add pyinstaller to dependcies

.gitignore

@@ -174,3 +174,8 @@ cython_debug/
 # PyPI configuration file
 .pypirc
 
+/individual_images
+*.xlsx
+*.csv
+*.snirf
+*.json

README.md

@@ -41,4 +41,4 @@ There are no conditions for Linux users at this time.
 
 FLARES is distributed under the GPL-3.0 license.
 
-Copyright (C) 2025 Tyler de Zeeuw
+Copyright (C) 2025-2026 Tyler de Zeeuw

changelog.md

@@ -1,7 +1,86 @@
+# Version 1.2.2
+
+- Added 'Update events in snirf file (BLAZES)...' and renamed 'Update events in snirf file...' to 'Update events in snirf file (BORIS)...'
+- The BLAZES option will assign events that are exported directly from the software [BLAZES](https://git.research.dezeeuw.ca/tyler/blazes)
+- Moved the updating logic to a seperate file for better reusability and generalization
+- Fixed 'Toggle Status Bar' having no effect on the visibility of the status bar
+- Fixed a bug when updating optode positions that would prevent .txt files from being selected. Fixes [Issue 54](https://git.research.dezeeuw.ca/tyler/flares/issues/54)
+- Fixed a missing dependency in the standalone application when attempting to use an .xlsx file to update optode positions
+
+
+# Version 1.2.1
+
+- Added a requirements.txt file to ensure compatibility
+- Added new options 'Missing Events Bypass' and 'Analysis Clearing Bypass' to the Preferences Menu
+- Missing Events Bypass allows comparing events in the Group Viewers even if not all participants in the group have the event present. Fixes [Issue 28](https://git.research.dezeeuw.ca/tyler/flares/issues/28)
+- Clicking Process after an analysis has been performed will now clear the existing analysis by default with a popup warning that the analysis will be cleared
+- Analysis Clearing Bypass will prevent the popup and will not clear the existing analysis data. Fixes [Issue 41](https://git.research.dezeeuw.ca/tyler/flares/issues/41)
+- Clicking 'Clear' should now actually properly clear all data. Hopefully fixes [Issue 9](https://git.research.dezeeuw.ca/tyler/flares/issues/9) for good
+- Setting SHORT_CHANNEL to False will now grey out SHORT_CHANNEL_REGRESSION, as it is impossible to regress what does not exist. Sets SHORT_CHANNEL_REGRESSION to False under the hood when it is greyed out regardless of what is displayed. Fixes [Issue 47](https://git.research.dezeeuw.ca/tyler/flares/issues/47)
+- Projects can now be saves if files have different parent folders. Fixes [Issue 48](https://git.research.dezeeuw.ca/tyler/flares/issues/48)
+- It is no longer possible to attempt a save before any data has been processed. A popup will now display if a save is attempted with nothing to save
+- Fixed a bug where LONG_CHANNEL_THRESH was not being applied in the processing steps
+- Added a new option in the Analysis window for Group Functional Connectivity. Implements [Issue 50](https://git.research.dezeeuw.ca/tyler/flares/issues/50)
+- Group Functional connectivity is still in development and the results should currently be taken with a grain of salt
+- A warning is displayed when entering the Group Functional Connectivity Viewer disclosing this
+- Fixed a bug when updating optode positions that would prevent .txt files from being selected. Fixes [Issue 54](https://git.research.dezeeuw.ca/tyler/flares/issues/54)
+- Fixed a bug where the secondary download server would never get contacted if the primary failed
+- Automatic downloads will now ignore prerelease versions. Fixes [Issue 52](https://git.research.dezeeuw.ca/tyler/flares/issues/52)
+
+
+# Version 1.2.0
+
+- This is a save-breaking release due to a new save file format. Please update your project files to ensure compatibility. Fixes [Issue 30](https://git.research.dezeeuw.ca/tyler/flares/issues/30)
+- Added new parameters to the right side of the screen
+- These parameters include SHOW_OPTODE_NAMES, SECONDS_TO_STRIP_HR, MAX_LOW_HR, MAX_HIGH_HR, SMOOTHING_WINDOW_HR, HEART_RATE_WINDOW, BAD_CHANNELS_HANDLING, MAX_DIST, MIN_NEIGHBORS, L_TRANS_BANDWIDTH, H_TRANS_BANDWIDTH, RESAMPLE, RESAMPLE_FREQ, STIM_DUR, HRF_MODEL, HIGH_PASS, DRIFT_ORDER, FIR_DELAYS, MIN_ONSET, OVERSAMPLING, SHORT_CHANNEL_REGRESSION, NOISE_MODEL, BINS, and VERBOSITY.
+- Certain parameters now have dependencies on other parameters and will now grey out if they are not used
