typos, standardization, and file association for project extensions

src/analysis/intergroupbrainimage.py

@@ -21,7 +21,7 @@ from mne.io.base import BaseRaw
 from flares import aggregate_fnirs_group_geometry, plot_fir_model_results, brain_3d_visualization
 from src.shared.flaresbasewidget import InterGroupUIMixin, FlaresBaseWidget
 from src.shared.shareddata import APP_NAME
-from mne.io import BaseRaw
+
 
 PARAMETERIZED_INDEXES: dict[int, list[dict[str, Any]]] = {
     0: [
@@ -81,7 +81,6 @@ PARAMETERIZED_INDEXES: dict[int, list[dict[str, Any]]] = {
 }
 
 
-
 class InterGroupBrainImageWidget(InterGroupUIMixin, FlaresBaseWidget):
     def __init__(
         self,

src/analysis/intergroupfunctionalconnectivity.py

@@ -39,7 +39,6 @@ PARAMETERIZED_INDEXES: dict[int, list[dict[str, Any]]] = {
 }
 
 
-
 class InterGroupFunctionalConnectivityWidget(InterGroupUIMixin, FlaresBaseWidget):
     def __init__(
         self,

src/analysis/intergroupstats.py

@@ -157,7 +157,6 @@ DESCRIPTION = """0. ROI vs. Zero (run_roi_second_level_analysis)
 
 
 class InterGroupStatsWidget(InterGroupUIMixin, FlaresBaseWidget):
-    
     def __init__(
         self, 
         haemo_dict: dict[str | Path, BaseRaw], 

src/analysis/participantfunctionalconnectivity.py

@@ -87,7 +87,6 @@ PARAMETERIZED_INDEXES: dict[int, list[dict[str, Any]]] = {
 }
 
 
-
 class ParticipantFunctionalConnectivityWidget(ParticipantUIMixin, FlaresBaseWidget):
     def __init__(
         self,
@@ -106,7 +105,6 @@ class ParticipantFunctionalConnectivityWidget(ParticipantUIMixin, FlaresBaseWidg
         self.setup_participant_ui(["0 (Spectral Connectivity Epochs)", "1 (Envelope Correlation)", "2 (Betas)", "3 (Spectral Connectivity Epochs)",])
 
 
-
     def process_request(self):
         request = self.get_common_request_data(PARAMETERIZED_INDEXES)
         if request is None:
@@ -138,7 +136,6 @@ class ParticipantFunctionalConnectivityWidget(ParticipantUIMixin, FlaresBaseWidg
                     print(f"Skipping {self.participant_map[file_path]}: Event '{selected_event}' not found.")
                     continue
 
-
             for idx in selected_indexes:
                 if idx == 0:
 

src/analysis/participantimage.py

@@ -85,7 +85,6 @@ class ParticipantImageViewerWidget(FlaresBaseWidget):
         self.showMaximized()
 
 
-
     def show_selected_images(self):
         # Clear previous images
         while self.grid_layout.count():

src/window/about.py

@@ -7,11 +7,13 @@ Author: Tyler de Zeeuw
 License: GPL-3.0
 """
 
+# External library imports
 from PySide6.QtWidgets import QWidget, QVBoxLayout, QLabel
 from PySide6.QtCore import Qt
 
 from src.shared.shareddata import APP_NAME, APP_NAME_EXPANDED, CURRENT_VERSION
 
+
 class AboutWindow(QWidget):
     """
     Simple About window displaying basic application information.

src/window/terminal.py

@@ -7,16 +7,38 @@ Author: Tyler de Zeeuw
 License: GPL-3.0
 """
 
+# Built-in imports
 from typing import Any, Callable
 
+# External library imports
 from PySide6.QtWidgets import QWidget, QVBoxLayout, QTextEdit, QLineEdit
-from PySide6.QtCore import Qt
+from PySide6.QtCore import Qt, QThread, Signal
 
+from file_ext_registration import register_file_association, is_windows_admin
 from src.shared.shareddata import API_URL, API_URL_SECONDARY, APP_NAME, CURRENT_VERSION, PLATFORM_NAME
 from src.window.about import AboutWindow
 from updater import UpdateManager
 
 
+class _AssocWorker(QThread):
+    """
+    Runs register_file_association() off the UI thread. Only actually
+    needed for the force_admin=True path, since that blocks on
+    WaitForSingleObject while the UAC prompt is up and the elevated
+    child process runs — which would otherwise freeze the terminal
+    window. Used for the non-elevated path too for consistency.
+    """
+    result_ready = Signal(bool, str)
+ 
+    def __init__(self, force_admin: bool, parent: QWidget | None = None) -> None:
+        super().__init__(parent)
+        self._force_admin = force_admin
+ 
+    def run(self) -> None:
+        ok, msg = register_file_association(force_admin=self._force_admin)
+        self.result_ready.emit(ok, msg)
+
+
 class TerminalWindow(QWidget):
     def __init__(self, parent: QWidget | None = None) -> None:
         super().__init__(parent, Qt.WindowType.Window)
@@ -38,9 +60,13 @@ class TerminalWindow(QWidget):
             "help": self.cmd_help,
             "version": self.cmd_version,
             "about": self.cmd_about,
+            "assoc": self.cmd_assoc,
             "update": self.cmd_update,
         }
 
