further issue fixes

changelog.md

@@ -1,6 +1,14 @@
 # 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
 
 
 # Version 1.2.0

main.py

@@ -46,7 +46,7 @@ from PySide6.QtGui import QAction, QKeySequence, QIcon, QIntValidator, QDoubleVa
 from PySide6.QtSvgWidgets import QSvgWidget # needed to show svgs when app is not frozen
 
 
-CURRENT_VERSION = "1.2.0"
+CURRENT_VERSION = "1.2.1"
 
 API_URL = "https://git.research.dezeeuw.ca/api/v1/repos/tyler/flares/releases"
 API_URL_SECONDARY = "https://git.research2.dezeeuw.ca/api/v1/repos/tyler/flares/releases"
@@ -1480,11 +1480,11 @@ class ParamSection(QWidget):
                 }
     """
         
-    def __init__(self, section_data):
+    def __init__(self, section_data, global_widgets):
         super().__init__()
         layout = QVBoxLayout()
         self.setLayout(layout)
-        self.widgets = {}
+        self.widgets = global_widgets
         self.dependencies = []
         self.selected_path = None
 
@@ -1527,7 +1527,7 @@ class ParamSection(QWidget):
                 widget = QComboBox()
                 widget.addItems(["True", "False"])
                 widget.setCurrentText(str(param["default"]))
-                widget.currentTextChanged.connect(self.update_dependencies)
+                widget.currentTextChanged.connect(self.notify_global_update)
             elif param["type"] == int:
                 widget = QLineEdit()
                 widget.setValidator(QIntValidator())
@@ -1541,7 +1541,7 @@ class ParamSection(QWidget):
                     widget = QComboBox()
                     widget.addItems(param.get("options", []))
                     widget.setCurrentText(str(param.get("default", "<None Selected>")))
-                    widget.currentTextChanged.connect(self.update_dependencies)
+                    widget.currentTextChanged.connect(self.notify_global_update)
                 else:
                     widget = self._create_multiselect_dropdown(None)
             elif param["type"] == range:
@@ -1580,6 +1580,16 @@ class ParamSection(QWidget):
 
         self.update_dependencies()
 
+    def notify_global_update(self):
+        """
+        Since dependencies can cross sections, we need to tell 
+        all sections to refresh their enabled/disabled states.
+        """
+        # If you have a reference to the parent container, call its update.
+        # Otherwise, you can iterate through the known param_sections:
+        for section in self.parent().findChildren(ParamSection):
+            section.update_dependencies()
+
     def update_dependencies(self):
         """Disables/Enables widgets based on parent selection values."""
         for dep in self.dependencies:
@@ -1691,6 +1701,12 @@ class ParamSection(QWidget):
             widget = info["widget"]
             expected_type = info["type"]
 
+            if name == "SHORT_CHANNEL_REGRESSION":
+                # If the widget is disabled (greyed out), force False
+                if not widget.isEnabled():
+                    values[name] = False
+                    continue
+
             if expected_type == bool:
                 values[name] = widget.currentText() == "True"
             elif expected_type == list:
@@ -4061,6 +4077,7 @@ class MainApplication(QMainWindow):
         self.is_2d_bypass = False
         self.incompatible_save_bypass = False
         self.missing_events_bypass = False
+        self.analysis_clearing_bypass = False
 
         self.files_total = 0        # total number of files to process
         self.files_done = set()     # set of file paths done (success or fail)
@@ -4313,7 +4330,8 @@ class MainApplication(QMainWindow):
         preferences_actions = [
             ("2D Data Bypass", "", self.is_2d_bypass_func, resource_path("icons/info_24dp_1F1F1F.svg")),
             ("Incompatible Save Bypass", "", self.incompatable_save_bypass_func, resource_path("icons/info_24dp_1F1F1F.svg")),
-            ("Missing Events Bypass", "", self.missing_events_bypass_func, resource_path("icons/info_24dp_1F1F1F.svg"))
+            ("Missing Events Bypass", "", self.missing_events_bypass_func, resource_path("icons/info_24dp_1F1F1F.svg")),
+            ("Analysis Clearing Bypass", "", self.analysis_clearing_bypass_func, resource_path("icons/info_24dp_1F1F1F.svg"))
         ]
         for name, shortcut, slot, icon in preferences_actions:
             preferences_menu.addAction(make_action(name, shortcut, slot, icon=icon, checkable=True, checked=False))
@@ -4337,13 +4355,18 @@ class MainApplication(QMainWindow):
                 widget.deleteLater()
         self.param_sections.clear()
 
