pylance fixes and terminal plugin launching

main.py

@@ -1337,7 +1337,7 @@ class MainApplication(QMainWindow):
 
     def terminal_gui(self):
         if self.terminal is None or not self.terminal.isVisible():
-            self.terminal = TerminalWindow(self)
+            self.terminal = TerminalWindow(self, self.plugin_manager)
             self.terminal.show()
 
     def update_optode_positions(self):

plugin_manager.py

@@ -1,6 +1,7 @@
 """
 Filename: plugin_manager.py
 Description: Manager file for anything plugin related
+Note: Compliant with pylance strict type checking
 
 Author: Tyler de Zeeuw
 License: GPL-3.0
@@ -117,7 +118,7 @@ class PluginManager(QObject):
 
             print(f"[PluginManager] {summary_msg}")
 
-            parent_widget = getattr(self, "main_window", None) or self
+            parent_widget = getattr(self, "main_window", None)
             QMessageBox.warning(
                 parent_widget,
                 "Plugin Load Failures",
@@ -166,7 +167,9 @@ class PluginManager(QObject):
         for action in menubar.actions():
             clean_text = action.text().replace("&", "").strip().lower()
             if clean_text == "plugins":
-                plugins_menu = action.menu()
+                menu = action.menu()
+                if isinstance(menu, QMenu):
+                    plugins_menu = menu
                 break
 
         # If it doesn't exist yet, create it
@@ -191,8 +194,9 @@ class PluginManager(QObject):
         plugins_menu.addSeparator()
         manager_action = plugins_menu.addAction("Manage Plugins...")
 
-        if hasattr(self.main_window, "plugins_gui") and callable(self.main_window.plugins_gui):
+        plugins_gui_func = getattr(self.main_window, "plugins_gui", None)
-            manager_action.triggered.connect(self.main_window.plugins_gui)
+        if callable(plugins_gui_func):
+            manager_action.triggered.connect(plugins_gui_func)
 
     def unload_plugins(self) -> None:
         """Clears current active plugin instances."""

pylance_progress

@@ -1,4 +1,4 @@
-src\analysis\participantfoldchannels.py  158
+src\analysis\participantfoldchannels.py  84
 src\shared\flaresbasewidget.py  1155
 flares.py  2900
 main_unit_tests.py  152

src/analysis/participantfoldchannels.py

@@ -8,29 +8,31 @@ License: GPL-3.0
 
 # Built-in Imports
 import os
-from pathlib import Path
 import time
 import traceback
+
+from pathlib import Path
 from multiprocessing import Process, current_process, Manager
-from typing import Any, Dict, List, Optional, Tuple, Union
+from typing import Any, Callable, Dict, List, Optional, Tuple, Union
 
 # External library imports
-from matplotlib.backend_bases import Event
 import numpy as np
+from pandas import DataFrame
 
 import matplotlib.pyplot as plt
 import matplotlib.image as mpimg
 from matplotlib.figure import Figure
+from matplotlib.backend_bases import Event
 from matplotlib.backends.backend_qtagg import FigureCanvasQTAgg as FigureCanvas
 
 from PySide6.QtWidgets import QFrame, QGridLayout, QHBoxLayout, QLabel, QLayout, QProgressBar, QPushButton, QScrollArea, QSizePolicy, QWidget, QDialog, QVBoxLayout
 from PySide6.QtCore import QThread, Qt, QSize, QTimer, QObject, Signal
 from PySide6.QtGui import QCloseEvent, QMouseEvent, QPixmap, QImage
-from pandas import DataFrame
 
 from mne.io.base import BaseRaw
 from src.shared.flaresbasewidget import FlaresBaseWidget
 from src.shared.shareddata import APP_NAME, resource_path
+from flares import fold_channels
 
 
 class MultiProgressDialog(QDialog):
@@ -82,7 +84,6 @@ def single_participant_worker(
     """ Runs inside its own dedicated process """
     p_name = os.path.basename(file_path)
     try:
-        from flares import fold_channels
         # Perform the heavy fold_channels logic
         channel_results = fold_channels(raw=raw_data, p_name=p_name, progress_queue=progress_queue)
         
