finalcif 146__tar.gz → 148__tar.gz

{finalcif-146 → finalcif-148}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: finalcif
-Version: 146
+Version: 148
 Summary: CIF file editor
 Project-URL: Homepage, https://dkratzert.de/finalcif.html
 Project-URL: Bug Tracker, https://github.com/dkratzert/FinalCif/issues

finalcif-148/finalcif/__init__.py

@@ -0,0 +1,2 @@
+
+VERSION = 148

{finalcif-146 → finalcif-148}/finalcif/appwindow.py

@@ -1604,8 +1604,11 @@ class AppWindow(QMainWindow):
         """
         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)
+        try:
+            # noinspection PyTypeChecker
+            longest_string: str = max(self.ui.cif_main_table.vheaderitems, key=len)
+        except ValueError:
+            longest_string = '_chemical_formula_sum_foo'
         vheader.setMaximumWidth(fm.width(longest_string + 'O'))
 
     def changes_cif_has_values(self) -> bool:

{finalcif-146 → finalcif-148}/finalcif/cif/cif_file_io.py

@@ -42,7 +42,6 @@ class CifContainer():
                        the existing document is opened.
         """
         self.picometer: bool = False
-        self._hkl_file: str = ''
         self._abs_hkl_details: Dict[str, str] = {}
         if isinstance(file, str):
             self.fileobj = Path(file)
@@ -347,14 +346,10 @@ class CifContainer():
     def hkl_file(self) -> str:
         hkl_loop: Loop = self.get_loop('_diffrn_refln_index_h')
         if hkl_loop and hkl_loop.width() > 4:
-            if not self._hkl_file:
-                self._hkl_file = self._hkl_from_cif_format(hkl_loop)
-            return self._hkl_file
+            return self._hkl_from_cif_format(hkl_loop)
         else:
             # returns an empty string if no cif hkl was found:
-            if not self._hkl_file:
-                self._hkl_file = self._hkl_from_shelx()
-            return self._hkl_file
+            return self._hkl_from_shelx()
 
     def _hkl_from_cif_format(self, hkl_loop: Loop) -> str:
         hkl_list = []
@@ -400,7 +395,7 @@ class CifContainer():
         return HKL(self.hkl_file, self.block.name, hklf_type=self.hklf_number).get_hkl_min_max()
 
     def _hklf_number_from_shelxl_file(self) -> int:
-        if self.shx.hklf:
+        if self.shx and self.shx.hklf:
             return self.shx.hklf.n if self.shx.hklf.n != 0 else 4
         else:
             return 4
@@ -524,8 +519,11 @@ class CifContainer():
 
     def add_loop_from_columns(self, loop_tags: List[str],
                               column_values: Union[List[List[str]], Tuple[Tuple[str]]]) -> gemmi.cif.Loop:
-        gemmi_loop = self.init_loop(loop_tags)
-        gemmi_loop.set_all_values(column_values)
+        try:
+            gemmi_loop = self.init_loop(loop_tags)
+            gemmi_loop.set_all_values(column_values)
+        except RuntimeError as err:
+            raise Exception('Gemmi raised an exception') from err
         return gemmi_loop
 
     @property

{finalcif-146 → finalcif-148}/finalcif/finalcif_start.py

@@ -14,8 +14,7 @@ from typing import Type
 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
-from finalcif.gui.dialogs import show_general_warning
+from finalcif.gui.dialogs import show_bug_found_warning, show_general_warning
 
 
 def my_exception_hook(exctype: Type[BaseException], value: BaseException, error_traceback: traceback,
@@ -30,10 +29,26 @@ def my_exception_hook(exctype: Type[BaseException], value: BaseException, error_
                  f'Date: {time.asctime(time.localtime(time.time()))}\n'
                  f'Finalcif crashed during the following operation:\n\n'
                  f'{"-" * 120}\n'
-                 f'{"".join(traceback.format_tb(error_traceback))}\n'
-                 f'{str(exctype.__name__)}: '
-                 f'{str(value)} \n'
-                 f'{"-" * 120}\n')
+                 # f'{"".join(traceback.format_tb(error_traceback))}\n'
+                 # f'{str(exctype.__name__)}: '
+                 # f'{str(value)} \n'
+                 # f'{"-" * 120}\n'
+                 )
+
+    # Walk through the traceback and extract local variables
+    for frame, _ in traceback.walk_tb(error_traceback):
+        errortext += (f'File "{frame.f_code.co_filename}", line {frame.f_lineno}, in '
+                      f'{frame.f_code.co_qualname}(...):\n')
+        newline = '\n'
+        errortext += f'  Locals: \n    '
+        errortext += "    ".join(
+            [f"  {k}:{newline}          {'          '.join([x + newline for x in repr(v).splitlines()])}" for k, v in
+             frame.f_locals.items()]) + '\n\n'
+
+    errortext += f'{"-" * 120}\n'
+    errortext += f'{str(exctype.__name__)}: {str(value)} \n'
+    errortext += f'{"-" * 120}\n'
+
     logfile = Path.home().joinpath(Path(r'finalcif-crash.txt'))
     try:
         logfile.write_text(errortext)

{finalcif-146 → finalcif-148}/finalcif/gui/finalcif_gui_ui.py

@@ -414,7 +414,7 @@ class Ui_FinalCifWindow(object):
         self.page_MainTable = QtWidgets.QWidget()
         self.page_MainTable.setObjectName("page_MainTable")
         self.verticalLayout = QtWidgets.QVBoxLayout(self.page_MainTable)
-        self.verticalLayout.setContentsMargins(0, 0, 0, 0)
+        self.verticalLayout.setContentsMargins(0, 6, 0, 0)
         self.verticalLayout.setSpacing(0)
         self.verticalLayout.setObjectName("verticalLayout")
         self.cif_main_table = MyCifTable(self.page_MainTable)
@@ -614,6 +614,7 @@ class Ui_FinalCifWindow(object):
         font.setFamily("Courier New")
         font.setPointSize(11)
         font.setBold(True)
+        font.setWeight(75)
         self.shelx_warn_TextEdit.setFont(font)
         self.shelx_warn_TextEdit.setUndoRedoEnabled(False)
         self.shelx_warn_TextEdit.setLineWrapMode(QtWidgets.QPlainTextEdit.NoWrap)
@@ -651,6 +652,7 @@ class Ui_FinalCifWindow(object):
         font = QtGui.QFont()
         font.setBold(False)
         font.setItalic(False)
+        font.setWeight(50)
         self.wR2Label.setFont(font)
         self.wR2Label.setAlignment(QtCore.Qt.AlignRight|QtCore.Qt.AlignTrailing|QtCore.Qt.AlignVCenter)
         self.wR2Label.setObjectName("wR2Label")
@@ -663,6 +665,7 @@ class Ui_FinalCifWindow(object):
         font = QtGui.QFont()
         font.setBold(False)
         font.setItalic(False)
+        font.setWeight(50)
         self.r1Label.setFont(font)
         self.r1Label.setAlignment(QtCore.Qt.AlignRight|QtCore.Qt.AlignTrailing|QtCore.Qt.AlignVCenter)
         self.r1Label.setObjectName("r1Label")
@@ -690,6 +693,7 @@ class Ui_FinalCifWindow(object):
         self.completeLabel = QtWidgets.QLabel(self.groupBox_3)
         font = QtGui.QFont()
         font.setBold(False)
+        font.setWeight(50)
         self.completeLabel.setFont(font)
         self.completeLabel.setAlignment(QtCore.Qt.AlignRight|QtCore.Qt.AlignTrailing|QtCore.Qt.AlignVCenter)
         self.completeLabel.setObjectName("completeLabel")
@@ -737,6 +741,7 @@ class Ui_FinalCifWindow(object):
         self.dataReflnsLabel = QtWidgets.QLabel(self.groupBox_3)
         font = QtGui.QFont()
         font.setBold(False)
+        font.setWeight(50)
         self.dataReflnsLabel.setFont(font)
         self.dataReflnsLabel.setAlignment(QtCore.Qt.AlignRight|QtCore.Qt.AlignTrailing|QtCore.Qt.AlignVCenter)
         self.dataReflnsLabel.setObjectName("dataReflnsLabel")
@@ -803,6 +808,7 @@ class Ui_FinalCifWindow(object):
         self.rintLabel = QtWidgets.QLabel(self.groupBox_3)
         font = QtGui.QFont()
         font.setBold(False)
+        font.setWeight(50)
         self.rintLabel.setFont(font)
         self.rintLabel.setAlignment(QtCore.Qt.AlignRight|QtCore.Qt.AlignTrailing|QtCore.Qt.AlignVCenter)
         self.rintLabel.setObjectName("rintLabel")
@@ -814,6 +820,7 @@ class Ui_FinalCifWindow(object):
         self.rsigmaLabel = QtWidgets.QLabel(self.groupBox_3)
         font = QtGui.QFont()
         font.setBold(False)
+        font.setWeight(50)
         self.rsigmaLabel.setFont(font)
         self.rsigmaLabel.setAlignment(QtCore.Qt.AlignRight|QtCore.Qt.AlignTrailing|QtCore.Qt.AlignVCenter)
         self.rsigmaLabel.setObjectName("rsigmaLabel")
@@ -849,6 +856,7 @@ class Ui_FinalCifWindow(object):
         self.dLabel = QtWidgets.QLabel(self.groupBox_3)
         font = QtGui.QFont()
         font.setBold(False)
+        font.setWeight(50)
         self.dLabel.setFont(font)
         self.dLabel.setAlignment(QtCore.Qt.AlignRight|QtCore.Qt.AlignTrailing|QtCore.Qt.AlignVCenter)
         self.dLabel.setObjectName("dLabel")
@@ -1128,7 +1136,7 @@ class Ui_FinalCifWindow(object):
         self.page_Loops = QtWidgets.QWidget()
         self.page_Loops.setObjectName("page_Loops")
         self.verticalLayout_9 = QtWidgets.QVBoxLayout(self.page_Loops)
-        self.verticalLayout_9.setContentsMargins(0, 0, 0, 0)
+        self.verticalLayout_9.setContentsMargins(0, 12, 0, 0)
         self.verticalLayout_9.setObjectName("verticalLayout_9")
         self.LoopsTabWidget = QtWidgets.QTabWidget(self.page_Loops)
         self.LoopsTabWidget.setObjectName("LoopsTabWidget")
@@ -1839,7 +1847,7 @@ class Ui_FinalCifWindow(object):
         self.retranslateUi(FinalCifWindow)
         self.TemplatesStackedWidget.setCurrentIndex(0)
         self.EquipmentTemplatesStackedWidget.setCurrentIndex(0)
-        self.MainStackedWidget.setCurrentIndex(4)
+        self.MainStackedWidget.setCurrentIndex(5)
         self.PropertiesTemplatesStackedWidget.setCurrentIndex(1)
         self.LoopsTabWidget.setCurrentIndex(0)
         self.authorEditTabWidget.setCurrentIndex(1)

{finalcif-146 → finalcif-148}/finalcif/gui/finalcif_gui_ui.ui

@@ -1013,7 +1013,7 @@
         <item row="2" column="0" colspan="13">
          <widget class="MyMainStackedWidget" name="MainStackedWidget">
           <property name="currentIndex">
-           <number>4</number>
+           <number>5</number>
           </property>
           <widget class="QWidget" name="page_MainTable">
            <layout class="QVBoxLayout" name="verticalLayout">
@@ -1024,7 +1024,7 @@
              <number>0</number>
             </property>
             <property name="topMargin">
-             <number>0</number>
+             <number>6</number>
             </property>
             <property name="rightMargin">
              <number>0</number>
@@ -1536,6 +1536,7 @@
                   <font>
                    <family>Courier New</family>
                    <pointsize>11</pointsize>
+                   <weight>75</weight>
                    <bold>true</bold>
                   </font>
                  </property>
@@ -1602,6 +1603,7 @@
                   <widget class="QLabel" name="wR2Label">
                    <property name="font">
                     <font>
+                     <weight>50</weight>
                      <italic>false</italic>
                      <bold>false</bold>
                     </font>
@@ -1625,6 +1627,7 @@
                   <widget class="QLabel" name="r1Label">
                    <property name="font">
                     <font>
+                     <weight>50</weight>
                      <italic>false</italic>
                      <bold>false</bold>
                     </font>
@@ -1682,6 +1685,7 @@
                   <widget class="QLabel" name="completeLabel">
                    <property name="font">
                     <font>
+                     <weight>50</weight>
                      <bold>false</bold>
                     </font>
                    </property>
@@ -1797,6 +1801,7 @@
                   <widget class="QLabel" name="dataReflnsLabel">
                    <property name="font">
                     <font>
+                     <weight>50</weight>
                      <bold>false</bold>
                     </font>
                    </property>
@@ -1944,6 +1949,7 @@
                   <widget class="QLabel" name="rintLabel">
                    <property name="font">
                     <font>
+                     <weight>50</weight>
                      <bold>false</bold>
                     </font>
                    </property>
@@ -1966,6 +1972,7 @@
                   <widget class="QLabel" name="rsigmaLabel">
                    <property name="font">
                     <font>
+                     <weight>50</weight>
                      <bold>false</bold>
                     </font>
                    </property>
@@ -2039,6 +2046,7 @@
                   <widget class="QLabel" name="dLabel">
                    <property name="font">
                     <font>
+                     <weight>50</weight>
                      <bold>false</bold>
                     </font>
                    </property>
@@ -2617,6 +2625,9 @@ The data source will be ignored until next program restart.</string>
           </widget>
           <widget class="QWidget" name="page_Loops">
            <layout class="QVBoxLayout" name="verticalLayout_9">
+            <property name="topMargin">
+             <number>12</number>
+            </property>
             <item>
              <widget class="QTabWidget" name="LoopsTabWidget">
               <property name="currentIndex">

{finalcif-146 → finalcif-148}/finalcif/report/templated_report.py

@@ -1105,7 +1105,9 @@ class TemplatedReport():
         context, tpl_doc = self.prepare_report_data(self.cif, self.options, picfile, tpl_doc)
         # Filter definition for {{foobar|filter}} things:
         jinja_env = jinja2.Environment()
+        jinja_env.globals.update(zip=zip)
         jinja_env.globals.update(strip=str.strip)
+        jinja_env.filters['utf8'] = report_text.utf8
         jinja_env.filters['inv_article'] = report_text.get_inf_article
         jinja_env.filters['to_pm'] = angstrom_to_pm if self.options.use_picometers else do_nothing
         jinja_env.filters['to_nm'] = angstrom_to_nanometers if self.options.use_picometers else do_nothing
@@ -1144,6 +1146,7 @@ class TemplatedReport():
                                        autoescape=select_autoescape(['html', 'htm', 'xml']))
         # Add zip() method to global namespace of the template:
         jinja_env.globals.update(zip=zip)
+        jinja_env.globals.update(strip=str.strip)
         jinja_env.filters['to_pm'] = angstrom_to_pm if self.options.use_picometers else do_nothing
         jinja_env.filters['to_nm'] = angstrom_to_nanometers if self.options.use_picometers else do_nothing
         jinja_env.filters['inv_article'] = report_text.get_inf_article

finalcif-146/finalcif/__init__.py

@@ -1,2 +0,0 @@
-
-VERSION = 146