fixes to cross platform saves

flares.py

@@ -3070,4 +3070,15 @@ def process_participant(file_path, progress_callback=None):
     if progress_callback: progress_callback(20)
     logger.info("20")
         
+    sanitize_paths_for_pickle(raw_haemo, epochs)
+
     return raw_haemo, epochs, fig_bytes, cha, contrast_results, df_ind, design_matrix, AGE, GENDER, GROUP, True
+
+def sanitize_paths_for_pickle(raw_haemo, epochs):
+    # Fix raw_haemo._filenames
+    if hasattr(raw_haemo, '_filenames'):
+        raw_haemo._filenames = [str(p) for p in raw_haemo._filenames]
+
+    # Fix epochs._raw._filenames
+    if hasattr(epochs, '_raw') and hasattr(epochs._raw, '_filenames'):
+        epochs._raw._filenames = [str(p) for p in epochs._raw._filenames]

main.py

@@ -19,7 +19,7 @@ import zipfile
 import platform
 import traceback
 import subprocess
-from pathlib import Path
+from pathlib import Path, PurePosixPath
 from datetime import datetime
 from multiprocessing import Process, current_process, freeze_support, Manager
 
@@ -4276,12 +4276,26 @@ class MainApplication(QMainWindow):
             return
 
         try:
-            project_data = {
-                "file_list": [bubble.file_path for bubble in self.bubble_widgets.values()],
-                "progress_states": {
-                    bubble.file_path: bubble.current_step for bubble in self.bubble_widgets.values()
-                },
+            # Ensure the filename has the proper extension
+            if not filename.endswith(".flare"):
+                filename += ".flare"
 
+            project_path = Path(filename).resolve()
+            project_dir = project_path.parent
+            
+            file_list = [
+                str(PurePosixPath(Path(bubble.file_path).resolve().relative_to(project_dir)))
+                for bubble in self.bubble_widgets.values()
+            ]
+
+            progress_states = {
+                str(PurePosixPath(Path(bubble.file_path).resolve().relative_to(project_dir))): bubble.current_step
+                for bubble in self.bubble_widgets.values()
+            }
+
+            project_data = {
+                "file_list": file_list,
+                "progress_states": progress_states,
                 "raw_haemo_dict": self.raw_haemo_dict,
                 "epochs_dict": self.epochs_dict,
                 "fig_bytes_dict": self.fig_bytes_dict,
@@ -4295,6 +4309,17 @@ class MainApplication(QMainWindow):
                 "valid_dict": self.valid_dict,
             }
             
+            def sanitize(obj):
+                if isinstance(obj, Path):
+                    return str(PurePosixPath(obj))
+                elif isinstance(obj, dict):
+                    return {sanitize(k): sanitize(v) for k, v in obj.items()}
+                elif isinstance(obj, list):
+                    return [sanitize(i) for i in obj]
+                return obj
+
+            project_data = sanitize(project_data)
+
             with open(filename, "wb") as f:
                 pickle.dump(project_data, f)
 
@@ -4328,8 +4353,19 @@ class MainApplication(QMainWindow):
             self.group_dict = data.get("group_dict", {})
             self.valid_dict = data.get("valid_dict", {})
 
-            # Restore bubbles and progress
-            self.show_files_as_bubbles_from_list(data["file_list"], data.get("progress_states", {}), filename)
+            project_dir = Path(filename).parent
+
+            # Convert saved relative paths to absolute paths
+            file_list = [str((project_dir / Path(rel_path)).resolve()) for rel_path in data["file_list"]]
+
+            # Also resolve progress_states with updated paths
+            raw_progress = data.get("progress_states", {})
+            progress_states = {
+                str((project_dir / Path(rel_path)).resolve()): step
+                for rel_path, step in raw_progress.items()
+            }
+
+            self.show_files_as_bubbles_from_list(file_list, progress_states, filename)
             
             # Re-enable buttons
             # self.button1.setVisible(True)