Feat/pyqt6 napari07 migration

software/Python 3.14 Compatibility Check.md

@@ -0,0 +1,66 @@
+# Python 3.14 Compatibility -- Squid Dependencies
+
+## Supported (confirmed)
+| Package | Notes |
+|---------|-------|
+| numpy | Wheels for 3.14 since v2.3+ |
+| scipy | Supported |
+| pandas | Supported |
+| pydantic (v2) | Supported -- but **pydantic v1** (used by old napari) is **NOT** |
+| Pillow | Supported |
+| matplotlib | Supported |
+| PyYAML | Supported |
+| filelock | Supported |
+| platformdirs | Supported |
+| scikit-image | Wheels for 3.14 since v0.26 |
+| napari (latest) | Supported -- requires PyQt6, not PyQt5 |
+| opencv-python-headless | Uses stable ABI (cp37-abi3), works |
+| opencv-contrib-python-headless | Same stable ABI, works |
+| torch (PyTorch) | Supported since ~2.13 |
+| dask | Active releases in 2026 |
+| zarr | Supported |
+| tifffile | Supported |
+| imageio | Supported |
+| pyqtgraph | Pure Python, likely works |
+| qtpy | Pure Python abstraction layer, works |
+
+## Blocked / Incompatible
+| Package | Issue |
+|---------|-------|
+| **PyQt5** | **No Python 3.14 support -- this is the main blocker** |
+| **pydantic v1** | Explicitly incompatible with 3.14 (the `__slots__` error) |
+
+## Uncertain / Likely OK but unconfirmed
+| Package | Notes |
+|---------|-------|
+| pyserial | Pure Python, last release 2020 -- probably works but untested |
+| pyvisa | Likely works |
+| hidapi | Cython extension -- no 3.14 wheels confirmed |
+| GitPython | Marked as NOT supporting 3.14 on pyreadiness.org |
+| aicsimageio | Unclear, niche package |
+| basicpy | Unclear |
+| ome-zarr | Unclear |
+| pydantic-xml | Likely works if pydantic v2 is used |
+| pyreadline3 | Windows-specific, unclear |
+| qtconsole | Depends on Qt backend |
+| lxml / lxml_html_clean | C extension -- needs checking |
+| mcp | Unclear |
+| Hardware drivers (PySpin, pyAndorSDK3, ids_peak, pyvcam, pm16) | Vendor-specific, unlikely to have 3.14 builds yet |
+
+## Bottom Line
+
+The **two hard blockers** are **PyQt5** and **pydantic v1** (via old napari). Migrating to Python 3.14 would require:
+1. Switching from PyQt5 to PyQt6 (non-trivial API changes)
+2. Upgrading napari to a version that uses pydantic v2
+3. Verifying all hardware vendor SDKs have 3.14 builds
+
+**Recommendation: Stay on Python 3.10** for production use. It's the sweet spot where everything works.
+
+## Sources
+- [Python 3.14 Readiness](https://pyreadiness.org/3.14/)
+- [NumPy 2.3.0 Release Notes](https://numpy.org/devdocs/release/2.3.0-notes.html)
+- [PyQt5 on PyPI](https://pypi.org/project/PyQt5/)
+- [napari Installation](https://napari.org/stable/getting_started/installation.html)
+- [PyTorch torch.compile Python 3.14 support](https://dev-discuss.pytorch.org/t/torch-compile-support-for-python-3-14-completed/3276)
+- [Pydantic v1 Python 3.14 issue](https://github.com/pydantic/pydantic/issues/12618)
+- [Anaconda Python 3.14 overview](https://www.anaconda.com/blog/python-3-14-what-data-scientists-developers-need-know)

software/control/console.py

@@ -1,7 +1,7 @@
 import os
 
 # set QT_API environment variable
-os.environ["QT_API"] = "pyqt5"
+os.environ["QT_API"] = "pyqt6"
 
 import qtpy
 from qtpy.QtWidgets import QApplication, QMainWindow, QWidget, QVBoxLayout, QPushButton, QLabel

software/control/core/core.py

@@ -4,7 +4,7 @@
 import tempfile
 
 # qt libraries
-os.environ["QT_API"] = "pyqt5"
+os.environ["QT_API"] = "pyqt6"
 import qtpy
 import pyqtgraph as pg
 from qtpy.QtCore import *
@@ -1677,9 +1677,6 @@ def update_wellplate_settings(
         rows,
         cols,
     ):
-        if isinstance(sample_format, QVariant):
-            sample_format = sample_format.value()
-
         if sample_format == "glass slide":
             if IS_HCS:
                 sample = "4 glass slide"

software/control/core_PDAF.py

@@ -1,7 +1,7 @@
 # set QT_API environment variable
 import os
 
-os.environ["QT_API"] = "pyqt5"
+os.environ["QT_API"] = "pyqt6"
 