+- All the new parameters have default values matching the underlying values in version 1.1.7
+- The order of the parameters have changed to match the order that the code runs when the Process button is clicked
+- Moved TIME_WINDOW_START and TIME_WINDOW_END to the 'Other' category
+- Fixed a bug causing SCI to not work when HEART_RATE was set to False
+- Bad channels can now be dealt with by taking no action, removing them completely, or interpolating them based on their neighbours. Interpolation remains the default option
+- Fixed an underlying deprecation warning
+- Fixed an issue causing some overlay elements to not render on the brain for certain devices
+- Fixed a crash when rendering some Inter-Group images with only one participant in a group
+- Fixed a crash when attempting to fOLD channels without the fOLD dataset installed
+- Lowered the number of rectangles in the progress bar to 24 after combining some actions
+- Fixed the User Guide window to properly display information about the 24 stages and added a link to the Git wiki page
+- MAX_WORKERS should now properly repect the value set
+- Added a new CSV export option to be used by other applications
+- Added support for updating optode positions directly from an .xlsx file from a Polhemius system
+- Fixed an issue where the dropdowns in the Viewer windows would immediately open and close when using a trackpad
+- glover and spm hrf models now function as intended without crashing. Currently, group analysis is still only supported by fir. Fixes [Issue 8](https://git.research.dezeeuw.ca/tyler/flares/issues/8)
+- Clicking 'Clear' should now properly clear all data. Fixes [Issue 9](https://git.research.dezeeuw.ca/tyler/flares/issues/9)
+- Revamped the fold channels viewer to not hang the application and to better process multiple participants at once. Fixes [Issue 34](https://git.research.dezeeuw.ca/tyler/flares/issues/34), [Issue 31](https://git.research.dezeeuw.ca/tyler/flares/issues/31)
+- Added a Preferences menu to the navigation bar
+- Two preferences have been added allowing to bypass the warning of 2D data detected and save files being from previous, potentially breaking versions
+- Fixed a typo when saving a CSV that stated a SNIRF was being saved
+- Loading a save file now properly restores AGE, GENDER, and GROUP. Fixes [Issue 40](https://git.research.dezeeuw.ca/tyler/flares/issues/40)
+- Saving a project now no longer makes the main window go not responding. Fixes [Issue 43](https://git.research.dezeeuw.ca/tyler/flares/issues/43)
+- Memory usage should no longer grow when generating lots of images multiple times. Fixes [Issue 36](https://git.research.dezeeuw.ca/tyler/flares/issues/36)
+- Added a new option in the Analysis window for Functional Connectivity
+- Functional connectivity is still in development and the results should currently be taken with a grain of salt
+- A warning is displayed when entering the Functional Connectivity Viewer disclosing this
+
+
+# Version 1.1.7
+
+- Fixed a bug where having both a L_FREQ and H_FREQ would cause only the L_FREQ to be used
+- Changed the default H_FREQ from 0.7 to 0.3
+- Added a PSD graph, along with 2 heart rate images to the individual participant viewer
+- The PSD graph is used to help calculate the heart rate, whereas the other 2 are currently just for show
+- SCI is now done using a .6hz window around the calculated heart rate compared to a window around an average heart rate
+- Fixed an issue with some epochs figures not showing under the participant analysis
+- Removed SECONDS_TO_STRIP from the preprocessing options
+- Added new parameters to the right side of the screen
+- These parameters include TRIM, SECONDS_TO_KEEP, OPTODE_PLACEMENT, HEART_RATE, WAVELET, IQR, WAVELET_TYPE, WAVELET_LEVEL, ENHANCE_NEGATIVE_CORRELATION, SHORT_CHANNEL_THRESH, LONG_CHANNEL_THRESH, and DRIFT_MODEL
+- Changed number of rectangles in the progress bar to 25 to account for the new options
+
+
 # Version 1.1.6
 
 - Fixed Process button from appearing when no files are selected
-- Fix for instand child process crash on Windows
+- Fixed a bug that would cause an instant child process crash on Windows
 - Added L_FREQ and H_FREQ parameters for more user control over low and high pass filtering
 
