Update to Python 3.10 (#1989)

* Bump version to 1.4.1a3

* Trigger workflows

* Force full viewport rendering

* Remove env flag workaround for Qt bug

* Fix threading errors

* More threading cleanup

* networkx backward compatibility

* Remove rendering mode hack

* Disable albumentations update check.

* Add safer thread/timer stopping

* networkx backwards compatibility

* networkx backwards compatibility

* Update tf.data APIs

* Use legacy optimizer on Apple Silicon

* Lazy loading for OpenCV

* Fix backwards compatibility with tensorflow

* Lint

* More lint

---------

Co-authored-by: Talmo Pereira <[email protected]>

.conda_mac/meta.yaml

@@ -58,6 +58,7 @@ requirements:
     - conda-forge::qudida
     - conda-forge::albumentations >=1.4.15 # Handle Nan keypoints
     - conda-forge::ndx-pose <0.2.0
+    - conda-forge::lazy_loader
 
   run:
     - conda-forge::python >=3.10.0,<3.11.0
@@ -89,3 +90,4 @@ requirements:
     - conda-forge::qudida
     - conda-forge::albumentations >=1.4.15 # Handle Nan keypoints
     - conda-forge::ndx-pose <0.2.0
+    - conda-forge::lazy_loader

.github/ISSUE_TEMPLATE/bug_report.md

@@ -28,7 +28,7 @@ Please include information about how you installed.
 - OS:
 <!-- [e.g. ubuntu 20.04, macOS 11.0] -->
 - Version(s):
-<!-- e.g. [SLEAP v1.4.1a2, python 3.8] --->
+<!-- e.g. [SLEAP v1.4.1a3, python 3.8] --->
 - SLEAP installation method (listed [here](https://sleap.ai/installation.html#)):
   - [ ] [Conda from package](https://sleap.ai/installation.html#conda-package)
   - [ ] [Conda from source](https://sleap.ai/installation.html#conda-from-source)

.github/workflows/build_conda_ci.yml

@@ -11,7 +11,7 @@ on:
       - "requirements.txt"
       - "dev_requirements.txt"
       - "environment_build.yml"
-      - ".github/workflows/build_conda_ci.yml"
+      - ".github/workflows/build_conda_ci.yml"  # Run
 
 # If RUN_BUILD_JOB is set to true, then RUN_ID will be overwritten to the current run id
 env:

.github/workflows/build_pypi_ci.yml

@@ -11,7 +11,7 @@ on:
       - "jupyter_requirements.txt"
       - "pypi_requirements.txt"
       - "environment_build.yml"
-      - ".github/workflows/build_pypi_ci.yml"
+      - ".github/workflows/build_pypi_ci.yml"  # Run
 
 jobs:
   build:

.github/workflows/website.yml

@@ -8,7 +8,7 @@ on:
       # 'main' triggers updates to 'sleap.ai', all others to 'sleap.ai/develop'
       - main
       - develop
-      - liezl/remove-python-version-from-website-build-yml
+      - liezl/bump-to-1.4.1a3-py310
     paths:
       - "docs/**"
       - "README.rst"

.gitignore

@@ -117,3 +117,5 @@ venv.bak/
 
 # OS generated files
 .DS_Store
+
+models/

docs/conf.py

@@ -28,15 +28,15 @@
 copyright = f"2019–{date.today().year}, Talmo Lab"
 
 # The short X.Y version
-version = "1.4.1a2"
+version = "1.4.1a3"
 
 # Get the sleap version
 # with open("../sleap/version.py") as f:
 #     version_file = f.read()
 #     version = re.search("\d.+(?=['\"])", version_file).group(0)
 
