Fixed build

.vscode/tasks.json

@@ -4,7 +4,7 @@
         {
             "label": "Compile UI",
             "type": "shell",
-            "command": "pyside6-uic wgse/gui/form.ui -o wgse/gui/ui_form.py && pyside6-uic wgse/gui/header.ui -o wgse/gui/header.py",
+            "command": "pyside6-uic wgse/gui/form.ui -o wgse/gui/ui_form.py",
             "problemMatcher": [],
             "group": {
                 "kind": "build",

wgse/gui/main.py

@@ -2,27 +2,45 @@
 import webbrowser
 from pathlib import Path
 
-from PySide6.QtCore import QModelIndex, Qt
+from PyQt6.QtCore import QObject, pyqtSignal
+from PyQt6.QtWidgets import QApplication, QMainWindow
+from PySide6.QtCore import QModelIndex
 from PySide6.QtWidgets import (QApplication, QFileDialog, QMainWindow,
-                               QMessageBox, QTableWidgetItem, QLabel)
+                               QMessageBox, QTableWidgetItem)
 
-from wgse.adapters.alignment_map_file_info_adapter import AlignmentMapFileInfoAdapter
 from wgse.adapters.alignment_stats_adapter import AlignmentStatsAdapter
-from wgse.adapters.header_adapter import HeaderAdapter, HeaderCommentsAdapter, HeaderProgramsAdapter, HeaderReadGroupAdapter, HeaderSequenceAdapter
+from wgse.adapters.header_adapter import (HeaderCommentsAdapter,
+                                          HeaderProgramsAdapter,
+                                          HeaderReadGroupAdapter,
+                                          HeaderSequenceAdapter)
 from wgse.adapters.index_stats_adapter import IndexStatsAdapter
 from wgse.alignment_map.alignment_map_file import AlignmentMapFile
 from wgse.configuration import MANAGER_CFG
 from wgse.data.gender import Gender
 from wgse.data.sorting import Sorting
-from wgse.gui.table_dialog import ListTableDialog, TableDialog
-from wgse.utility.external import External
-from wgse.fasta.reference import Reference
-from wgse.gui.alignment_statistics_dialog import AlignmentStatisticsDialog
-from wgse.gui.header_dialog import HeaderDialog
 from wgse.gui.extract import ExtractDialog
-from wgse.gui.index_statistics_dialog import IndexStatisticsDialog
+from wgse.gui.table_dialog import ListTableDialog, TableDialog
 from wgse.gui.ui_form import Ui_MainWindow
-from wgse.renderers.html_aligned_file_report import HTMLAlignedFileReport
+from wgse.utility.external import External
+
+
+class Worker(QObject):
+    def __init__(self, f, parent=None) -> None:
+        super().__init__(parent)
+        self.finished = pyqtSignal()
+        self.progress = pyqtSignal(int)  # Optional progress signal
+        self.f = f
+
+    def run(self):
+        """Long-running task goes here."""
+        try:
+            self.f()
+            # Emit progress updates (optional)
+            # self.progress.emit(percentage)
+            pass
+        finally:
+            self.finished.emit()  # Always emit finished, even with errors
+
 
 class WGSEWindow(QMainWindow):
     def launch():
@@ -34,19 +52,14 @@ def launch():
     def __init__(
         self,
         parent=None,
-        config = MANAGER_CFG.GENERAL,
+        config=MANAGER_CFG.GENERAL,
         external: External = External(),
     ):
         super().__init__(parent)
         self._external = external
         self.config = config
         self.switch_to_main()
         return
-        # self.ui = Ui_Drop()
-        # self.ui.setupUi(self)
-        # self.setAlignment(Qt.AlignmentFlag.AlignCenter)
-        # self.setCentralWidget(self.ui.groupBox)
-        # self.setAcceptDrops(True)
 
     def switch_to_main(self):
         self.ui = Ui_MainWindow()
@@ -77,7 +90,6 @@ def dropEvent(self, event):
             print("Dropped file:", file_path)
             # Do something with the dropped file
 
-
     def export(self):
         if self.current_file is None:
             return
@@ -180,7 +192,7 @@ def file_item_clicked(self, index: QModelIndex):
             "Alignment stats": self._show_alignment_stats,
             "Index stats": self._show_index_stats,
             "Coverage stats": self._show_coverage_stats,
-        }
+        } 
         item = self.ui.fileInformationTable.verticalHeaderItem(index.row())
         if item.text() not in handlers:
             return
@@ -253,7 +265,9 @@ def _show_index_stats(self):
                 return
             self._do_indexing(user_informed=True)
         dialog = TableDialog("Index Statistics", self)
-        dialog.set_data(IndexStatsAdapter.adapt(self.current_file.file_info.index_stats))
+        dialog.set_data(
+            IndexStatsAdapter.adapt(self.current_file.file_info.index_stats)
+        )
         dialog.exec()
 
     def _show_coverage_stats(self):
@@ -266,22 +280,28 @@ def _show_alignment_stats(self):
         if self.current_file is None:
             return
         dialog = TableDialog("Alignment statistics", self)
-        dialog.set_data(AlignmentStatsAdapter.adapt(self.current_file.file_info.alignment_stats))
+        dialog.set_data(
+            AlignmentStatsAdapter.adapt(self.current_file.file_info.alignment_stats)
+        )
         dialog.exec()
 
     def _show_header(self):
         if self.current_file is None:
             return
-        
+
         dialog = ListTableDialog("Header", self)
         data = {
-            "Sequences": HeaderSequenceAdapter.adapt(self.current_file.header.sequences.values()),
+            "Sequences": HeaderSequenceAdapter.adapt(
+                self.current_file.header.sequences.values()
+            ),
             "Programs": HeaderProgramsAdapter.adapt(self.current_file.header.programs),
-            "Read groups": HeaderReadGroupAdapter.adapt(self.current_file.header.read_groups),
-            "Comments" : HeaderCommentsAdapter.adapt(self.current_file.header.comments)
+            "Read groups": HeaderReadGroupAdapter.adapt(
+                self.current_file.header.read_groups
+            ),
+            "Comments": HeaderCommentsAdapter.adapt(self.current_file.header.comments),
         }
         dialog.set_data(data)
         dialog.exec()
 
     def _gender_determined(self, gender: Gender):
-        pass
+        pass