 
@@ -72,7 +151,7 @@
 - Added a group option when clicking on a participant's file
 - If no group is specified, the participant will be added to the "Default" group
 - Added option to update the optode positions in a snirf file from the Options menu (F6)
-- Fixed [Issue 3](https://git.research.dezeeuw.ca/tyler/flares/issues/3), [Issue 4](https://git.research.dezeeuw.ca/tyler/flares/issues/4), [Issue 17](https://git.research.dezeeuw.ca/tyler/flares/issues/17), [Issue 21](https://git.research.dezeeuw.ca/tyler/flares/issues/21), [Issue 22](https://git.research.dezeeuw.ca/tyler/flares/issues/22)
+- Fixed [Issue 3](https://git.research.dezeeuw.ca/tyler/flares/issues/3), [Issue 5](https://git.research.dezeeuw.ca/tyler/flares/issues/5), [Issue 17](https://git.research.dezeeuw.ca/tyler/flares/issues/17), [Issue 21](https://git.research.dezeeuw.ca/tyler/flares/issues/21), [Issue 22](https://git.research.dezeeuw.ca/tyler/flares/issues/22)
 
 
 # Version 1.0.1

flares_updater.py

@@ -18,11 +18,12 @@ import subprocess
 from datetime import datetime
 
 PLATFORM_NAME = platform.system().lower()
+APP_NAME = "flares"
 
 if PLATFORM_NAME == 'darwin':
-    LOG_FILE = os.path.join(os.path.dirname(sys.executable), "../../../flares_updater.log")
+    LOG_FILE = os.path.join(os.path.dirname(sys.executable), f"../../../{APP_NAME}_updater.log")
 else:
-    LOG_FILE = os.path.join(os.getcwd(), "flares_updater.log")
+    LOG_FILE = os.path.join(os.getcwd(), f"{APP_NAME}_updater.log")
 
 
 def log(msg):
@@ -147,7 +148,7 @@ def copy_update_files_darwin(src_folder, dest_folder, updater_name):
 
 def remove_quarantine(app_path):
     script = f'''
-    do shell script "xattr -d -r com.apple.quarantine {shlex.quote(app_path)}" with administrator privileges with prompt "FLARES needs privileges to finish the update. (1/2)"
+    do shell script "xattr -d -r com.apple.quarantine {shlex.quote(app_path)}" with administrator privileges with prompt "{APP_NAME} needs privileges to finish the update. (1/2)"
     '''
     try:
         subprocess.run(['osascript', '-e', script], check=True)
@@ -162,7 +163,7 @@ def main():
         log(f"[Updater] sys.argv: {sys.argv}")
 
         if len(sys.argv) != 3:
-            log("Invalid arguments. Usage: flares_updater <update_folder> <main_app_executable>")
+            log(f"Invalid arguments. Usage: {APP_NAME}_updater <update_folder> <main_app_executable>")
             sys.exit(1)
 
         update_folder = sys.argv[1]
@@ -215,7 +216,7 @@ def main():
         if PLATFORM_NAME == 'darwin':
             log(f'Attempting to delete {ppparent_dir}')
             delete_path(ppparent_dir)
-            update_folder = os.path.join(sys.argv[1], "flares-darwin")
+            update_folder = os.path.join(sys.argv[1], f"{APP_NAME}-darwin")
             copy_update_files_darwin(update_folder, pppparent_dir, updater_name)
 
         else:

mne/transforms.py

@@ -12,7 +12,7 @@ from pathlib import Path
 import numpy as np
 from scipy import linalg
 from scipy.spatial.distance import cdist
-from scipy.special import sph_harm
+from scipy.special import sph_harm_y
 
 from ._fiff.constants import FIFF
 from ._fiff.open import fiff_open

mne/viz/_3d.py

@@ -1025,7 +1025,7 @@ def _handle_sensor_types(meg, eeg, fnirs):
         fnirs=dict(channels="fnirs", pairs="fnirs_pairs"),
     )
     sensor_alpha = {
-        key: dict(meg_helmet=0.25, meg=0.25).get(key, 0.8)
+        key: dict(meg_helmet=0.25, meg=0.25).get(key, 1.0)
         for ch_dict in alpha_map.values()
         for key in ch_dict.values()
     }

