Add parents to all widgets

finalcif/appwindow.py

@@ -475,7 +475,7 @@ def import_text_template(self):
             doc = read_document_from_cif_file(filename)
             block: gemmi.cif.Block = doc.sole_block()
         except Exception:
-            show_general_warning('This file is not readable.')
+            show_general_warning(self, 'This file is not readable.')
             return
         text_list = []
         for i in block:
@@ -500,7 +500,7 @@ def export_text_template(self) -> None:
             loop = block.init_loop(blockname, [''])
         except RuntimeError:
             # Not a valid loop key
-            show_general_warning('"{}" is not a valid cif keyword.'.format(blockname))
+            show_general_warning(self, '"{}" is not a valid cif keyword.'.format(blockname))
             return
         for value in textlist:
             if value:
@@ -514,7 +514,7 @@ def export_text_template(self) -> None:
         except PermissionError:
             if Path(filename).is_dir():
                 return
-            show_general_warning('No permission to write file to {}'.format(Path(filename).resolve()))
+            show_general_warning(self, 'No permission to write file to {}'.format(Path(filename).resolve()))
         self.status_bar.show_message(f'Template exported to {filename}.', timeout=10)
 
     def delete_text_template(self) -> None:
@@ -703,7 +703,7 @@ def is_update_necessary(self, content: bytes) -> None:
             remote_version = int(content.decode('ascii', errors='ignore'))
         if remote_version > VERSION:
             print('Version {} is outdated (actual is {}).'.format(VERSION, remote_version))
-            show_update_warning(remote_version)
+            show_update_warning(self, remote_version)
         else:
             print('Version {} is up-to-date.'.format(VERSION))
 
@@ -1127,13 +1127,13 @@ def make_report_tables(self) -> None:
                 raise
             print('Unable to make report from cif file.')
             not_ok = e
-            show_general_warning("The report templates could not be found:\n" + str(not_ok))
+            show_general_warning(self, "The report templates could not be found:\n" + str(not_ok))
             return
         except PermissionError:
             if DEBUG:
                 raise
             print('Unable to open cif file')
-            show_general_warning('The report document {} could not be opened.\n'
+            show_general_warning(self, 'The report document {} could not be opened.\n'
                                  'Is the file already opened?'.format(report_filename.name))
             return
         if not self.running_inside_unit_test:
@@ -1219,7 +1219,7 @@ def save_current_cif_file(self) -> Union[bool, None]:
         except Exception as e:
             print('Unable to save file:')
             print(e)
-            show_general_warning('Can not save file: ' + str(e))
+            show_general_warning(self, 'Can not save file: ' + str(e))
             return False
 