@@ -284,7 +285,7 @@ class StaticChannelCanvas(FigureCanvas):
 
 
 class StandaloneLegendDialog(QWidget):
-    def __init__(self, canvas_engine, title_prefix, parent=None):
+    def __init__(self, canvas_engine: Any, title_prefix: str, parent: QWidget | None = None) -> None:
         super().__init__(None)
         self.setWindowTitle("Full View - Brodmann Legend")
         self.setMinimumSize(500, 600)
@@ -302,7 +303,14 @@ class InteractiveParticipantGridCanvas(FigureCanvas):
     """The Big Grid Canvas.
     Dynamically scales row and column configurations to maintain a crisp 16:9 layout orientation.
     """
-    def __init__(self, channels_data, color_map, is_fullscreen_copy=False, parent=None):
+    def __init__(
+        self, 
+        channels_data: dict[str, list[dict[str, Any]]], 
+        color_map: dict[str, str], 
+        is_fullscreen_copy: bool = False, 
+        parent: QWidget | None = None
+    ) -> None:
+        
         self.channels_data = channels_data
         self.color_map = color_map
         self.is_fullscreen_copy = is_fullscreen_copy
@@ -494,7 +502,7 @@ class InteractiveParticipantGridCanvas(FigureCanvas):
         self._fullscreen_refs.append(fullscreen_window)
 
 
-    def _calculate_total_brodmann_profile(self, channels_data: Dict[str, Any]):
+    def _calculate_total_brodmann_profile(self, channels_data: dict[str, list[dict[str, Any]]]) -> list[dict[str, Any]]:
         """Sums and normalizes the specificity profile across all channels."""
         totals = {}
         num_channels = len(channels_data)
@@ -503,7 +511,7 @@ class InteractiveParticipantGridCanvas(FigureCanvas):
             return []
 
         # Sum up specificities across all channels
-        for channel_name, data_list in channels_data.items():
+        for _, data_list in channels_data.items():
             for entry in data_list:
                 landmark = entry['Landmark']
                 specificity = entry['Specificity']
@@ -532,7 +540,7 @@ class InteractiveParticipantGridCanvas(FigureCanvas):
 
         return normalized_data_list
 
-    def _open_expanded_view(self, channel_name, data_list):
+    def _open_expanded_view(self, channel_name: str, data_list: list[dict[str, Any]]) -> None:
         # 1. Create a plain QWidget with NO parent (None)
         # This instantly makes it a top-level desktop window
         popup = QWidget(None) 
@@ -746,11 +754,12 @@ class ProcessOrchestrator(QObject):
     setup_finished = Signal(object, object, object, list)
     setup_failed = Signal(str)
 
-    def __init__(self,
+    def __init__(
-        selected_files,
+        self,
-        haemo_dict: dict[str, BaseRaw],
+        selected_files: list[str],
-        worker_func
+        haemo_dict: dict[str, Any],
-    ):
+        worker_func: Callable[..., Any]
+    ) -> None:
         
         super().__init__()
         self.selected_files = selected_files
@@ -810,9 +819,6 @@ class ParticipantFoldChannelsWidget(FlaresBaseWidget):
               
         self.index_texts = [
             "0 (Fold Channels)",
-            # "1 (second image)",
-            # "2 (third image)",
-            # "3 (fourth image)",
             ]
 
         self.image_index_dropdown = self._create_multiselect_dropdown(self.index_texts)
@@ -888,13 +894,8 @@ class ParticipantFoldChannelsWidget(FlaresBaseWidget):
             
             self.multi_progress.add_participant(os.path.basename(file_path), total_channels)
 
