finalcif 154__tar.gz → 156__tar.gz

{finalcif-154 → finalcif-156}/.gitignore

@@ -227,3 +227,11 @@ tests/examples/work/cu_BruecknerJK_153F40_0m.lxt
 finalcif_keys_order.cif
 !/.python-version
 /platon/*.mod
+/work/test.aux
+/work/test.pdf
+/work/test.synctex.gz
+/work/test.tex
+/tests/examples/work/cu_BruecknerJK_153F40_0m-finalcif-1.zip
+/tests/examples/work/cu_BruecknerJK_153F40_0m-finalcif-2.zip
+/tests/examples/work/cu_BruecknerJK_153F40_0m_video-finalcif.png
+/tests/examples/work/report_cu_BruecknerJK_153F40_0m-finalcif.html

{finalcif-154 → finalcif-156}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: finalcif
-Version: 154
+Version: 156
 Summary: CIF file editor
 Project-URL: Homepage, https://dkratzert.de/finalcif.html
 Project-URL: Bug Tracker, https://github.com/dkratzert/FinalCif/issues

finalcif-156/finalcif/__init__.py

@@ -0,0 +1,2 @@
+
+VERSION = 156

{finalcif-154 → finalcif-156}/finalcif/appwindow.py

@@ -5,14 +5,21 @@
 #   and you think this stuff is worth it, you can buy me a beer in return.
 #   ----------------------------------------------------------------------------
 import os
+import pickle
 import subprocess
 import sys
 import threading
 import time
+import warnings
 from contextlib import suppress
 from datetime import datetime
 from math import sin, radians
 from pathlib import Path, WindowsPath
+from typing import cast
+
+from finalcif.gui.vzs_viewer import VZSImageViewer
+
+warnings.filterwarnings("ignore", category=RuntimeWarning, module="shibokensupport.signature.parser")
 
 import gemmi
 
@@ -43,7 +50,8 @@ from finalcif.gui.custom_classes import Column, MyTableWidgetItem, light_green,
     white
 from finalcif.gui.dialogs import show_update_warning, unable_to_open_message, show_general_warning, \
     cif_file_open_dialog, \
-    bad_z_message, show_res_checksum_warning, show_hkl_checksum_warning, cif_file_save_dialog, show_yes_now_question
+    bad_z_message, show_res_checksum_warning, show_hkl_checksum_warning, cif_file_save_dialog, show_yes_now_question, \
+    video_file_open_dialog
 from finalcif.gui.finalcif_gui_ui import Ui_FinalCifWindow
 from finalcif.gui.import_selector import ImportSelector
 from finalcif.gui.loop_creator import LoopCreator
@@ -124,6 +132,9 @@ class AppWindow(QMainWindow):
         self.ui.TemplatesStackedWidget.setCurrentIndex(0)
         self.ui.MainStackedWidget.got_to_main_page()
         self.set_initial_button_states()
+        self.video = VZSImageViewer(self)
+        self.ui.picturesTabWidget.setCurrentIndex(0)
+        self.ui.video_vLayout.addWidget(self.video)
         if file:
             self.load_cif_file(file)
         self.load_recent_cifs_list()
@@ -143,7 +154,9 @@ class AppWindow(QMainWindow):
             "            Spek, A.L. (2020). Acta Cryst. E76, 1-11.\n"
             "  \n"
             "  \n"
-            "  - Recent versions of PLATON may be obtained from: https://platonsoft.nl/xraysoft\n"
+            "  - Recent versions of PLATON may be obtained from: https://platonsoft.nl/xraysoft\n\n"
+            " PLATON is free of charge for Academics.\n"
+            " For-profit organisations should contact Anthony L. Spek, a.l.spek@uu.nl for a license." 
             "  "
         )
         self.set_checkcif_output_font(self.ui.CheckcifPlaintextEdit)
@@ -161,7 +174,7 @@ class AppWindow(QMainWindow):
         # self.set_font_sizes()
 