 # qt libraries
 from qtpy.QtCore import *

software/control/core_displacement_measurement.py

@@ -1,7 +1,7 @@
 # set QT_API environment variable
 import os
 
-os.environ["QT_API"] = "pyqt5"
+os.environ["QT_API"] = "pyqt6"
 import qtpy
 
 # qt libraries

software/control/core_usbspectrometer.py

@@ -1,7 +1,7 @@
 # set QT_API environment variable
 import os
 
-os.environ["QT_API"] = "pyqt5"
+os.environ["QT_API"] = "pyqt6"
 import qtpy
 
 # qt libraries

software/control/core_volumetric_imaging.py

@@ -1,7 +1,7 @@
 # set QT_API environment variable
 import os
 
-os.environ["QT_API"] = "pyqt5"
+os.environ["QT_API"] = "pyqt6"
 import qtpy
 
 # qt libraries
@@ -173,8 +173,8 @@ def __init__(self, window_title=""):
         self.setCentralWidget(self.widget)
 
         # set window size
-        desktopWidget = QDesktopWidget()
-        width = min(desktopWidget.height() * 0.9, 1000)  # @@@TO MOVE@@@#
+        screen_height = QApplication.primaryScreen().size().height()
+        width = int(min(screen_height * 0.9, 1000))  # @@@TO MOVE@@@#
         height = width
         self.setFixedSize(width, height)
 

software/control/gui_hcs.py

@@ -15,7 +15,7 @@
     ClearedScanCoordinates,
 )
 
-os.environ["QT_API"] = "pyqt5"
+os.environ["QT_API"] = "pyqt6"
 import re
 import time
 from enum import Enum, auto
@@ -1426,8 +1426,7 @@ def _getMainWindowMinimumSize(self):
         We want our main window to fit on the primary screen, so grab the users primary screen and return
         something slightly smaller than that.
         """
-        desktop_info = QDesktopWidget()
-        primary_screen_size = desktop_info.screen(desktop_info.primaryScreen()).size()
+        primary_screen_size = QApplication.primaryScreen().size()
 
         height_min = int(0.9 * primary_screen_size.height())
         width_min = int(0.96 * primary_screen_size.width())
@@ -1819,33 +1818,42 @@ def makeNapariConnections(self):
             self.updateNapariConnections()
 
     def updateNapariConnections(self):
-        # Update Napari connections based on performance mode. Live widget connections are preserved
+        # Update Napari connections based on performance mode.
         # Connection tuples can be:
         #   (signal, slot) - uses default Qt.AutoConnection
         #   (signal, slot, connection_type) - uses specified connection type (e.g., Qt.QueuedConnection)
+        #
+        # The live widget is always kept connected. In performance mode the mosaic's
+        # data feed is ALSO kept connected: its canvas still builds during acquisition,
+        # but rendering is deferred while its tab is hidden and flushed once when the run
+        # finishes (see UnifiedMosaicWidget.showEvent and toggleAcquisitionStart). Only
+        # the remaining napari views (e.g. multichannel) are disconnected in performance mode.
         for widget_name, connections in self.napari_connections.items():
-            if widget_name != "napariLiveWidget":  # Always keep the live widget connected
-                widget = getattr(self, widget_name, None)
-                if widget:
-                    for conn in connections:
-                        signal = conn[0]
-                        slot = conn[1]
-                        connection_type = conn[2] if len(conn) > 2 else None
-                        if self.performance_mode:
-                            try:
-                                signal.disconnect(slot)
-                            except TypeError:
-                                # Connection might not exist, which is fine
-                                pass
+            if widget_name == "napariLiveWidget":  # always kept connected (wired at init)
+                continue
+            keep_connected = (not self.performance_mode) or widget_name == "unifiedMosaicWidget"
+            widget = getattr(self, widget_name, None)
+            if not widget:
+                continue
+            for conn in connections:
+                signal = conn[0]
+                slot = conn[1]
+                connection_type = conn[2] if len(conn) > 2 else None
+                if keep_connected:
+                    try:
+                        if connection_type is not None:
+                            signal.connect(slot, connection_type)
                         else:
-                            try:
-                                if connection_type is not None:
-                                    signal.connect(slot, connection_type)
-                                else:
-                                    signal.connect(slot)
-                            except TypeError:
-                                # Connection might already exist, which is fine
-                                pass
+                            signal.connect(slot)
+                    except TypeError:
+                        # Connection might already exist, which is fine
+                        pass
+                else:
+                    try:
+                        signal.disconnect(slot)
+                    except TypeError:
+                        # Connection might not exist, which is fine
+                        pass
 