mne/viz/backends/_pyvista.py

@@ -586,7 +586,7 @@ class _PyVistaRenderer(_AbstractRenderer):
                 color = None
             else:
                 scalars = None
-            tube = line.tube(radius, n_sides=self.tube_n_sides)
+            tube = line.tube(radius=radius, n_sides=self.tube_n_sides)
             actor = _add_mesh(
                 plotter=self.plotter,
                 mesh=tube,

updater.py

@@ -0,0 +1,539 @@
+"""
+Filename: updater.py
+Description: Generic updater file
+
+Author: Tyler de Zeeuw
+License: GPL-3.0
+"""
+
+# Built-in imports
+import os
+import re
+import sys
+import time
+import shlex
+import shutil
+import zipfile
+import traceback
+import subprocess
+
+# External library imports
+import psutil
+import requests
+
+from PySide6.QtWidgets import QMessageBox
+from PySide6.QtCore import QThread, Signal, QObject
+
+
+class UpdateDownloadThread(QThread):
+    """
+    Thread that downloads and extracts an update package and emits a signal on completion or error.
+
+    Args:
+        download_url (str): URL of the update zip file to download.
+        latest_version (str): Version string of the latest update.
+    """
+        
+    update_ready = Signal(str, str)
+    error_occurred = Signal(str)
+
+    def __init__(self, download_url, latest_version, platform_name, app_name):
+        super().__init__()
+        self.download_url = download_url
+        self.latest_version = latest_version
+        self.platform_name = platform_name
+        self.app_name = app_name
+
+    def run(self):
+        try:
+            local_filename = os.path.basename(self.download_url)
+
+            if self.platform_name == 'darwin':
+                tmp_dir = f'/tmp/{self.app_name}tempupdate'
+                os.makedirs(tmp_dir, exist_ok=True)
+                local_path = os.path.join(tmp_dir, local_filename)
+            else:
+                local_path = os.path.join(os.getcwd(), local_filename)
+
+            # Download the file
+            with requests.get(self.download_url, stream=True, timeout=15) as r:
+                r.raise_for_status()
+                with open(local_path, 'wb') as f:
+                    for chunk in r.iter_content(chunk_size=8192):
+                        if chunk:
+                            f.write(chunk)
+
+            # Extract folder name (remove .zip)
+            if self.platform_name == 'darwin':
+                extract_folder = os.path.splitext(local_filename)[0]
+                extract_path = os.path.join(tmp_dir, extract_folder)
+
+            else:
+                extract_folder = os.path.splitext(local_filename)[0]
+                extract_path = os.path.join(os.getcwd(), extract_folder)
+
+            # Create the folder if not exists
+            os.makedirs(extract_path, exist_ok=True)
+
+            # Extract the zip file contents
+            if self.platform_name == 'darwin':
+                subprocess.run(['ditto', '-xk', local_path, extract_path], check=True)
+            else:
+                with zipfile.ZipFile(local_path, 'r') as zip_ref:
+                    zip_ref.extractall(extract_path)
+
+            # Remove the zip once extracted and emit a signal
+            os.remove(local_path)
+            self.update_ready.emit(self.latest_version, extract_path)
+
+        except Exception as e:
+            # Emit a signal signifying failure
+            self.error_occurred.emit(str(e))
+
+
+
+class UpdateCheckThread(QThread):
+    """
+    Thread that checks for updates by querying the API and emits a signal based on the result.
+
+    Signals:
+        download_requested(str, str): Emitted with (download_url, latest_version) when an update is available.
+        no_update_available(): Emitted when no update is found or current version is up to date.
+        error_occurred(str): Emitted with an error message if the update check fails.
+    """
+
+    download_requested = Signal(str, str)
+    no_update_available = Signal()
+    error_occurred = Signal(str)
+
+    def __init__(self, api_url, api_url_sec, current_version, platform_name, app_name):
+        super().__init__()
+        self.api_url = api_url
+        self.api_url_sec = api_url_sec
+        self.current_version = current_version
+        self.platform_name = platform_name
+        self.app_name = app_name
+
+    def run(self):
+        # if not getattr(sys, 'frozen', False):
+        #     self.error_occurred.emit("Application is not frozen (Development mode).")
+        #     return
+        try:
+            latest_version, download_url = self.get_latest_release_for_platform()
+            if not latest_version:
+                self.no_update_available.emit()
+                return
+
+            if not download_url:
