgets.QAction(MainWindow)
+        self.actionOvernight = QtGui.QAction(MainWindow)
         self.actionOvernight.setCheckable(True)
         self.actionOvernight.setObjectName("actionOvernight")
-        self.actionAdd_multiple = QtWidgets.QAction(MainWindow)
+        self.actionAdd_multiple = QtGui.QAction(MainWindow)
         self.actionAdd_multiple.setObjectName("actionAdd_multiple")
         self.menuDeepEthogram.addAction(self.actionNew_Project)
         self.menuDeepEthogram.addAction(self.actionSave_Project)

deepethogram/gui/menus_and_popups.py

@@ -1,7 +1,7 @@
 import pathlib
 import warnings
 
-from PySide2 import QtCore, QtWidgets
+from PySide6 import QtCore, QtWidgets
 
 
 def simple_popup_question(parent, message: str):
@@ -25,7 +25,7 @@ def overwrite_or_not(parent):
     )
     overwrite = msgBox.addButton("Overwrite", QtWidgets.QMessageBox.YesRole)
     unlabeled = msgBox.addButton("Only import unlabeled", QtWidgets.QMessageBox.NoRole)
-    msgBox.exec_()
+    msgBox.exec()
     if msgBox.clickedButton() is overwrite:
         return True
     elif msgBox.clickedButton() is unlabeled:
@@ -46,7 +46,7 @@ def __init__(self, parent=None):
         )
         msgBox.addButton(QtWidgets.QPushButton("Overwrite"), QtWidgets.QMessageBox.YesRole)
         msgBox.addButton(QtWidgets.QPushButton("Only import unlabeled"), QtWidgets.QMessageBox.NoRole)
-        msgBox.exec_()
+        msgBox.exec()
 
 
 class CreateProject(QtWidgets.QDialog):
@@ -148,8 +148,8 @@ def get_outputs(self):
     form = ShouldRunInference(
         ["M134_20141203_v001", "M134_20141203_v002", "M134_20141203_v004"] * num, [True, True, False] * num
     )
-    ret = form.exec_()
+    ret = form.exec()
     if ret:
         print(form.get_outputs())
-    # ret = app.exec_()
+    # ret = app.exec()
     # print(ret)

docker/Dockerfile-full

@@ -31,10 +31,11 @@ RUN curl -sLo ~/miniconda.sh https://repo.continuum.io/miniconda/Miniconda3-py39
 
 # install
 RUN conda install python=3.7 -y
-RUN pip install setuptools --upgrade && pip install --upgrade "pip<24.0"
-RUN pip install torch==1.11.0+cu115 torchvision==0.12.0+cu115 -f https://download.pytorch.org/whl/torch_stable.html
-
+RUN pip install --upgrade pip
+# Install deepethogram with dev dependencies
 ADD . /app/deepethogram
 WORKDIR /app/deepethogram
+# Use Python 3.7 compatible pyproject.toml
+RUN cp pyproject_py37.toml pyproject.toml
 ENV DEG_VERSION='full'
-RUN pip install -e .
+RUN pip install -e ".[dev]"

docker/Dockerfile-gui

@@ -35,13 +35,16 @@ RUN curl -sLo ~/miniconda.sh https://repo.continuum.io/miniconda/Miniconda3-py39
 
 # install
 RUN conda install python=3.7 -y
-RUN pip install setuptools --upgrade && pip install --upgrade pip
+RUN pip install --upgrade pip
 
 # TODO: REFACTOR CODE SO IT'S POSSIBLE TO RUN GUI WITHOUT TORCH
-RUN conda install pytorch cpuonly -c pytorch
+# Install PyTorch CPU via pip to avoid conda issues with Python 3.7
+RUN pip install torch==1.11.0+cpu torchvision==0.12.0+cpu -f https://download.pytorch.org/whl/torch_stable.html
 
-# # needed for pandas for some reason
+# Install deepethogram with dev dependencies
 ADD . /app/deepethogram
 WORKDIR /app/deepethogram
+# Use Python 3.7 compatible pyproject.toml
+RUN cp pyproject_py37.toml pyproject.toml
 ENV DEG_VERSION='gui'
-RUN pip install -e .
+RUN pip install -e ".[dev]"

docker/Dockerfile-headless

@@ -33,11 +33,13 @@ RUN curl -sLo ~/miniconda.sh https://repo.continuum.io/miniconda/Miniconda3-py39
 
 # install
 RUN conda install python=3.7 -y
-RUN pip install setuptools --upgrade && pip install --upgrade pip
-RUN conda install pytorch torchvision torchaudio cudatoolkit=11.3 -c pytorch
+RUN pip install --upgrade pip
+# RUN conda install pytorch torchvision torchaudio cudatoolkit=11.3 -c pytorch
 
-# # needed for pandas for some reason
+# Install deepethogram with dev dependencies
 ADD . /app/deepethogram
 WORKDIR /app/deepethogram
+# Use Python 3.7 compatible pyproject.toml
+RUN cp pyproject_py37.toml pyproject.toml
 ENV DEG_VERSION='headless'
-RUN pip install -e .
+RUN pip install -e ".[dev]"