     def load_fontsize_from_settings(self):
-        fontsize = self.settings.load_value_of_key('global_font_size')
+        fontsize = cast(int, self.settings.load_value_of_key('global_font_size'))
         if fontsize is not None and fontsize >= 8:
             self.set_global_font(fontsize)
             self.ui.textSizeSpinBox.setValue(fontsize)
@@ -428,6 +441,23 @@ class AppWindow(QMainWindow):
         self.ui.ImportAllTemplatesPushButton.clicked.connect(self.import_all_templates)
         self.ui.searchMainTableLineEdit.textChanged.connect(self.ui.cif_main_table.search)
         self.ui.textSizeSpinBox.valueChanged.connect(self.set_global_font)
+        # video:
+        self.ui.SelectVideo_PushButton.clicked.connect(lambda x: self._select_crystal_video())
+        self.ui.videoRightToolButton.clicked.connect(self.video.next)
+        self.ui.videoLeftToolButton.clicked.connect(self.video.previous)
+        self.ui.setVideoPicturePushButton.clicked.connect(self.set_video_image_for_report)
+
+    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
+
+    def _select_crystal_video(self, video_file: Path | None = None) -> None:
+        if video_file is None:
+            video_file = Path(video_file_open_dialog(parent=self, last_dir=self.get_last_workdir()))
+        if video_file is not None and video_file.is_file() and video_file.exists():
+            self.ui.videoLineEdit.setText(str(video_file.resolve()))
+            self.video.load_file(video_file)
 
     @property
     def finalcif_changes_filename(self):
@@ -437,8 +467,7 @@ class AppWindow(QMainWindow):
         self.make_loops_tables()
         self.ui.MainStackedWidget.go_to_loops_page()
 
-    def export_all_templates(self, filename: Path | None = None):
-        import pickle
+    def export_all_templates(self, filename: Path | None = None) -> None:
         if not filename:
             filename, _ = compat.getsavefilename(parent=self,
                                                  basedir=str(Path(self.get_last_workdir()).joinpath(
@@ -461,7 +490,7 @@ class AppWindow(QMainWindow):
         except pickle.PickleError as e:
             self.status_bar.show_message(f'Saving templates failed: {e!s}')
 
-    def import_all_templates(self, filename: Path | None = None):
+    def import_all_templates(self, filename: Path | None = None) -> None:
         import pickle
         if not filename:
             filename, _ = compat.getopenfilename(parent=self,
@@ -737,7 +766,7 @@ class AppWindow(QMainWindow):
         if self.options.track_changes and self.changes_answer == QMessageBox.StandardButton.Yes:
             self.delete_key_from_changes_cif(key)
 
-    def delete_key_from_changes_cif(self, key):
+    def delete_key_from_changes_cif(self, key: str) -> None:
         changes_cif = self.get_changes_cif(self.finalcif_changes_filename)
         del changes_cif[key]
         if changes_cif.is_empty():
@@ -921,7 +950,10 @@ class AppWindow(QMainWindow):
         url = QtCore.QUrl.fromLocalFile(str(self.htmlfile.resolve()))
         self.ui.MainStackedWidget.go_to_checkcif_page()
         self.ui.CheckCIFResultsTabWidget.setCurrentIndex(1)  # Index 1 is html page
-        self.checkcif_browser.load(url)
+        try:
+            self.checkcif_browser.setHtml(self.htmlfile.resolve().read_text('utf-8', 'ignore'))
+        except FileNotFoundError:
+            print(f'{self.htmlfile} not found')
         self.ui.ResponsesTabWidget.setCurrentIndex(0)
         threading.Thread(target=self._display_structure_factor_report, args=(parser,)).start()
         # The picture file linked in the html file:
@@ -979,7 +1011,8 @@ class AppWindow(QMainWindow):
         self.ckf = CheckCif(parent=self, cif=self.cif, outfile=self.htmlfile,
                             hkl_upload=(not self.ui.structfactCheckBox.isChecked()), pdf=False,
                             url=self.options.checkcif_url,
-                            full_iucr=self.ui.fullIucrCheckBox.isChecked())
+                            full_iucr=self.ui.fullIucrCheckBox.isChecked(),
+                            check_duplicates=self.ui.checkDuplicatesCheckBox.isChecked())
         self.ckf.progress.connect(self._ckf_progress)
         self.ckf.failed.connect(self._checkcif_failed)
         self.ckf.finished.connect(self._checkcif_finished)
@@ -1052,7 +1085,8 @@ class AppWindow(QMainWindow):
         self.ckf = CheckCif(parent=self, cif=self.cif, outfile=htmlfile,
                             hkl_upload=(not self.ui.structfactCheckBox.isChecked()),
                             pdf=True, url=self.options.checkcif_url,
-                            full_iucr=self.ui.fullIucrCheckBox.isChecked())
+                            full_iucr=self.ui.fullIucrCheckBox.isChecked(),
+                            check_duplicates=self.ui.checkDuplicatesCheckBox.isChecked())
         self.ckf.failed.connect(self._checkcif_failed)
         # noinspection PyUnresolvedReferences
         self.ckf.finished.connect(self._pdf_checkcif_finished)
@@ -1136,10 +1170,12 @@ class AppWindow(QMainWindow):
                                                  caption='Open a Report Picture')
             self.set_report_picture_path(filename)
 