-        from datetime import datetime
-
-        print(f"Before: {datetime.now()}")
         self.multi_progress.show()
 
-        print(f"After 1: {datetime.now()}")
-
         if current_process().name == 'MainProcess':
             # Create a clean background thread worker execution channel
             self.orchestrator_thread = QThread()
@@ -914,7 +915,6 @@ class ParticipantFoldChannelsWidget(FlaresBaseWidget):
             self.orchestrator.setup_failed.connect(self.orchestrator.deleteLater)
 
             self.orchestrator_thread.start()
-        print(f"After 4: {datetime.now()}")
 
     def on_orchestration_success(
         self, 
@@ -1102,7 +1102,7 @@ class ParticipantFoldChannelsWidget(FlaresBaseWidget):
         vbox = QVBoxLayout(container)
         
         title = QLabel("<b>Brodmann Area Legend</b>")
-        title.setAlignment(Qt.AlignCenter)
+        title.setAlignment(Qt.AlignmentFlag.AlignCenter)
         vbox.addWidget(title)
         
         pixmap = self._bytes_to_pixmap(legend_bytes)
@@ -1110,10 +1110,10 @@ class ParticipantFoldChannelsWidget(FlaresBaseWidget):
         # Legends are usually tall, so we scale it differently or keep it smaller
         legend_label.setPixmap(pixmap.scaled(
             self.thumb_size, 
-            Qt.KeepAspectRatio, 
+            Qt.AspectRatioMode.KeepAspectRatio, 
-            Qt.SmoothTransformation
+            Qt.TransformationMode.SmoothTransformation
         ))
-        legend_label.setAlignment(Qt.AlignCenter)
+        legend_label.setAlignment(Qt.AlignmentFlag.AlignCenter)
         legend_label.mousePressEvent = lambda e, p=pixmap: self._open_full_size(p, "Brodmann Legend")
         
         vbox.addWidget(legend_label)

src/window/plugins.py

@@ -1,13 +1,15 @@
 """
 Filename: plugins.py
 Description: Plugins window
+Note: Compliant with pylance strict type checking
 
 Author: Tyler de Zeeuw
 License: GPL-3.0
 """
 
 # Built-in imports
-from typing import Any
+from pathlib import Path
+from typing import Any, cast
 
 # External library imports
 from PySide6.QtCore import Qt, QThread, Signal
@@ -104,12 +106,14 @@ class PluginsWindow(QWidget):
             self._clear_details_panel()
             return
 
-        name = info.get("name", "Unknown")
+        plugin_info = cast(dict[str, Any], info)
-        version = info.get("version", "1.0.0")
+
-        author = info.get("author", "Unknown")
+        name = str(plugin_info.get("name", "Unknown"))
-        desc = info.get("description", "No description provided.")
+        version = str(plugin_info.get("version", "1.0.0"))
-        is_disabled = info.get("is_disabled", False)
+        author = str(plugin_info.get("author", "Unknown"))
-        path = info.get("path", "")
+        desc = str(plugin_info.get("description", "No description provided."))
+        is_disabled = bool(plugin_info.get("is_disabled", False))
+        path = str(plugin_info.get("path", ""))
 
         self.lbl_plugin_title.setText(name)
         self.lbl_plugin_meta.setText(f"<b>Version:</b> {version} &nbsp;|&nbsp; <b>Author:</b> {author}")
@@ -134,25 +138,37 @@ class PluginsWindow(QWidget):
         selected = self.installed_list.currentItem()
         if not selected:
             return
-        info = selected.data(Qt.ItemDataRole.UserRole)
+        raw_info = selected.data(Qt.ItemDataRole.UserRole)
-        if isinstance(info, dict) and "path" in info:
+        if isinstance(raw_info, dict):
-            self.manager.toggle_plugin_state(info["path"])
+            info = cast(dict[str, Any], raw_info)
+            plugin_path = info.get("path")
+            if isinstance(plugin_path, str) and plugin_path:
+                self.manager.toggle_plugin_state(Path(plugin_path))
 