     def store_data_from_table_rows(self) -> None:
@@ -1232,7 +1232,7 @@ def store_data_from_table_rows(self) -> None:
                 changes_cif = self.get_changes_cif(self.finalcif_changes_filename)
             except Exception as e:
                 print('Unable to create changes CIF:', e)
-                unable_to_open_message(filepath=self.finalcif_changes_filename, not_ok=e)
+                unable_to_open_message(parent=self, filepath=self.finalcif_changes_filename, not_ok=e)
                 changes_cif = None
         # makes sure also the currently edited item is saved:
         self.ui.cif_main_table.setCurrentItem(None)
@@ -1360,24 +1360,24 @@ def import_additional_cif(self, filename: str):
         try:
             imp_cif = CifContainer(Path(filename))
         except RuntimeError as e:
-            show_general_warning('Could not import {}:\n'.format(filename) + str(e))
+            show_general_warning(self, 'Could not import {}:\n'.format(filename) + str(e))
             return
         except ValueError as e:
             warning = 'Problems parsing file: {}:\n'.format(filename) + str(e)
             if 'data_' in str(e):
                 warning = warning + "\n\nA CIF needs to start with 'data_[some_name]'."
-            show_general_warning(warning)
+            show_general_warning(self, warning)
             return
         except IOError as e:
-            show_general_warning('Unable to open file {}:\n'.format(filename) + str(e))
+            show_general_warning(self, 'Unable to open file {}:\n'.format(filename) + str(e))
             return
         self.check_cif_for_missing_values_before_really_open_it()
         try:
             self.import_key_value_pairs(imp_cif)
             self.import_loops(imp_cif)
         except Exception as e:
             print(e)
-            unable_to_open_message(Path(self.cif.filename), e)
+            unable_to_open_message(self, Path(self.cif.filename), e)
         # I think I leave the user possibilities to change the imported values:
         # self.save_current_cif_file()
         # self.load_cif_file(str(self.cif.finalcif_file))
@@ -1450,7 +1450,7 @@ def load_cif_file(self, filepath: Path, block=0, load_changes: bool = True) -> N
             print(e)
             not_ok = e
         if not_ok:
-            unable_to_open_message(filepath, not_ok)
+            unable_to_open_message(self, filepath, not_ok)
             return
         if not self.cif.chars_ok:
             self.warn_about_bad_cif()
@@ -1487,7 +1487,7 @@ def _load_block(self, index: int, load_changes: bool = True) -> None:
             self.fill_cif_table()
         except UnicodeDecodeError:
             nums = self.cif.get_line_numbers_of_bad_characters(Path(self.cif.doc.source))
-            show_general_warning(window_title='Unable to open file',
+            show_general_warning(parent=self, window_title='Unable to open file',
                                  warn_text='Invalid characters in file!',
                                  info_text=f'The file "{Path(self.cif.doc.source)}" has invalid '
                                            f'characters in line(s)'
@@ -1516,7 +1516,7 @@ def _load_block(self, index: int, load_changes: bool = True) -> None:
                 try:
                     self.load_changes_cif()
                 except Exception as e:
-                    unable_to_open_message(filepath=self.finalcif_changes_filename, not_ok=e)
+                    unable_to_open_message(parent=self, filepath=self.finalcif_changes_filename, not_ok=e)
             if self.running_inside_unit_test and changes_exist:
                 self.load_changes_cif()
         self.make_loops_tables()
@@ -1576,9 +1576,9 @@ def append_cif(self, cif_file: Path):
             return
         cif2 = CifContainer(cif_file)
         if cif2.is_multi_cif:
-            show_general_warning('Can add single data CIFs only!')
+            show_general_warning(self, 'Can add single data CIFs only!')
         if cif2.block.name in [x.name for x in self.cif.doc]:
-            show_general_warning(warn_text='Duplicate block', info_text='Data block name "<b>{}</b>" already present '
+            show_general_warning(self, warn_text='Duplicate block', info_text='Data block name "<b>{}</b>" already present '
                                                                         'in current CIF!'.format(self.cif.block.name))
             return
         self.cif.doc.add_copied_block(block=cif2.block, pos=-1)
@@ -1604,7 +1604,7 @@ def check_cif_for_missing_values_before_really_open_it(self) -> None:
             print(str(e))
             errlist = str(e).split(':')
             if len(errlist) > 1:
-                show_general_warning(
+                show_general_warning(self,
                     f"Attention in CIF line {errlist[1]}:\n'{errlist[2].split()[0]}' has no value.")
 
     def get_last_workdir(self):
@@ -1625,15 +1625,15 @@ def set_path_display_in_file_selector(self, fname: str) -> None:
 
     def able_to_open(self, filepath: Path) -> bool:
         if not filepath.exists():
-            show_general_warning("The file you tried to open does not exist!")
+            show_general_warning(self, "The file you tried to open does not exist!")
             return False
         if filepath.stat().st_size == 0:
-            show_general_warning('This file has zero byte size!')
+            show_general_warning(self, 'This file has zero byte size!')
             return False
         return True
 
     def warn_about_bad_cif(self):
-        show_general_warning("You have non-ascii characters like umlauts in the SHELX file "
+        show_general_warning(self, "You have non-ascii characters like umlauts in the SHELX file "
                              "attached to this CIF.\n\n"
                              "FinalCif tries to convert them, but be warned "
                              "(they are not allowed in CIF1 files anyway).\n")
@@ -1744,7 +1744,7 @@ def check_Z(self) -> None:
                                or csystem == 'hexagonal' or csystem == 'cubic'):
             bad = True
         if bad:
-            bad_z_message(Z)
+            bad_z_message(self, Z)
 
     def get_data_sources(self) -> None:
         """
@@ -1848,9 +1848,9 @@ def fill_cif_table(self) -> None:
                 #threading.Thread(target=self.ui.cif_main_table.resizeRowsToContents).start()
             # print(key, value)
         if not self.cif.test_res_checksum():
-            show_res_checksum_warning()
+            show_res_checksum_warning(parent=self)
         if not self.cif.test_hkl_checksum():
-            show_hkl_checksum_warning()
+            show_hkl_checksum_warning(parent=self)
         if self.cif.is_multi_cif:
             self.refresh_combo_boxes()
         else:
@@ -1904,7 +1904,7 @@ def add_res_file_to_loops(self) -> None:
         textedit.setReadOnly(True)
 
     def _go_to_new_loop_page(self):
-        self.loopcreate = LoopCreator(cif=self.cif)
+        self.loopcreate = LoopCreator(parent=self, cif=self.cif)
         self.ui.LoopsTabWidget.addTab(self.loopcreate, 'Create Loops')
         self.ui.LoopsTabWidget.setCurrentIndex(self.ui.LoopsTabWidget.count() - 1)
         self.ui.revertLoopsPushButton.hide()