-    def set_report_picture_path(self, filename: str):
+    def set_report_picture_path(self, filename: str) -> None:
+        if not filename:
+            return None
         with suppress(Exception):
             self.report_picture_path = Path(filename)
-        if self.report_picture_path.exists() and self.report_picture_path.is_file():
+        if self.report_picture_path and self.report_picture_path.exists() and self.report_picture_path.is_file():
             with suppress(Exception):
                 self.set_picture_button_icon()
 
@@ -1179,9 +1215,9 @@ class AppWindow(QMainWindow):
         self.cif.picometer = self.options.use_picometers
         # The picture after the header:
         if self.report_picture_path:
-            picfile = self.report_picture_path
+            self.options.structure_figure = self.report_picture_path
         else:
-            picfile = self.cif.finalcif_file.with_suffix('.gif')
+            self.options.structure_figure = self.cif.finalcif_file.with_suffix('.gif')
         try:
             print('Report with templates')
             template_path = Path(self.get_checked_templates_list_text())
@@ -1189,7 +1225,6 @@ class AppWindow(QMainWindow):
             if template_path.suffix in ('.docx',):
                 t = TemplatedReport(format=ReportFormat.RICHTEXT, options=self.options, cif=self.cif)
                 ok = t.make_templated_docx_report(output_filename=str(report_filename),
-                                                  picfile=picfile,
                                                   template_path=Path(self.get_checked_templates_list_text()))
                 if self.cif.is_multi_cif and self.cif.doc[0].name != 'global':
                     make_multi_tables(cif=self.cif, output_filename=str(multi_table_document))
@@ -1197,7 +1232,6 @@ class AppWindow(QMainWindow):
                 t = TemplatedReport(format=ReportFormat.HTML, options=self.options, cif=self.cif)
                 report_filename = report_filename.with_suffix('.html')
                 ok = t.make_templated_html_report(output_filename=str(report_filename),
-                                                  picfile=picfile,
                                                   template_path=template_path.parent,
                                                   template_file=template_path.name)
             if not ok:
@@ -1211,10 +1245,11 @@ class AppWindow(QMainWindow):
             return
         except PermissionError:
             if DEBUG:
+                print('dbg> Unable to open report or CIF file')
                 raise
-            print('Unable to open cif file')
-            show_general_warning(self, f'The report document {report_filename.name} could not be opened.\n'
-                                       'Is the file already opened?')
+            show_general_warning(self,
+                                 f'The document {report_filename.name} could not be opened to '
+                                 f'write the report.\nIs the file already opened?')
             return
         if not self.running_inside_unit_test:
             self.open_report_document(report_filename, multi_table_document)
@@ -1494,12 +1529,12 @@ class AppWindow(QMainWindow):
         self.set_path_display_in_file_selector(str(filepath))
         try:
             if not self.able_to_open(filepath):
-                return
+                return None
         except (OSError, IndexError):
             print('Something failed during cif file opening...')
             if DEBUG:
                 raise
-            return
+            return None
         not_ok = None
         try:
             e = None
@@ -1513,7 +1548,7 @@ class AppWindow(QMainWindow):
         if not_ok:
             unable_to_open_message(self, filepath, not_ok)
             return None
-        if not self.cif.is_valid_structure_cif and not self.cif.doc.find_block('global'):
+        if not self.cif.is_valid_structure_cif:
             show_general_warning(self, "The CIF file you are about to open contains no structure.\n\n"
                                        "Use the Import button below to import metadata.")
             return None
@@ -1529,9 +1564,18 @@ class AppWindow(QMainWindow):
         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)
 