+        self.global_param_widgets = {}
+
         # Add ParamSection widgets from SECTIONS
         for section in SECTIONS:
-            self.section_widget = ParamSection(section)
+            self.section_widget = ParamSection(section, self.global_param_widgets)
             self.rows_layout.addWidget(self.section_widget)
 
             self.param_sections.append(self.section_widget)
 
+            for sec in self.param_sections:
+                sec.update_dependencies()
+
 
     def clear_all(self):
         
@@ -4358,6 +4381,11 @@ class MainApplication(QMainWindow):
             if widget:
                 widget.deleteLater()
 
+        if hasattr(self, "selected_paths"):
+            self.selected_paths = []
+        if hasattr(self, "selected_path"):
+            self.selected_path = None
+
         # Clear file data
         self.bubble_widgets.clear()
         self.statusBar().clearMessage()
@@ -4405,6 +4433,9 @@ class MainApplication(QMainWindow):
     def missing_events_bypass_func(self, checked):
         self.missing_events_bypass = checked
 
+    def analysis_clearing_bypass_func(self, checked):
+        self.analysis_clearing_bypass = checked
+
     def about_window(self):
         if self.about is None or not self.about.isVisible():
             self.about = AboutWindow(self)
@@ -4533,6 +4564,15 @@ class MainApplication(QMainWindow):
 
     def save_project(self, onCrash=False):
 
+        if not getattr(self, 'raw_haemo_dict', None):
+            if not onCrash: # Don't show popups during a crash/autosave
+                QMessageBox.warning(
+                    self, 
+                    "Save Project", 
+                    "There is no processed data to save. Please process some data before saving."
+                )
+            return
+
         if not onCrash:
             filename, _ = QFileDialog.getSaveFileName(
                 self, "Save Project", "", "FLARE Project (*.flare)"
@@ -4554,12 +4594,12 @@ class MainApplication(QMainWindow):
             project_dir = project_path.parent
             
             file_list = [
-                str(PurePosixPath(Path(bubble.file_path).resolve().relative_to(project_dir)))
+                str(PurePosixPath(os.path.relpath(Path(bubble.file_path).resolve(), 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
+                str(PurePosixPath(os.path.relpath(Path(bubble.file_path).resolve(), project_dir))): bubble.current_step
                 for bubble in self.bubble_widgets.values()
             }
 
@@ -5061,6 +5101,39 @@ class MainApplication(QMainWindow):
     '''MODULE FILE'''
     def on_run_task(self):
 
+        #do the check
+        if not self.analysis_clearing_bypass:
+            if self.button3.isVisible():
+                msg = QMessageBox(self)
+                msg.setWindowTitle("Confirm - FLARES")
+                msg.setText("Processing new data will clear the current analysis. Continue? (If you do not want this dialog box to appear, toggle 'Analysis Clearing Bypass' from the Preferences menu.)")
+                
+                # Add the OK and Cancel buttons
+                msg.setStandardButtons(QMessageBox.StandardButton.Ok | QMessageBox.StandardButton.Cancel)
+                
+                # Set the default button (highlighted)
+                msg.setDefaultButton(QMessageBox.StandardButton.Cancel)
+
+                # Capture the result
+                response = msg.exec()
+
+                if response == QMessageBox.StandardButton.Ok:
+                    print("User clicked OK")
+                else:
+                    return
+
+            self.button3.setVisible(False)
+    
+            self.raw_haemo_dict = {}
+            self.config_dict = {}
+            self.epochs_dict = {}
+            self.fig_bytes_dict = {}
+            self.cha_dict = {}
+            self.contrast_results_dict = {}
+            self.df_ind_dict = {}
+            self.design_matrix_dict = {}
+            self.valid_dict = {}
+            
         self.button1.clicked.disconnect(self.on_run_task)
         self.button1.setText("Cancel")
         self.button1.clicked.connect(self.cancel_task)