+                self.error_occurred.emit(f"No download available for platform '{self.platform_name}'")
+                return
+
+            if self.version_compare(latest_version, self.current_version) > 0:
+                self.download_requested.emit(download_url, latest_version)
+            else:
+                self.no_update_available.emit()
+
+        except Exception as e:
+            self.error_occurred.emit(f"Update check failed: {e}")
+
+    def version_compare(self, v1, v2):
+        def normalize(v): return [int(x) for x in v.split(".")]
+        return (normalize(v1) > normalize(v2)) - (normalize(v1) < normalize(v2))
+
+    def get_latest_release_for_platform(self):
+        urls = [self.api_url, self.api_url_sec]
+        for url in urls:
+            try:
+                    
+                response = requests.get(url, timeout=5)
+                response.raise_for_status()
+                releases = response.json()
+
+                if not releases:
+                    continue
+
+                latest = next((r for r in releases if not r.get("prerelease") and not r.get("draft")), None)
+
+                if not latest:
+                    continue
+                
+                tag = latest["tag_name"].lstrip("v")
+
+                for asset in latest.get("assets", []):
+                    if self.platform_name in asset["name"].lower():
+                        return tag, asset["browser_download_url"]
+
+                return tag, None
+            except (requests.RequestException, ValueError) as e:
+                continue
+        return None, None
+
+
+class LocalPendingUpdateCheckThread(QThread):
+    """
+    Thread that checks for locally pending updates by scanning the download directory and emits a signal accordingly.
+
+    Args:
+        current_version (str): Current application version.
+        platform_suffix (str): Platform-specific suffix to identify update folders.
+    """
+
+    pending_update_found = Signal(str, str)
+    no_pending_update = Signal()
+
+    def __init__(self, current_version, platform_suffix, platform_name, app_name):
+        super().__init__()
+        self.current_version = current_version
+        self.platform_suffix = platform_suffix
+        self.platform_name = platform_name
+        self.app_name = app_name
+
+    def version_compare(self, v1, v2):
+        def normalize(v): return [int(x) for x in v.split(".")]
+        return (normalize(v1) > normalize(v2)) - (normalize(v1) < normalize(v2))
+
+    def run(self):
+        if self.platform_name == 'darwin':
+            cwd = f'/tmp/{self.app_name}tempupdate'
+        else:
+            cwd = os.getcwd()
+
+        pattern = re.compile(r".*-(\d+\.\d+\.\d+)" + re.escape(self.platform_suffix) + r"$")
+        found = False
+
+        try:
+            for item in os.listdir(cwd):
+                folder_path = os.path.join(cwd, item)
+                if os.path.isdir(folder_path) and item.endswith(self.platform_suffix):
+                    match = pattern.match(item)
+                    if match:
+                        folder_version = match.group(1)
+                        if self.version_compare(folder_version, self.current_version) > 0:
+                            self.pending_update_found.emit(folder_version, folder_path)
+                            found = True
+                            break
+        except:
+            pass
+        
+        if not found:
+            self.no_pending_update.emit()
+
+
+
+
+
+class UpdateManager(QObject):
+    """
+    Orchestrates the update process. 
+    Main apps should instantiate this and call check_for_updates().
+    """
+    
+    def __init__(self, main_window, api_url, api_url_sec, current_version, platform_name, platform_suffix, app_name):
+        super().__init__()
+        self.parent = main_window
+        self.api_url = api_url
+        self.api_url_sec = api_url_sec
+        self.current_version = current_version
+        self.platform_name = platform_name
+        self.platform_suffix = platform_suffix
+        self.app_name = app_name
+        
+        self.pending_update_version = None
+        self.pending_update_path = None
+
+
+    def manual_check_for_updates(self):
+        self.local_check_thread = LocalPendingUpdateCheckThread(self.current_version, self.platform_suffix, self.platform_name, self.app_name)
+        self.local_check_thread.pending_update_found.connect(self.on_pending_update_found)
+        self.local_check_thread.no_pending_update.connect(self.on_no_pending_update)
+        self.local_check_thread.start()
+
+    def on_pending_update_found(self, version, folder_path):
+        self.parent.statusBar().showMessage(f"Pending update found: version {version}")
+        self.pending_update_version = version