finalcif/cif/cod/deposit.py

@@ -299,7 +299,7 @@ def prepare_upload(self, username, password, author_name, author_email,
         data = self._enrich_upload_data(author_email, author_name, data, deposition_type, embargo_time)
         files = self._get_files_data_for_upload()
         if 'hkl' not in files and not self.cif.hkl_file \
-            and not show_ok_cancel_warning('You are attempting to upload a CIF without hkl data.\n'
+            and not show_ok_cancel_warning(self.ui.Mainwidget, 'You are attempting to upload a CIF without hkl data.\n'
                                            'Do you really want to proceed?'):
             self.ui.depositOutputTextBrowser.setText('Deposition aborted.')
             return
@@ -386,14 +386,14 @@ def _set_external_hkl_file(self) -> None:
             cif = CifContainer(file)
             list_code = cif['_shelx_refln_list_code']
             if list_code != '4':
-                show_general_warning('Only plain hkl or fcf (LIST 4 style) files should be uploaded.')
+                show_general_warning(self.ui.Mainwidget, 'Only plain hkl or fcf (LIST 4 style) files should be uploaded.')
                 return
             self.hkl_file = io.StringIO(Path(file).read_text())
             self.hkl_file.name = Path(file).name
         elif file == '':
             self.hkl_file = None
         else:
-            show_general_warning('Only plain hkl or fcf (LIST 4 style) files should be uploaded.')
+            show_general_warning(self.ui.Mainwidget, 'Only plain hkl or fcf (LIST 4 style) files should be uploaded.')
 
 
 if __name__ == '__main__':

finalcif/datafiles/bruker_data.py

@@ -115,22 +115,22 @@ def __init__(self, app, cif: CifContainer):
             temperature = ''
         if (self.cif['_diffrn_ambient_temperature'].split('(')[0] or
             self.cif['_cell_measurement_temperature']).split('(')[0] == '0':
-            show_general_warning('<b>Warning of impossible temperature specification</b>:<br>'
-                                 'You probably entered &minus;273.15 °C instead '
-                                 'of &minus;173.15 °C into the SHELX instruction file.<br>'
-                                 'A temperature of 0 K is likely to be wrong.')
+            show_general_warning(self.app, '<b>Warning of impossible temperature specification</b>:<br>'
+                                           'You probably entered &minus;273.15 °C instead '
+                                           'of &minus;173.15 °C into the SHELX instruction file.<br>'
+                                           'A temperature of 0 K is likely to be wrong.')
         try:
             if abs(int(self.cif['_diffrn_ambient_temperature'].split('(')[0]) - int(temperature)) >= 2 and \
-                not self.app.temperature_warning_displayed:
+                    not self.app.temperature_warning_displayed:
                 self.app.temperature_warning_displayed = True
-                show_general_warning('<b>Warning</b>: The temperature from the measurement and '
-                                     'from SHELX differ. Please double-check for correctness.<br><br>'
-                                     'SHELX says: {} K<br>'
-                                     'The P4P file says: {} K<br>'
-                                     'Frame header says: {} K<br><br>'
-                                     'You may add a '
-                                     '<a href="http://shelx.uni-goettingen.de/shelxl_html.php#TEMP">TEMP</a> '
-                                     'instruction to your SHELX file (in °C).'
+                show_general_warning(self.app, '<b>Warning</b>: The temperature from the measurement and '
+                                               'from SHELX differ. Please double-check for correctness.<br><br>'
+                                               'SHELX says: {} K<br>'
+                                               'The P4P file says: {} K<br>'
+                                               'Frame header says: {} K<br><br>'
+                                               'You may add a '
+                                               '<a href="http://shelx.uni-goettingen.de/shelxl_html.php#TEMP">TEMP</a> '
+                                               'instruction to your SHELX file (in °C).'
                                      .format(self.cif['_diffrn_ambient_temperature'].split('(')[0],
                                              round(temp2, 1),
                                              round(temp1, 1)))

finalcif/equip_property/author_loop_templates.py

@@ -166,7 +166,7 @@ def check_if_loop_and_row_size_fit_together(self, gemmi_loop: gemmi.cif.Loop, ro
             if cut_row not in gemmi_loop.values:
                 gemmi_loop.add_row(cut_row)
         elif gemmi_loop.width() > len(row):
-            show_general_warning('An author loop with larger size is already in the CIF. Can not proceed.')
+            show_general_warning(self, 'An author loop with larger size is already in the CIF. Can not proceed.')
         else:
             if row not in gemmi_loop.values:
                 gemmi_loop.add_row(row)
@@ -283,7 +283,7 @@ def export_author_template(self, filename: str = None) -> None:
         except (PermissionError, IOError):
             if Path(filename).is_dir():
                 return
-            show_general_warning('No permission to write file to {}'.format(Path(filename).resolve()))
+            show_general_warning(self, 'No permission to write file to {}'.format(Path(filename).resolve()))
 
