finalcif 136__tar.gz → 137__tar.gz

{finalcif-136 → finalcif-137}/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.3
 Name: finalcif
-Version: 136
+Version: 137
 Summary: CIF file editor
 Project-URL: Homepage, https://dkratzert.de/finalcif.html
 Project-URL: Bug Tracker, https://github.com/dkratzert/FinalCif/issues

finalcif-137/finalcif/__init__.py

@@ -0,0 +1,2 @@
+
+VERSION = 137

{finalcif-136 → finalcif-137}/finalcif/appwindow.py

@@ -13,12 +13,11 @@ from contextlib import suppress
 from datetime import datetime
 from math import sin, radians
 from pathlib import Path, WindowsPath
-from shutil import which
 from typing import Union, Dict, Tuple, List, Optional
 
 import gemmi.cif
 import requests  # type: ignore
-from PyQt5 import QtCore, QtGui, QtWebEngineWidgets
+from PyQt5 import QtCore, QtGui, QtWebEngineWidgets, QtWidgets
 from PyQt5.QtCore import Qt, QEvent
 from PyQt5.QtWidgets import QMainWindow, QShortcut, QCheckBox, QListWidgetItem, QApplication, \
     QPlainTextEdit, QFileDialog, QMessageBox, QScrollBar
@@ -61,6 +60,8 @@ from finalcif.tools.space_groups import SpaceGroups
 from finalcif.tools.statusbar import StatusBar
 from finalcif.tools.sumformula import formula_str_to_dict, sum_formula_to_html
 
+# QtCore.QCoreApplication.setAttribute(QtCore.Qt.AA_EnableHighDpiScaling)
+
 DEBUG = False
 app = QApplication.instance()
 if app is None:
@@ -633,10 +634,9 @@ class AppWindow(QMainWindow):
 
     def setTextEditSizes(self):
         for ui in [self.ui.Spacegroup_top_LineEdit, self.ui.CCDCNumLineEdit, self.ui.SumFormMainLineEdit]:
-            ui.setFixedHeight(self.ui.appendCifPushButton.height() + 6)
-            ui.setFixedHeight(self.ui.appendCifPushButton.height() + 6)
-            ui.setFixedHeight(self.ui.appendCifPushButton.height() + 6)
+            ui.setFixedHeight(self.ui.appendCifPushButton.height())
             vScrollBar = ui.verticalScrollBar()
+            # Scroll down a bit, or text will not be in the vertical center:
             vScrollBar.triggerAction(QScrollBar.SliderSingleStepAdd)
 
     def moveEvent(self, a0: QtGui.QMoveEvent) -> None:
@@ -1035,7 +1035,7 @@ class AppWindow(QMainWindow):
                               log_widget=self.ui.CheckCifLogPlainTextEdit,
                               output_widget=self.ui.CheckcifPlaintextEdit,
                               cif_file=self.cif.fileobj)
-        if not Path(which(runner.platon_exe)).exists():
+        if runner.platon_exe is not None and not Path(runner.platon_exe).exists():
             self.ui.CheckCifLogPlainTextEdit.setPlainText('\nPlaton executable not found!')
             self.ui.CheckCifLogPlainTextEdit.appendPlainText(
                 'You can download Platon at http://www.platonsoft.nl/platon/\n')
@@ -1135,12 +1135,20 @@ class AppWindow(QMainWindow):
                     make_multi_tables(cif=self.cif, output_filename=str(multi_table_document))
             else:
                 print('Report with templates')
-                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()))
-                # t = TemplatedReport(format=ReportFormat.HTML, options=self.options, cif=self.cif)
-                # t.make_templated_html_report(options=self.options, picfile=picfile)
+                template_path = Path(self.get_checked_templates_list_text())
+                ok = False
+                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()))
+                elif template_path.suffix in ('.html', '.tmpl'):
+                    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:
                     return None
         except FileNotFoundError as e:
@@ -1513,6 +1521,7 @@ class AppWindow(QMainWindow):
             raise
             # unable_to_open_message(Path(self.cif.filename), not_ok)
         self.load_recent_cifs_list()
+        self.set_vertical_header_width()
         if self.options.track_changes and load_changes:
             changes_exist = False
             if self.changes_cif_has_zero_size():
@@ -1557,6 +1566,16 @@ class AppWindow(QMainWindow):
             t = QtCore.QTimer(self)
             t.singleShot(1000, self.check_cecksums)
 