+        self.pending_update_path = folder_path
+        self.show_pending_update_popup()
+
+    def on_no_pending_update(self):
+        # No pending update found locally, start server check directly
+        self.parent.statusBar().showMessage("No pending local update found. Checking server...")
+        self.start_update_check_thread()
+
+    def show_pending_update_popup(self):
+        msg_box = QMessageBox(self.parent)
+        msg_box.setWindowTitle("Pending Update Found")
+        msg_box.setText(f"A previously downloaded update for {self.app_name.upper()} (version {self.pending_update_version}) is available at:\n{self.pending_update_path}\nWould you like to install it now?")
+        install_now_button = msg_box.addButton("Install Now", QMessageBox.ButtonRole.AcceptRole)
+        install_later_button = msg_box.addButton("Install Later", QMessageBox.ButtonRole.RejectRole)
+        msg_box.exec()
+
+        if msg_box.clickedButton() == install_now_button:
+            self.install_update(self.pending_update_path)
+        else:
+            self.parent.statusBar().showMessage("Pending update available. Install later.")
+            # After user dismisses, still check the server for new updates
+            self.start_update_check_thread()
+
+    def start_update_check_thread(self):
+        self.check_thread = UpdateCheckThread(self.api_url, self.api_url_sec, self.current_version, self.platform_name, self.app_name)
+        self.check_thread.download_requested.connect(self.on_server_update_requested)
+        self.check_thread.no_update_available.connect(self.on_server_no_update)
+        self.check_thread.error_occurred.connect(self.on_error)
+        self.check_thread.start()
+
+    def on_server_no_update(self):
+        self.parent.statusBar().showMessage("No new updates found on server.", 5000)
+
+    def on_server_update_requested(self, download_url, latest_version):
+        if self.pending_update_version:
+            cmp = self.version_compare(latest_version, self.pending_update_version)
+            if cmp > 0:
+                # Server version is newer than pending update
+                self.parent.statusBar().showMessage(f"Newer version {latest_version} available on server. Removing old pending update...")
+                try:
+                    shutil.rmtree(self.pending_update_path)
+                    self.parent.statusBar().showMessage(f"Deleted old update folder: {self.pending_update_path}")
+                except Exception as e:
+                    self.parent.statusBar().showMessage(f"Failed to delete old update folder: {e}")
+                    
+                # Clear pending update info so new download proceeds
+                self.pending_update_version = None
+                self.pending_update_path = None
+
+                # Download the new update
+                self.download_update(download_url, latest_version)
+            elif cmp == 0:
+                # Versions equal, no download needed
+                self.parent.statusBar().showMessage(f"Pending update version {self.pending_update_version} is already latest. No download needed.")
+            else:
+                # Server version older than pending? Unlikely but just keep pending update
+                self.parent.statusBar().showMessage(f"Pending update version {self.pending_update_version} is newer than server version. No action.")
+        else:
+            # No pending update, just download
+            self.download_update(download_url, latest_version)
+
+    def download_update(self, download_url, latest_version):
+        self.parent.statusBar().showMessage("Downloading update...")
+        self.download_thread = UpdateDownloadThread(download_url, latest_version, self.platform_name, self.app_name)
+        self.download_thread.update_ready.connect(self.on_update_ready)
+        self.download_thread.error_occurred.connect(self.on_error)
+        self.download_thread.start()
+
+    def on_update_ready(self, latest_version, extract_folder):
+        self.parent.statusBar().showMessage("Update downloaded and extracted.")
+
+        msg_box = QMessageBox(self.parent)
+        msg_box.setWindowTitle("Update Ready")
+        msg_box.setText(f"Version {latest_version} has been downloaded and extracted to:\n{extract_folder}\nWould you like to install it now?")
+        install_now_button = msg_box.addButton("Install Now", QMessageBox.ButtonRole.AcceptRole)
+        install_later_button = msg_box.addButton("Install Later", QMessageBox.ButtonRole.RejectRole)
+
+        msg_box.exec()
+
+        if msg_box.clickedButton() == install_now_button:
+            self.install_update(extract_folder)
+        else:
+            self.parent.statusBar().showMessage("Update ready. Install later.")