+    def _find_video(self) -> None:
+        self.video.reset()
+        self.ui.videoLineEdit.setText('')
+        path = self.cif.fileobj.parent.parent
+        videos = list(path.glob('*.vzs'))
+        if videos:
+            self._select_crystal_video(videos[0])
+
     def find_widgets_without_parent(self) -> None:
         print('Finding parents...')
         all_widgets = app.allWidgets()

{finalcif-154 → finalcif-156}/finalcif/cif/all_cif_dicts.py

@@ -105,6 +105,11 @@ additional_keywords = {
                                                 'The O(CH2CH3)2 solvent molecule (42 electrons) disordred around '
                                                 'an inverstion center was treated by SQUEEZE. '
                                                 '<br><p><h4>Type:</h4> string </p>\n',
+    '_exptl_bruker_absorpt_correction_T_ratio': '<pre><h2>_exptl_bruker_absorpt_correction_T_ratio</h2>'
+                                                'SADABS (and other scaling programs) can only determine the RATIO of '
+                                                'absorpt_correction_Tmin/Tmax, so this value determined by SHELXL is used to '
+                                                'scale the transmission values from SADABS.</pre>'
+                                                '<br><p><h4>Type:</h4> number (float) </p>\n',
 }
 
 cif_all_dict = {}

{finalcif-154 → finalcif-156}/finalcif/cif/checkcif/checkcif.py

@@ -25,7 +25,7 @@ class CheckCif(QThread):
     failed = Signal(str)
 
     def __init__(self, parent, cif: CifContainer, outfile: Path, hkl_upload: bool = True,
-                 pdf: bool = False, url: str = '', full_iucr: bool = False):
+                 pdf: bool = False, url: str = '', full_iucr: bool = False, check_duplicates: bool = True):
         # hkl == False means no hkl upload
         super().__init__(parent=parent)
         self.hkl_upload = hkl_upload
@@ -34,6 +34,7 @@ class CheckCif(QThread):
         self.pdf = pdf
         self.checkcif_url = url
         self.full_iucr = full_iucr
+        self.check_duplicates = check_duplicates
 
     def _html_check(self) -> None:
         if self.hkl_upload:
@@ -63,11 +64,13 @@ class CheckCif(QThread):
             validation_type = 'checkcif_with_hkl'
         vrf = self.get_vrf()
         headers = {
+            "from_index": "from_index",
             "runtype"   : "symmonly",
             "referer"   : "checkcif_server",
             "outputtype": 'PDF' if self.pdf else 'HTML',
             "validtype" : validation_type,
             "valout"    : vrf,
+            "duplic"    : "duplicyes" if self.check_duplicates else "duplicno",
         }
         t1 = time.perf_counter()
         self.progress.emit('Report request sent. Please wait...')

{finalcif-154 → finalcif-156}/finalcif/cif/cif_order.py

@@ -14,6 +14,10 @@ special_keys = ['_iucr_refine_instructions_details',
                 '_refln_F_squared_sigma',
                 '_refln_F_calc',
                 '_refln_F_squared_calc',
+
+                '_shelx_include_file_name',
+                '_shelx_include_file',
+                '_shelx_include_file_checksum',
                 ]
 
 order = [
@@ -349,19 +353,19 @@ order = [
     '_geom_details',
     '_geom_special_details',
 