 # Release should be the full branch name
-release = "v1.4.1a2"
+release = "v1.4.1a3"
 
 html_title = f"SLEAP ({release})"
 html_short_title = "SLEAP"

docs/installation.md

@@ -5,12 +5,12 @@ SLEAP can be installed as a Python package on Windows, Linux, and Mac OS. For qu
 ````{tabs}
    ```{group-tab} Windows and Linux
       ```bash
-      conda create -y -n sleap -c conda-forge -c nvidia -c sleap -c anaconda sleap=1.4.1a2
+      conda create -y -n sleap -c conda-forge -c nvidia -c sleap -c anaconda sleap=1.4.1a3
       ```
    ```
    ```{group-tab} Mac OS
       ```bash
-      conda create -y -n sleap -c conda-forge -c anaconda -c sleap sleap=1.4.1a2
+      conda create -y -n sleap -c conda-forge -c anaconda -c sleap sleap=1.4.1a3
       ```
    ```
 ````
@@ -147,7 +147,7 @@ SLEAP can be installed three different ways: via {ref}`conda package<condapackag
       ````{tabs}
          ```{group-tab} Windows and Linux
             ```bash
-            conda create -y -n sleap -c conda-forge -c nvidia -c sleap -c anaconda sleap=1.4.1a2
+            conda create -y -n sleap -c conda-forge -c nvidia -c sleap -c anaconda sleap=1.4.1a3
             ```  
             ```{note}
             - This comes with CUDA to enable GPU support. All you need is to have an NVIDIA GPU and [updated drivers](https://nvidia.com/drivers).
@@ -157,7 +157,7 @@ SLEAP can be installed three different ways: via {ref}`conda package<condapackag
          ```
          ```{group-tab} Mac OS
             ```bash
-            conda create -y -n sleap -c conda-forge -c anaconda -c sleap sleap=1.4.1a2
+            conda create -y -n sleap -c conda-forge -c anaconda -c sleap sleap=1.4.1a3
             ```
             ```{note}
             This will also work in CPU mode if you don't have a GPU on your machine.
@@ -240,7 +240,7 @@ SLEAP can be installed three different ways: via {ref}`conda package<condapackag
                ```
             3. Finally, we can perform the `pip install`:
                ```bash
-               pip install sleap[pypi]==1.4.1a2
+               pip install sleap[pypi]==1.4.1a3
                ```
                ```{note}
                The pypi distributed package of SLEAP ships with the following extras:

environment.yml

@@ -7,7 +7,6 @@ channels:
     - conda-forge
     - nvidia
     - sleap
-    - anaconda
 
 dependencies:
     # Packages SLEAP uses directly
@@ -42,6 +41,7 @@ dependencies:
     - conda-forge::qudida
     - conda-forge::albumentations >=1.4.15 # Handle Nan keypoints
     - conda-forge::ndx-pose <0.2.0
+    - conda-forge::lazy_loader
 
     # Packages required by tensorflow to find/use GPUs
     - conda-forge::cudatoolkit ==11.3.1

environment_mac.yml

@@ -40,5 +40,6 @@ dependencies:
     - conda-forge::qudida
     - conda-forge::albumentations >=1.4.15 # Handle Nan keypoints
     - conda-forge::ndx-pose <0.2.0
+    - conda-forge::lazy_loader
     - pip:
-          - "--editable=.[conda_dev]"
+        - "--editable=.[conda_dev]"

environment_no_cuda.yml

@@ -42,6 +42,6 @@ dependencies:
     - conda-forge::qudida
     - conda-forge::albumentations >=1.4.15 # Handle Nan keypoints
     - conda-forge::ndx-pose <0.2.0
-
+    - conda-forge::lazy_loader
     - pip:
           - "--editable=.[conda_dev]"

pypi_requirements.txt

@@ -28,13 +28,15 @@ scipy>=1.7.0
 scikit-image
 scikit-learn>=1.0.0
 seaborn
-tensorflow==2.9.2; platform_machine != 'arm64'
-tensorflow-hub
-albumentations>=1.4.15 # Handle Nan keypoints
+albumentations
 ndx-pose<0.2.0
+lazy-loader
+tensorflow==2.9.2; platform_machine != 'arm64'
+tensorflow-hub; platform_machine != 'arm64'
 # Silicon Mac specific packages
+tensorflow-hub >=0.14.0,<=0.16.1; sys_platform == 'darwin' and platform_machine == 'arm64'
 tensorflow-macos >=2.10.0,<2.13.0; sys_platform == 'darwin' and platform_machine == 'arm64'
-tensorflow-metal; sys_platform == 'darwin' and platform_machine == 'arm64'
+tensorflow-metal >=0.8.0,<=1.1.0; sys_platform == 'darwin' and platform_machine == 'arm64'
 