+
+
+    def install_update(self, extract_folder):
+        # Path to updater executable
+
+        if self.platform_name == 'windows':
+            updater_path = os.path.join(os.getcwd(), f"{self.app_name}_updater.exe")
+        elif self.platform_name == 'darwin':
+            if getattr(sys, 'frozen', False):
+                updater_path = os.path.join(os.path.dirname(sys.executable), f"../../../{self.app_name}_updater.app")
+            else:
+                updater_path = os.path.join(os.getcwd(), f"../{self.app_name}_updater.app")
+
+        elif self.platform_name == 'linux':
+            updater_path = os.path.join(os.getcwd(), f"{self.app_name}_updater")
+        else:
+            updater_path = os.getcwd()
+
+        if not os.path.exists(updater_path):
+            QMessageBox.critical(self.parent, "Error", f"Updater not found at:\n{updater_path}. The absolute path was {os.path.abspath(updater_path)}")
+            return
+
+        # Launch updater with extracted folder path as argument
+        try:
+            # Pass current app's executable path for updater to relaunch
+            main_app_executable = os.path.abspath(sys.argv[0])
+
+            print(f'Launching updater with: "{updater_path}" "{extract_folder}" "{main_app_executable}"')
+
+            if self.platform_name == 'darwin':
+                subprocess.Popen(['open', updater_path, '--args', extract_folder, main_app_executable])
+            else:
+                subprocess.Popen([updater_path, f'{extract_folder}', f'{main_app_executable}'], cwd=os.path.dirname(updater_path))
+
+            # Close the current app so updater can replace files
+            sys.exit(0)
+
+        except Exception as e:
+            QMessageBox.critical(self.parent, "Error", f"[Updater Launch Failed]\n{str(e)}\n{traceback.format_exc()}")
+
+    def on_error(self, message):
+        # print(f"Error: {message}")
+        self.parent.statusBar().showMessage(f"Error occurred during update process. {message}")
+
+    def version_compare(self, v1, v2):
+        def normalize(v): return [int(x) for x in v.split(".")]
+        return (normalize(v1) > normalize(v2)) - (normalize(v1) < normalize(v2))
+
+
+def wait_for_process_to_exit(process_name, timeout=10):
+    """
+    Waits for a process with the specified name to exit within a timeout period.
+
+    Args:
+        process_name (str): Name (or part of the name) of the process to wait for.
+        timeout (int, optional): Maximum time to wait in seconds. Defaults to 10.
+
+    Returns:
+        bool: True if the process exited before the timeout, False otherwise.
+    """
+
+    print(f"Waiting for {process_name} to exit...")
+    deadline = time.time() + timeout
+    while time.time() < deadline:
+        still_running = False
+        for proc in psutil.process_iter(['name']):
+            try:
+                if proc.info['name'] and process_name.lower() in proc.info['name'].lower():
+                    still_running = True
+                    print(f"Still running: {proc.info['name']} (PID: {proc.pid})")
+                    break
+            except (psutil.NoSuchProcess, psutil.AccessDenied):
+                continue
+        if not still_running:
+            print(f"{process_name} has exited.")
+            return True
+        time.sleep(0.5)
+    print(f"{process_name} did not exit in time.")
+    return False
+
+
+def finish_update_if_needed(platform_name, app_name):
+    """
+    Completes a pending application update if '--finish-update' is present in the command-line arguments.
+    """
+
+    if "--finish-update" in sys.argv:
+        print("Finishing update...")
+
+        if platform_name == 'darwin':
+            app_dir = f'/tmp/{app_name}tempupdate'
+        else:
+            app_dir = os.getcwd()
+
+        # 1. Find update folder
+        update_folder = None
+        for entry in os.listdir(app_dir):
+            entry_path = os.path.join(app_dir, entry)
+            if os.path.isdir(entry_path) and entry.startswith(f"{app_name}-") and entry.endswith("-" + platform_name):
+                update_folder = os.path.join(app_dir, entry)
+                break
+
+        if update_folder is None:
+            print("No update folder found. Skipping update steps.")
+            return
+        
+        if platform_name == 'darwin':
+            update_folder = os.path.join(update_folder, f"{app_name}-darwin")
+
+        # 2. Wait for updater to exit
+        print(f"Waiting for {app_name}_updater to exit...")
+        for proc in psutil.process_iter(['pid', 'name']):
+            if proc.info['name'] and f"{app_name}_updater" in proc.info['name'].lower():
+                try:
+                    proc.wait(timeout=5)
+                except psutil.TimeoutExpired:
+                    print(f"Force killing lingering {app_name}_updater")
+                    proc.kill()
+
+        # 3. Replace the updater
+        if platform_name == 'windows':
+            new_updater = os.path.join(update_folder, f"{app_name}_updater.exe")
+            dest_updater = os.path.join(app_dir, f"{app_name}_updater.exe")
+
+        elif platform_name == 'darwin':
+            new_updater = os.path.join(update_folder, f"{app_name}_updater.app")
+            dest_updater = os.path.abspath(os.path.join(sys.executable, f"../../../../{app_name}_updater.app"))
+
+        elif platform_name == 'linux':
+            new_updater = os.path.join(update_folder, f"{app_name}_updater")
+            dest_updater = os.path.join(app_dir, f"{app_name}_updater")
+
+        else:
+            print("Unknown Platform")
+            new_updater = os.getcwd()
+            dest_updater = os.getcwd()
+
+        print(f"New updater is {new_updater}")
+        print(f"Dest updater is {dest_updater}")
+
+        print("Writable?", os.access(dest_updater, os.W_OK))
+        print("Executable path:", sys.executable)
+        print("Trying to copy:", new_updater, "->", dest_updater)
+
+        if os.path.exists(new_updater):
+            try:
+                if os.path.exists(dest_updater):
+                    if platform_name == 'darwin':
+                        try:
+                            if os.path.isdir(dest_updater):
+                                shutil.rmtree(dest_updater)
+                                print(f"Deleted directory: {dest_updater}")
+                            else:
+                                os.remove(dest_updater)
+                                print(f"Deleted file: {dest_updater}")
+                        except Exception as e:
+                            print(f"Error deleting {dest_updater}: {e}")
+                    else:
+                        os.remove(dest_updater)
+
+                if platform_name == 'darwin':
+                    wait_for_process_to_exit(f"{app_name}_updater", timeout=10)
+                    subprocess.check_call(["ditto", new_updater, dest_updater])
+                else:
+                    shutil.copy2(new_updater, dest_updater)
+
+                if platform_name in ('linux', 'darwin'):
+                    os.chmod(dest_updater, 0o755)
+
+                if platform_name == 'darwin':
+                    remove_quarantine(dest_updater, app_name)
+
+                print(f"{app_name}_updater replaced.")
+            except Exception as e:
+                print(f"Failed to replace {app_name}_updater: {e}")
+
+        # 4. Delete the update folder
+        try:
+            if platform_name == 'darwin':
+                shutil.rmtree(app_dir)
+            else:
+                shutil.rmtree(update_folder)
+        except Exception as e:
+            print(f"Failed to delete update folder: {e}")
+
+        QMessageBox.information(None, "Update Complete", "The application has been successfully updated.")
+        sys.argv.remove("--finish-update")
+
+
+def remove_quarantine(app_path, app_name):
+    """
+    Removes the macOS quarantine attribute from the specified application path.
+    """
+
+    script = f'''
+    do shell script "xattr -d -r com.apple.quarantine {shlex.quote(app_path)}" with administrator privileges with prompt "{app_name.upper()} needs privileges to finish the update. (2/2)"
+    '''
+    try:
+        subprocess.run(['osascript', '-e', script], check=True)
+        print("✅ Quarantine attribute removed.")
+    except subprocess.CalledProcessError as e:
+        print("❌ Failed to remove quarantine attribute.")
+        print(e)

version_main.txt

@@ -18,7 +18,7 @@ VSVersionInfo(
            StringStruct('FileDescription', 'FLARES main application'),
            StringStruct('FileVersion', '1.0.0.0'),
            StringStruct('InternalName', 'flares.exe'),
-           StringStruct('LegalCopyright', '© 2025 Tyler de Zeeuw'),
+           StringStruct('LegalCopyright', '© 2025-2026 Tyler de Zeeuw'),
            StringStruct('OriginalFilename', 'flares.exe'),
            StringStruct('ProductName', 'FLARES'),
            StringStruct('ProductVersion', '1.0.0.0')])

version_updater.txt

@@ -18,7 +18,7 @@ VSVersionInfo(
            StringStruct('FileDescription', 'FLARES updater application'),
            StringStruct('FileVersion', '1.0.0.0'),
            StringStruct('InternalName', 'main.exe'),
-           StringStruct('LegalCopyright', '© 2025 Tyler de Zeeuw'),
+           StringStruct('LegalCopyright', '© 2025-2026 Tyler de Zeeuw'),
            StringStruct('OriginalFilename', 'flares_updater.exe'),
            StringStruct('ProductName', 'FLARES Updater'),
            StringStruct('ProductVersion', '1.0.0.0')])