+    def set_vertical_header_width(self):
+        """
+        Sets the width of the vertical header to the length of the longest string in the list.
+        """
+        vheader: QtWidgets.QHeaderView = self.ui.cif_main_table.verticalHeader()
+        fm = QtGui.QFontMetrics(vheader.font(), self)
+        # noinspection PyTypeChecker
+        longest_string: str = max(self.ui.cif_main_table.vheaderitems, key=len)
+        vheader.setMaximumWidth(fm.width(longest_string + 'O'))
+
     def changes_cif_has_values(self) -> bool:
         try:
             return not self.get_changes_cif(self.finalcif_changes_filename).is_empty()

{finalcif-136 → finalcif-137}/finalcif/cif/cif_dict_foo.py

@@ -21,6 +21,15 @@ def format_definition(definition: str):
     return newdef
 
 
+formats = {
+    'char' : 'string',
+    'uchar': 'case-insensitive string',
+    'numb' : 'number (int or float)',
+    'null' : '? (unknown)' or '. (not applicable)',
+    ''     : '--'
+}
+
+
 def process_cif_dict(cdic):
     """
     Creates a dictionary with cif keywords as key and help text as value.
@@ -36,6 +45,7 @@ def process_cif_dict(cdic):
                 example_detail = item.get('_example_detail', '')
                 enumeration = item.get('_enumeration', '')
                 enumeration_detail = item.get('_enumeration_detail', '')
+                default = item.get('_enumeration_default', '')
                 if example:
                     if isinstance(example, list) and not enumeration_detail:
                         example = '\n'.join([str(x) for x in example])
@@ -52,15 +62,29 @@ def process_cif_dict(cdic):
                             ["{}\n\t{}\n".format(str(x), str(y)) for x, y in zip(enumeration, enumeration_detail)])
                     enumeration = format_definition(escape(str(enumeration)))
                     definition = '{}\n\n<h3>Example:</h3>\n{}'.format(definition, enumeration)
+                type_format = item.get("_type", "")
+                enum_range = item.get('_enumeration_range', '')
                 if isinstance(name, list):
                     for n in name:
                         # For keys like 'atom_site_aniso_b_[]' where the name has several subnames:
-                        alldic[n] = '<pre><h2>{}</h2>{}</pre>'.format(n, format_definition(definition))
+                        alldic[n] = help_text(definition, n, type_format, enum_range, default)
                 else:
-                    alldic[name] = '<pre><h2>{}</h2>{}</pre>'.format(name, format_definition(definition))
+                    alldic[name] = help_text(definition, name, type_format, enum_range, default)
     return alldic
 
 
+def help_text(definition: str, name: str, type_format: str, enum_range: str, enum_default) -> str:
+    if enum_range.endswith(':'):
+        enum_range = enum_range + '∞'
+    limits = f'\n<br><p><h4>Limits:</h4> {enum_range} </p>'
+    default = f'\n<br><p><h4>Default:</h4> {enum_default} </p>'
+    return (f'<pre><h2>{name}</h2>{format_definition(definition)}</pre>'
+            f'\n<br><p><h4>Type:</h4> {formats.get(type_format, "")}</p>'
+            f'{limits if enum_range else ""}'
+            f'{default if enum_default else ""}'
+            )
+
+
 def load_cif_as_dictionary(link, path_to_cif):
     if not path_to_cif.exists():
         get_dictionary_cif(link, path_to_cif)

{finalcif-136 → finalcif-137}/finalcif/cif/cif_file_io.py

@@ -94,7 +94,7 @@ class CifContainer():
         The suffix needs '-finalcif' in order to contain the finalcif ending.
         "foo/bar/baz-finalcif.cif"
 
-        :param forece_strip: Forces to strip the filename also after the '-finalcif' string.
+        :param force_strip: Forces to strip the filename also after the '-finalcif' string.
         """
         file_witout_finalcif = strip_finalcif_of_name(Path(self.filename).stem, till_name_ends=force_strip)
         filename = self.path_base.joinpath(Path(prefix + file_witout_finalcif + suffix))

{finalcif-136 → finalcif-137}/finalcif/cif/cif_order.py

@@ -17,6 +17,13 @@ special_keys = ['_iucr_refine_instructions_details',
                 ]
 
 order = [
+    '_audit_update_record',
+    '_audit_contact_author',
+    '_audit_contact_author_name',
+    '_audit_contact_author_phone',
+    '_audit_contact_author_email',
+    '_audit_contact_author_fax',
+    '_audit_contact_author_address',
     '_audit_author_id',
     '_audit_author_id_audit',
     '_audit_author_name',
@@ -128,7 +135,6 @@ order = [
     '_publ_contact_author_id_orcid',
     '_publ_contact_author_footnote',
 
-
     '_shelx_SHELXL_version_number',
     '_chemical_name_systematic',
     '_chemical_name_common',
@@ -341,4 +347,17 @@ 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',
 ]