fixup! transitioned RNAlysis to Qt6

rnalysis/gui/gui.py

@@ -3386,28 +3386,27 @@ def new_table_from_folder_htseqcount(self):
 
     def load_multiple_files(self):
         filenames, _ = QtWidgets.QFileDialog.getOpenFileNames(self, "Choose files")
-        if filenames:
-            if len(filenames) > 0:
-                window = MultiOpenWindow(filenames, self)
-                accepted = window.exec()
-                if accepted:
-                    paths, types, names, kwargs = window.result()
-                    tabs_to_close = None
-                    if self.tabs.currentWidget().is_empty():
-                        tabs_to_close = self.tabs.currentIndex()
-
-                    for filename in filenames:
-                        path = paths[filename]
-                        table_type = FILTER_OBJ_TYPES[types[filename]]
-                        name = names[filename]
-                        filter_obj = table_type(path, **kwargs[filename])
-                        if name == '':
-                            self.new_tab_from_filter_obj(filter_obj, JOB_COUNTER.get_id())
-                        else:
-                            self.new_tab_from_filter_obj(filter_obj, JOB_COUNTER.get_id(), name)
-                        QtWidgets.QApplication.processEvents()
-                    if tabs_to_close is not None:
-                        self.tabs.removeTab(tabs_to_close)
+        if len(filenames) > 0:
+            window = MultiOpenWindow(filenames, self)
+            accepted = window.exec()
+            if accepted:
+                paths, types, names, kwargs = window.result()
+                tabs_to_close = None
+                if self.tabs.currentWidget().is_empty():
+                    tabs_to_close = self.tabs.currentIndex()
+
+                for filename in filenames:
+                    path = paths[filename]
+                    table_type = FILTER_OBJ_TYPES[types[filename]]
+                    name = names[filename]
+                    filter_obj = table_type(path, **kwargs[filename])
+                    if name == '':
+                        self.new_tab_from_filter_obj(filter_obj, JOB_COUNTER.get_id())
+                    else:
+                        self.new_tab_from_filter_obj(filter_obj, JOB_COUNTER.get_id(), name)
+                    QtWidgets.QApplication.processEvents()
+                if tabs_to_close is not None:
+                    self.tabs.removeTab(tabs_to_close)
 
     @QtCore.pyqtSlot(filtering.Filter, int, str)
     @QtCore.pyqtSlot(filtering.Filter, int)
@@ -3631,18 +3630,15 @@ def import_pipeline(self):
             self._import_pipeline_from_str(pipeline_name, content)
 
     def import_multiple_gene_sets(self):
-        dialog = gui_windows.MultiFileSelectionDialog()
-        accepted = dialog.exec()
-        if accepted == QtWidgets.QDialog.DialogCode.Accepted:
-            filenames = dialog.result()
-            tabs_to_close = None
-            if len(filenames) > 0 and self.tabs.currentWidget().is_empty():
-                tabs_to_close = self.tabs.currentIndex()
-            for filename in filenames:
-                gene_set = self._filename_to_gene_set(filename)
-                self.new_tab_from_gene_set(gene_set, JOB_COUNTER.get_id(), Path(filename).stem)
-            if tabs_to_close is not None:
-                self.tabs.removeTab(tabs_to_close)
+        filenames, _ = QtWidgets.QFileDialog.getOpenFileNames(self, "Choose files")
+        tabs_to_close = None
+        if len(filenames) > 0 and self.tabs.currentWidget().is_empty():
+            tabs_to_close = self.tabs.currentIndex()
+        for filename in filenames:
+            gene_set = self._filename_to_gene_set(filename)
+            self.new_tab_from_gene_set(gene_set, JOB_COUNTER.get_id(), Path(filename).stem)
+        if tabs_to_close is not None:
+            self.tabs.removeTab(tabs_to_close)
 
     def import_gene_set(self):
         filename, _ = QtWidgets.QFileDialog.getOpenFileName(self, "Choose a file", filter=

rnalysis/gui/gui_windows.py

@@ -419,7 +419,7 @@ def save_settings(self):
             dbs = []
             for i in range(self.appearance_widgets['databases'].count()):
                 item = self.appearance_widgets['databases'].item(i)
-                if item.checkState():
+                if item.checkState() == QtCore.Qt.CheckState.Checked:
                     dbs.append(item.text())
 
             settings.set_gui_settings(font, font_size, theme, dbs, show_tutorial, prompt_report_gen)

tests/test_gui.py

@@ -2439,8 +2439,8 @@ def test_MainWindow_multiple_new_tables(main_window, monkeypatch):
     def mock_exec(self):
         return True
 
-    def mock_multi_selection_result(self):
-        return filenames
+    def mock_multi_selection_result(self, _):
+        return filenames, ''
 
     def mock_multi_open_result(self):
         filename_dict = {fname: fname for fname in filenames}
@@ -2451,9 +2451,8 @@ def mock_multi_open_result(self):
                        filenames[2]: {'numerator_name': 'num', 'denominator_name': 'denom'}}
         return filename_dict, types_dict, names_dict, kwargs_dict
 
-    monkeypatch.setattr(gui_windows.MultiFileSelectionDialog, 'exec', mock_exec)
     monkeypatch.setattr(MultiOpenWindow, 'exec', mock_exec)
-    monkeypatch.setattr(gui_windows.MultiFileSelectionDialog, 'result', mock_multi_selection_result)
+    monkeypatch.setattr(QtWidgets.QFileDialog, 'getOpenFileNames', mock_multi_selection_result)
     monkeypatch.setattr(MultiOpenWindow, 'result', mock_multi_open_result)
     main_window.new_multiple_action.trigger()
 
@@ -2507,11 +2506,10 @@ def test_MainWindow_import_multiple_gene_sets(main_window_with_tabs, monkeypatch
         truth_featureset = enrichment.FeatureSet(truth_set, Path(filename).stem)
         truth.append(truth_featureset)
 
-    def mock_get_files(*args, **kwargs):
-        return filenames
+    def mock_multi_selection_result(self, _):
+        return filenames, ''
 
-    monkeypatch.setattr(gui_windows.MultiFileSelectionDialog, 'result', mock_get_files)
-    monkeypatch.setattr(gui_windows.MultiFileSelectionDialog, 'exec', lambda *args, **kwargs: True)
+    monkeypatch.setattr(QtWidgets.QFileDialog, 'getOpenFileNames', mock_multi_selection_result)
     main_window_with_tabs.import_multiple_sets_action.trigger()
     assert main_window_with_tabs.tabs.count() == 5 + len(filenames)
     assert isinstance(main_window_with_tabs.tabs.currentWidget(), SetTabPage)