-    '_bruker_diffrn_runs_wavelength',
-    '_bruker_diffrn_runs_temperature',
-    '_bruker_diffrn_runs_current',
-    '_bruker_diffrn_runs_voltage',
-    '_bruker_diffrn_runs_images',
-    '_bruker_diffrn_runs_time',
-    '_bruker_diffrn_runs_width',
     '_bruker_diffrn_runs_axis',
-    '_bruker_diffrn_runs_chi',
-    '_bruker_diffrn_runs_phi',
-    '_bruker_diffrn_runs_omega',
-    '_bruker_diffrn_runs_theta',
     '_bruker_diffrn_runs_distance',
+    '_bruker_diffrn_runs_theta',
+    '_bruker_diffrn_runs_omega',
+    '_bruker_diffrn_runs_phi',
+    '_bruker_diffrn_runs_chi',
+    '_bruker_diffrn_runs_width',
+    '_bruker_diffrn_runs_images',
+    '_bruker_diffrn_runs_time',
+    '_bruker_diffrn_runs_wavelength',
+    '_bruker_diffrn_runs_voltage',
+    '_bruker_diffrn_runs_current',
+    '_bruker_diffrn_runs_temperature',
 ]
 
 

{finalcif-154 → finalcif-156}/finalcif/ciforder/order_ui.py

@@ -113,8 +113,6 @@ class Ui_CifOrderForm(object):
 
 
         self.retranslateUi(CifOrderForm)
-
-        QMetaObject.connectSlotsByName(CifOrderForm)
     # setupUi
 
     def retranslateUi(self, CifOrderForm):

{finalcif-154 → finalcif-156}/finalcif/equip_property/author_loop_templates.py

@@ -381,7 +381,7 @@ class AuthorLoops:
             authors.append(author_data)
         return authors
 
-    def import_raw_data(self, authors_data: list[Author]):
+    def import_raw_data(self, authors_data: list[Author]) -> None:
         """
         Import all authors from an external file"""
         for author in authors_data:
@@ -391,7 +391,7 @@ class AuthorLoops:
     def authors_list(self) -> list[str]:
         return self.settings.list_saved_items(property='authors_list')
 
-    def contact_author_checked(self, checked: bool):
+    def contact_author_checked(self, checked: bool) -> None:
         """
         :parameter checked: state of the ContactAuthorCheckBox
         """

{finalcif-154 → finalcif-156}/finalcif/equip_property/properties.py

@@ -276,9 +276,9 @@ class Properties(QtCore.QObject):
         return properties_list
 
     def import_raw_data(self, properties_list: list[dict]) -> None:
-        for prop in properties_list:
-            self.settings.save_settings_list(property='property', name=prop.get("name"),
-                                             items=[prop.get('cif_key'), prop.get('data')])
+        for property in properties_list:
+            self.settings.save_settings_list(property='property', name=property.get("name"),
+                                             items=[property.get('cif_key'), property.get('data')])
         self.show_properties()
 
     @staticmethod

{finalcif-154 → finalcif-156}/finalcif/gui/dialogs.py

@@ -3,11 +3,10 @@ import os
 import sys
 from pathlib import Path
 
+from finalcif import VERSION
 from qtpy import QtCore, compat
 from qtpy.QtWidgets import QMessageBox, QMainWindow, QVBoxLayout, QTextEdit, QPushButton, QFrame
 
-from finalcif import VERSION
-
 
 def do_update_program(version) -> None:
     updater_exe = str(Path(__file__).parent.parent.parent.joinpath('update.exe'))
@@ -229,6 +228,17 @@ def cif_file_save_dialog(filename: str, parent=None) -> str:
     return filename
 
 
+def video_file_open_dialog(parent: object = None, filter: str = "Video file (*.vzs; *.jpg)", last_dir='', options=None) -> str:
+    filename, _ = compat.getopenfilename(parent=parent,
+                                         caption='Open a crystal video file',
+                                         basedir=last_dir,
+                                         filters=filter,
+                                         selectedfilter=filter,
+                                         options=options
+                                         )
+    return filename
+
+
 if __name__ == '__main__':
     from qtpy import QtWidgets
     from qtpy.QtWidgets import QApplication