     def toggleNapariTabs(self):
         # Enable/disable Napari tabs based on performance mode
@@ -2386,9 +2394,6 @@ def onDisplayTabChanged(self, index):
             self.toggleWellSelector(False)
 
     def onWellplateChanged(self, format_):
-        if isinstance(format_, QVariant):
-            format_ = format_.value()
-
         # TODO(imo): Not sure why glass slide is so special here?  It seems like it's just a "1 well plate".
         if format_ == "glass slide":
             self.toggleWellSelector(False)
@@ -2501,13 +2506,29 @@ def toggleAcquisitionStart(self, acquisition_started):
                 self.live_scan_grid_was_on = False
             # NOTE: RAM monitor widget is connected via multipointController.signal_acquisition_start
             # which fires AFTER the memory monitor is created (see make_connections)
+
+            # Performance mode: keep the mosaic/multichannel napari tabs hidden and
+            # disabled for the duration of the run so the mosaic canvas builds without
+            # rendering (deferred), avoiding the per-tile GL stalls. A previous run's
+            # completion may have re-enabled/shown them, so re-apply the hidden state here.
+            if self.performance_mode:
+                self.toggleNapariTabs()
         else:
             self.log.info("FINISHED ACQUISITION")
             if self.live_scan_grid_was_on:
                 self.toggle_live_scan_grid(on=True)
                 self.live_scan_grid_was_on = False
             # NOTE: RAM monitor widget is disconnected via multipointController.acquisition_finished
 
+            # Performance mode: render the assembled mosaic once, now that the run is
+            # done. Re-enable the napari tabs and switch to the mosaic view; becoming
+            # visible flushes the single deferred refresh (UnifiedMosaicWidget.showEvent).
+            if self.performance_mode:
+                for i in range(self.imageDisplayTabs.count()):
+                    self.imageDisplayTabs.setTabEnabled(i, True)
+                if self.unifiedMosaicWidget is not None:
+                    self.imageDisplayTabs.setCurrentWidget(self.unifiedMosaicWidget)
+
         # click to move off during acquisition
         self.navigationWidget.set_click_to_move(not acquisition_started)
 

software/control/single_instance.py

@@ -11,7 +11,7 @@
 
 # Pin the Qt binding before importing qtpy, matching the convention used by
 # every other Qt-using module in this codebase.
-os.environ["QT_API"] = "pyqt5"
+os.environ["QT_API"] = "pyqt6"
 
 import getpass
 from typing import NamedTuple, Optional

software/control/widgets.py

@@ -31,7 +31,7 @@
 from squid.config import CameraPixelFormat
 
 # set QT_API environment variable
-os.environ["QT_API"] = "pyqt5"
+os.environ["QT_API"] = "pyqt6"
 
 # qt libraries
 import qtpy
@@ -4170,7 +4170,7 @@ def add_components(self, show_trigger_options, show_display_options, show_autole
         self.entry_displayFPS.valueChanged.connect(self.streamHandler.set_display_fps)
         self.slider_resolutionScaling.valueChanged.connect(self.streamHandler.set_display_resolution_scaling)
         self.slider_resolutionScaling.valueChanged.connect(self.liveController.set_display_resolution_scaling)
-        self.dropdown_modeSelection.activated[str].connect(self.select_new_microscope_mode_by_name)
+        self.dropdown_modeSelection.textActivated.connect(self.select_new_microscope_mode_by_name)
         self.dropdown_triggerManu.currentIndexChanged.connect(self.update_trigger_mode)
         self.btn_live.clicked.connect(self.toggle_live)
         self.entry_exposureTime.valueChanged.connect(self.update_config_exposure_time)