     def uninstall_plugin(self) -> None:
         selected = self.installed_list.currentItem()
         if not selected:
             return
-        info = selected.data(Qt.ItemDataRole.UserRole)
+        
-        if not isinstance(info, dict) or "path" not in info:
+        raw_info = selected.data(Qt.ItemDataRole.UserRole)
+        if not isinstance(raw_info, dict):
+            return
+
+        info = cast(dict[str, Any], raw_info)
+        plugin_path = info.get("path")
+        plugin_name = info.get("name", "this plugin")
+
+        if not isinstance(plugin_path, str) or not plugin_path:
             return
 
         reply = QMessageBox.question(
-            self, "Confirm Uninstall",
+            self, 
-            f"Are you sure you want to delete '{info['name']}'?",
+            "Confirm Uninstall",
+            f"Are you sure you want to delete '{plugin_name}'?",
             QMessageBox.StandardButton.Yes | QMessageBox.StandardButton.No,
         )
         if reply == QMessageBox.StandardButton.Yes:
-            self.manager.uninstall_plugin(info["path"])
+            self.manager.uninstall_plugin(Path(plugin_path))
 
     def fetch_remote_plugins(self) -> None:
         """Asynchronously fetches remote plugins on a background thread."""
@@ -197,7 +213,7 @@ class PluginsWindow(QWidget):
             p_id = plugin.get("id", "")
             version = plugin.get("version", "v0.0")
             desc = plugin.get("description", "")
-            platforms = plugin.get("platforms", [])
+            platforms = str(plugin.get("platforms", []))
             min_v_str = plugin.get("min_app_version", "0.0.0")
 
             is_platform_ok = not platforms or self.manager.current_platform in platforms

src/window/terminal.py

@@ -17,8 +17,10 @@ from PySide6.QtWidgets import QWidget, QVBoxLayout, QTextEdit, QLineEdit, QMainW
 from PySide6.QtCore import QProcess, Qt, QThread, Signal
 
 from file_ext_registration import register_file_association, is_windows_admin
+from plugin_manager import PluginManager
 from src.shared.shareddata import API_URL, API_URL_SECONDARY, APP_NAME, CURRENT_VERSION, PLATFORM_NAME
 from src.window.about import AboutWindow
+from src.window.plugins import PluginsWindow
 from updater import UpdateManager
 
 
@@ -42,7 +44,7 @@ class _AssocWorker(QThread):
 
 
 class TerminalWindow(QWidget):
-    def __init__(self, parent: QWidget | None = None) -> None:
+    def __init__(self, parent: QWidget | None, plugin_manager: PluginManager) -> None:
         super().__init__(parent, Qt.WindowType.Window)
         self.setWindowTitle(f"Terminal - {APP_NAME.upper()}")
         self.resize(320, 180)
@@ -58,6 +60,7 @@ class TerminalWindow(QWidget):
         self.setLayout(layout)
 
         self._process: QProcess | None = None
+        self.plugin_manager = plugin_manager
 
         self.commands: dict[str, Callable[..., Any]] = {
             "hello": self.cmd_hello,
@@ -66,6 +69,7 @@ class TerminalWindow(QWidget):
             "about": self.cmd_about,
             "assoc": self.cmd_assoc,
             "update": self.cmd_update,
+            "plugins": self.cmd_plugins,
             "utest": self.cmd_utest,
         }
 
@@ -122,6 +126,10 @@ class TerminalWindow(QWidget):
         self.about = AboutWindow(self)
         self.about.show()
 
+    def cmd_plugins(self, *args: Any) -> None:
+        self.about = PluginsWindow(self, self.plugin_manager)
+        self.about.show()
+
     def cmd_update(self, *args: Any) -> str:
         main_win = self.parent()
         if not isinstance(main_win, QMainWindow):