     def put_author_in_cif_object(self, blockname: str, filename: str) -> CifContainer:
         author = self.author_loopdata(author_name=self.get_selected_loop_name())

finalcif/equip_property/equipment.py

@@ -181,11 +181,11 @@ def save_equipment_template(self) -> None:
         for key, _ in table_data:
             if key not in cif_all_dict.keys():
                 if not key.startswith('_'):
-                    show_general_warning('"{}" is not a valid keyword! '
+                    show_general_warning(self.app, '"{}" is not a valid keyword! '
                                          '\nChange the name in order to save.\n'
                                          'Keys must start with an underscore.'.format(key))
                     return
-                show_general_warning('"{}" is not an official CIF keyword!'.format(key))
+                show_general_warning(self.app, '"{}" is not an official CIF keyword!'.format(key))
         self.settings.save_settings_list('equipment', self.selected_template_name(), table_data)
         self.app.ui.EquipmentTemplatesStackedWidget.setCurrentIndex(0)
         print('saved')
@@ -269,7 +269,7 @@ def export_equipment_template(self, filename: str = None) -> None:
         except PermissionError:
             if Path(filename).is_dir():
                 return
-            show_general_warning('No permission to write file to {}'.format(Path(filename).resolve()))
+            show_general_warning(self.app, 'No permission to write file to {}'.format(Path(filename).resolve()))
 
     def cancel_equipment_template(self) -> None:
         """

finalcif/equip_property/properties.py

@@ -172,7 +172,7 @@ def export_property_template(self, filename: str = '') -> None:
             loop = block.init_loop(cif_key, [''])
         except RuntimeError:
             # Not a valid loop key
-            show_general_warning('"{}" is not a valid cif keyword.'.format(cif_key))
+            show_general_warning(self.app, '"{}" is not a valid cif keyword.'.format(cif_key))
             return
         for value in table_data:
             if value:
@@ -186,7 +186,7 @@ def export_property_template(self, filename: str = '') -> None:
         except PermissionError:
             if Path(filename).is_dir():
                 return
-            show_general_warning('No permission to write file to {}'.format(Path(filename).resolve()))
+            show_general_warning(self.app, 'No permission to write file to {}'.format(Path(filename).resolve()))
 
     def selected_template_name(self) -> str:
         return self.app.ui.PropertiesTemplatesListWidget.currentIndex().data()

finalcif/equip_property/tools.py

@@ -15,7 +15,7 @@ def read_document_from_cif_file(filename: str) -> Union[gemmi.cif.Document, None
         warning = "{}\n{}".format('This CIF is invalid:', str(e))
         if 'data_' in str(e):
             warning =  f"{warning}\n\nA CIF needs to start with 'data_[some_name]'."
-        show_general_warning(warning)
+        show_general_warning(parent=None, warn_text=warning)
     except IOError as e:
-        show_general_warning(f'Unable to open file {filename}:\n{str(e)}')
+        show_general_warning(parent=None, warn_text=f'Unable to open file {filename}:\n{str(e)}')
     return doc

finalcif/finalcif_start.py

@@ -57,7 +57,7 @@ def main():
     if len(sys.argv) > 1:
         file = Path(sys.argv[1])
         if not file.is_file():
-            show_general_warning(warn_text=f'The file {file.resolve().absolute()} \nyou tried to open does not exist.',
+            show_general_warning(parent=None, warn_text=f'The file {file.resolve().absolute()} \nyou tried to open does not exist.',
                                  window_title='File not found')
             file = None
     app.setQuitOnLastWindowClosed(True)

finalcif/gui/custom_classes.py

@@ -37,10 +37,9 @@ class MyCifTable(QTableWidget, ItemTextMixin):
     new_key = QtCore.pyqtSignal(str)
 
     def __init__(self, parent: QWidget = None, *args, **kwargs):
-        super().__init__(*args, **kwargs)
+        super().__init__(parent=parent, *args, **kwargs)
         self.parent = parent
         self.setAttribute(QtCore.Qt.WA_DeleteOnClose)
-        self.setParent(parent)
         self.installEventFilter(self)
         self.setSizeAdjustPolicy(QAbstractScrollArea.AdjustToContents)
         self.setVerticalScrollBarPolicy(Qt.ScrollBarAsNeeded)