 # Dependencies of dependencies
 # tensorboard 2.11.2 has requirement protobuf<4,>=3.9.2

sleap/__init__.py

@@ -1,16 +1,21 @@
 import logging
 import sys
+import os
 
+# Disable albumentations update check before imports.
+os.environ["NO_ALBUMENTATIONS_UPDATE"] = "1"
 
 # Setup logging to stdout
 logging.basicConfig(stream=sys.stdout, level=logging.INFO)
 
 # Import submodules we want available at top-level
 from sleap.version import __version__, versions
-from sleap.io.dataset import Labels, load_file
+
 from sleap.io.video import Video, load_video
 from sleap.instance import LabeledFrame, Instance, PredictedInstance, Track
 from sleap.skeleton import Skeleton
+from sleap.io.dataset import Labels, load_file
+
 import sleap.nn
 from sleap.nn.data import pipelines
 from sleap.nn import inference

sleap/gui/app.py

@@ -230,9 +230,11 @@ def closeEvent(self, event):
         # Save preferences.
         prefs.save()
 
+        will_accept = False
+
         if not self.state["has_changes"]:
             # No unsaved changes, so accept event (close)
-            event.accept()
+            will_accept = True
         else:
             msgBox = QMessageBox()
             msgBox.setText("Do you want to save the changes to this project?")
@@ -249,12 +251,16 @@ def closeEvent(self, event):
                 event.ignore()
             elif ret_val == QMessageBox.Discard:
                 # don't save, just close
-                event.accept()
+                will_accept = True
             elif ret_val == QMessageBox.Save:
                 # save
                 self.commands.saveProject()
                 # accept event (closes window)
-                event.accept()
+                will_accept = True
+
+        if will_accept:
+            self.player.cleanup()
+            event.accept()
 
     def dragEnterEvent(self, event):
         # TODO: Parse filenames and accept only if valid ext (or folder)

sleap/gui/commands.py

@@ -39,7 +39,6 @@ class which inherits from `AppCommand` (or a more specialized class such as
 from typing import Callable, Dict, Iterator, List, Optional, Tuple, Type, Union, cast
 
 import attr
-import cv2
 import numpy as np
 from qtpy import QtCore, QtGui, QtWidgets
 
@@ -1794,8 +1793,7 @@ def ask(context: CommandContext, params: dict) -> bool:
         """Shows gui for replacing videos in project."""
 
         def _get_truncation_message(truncation_messages, path, video):
-            reader = cv2.VideoCapture(path)
-            last_vid_frame = int(reader.get(cv2.CAP_PROP_FRAME_COUNT))
+            last_vid_frame = len(Video.from_filename(path))
             lfs: List[LabeledFrame] = list(context.labels.get(video))
             if lfs is not None:
                 lfs.sort(key=lambda lf: lf.frame_idx)

sleap/gui/dialogs/importvideos.py

@@ -45,7 +45,9 @@
 
 import h5py
 import qimage2ndarray
-import cv2
+import lazy_loader
+
+cv2 = lazy_loader.load("cv2")
 
 from typing import Any, Dict, List, Optional
 

sleap/gui/dialogs/missingfiles.py

@@ -1,14 +1,10 @@
 """
 Gui for prompting the user to locate one or more missing files.
 """
-
 import os
-
 from pathlib import Path, PurePath
 from typing import Callable, List
-
 from qtpy import QtWidgets, QtCore, QtGui
-
 from sleap.io import pathutils
 from sleap.gui.dialogs.filedialog import FileDialog
 

sleap/gui/widgets/video.py

@@ -116,11 +116,21 @@ def __init__(self, *args, **kwargs):
         # event to event queue from the request handler.
         self.process.connect(self.doProcessing)
 