+        self._pending_assoc_confirmation: bool = False
+        self._assoc_worker: _AssocWorker | None = None
+
         self.output_area.append(f"Welcome to {APP_NAME.upper()}. You are running version {CURRENT_VERSION}.")
         self.output_area.append("Type 'help' for a list of available commands.\n")
 
@@ -52,6 +78,12 @@ class TerminalWindow(QWidget):
         self.input_line.clear()
 
         self.output_area.append(f"> {command_text}")
+
+        if self._pending_assoc_confirmation:
+            self._pending_assoc_confirmation = False
+            self._handle_assoc_confirmation(command_text.strip().lower())
+            return
+        
         parts = command_text.strip().split()
         if not parts:
             return
@@ -101,4 +133,34 @@ class TerminalWindow(QWidget):
         self.output_area.append("Checking for updates...")
         
         self.updater.manual_check_for_updates()
-        return "See status bar for update information."
+        return "See status bar for update information."
+
+    def cmd_assoc(self, *args: Any) -> str | None:
+        # Non-Windows platforms don't have the admin/non-admin split —
+        # just register directly.
+        if PLATFORM_NAME != "windows" or is_windows_admin():
+            self._run_assoc(force_admin=False)
+            return None
+ 
+        self._pending_assoc_confirmation = True
+        return "Not running as admin. Register system-wide via UAC elevation? (y/n)"
+ 
+    def _handle_assoc_confirmation(self, answer: str) -> None:
+        if answer in ("y", "yes"):
+            self._run_assoc(force_admin=True)
+        elif answer in ("n", "no"):
+            self._run_assoc(force_admin=False)
+        else:
+            self.output_area.append("Please answer 'y' or 'n'. Run 'assoc' again to retry.")
+ 
+    def _run_assoc(self, force_admin: bool) -> None:
+        if force_admin:
+            self.output_area.append("Requesting elevation. Check for a UAC prompt...")
+ 
+        self._assoc_worker = _AssocWorker(force_admin=force_admin, parent=self)
+        self._assoc_worker.result_ready.connect(self._on_assoc_result)
+        self._assoc_worker.start()
+ 
+    def _on_assoc_result(self, ok: bool, msg: str) -> None:
+        self.output_area.append(msg)
+        self._assoc_worker = None

src/window/userguide.py

@@ -1,11 +1,13 @@
 """
 Filename: userguide.py
-Description: User guide for FLARES
+Description: User guide window
+Note: Compliant with pylance strict type checking
 
 Author: Tyler de Zeeuw
 License: GPL-3.0
 """
 
+# External library imports
 from PySide6.QtWidgets import QWidget, QVBoxLayout, QLabel
 from PySide6.QtCore import Qt
 

src/window/welcome.py

@@ -1,18 +1,19 @@
 """
 Filename: welcome.py
-Description: Welcome dialog for FLARES
+Description: Welcome dialog window
 Note: Compliant with pylance strict type checking
 
 Author: Tyler de Zeeuw
 License: GPL-3.0
 """
 
+# External library imports
 from PySide6.QtWidgets import QTextBrowser, QVBoxLayout, QLabel, QDialog, QHBoxLayout, QPushButton
 from PySide6.QtGui import QDesktopServices, QIcon
 from PySide6.QtCore import QUrl
 from PySide6.QtNetwork import QNetworkAccessManager, QNetworkRequest, QNetworkReply
 
-from src.shared.shareddata import APP_NAME, CURRENT_VERSION, CHANGELOG_URL, resource_path
+from src.shared.shareddata import APP_NAME, PLATFORM_NAME, CURRENT_VERSION, CHANGELOG_URL, resource_path
 
 
 class WelcomeDialog(QDialog):
@@ -27,8 +28,8 @@ class WelcomeDialog(QDialog):
         header_layout = QHBoxLayout()
         logo_label = QLabel(self)
 
-        # NOTE: might not work on mac and need the icns file
-        logo_label.setPixmap(QIcon(resource_path("icons/main.ico")).pixmap(48, 48))
+        icon_ext = "icns" if PLATFORM_NAME == "darwin" else "ico"
+        logo_label.setPixmap(QIcon(resource_path(f"icons/main.{icon_ext}")).pixmap(48, 48))
         if first:
             title_label = QLabel(f"<h2>Welcome to {APP_NAME.upper()}!</h2>", self)
         elif direct: