finalcif 169__tar.gz → 170__tar.gz

{finalcif-169 → finalcif-170}/Finalcif_installer_win.spec

@@ -9,7 +9,7 @@ site_packages = next(p for p in sys.path if 'site-packages' in p)
 
 a = Analysis(['finalcif/finalcif_start.py'],
              pathex=['finalcif'],
-             binaries=[('update.exe', '.')],
+             binaries=[],
              datas=[('finalcif/gui', 'gui'),
                     (path.join(site_packages, "docx", "templates"), 'finalcif/docx/templates'),
                     ('finalcif/template', 'template'), ('finalcif/icon', 'icon'),

{finalcif-169 → finalcif-170}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: finalcif
-Version: 169
+Version: 170
 Summary: CIF file editor
 Project-URL: Homepage, https://dkratzert.de/finalcif.html
 Project-URL: Bug Tracker, https://github.com/dkratzert/FinalCif/issues

finalcif-170/finalcif/__init__.py

@@ -0,0 +1,3 @@
+
+VERSION = 170
+__version__ = VERSION

{finalcif-169 → finalcif-170}/finalcif/appwindow.py

@@ -70,13 +70,15 @@ from finalcif.gui.plaintextedit import MyQPlainTextEdit
 from finalcif.gui.validators import calculated_z_validator
 from finalcif.gui.checkcif_browser import CheckCifBrowser
 from finalcif.gui.text_value_editor import MyTextTemplateEdit, TextEditItem
+from finalcif.gui.timers import single_shot
 from finalcif.cif.vrf_entry import VRFEntry
 from finalcif.gui.vrf_classes import MyVRFContainer
 from finalcif.template.templates import ReportTemplates
 from finalcif.tools.download import MyDownloader
 from finalcif.tools.dsrmath import my_isnumeric
 from finalcif.tools.misc import (next_path, celltxt, to_float, is_database_number,
-                                 open_file, strip_finalcif_of_name, file_age_in_days, open_in_text_editor)
+                                 open_file, strip_finalcif_of_name, file_age_in_days, open_in_text_editor,
+                                 running_inside_unit_test as is_unit_test)
 from finalcif.tools.options import Options
 from finalcif.tools.platon import PlatonRunner
 from finalcif.tools.settings import FinalCifSettings
@@ -155,6 +157,7 @@ class _StructureFactorReportThread(QtCore.QThread):
 
 
 class AppWindow(QMainWindow):
+    thread_shutdown_timeout_ms = 10_000
 
     def __init__(self, file: Path | None = None):
         super().__init__()
@@ -163,6 +166,7 @@ class AppWindow(QMainWindow):
         self.thread_version = None
         self.worker = None
         self._z_thread: _ZEstimatorThread | None = None
+        self.structure_factor_thread: _StructureFactorReportThread | None = None
         self.setAttribute(QtCore.Qt.WidgetAttribute.WA_DeleteOnClose)
         # This prevents some things to happen during unit tests:
         # Open of target dir of shred cif,
@@ -269,9 +273,9 @@ class AppWindow(QMainWindow):
 
     @property
     def running_inside_unit_test(self):
-        if "RUNNING_TEST" in os.environ:
+        if is_unit_test():
             if DEBUG:
-                print(f'pytest process running: {os.environ["PYTEST_CURRENT_TEST"]}')
+                print(f'pytest process running: {os.environ.get("PYTEST_CURRENT_TEST")}')
             return True
         return False
 
@@ -540,8 +544,8 @@ class AppWindow(QMainWindow):
 
     def set_video_image_for_report(self):
         image_filename = self.cif.finalcif_file_prefixed(prefix='', suffix='_video-finalcif.png')
-        self.video.save_image(image_filename)
-        self.options.video_image = image_filename
+        if self.video.save_image(image_filename):
+            self.options.video_image = image_filename
 
     def _select_crystal_video(self, video_file: Path | None = None) -> None:
         if video_file is None:
@@ -875,8 +879,26 @@ class AppWindow(QMainWindow):
         with suppress(Exception):
             self._savesize()
         self.settings.flush()
+        self._stop_background_threads()
         super().closeEvent(event)
 
+    def _stop_background_threads(self) -> None:
+        """Finish all worker threads before Qt destroys them together with this window.
+
+        Qt aborts the whole process when a running QThread is deleted. findChildren()
+        is used instead of the individual attributes because a superseded worker may
+        still run after its attribute was cleared.
+        """
+        for thread in self.findChildren(QtCore.QThread):
+            if not thread.isRunning():
+                continue
+            # Prevent a result from being delivered into the dying window.
+            thread.blockSignals(True)
+            thread.quit()
+            if not thread.wait(self.thread_shutdown_timeout_ms):
+                thread.terminate()
+                thread.wait()
+
     def show_help(self) -> None:
         QtGui.QDesktopServices.openUrl(QtCore.QUrl('https://dkratzert.de/files/finalcif/docs/'))
 
@@ -916,7 +938,27 @@ class AppWindow(QMainWindow):
         dialog = SqueezeSolventDialog(cif=self.cif, mode=mode, parent=self)
         if dialog._cancelled:
             return False
-        return bool(dialog.exec())
+        accepted = bool(dialog.exec())
+        if accepted:
+            self._refresh_after_squeeze_dialog(dialog)
+        return accepted
+
+    def _refresh_after_squeeze_dialog(self, dialog: SqueezeSolventDialog) -> None:
+        """
+        Show the values written by the solvent dialog without leaving the current page.
+        """
+        self._update_squeeze_details_row(dialog.details_key, dialog.details_text)
+        if self.ui.MainStackedWidget.on_loops_page():
+            self.ui.loops_page.reload()
+
+    def _update_squeeze_details_row(self, key: str, text: str) -> None:
+        if not self.ui.cif_main_table.rowCount():
+            return
+        if not self.ui.cif_main_table.has_key(key):
+            if not text:
+                return
+            self.add_row(key=key, value=text, at_start=True)
+        self.ui.cif_main_table.setText(key=key, column=Column.EDIT, txt=text)
 
     def _ccdc_deposit(self) -> None:
         """
@@ -1727,8 +1769,7 @@ class AppWindow(QMainWindow):
         fixfont.setPointSize(fixfont.pointSize() + 2)
         doc.setDefaultFont(fixfont)
         final_textedit.setLineWrapMode(QPlainTextEdit.LineWrapMode.NoWrap)
-        final_textedit.setPlainText(self.cif.finalcif_file.read_text(encoding='utf-8', errors='ignore'))
-        QtCore.QTimer().singleShot(0, lambda: final_textedit.highlighter.setDocument(doc))
+        final_textedit.set_cif_text(self.cif.as_saved_string())
 
     def import_additional_cif(self, filename: str):
         """
@@ -1818,18 +1859,16 @@ class AppWindow(QMainWindow):
         if not self.cif.chars_ok:
             self.warn_about_bad_cif()
         # Do this only when sure we can load the file:
-        QtCore.QTimer.singleShot(0, lambda: self.save_current_recent_files_list(filepath))
+        single_shot(self, 0, lambda: self.save_current_recent_files_list(filepath))
         self._load_block(block, load_changes=load_changes)
         self.add_data_names_to_combobox()
         self.ui.datanameComboBox.setCurrentIndex(block)
         self.ui.datanameComboBox.blockSignals(False)
-        QtCore.QTimer.singleShot(500, self.ui.cif_main_table.resizeRowsToContents)
+        single_shot(self, 500, self.ui.cif_main_table.resizeRowsToContents)
         if self.cif.is_multi_cif:
             self._flash_block_combobox()
         self.cif.set_order_keys(self.ui.cifOrderWidget.order_keys)
-        QtCore.QTimer().singleShot(0, self._find_video)
-        # Enable to find widgets without parent:
-        # QtCore.QTimer(self).singleShot(1000, self.find_widgets_without_parent)
+        single_shot(self, 0, self._find_video)
 
     def _find_video(self) -> None:
         self.video.reset()
@@ -1853,8 +1892,8 @@ class AppWindow(QMainWindow):
         pal.setColor(QtGui.QPalette.ColorRole.Base, light_blue)
         self.ui.datanameComboBox.setAutoFillBackground(True)
         # short after start, because window size is not finished before:
-        QtCore.QTimer(self).singleShot(1500, lambda: self.ui.datanameComboBox.setPalette(pal))
-        QtCore.QTimer(self).singleShot(2600, lambda: self.ui.datanameComboBox.setPalette(orig_pal))
+        single_shot(self, 1500, lambda: self.ui.datanameComboBox.setPalette(pal))
+        single_shot(self, 2600, lambda: self.ui.datanameComboBox.setPalette(orig_pal))
 
     def add_data_names_to_combobox(self) -> None:
         self.ui.datanameComboBox.clear()
@@ -1932,8 +1971,7 @@ class AppWindow(QMainWindow):
                 self.show_residuals()
                 self.redraw_molecule()
             self._update_z_label()
-            t = QtCore.QTimer(self)
-            t.singleShot(1000, self.check_cecksums)
+            single_shot(self, 1000, self.check_cecksums)
 
     def _delete_current_block(self, index: int) -> None:
         self.cif.delete_block(index)
@@ -2132,8 +2170,7 @@ class AppWindow(QMainWindow):
             self.ui.peakLineEdit.setText("{} / {}".format(peak, self.cif['_refine_diff_density_min']))
         self._show_shelx_file()
         try:
-            QtCore.QTimer(self).singleShot(0, lambda: self.view_molecule(reset_view=True))
-            # threading.Thread(target=self.view_molecule).start()
+            single_shot(self, 0, lambda: self.view_molecule(reset_view=True))
         except Exception:
             print('Molecule view crashed!')
 
@@ -2577,7 +2614,7 @@ class AppWindow(QMainWindow):
         table.clearSelection()
 
     def check_cecksums(self):
-        if "RUNNING_TEST" in os.environ:
+        if self.running_inside_unit_test:
             return
         if not self.cif.test_res_checksum():
             show_res_checksum_warning(parent=self)

{finalcif-169 → finalcif-170}/finalcif/cif/cif_file_io.py

@@ -386,6 +386,20 @@ class CifContainer:
             else:
                 self.block.set_pair(key, quote(txt))
 
+    def write_options(self) -> gemmi.cif.WriteOptions:
+        """The gemmi write options used to save and to display the CIF."""
+        options = gemmi.cif.WriteOptions()
+        options.prefer_pairs = False
+        options.compact = False
+        options.align_pairs = 33
+        options.align_loops = 15
+        options.misuse_hash = False
+        return options
+
+    def as_saved_string(self) -> str:
+        """The CIF text exactly as :meth:`save` writes it to disk."""
+        return self.doc.as_string(options=self.write_options())
+
     def save(self, filename: Path | None = None) -> None:
         """
         Saves the current cif file. It uses the '[basename]-finalcif.cif' suffix by default.
@@ -400,16 +414,7 @@ class CifContainer:
             raise PermissionError(f'Failed to open {filename.resolve()} for writing: Operation not permitted')
         self.order_cif_keys()
         print('Saving CIF to', Path(filename).resolve())
-        if Version(gemmi.__version__) > Version('0.6.3'):
-            options = gemmi.cif.WriteOptions()
-            options.prefer_pairs = False
-            options.compact = False
-            options.align_pairs = 33
-            options.align_loops = 15
-            options.misuse_hash = False
-            self.doc.write_file(str(filename), options=options)
-        else:
-            self.doc.write_file(str(filename), gemmi.cif.Style.Indent35)
+        self.doc.write_file(str(filename), options=self.write_options())
 
     def is_writable(self, filepath: Path | str) -> bool:
         filepath = Path(filepath)
@@ -973,9 +978,9 @@ class CifContainer:
         publ_loop = self.block.find_loop('_geom_angle_publ_flag') or len(label1) * ['?']
         angle = namedtuple('angle', ('label1', 'label2', 'label3', 'angle_val', 'symm1', 'symm2'))
         for label1, label2, label3, angle_val, symm1, symm2, publ in (
-            zip(label1, label2, label3, angle_val, symm1, symm2, publ_loop, strict=False)):
+                zip(label1, label2, label3, angle_val, symm1, symm2, publ_loop, strict=False)):
             if ((without_H and (self.ishydrogen(label1) or self.ishydrogen(label2) or self.ishydrogen(label3))) or
-                self.yes_not_set(publ)):
+                    self.yes_not_set(publ)):
                 continue
             else:
                 yield angle(label1=label1, label2=label2, label3=label3, angle_val=angle_val,
@@ -1049,7 +1054,7 @@ class CifContainer:
         hydr = namedtuple('HydrogenBond', ('label_d', 'label_h', 'label_a', 'dist_dh', 'dist_ha', 'dist_da',
                                            'angle_dha', 'symm'))
         for label_d, label_h, label_a, dist_dh, dist_ha, dist_da, angle_dha, symm, publ in (
-            zip(label_d, label_h, label_a, dist_dh, dist_ha, dist_da, angle_dha, symm, publ_loop, strict=False)):
+                zip(label_d, label_h, label_a, dist_dh, dist_ha, dist_da, angle_dha, symm, publ_loop, strict=False)):
             if self.yes_not_set(publ):
                 continue
             if self.picometer:

{finalcif-169 → finalcif-170}/finalcif/equip_property/author_loop_templates.py

@@ -22,6 +22,7 @@ from finalcif.cif.text import utf8_to_str, quote, retranslate_delimiter, string_
 from finalcif.equip_property.tools import read_document_from_cif_file
 from finalcif.gui.dialogs import cif_file_save_dialog, show_general_warning, cif_file_open_dialog
 from finalcif.gui.finalcif_gui_ui import Ui_FinalCifWindow
+from finalcif.gui.timers import single_shot
 from finalcif.tools.misc import grouper
 from finalcif.tools.settings import FinalCifSettings
 
@@ -452,7 +453,7 @@ class AuthorLoops:
                 self._rename_old_name = item.text()
                 # Defer editItem() to the next event-loop tick so that all
                 # menu-close events are processed before Qt starts the editor.
-                QtCore.QTimer.singleShot(0, lambda: listw.editItem(item))
+                single_shot(listw, 0, lambda: listw.editItem(item))
 
         menu.triggered.connect(_on_triggered)
         menu.popup(listw.viewport().mapToGlobal(pos))

{finalcif-169 → finalcif-170}/finalcif/equip_property/equipment.py

@@ -14,6 +14,7 @@ from finalcif.cif.text import retranslate_delimiter, string_to_utf8
 from finalcif.equip_property.tools import read_document_from_cif_file
 from finalcif.gui.custom_classes import Column, light_green
 from finalcif.gui.dialogs import show_general_warning, cif_file_open_dialog, cif_file_save_dialog
+from finalcif.gui.timers import single_shot
 from finalcif.tools import misc
 from finalcif.tools.misc import include_equipment_imports
 from finalcif.tools.settings import FinalCifSettings
@@ -94,7 +95,7 @@ class Equipment:
                 self._rename_old_name = item.text()
                 # Defer editItem() to the next event-loop tick so that all
                 # menu-close events are processed before Qt starts the editor.
-                QtCore.QTimer.singleShot(0, lambda: listw.editItem(item))
+                single_shot(listw, 0, lambda: listw.editItem(item))
 
         menu.triggered.connect(_on_triggered)
         menu.popup(listw.viewport().mapToGlobal(pos))

{finalcif-169 → finalcif-170}/finalcif/equip_property/properties.py

@@ -14,6 +14,7 @@ from finalcif.cif.text import retranslate_delimiter, utf8_to_str
 from finalcif.equip_property.tools import read_document_from_cif_file
 from finalcif.gui.dialogs import cif_file_open_dialog, show_general_warning, cif_file_save_dialog
 from finalcif.gui.plaintextedit import PlainTextEditTemplate
+from finalcif.gui.timers import single_shot
 from finalcif.tools import misc
 from finalcif.tools.settings import FinalCifSettings
 
@@ -72,7 +73,7 @@ class Properties(QtCore.QObject):
             self.lb.setText(f'key {key} already exists')
             self.lb.move(self.app.ui.cifKeywordLineEdit.mapToGlobal(QtCore.QPoint(15, 25)))
             self.lb.show()
-            QtCore.QTimer().singleShot(5000, self.hide_label)
+            single_shot(self.lb, 5000, self.hide_label)
         else:
             self.app.ui.SavePropertiesButton.setEnabled(True)
             self.lb.hide()
@@ -118,7 +119,7 @@ class Properties(QtCore.QObject):
                 self._rename_old_name = item.text()
                 # Defer editItem() to the next event-loop tick so that all
                 # menu-close events are processed before Qt starts the editor.
-                QtCore.QTimer.singleShot(0, lambda: listw.editItem(item))
+                single_shot(listw, 0, lambda: listw.editItem(item))
 
         menu.triggered.connect(_on_triggered)
         menu.popup(listw.viewport().mapToGlobal(pos))

{finalcif-169 → finalcif-170}/finalcif/finalcif_start.py

@@ -17,6 +17,7 @@ from finalcif import VERSION
 from finalcif.app_path import application_path
 from finalcif.appwindow import AppWindow, DEBUG, app
 from finalcif.gui.dialogs import show_bug_found_warning, show_general_warning
+from finalcif.tools.selfupdate import create_running_mutex
 
 
 def my_exception_hook(exctype: type[BaseException], value: BaseException, error_traceback: traceback,
@@ -73,6 +74,8 @@ def my_exception_hook(exctype: type[BaseException], value: BaseException, error_
 def main():
     if not DEBUG:
         sys.excepthook = my_exception_hook
+    # The installer (AppMutex) must not overwrite the files of a running FinalCif:
+    create_running_mutex()
     # windows_style = QStyleFactory.create('Fusion')
     # app.setStyle(windows_style)
     file = None

{finalcif-169 → finalcif-170}/finalcif/gui/cif_table_view.py

@@ -15,6 +15,7 @@ from finalcif.gui.cif_table_model import CifTableModel, Column, blue, CifRowData
 from finalcif.gui.combobox import MyComboBox
 from finalcif.gui.dialogs import show_keyword_help
 from finalcif.gui.plaintextedit import MyQPlainTextEdit
+from finalcif.gui.timers import single_shot
 
 DEBUG = False
 
@@ -381,7 +382,7 @@ class CifTableView(QTableView):
         return QObject.eventFilter(self, widget, event)
 
     def resizeEvent(self, e: QtGui.QResizeEvent) -> None:
-        QtCore.QTimer(self).singleShot(0, self.resizeRowsToContents)
+        single_shot(self, 0, self.resizeRowsToContents)
         super().resizeEvent(e)