+        # Defer timer creation to worker thread construction time
+        self.timer = None
+
+    @QtCore.Slot()
+    def start_timers(self):
         # Start timer which will trigger processing events every 20 ms when we're free
-        self.timer = QtCore.QTimer()
+        self.timer = QtCore.QTimer(self)
         self.timer.timeout.connect(self.doProcessing)
         self.timer.start(20)
 
+    @QtCore.Slot()
+    def stop_timers(self):
+        if self.timer:
+            self.timer.stop()
+
     def doProcessing(self):
         self._last_process_time = time.time()
 
@@ -211,7 +221,7 @@ def __init__(
         *args,
         **kwargs,
     ):
-        super(QtVideoPlayer, self).__init__(*args, **kwargs)
+        super().__init__(*args, **kwargs)
 
         self.setAcceptDrops(True)
 
@@ -257,11 +267,12 @@ def __init__(
         self._loader_thread = QtCore.QThread()
         self._video_image_loader = LoadImageWorker()
         self._video_image_loader.moveToThread(self._loader_thread)
+        self._loader_thread.started.connect(self._video_image_loader.start_timers)
         self._loader_thread.start()
 
         # Connect signal so that image will be shown after it's loaded
         self._video_image_loader.result.connect(
-            lambda qimage: self.view.setImage(qimage)
+            self.on_new_frame, QtCore.Qt.QueuedConnection
         )
 
         def update_selection_state(a, b):
@@ -282,16 +293,27 @@ def update_selection_state(a, b):
 
         self.view.show()
 
-        # Call cleanup method when application exits to end worker thread
-        self.destroyed.connect(self.cleanup)
-        atexit.register(self.cleanup)
+        # Call cleanup method when application exits to end worker thread.
+        # Note: This is commented out in favor of the MainWindow.closeEvent() path.
+        # self.destroyed.connect(self.cleanup)
+        # app = QApplication.instance()
+        # if app:
+        #     app.aboutToQuit.connect(self.cleanup)
 
         if video is not None:
             self.load_video(video)
 
+    def on_new_frame(self, qimage):
+        self.view.setImage(qimage)
+
     def cleanup(self):
-        self._loader_thread.quit()
-        self._loader_thread.wait()
+        if self._loader_thread.isRunning():
+            QtCore.QMetaObject.invokeMethod(
+                self._video_image_loader, "stop_timers", QtCore.Qt.QueuedConnection
+            )
+            QtWidgets.QApplication.processEvents()
+            self._loader_thread.quit()
+            self._loader_thread.wait()
 
     def dragEnterEvent(self, event):
         if self.parentWidget():

sleap/info/feature_suggestions.py

@@ -12,8 +12,6 @@
 from time import time
 from typing import Dict, List, Optional, Tuple
 
-import cv2
-
 from sklearn.decomposition import PCA
 from sklearn.cluster import KMeans
 
@@ -22,6 +20,9 @@
 from skimage.util.shape import view_as_windows
 
 from sleap.io.video import Video
+import lazy_loader
+
+cv2 = lazy_loader.load("cv2")
 
 logger = logging.getLogger(__name__)
 

sleap/io/dataset.py

@@ -76,14 +76,13 @@
     make_instance_cattr,
     PredictedInstance,
 )
-
 from sleap.io import pathutils
 from sleap.io.video import Video, ImgStoreVideo, HDF5Video
 from sleap.gui.suggestions import SuggestionFrame
-from sleap.gui.dialogs.missingfiles import MissingFilesDialog
 from sleap.rangelist import RangeList
 from sleap.util import uniquify, json_dumps
 
+
 """
 The version number to put in the Labels JSON format.
 """
@@ -2657,6 +2656,8 @@ def video_callback(
                         context["changed_on_load"] = True
 
             if use_gui:
+                from sleap.gui.dialogs.missingfiles import MissingFilesDialog
+
                 # If there are still missing paths, prompt user
                 if sum(missing):
                     # If we are using dummy for any video not found by user