Small refactoring and imports improved

finalcif/equip_property/author_loop_templates.py

@@ -1,11 +1,11 @@
+from __future__ import annotations
 #   ----------------------------------------------------------------------------
 #   "THE BEER-WARE LICENSE" (Revision 42):
 #   Daniel Kratzert <[email protected]> wrote this file.  As long as you retain
 #   this notice you can do whatever you want with this stuff. If we meet some day,
 #   and you think this stuff is worth it, you can buy me a beer in return.
 #   ----------------------------------------------------------------------------
 import re
-from contextlib import suppress
 from dataclasses import dataclass
 from enum import Enum
 from pathlib import Path
@@ -51,7 +51,7 @@ class Author:
 
 
 class AuthorLoops():
-    def __init__(self, ui: Ui_FinalCifWindow, cif: CifContainer, app: 'AppWindow'):
+    def __init__(self, ui: Ui_FinalCifWindow, cif: CifContainer, app: AppWindow):
         self.ui = ui
         self.cif = cif
         self.app = app

finalcif/equip_property/equipment.py

@@ -1,3 +1,4 @@
+from __future__ import annotations
 from bisect import bisect
 from pathlib import Path
 from typing import List, Dict
@@ -22,7 +23,7 @@
 
 class Equipment:
 
-    def __init__(self, app: 'AppWindow', settings: FinalCifSettings):
+    def __init__(self, app: AppWindow, settings: FinalCifSettings):
         self.app = app
         self.settings = settings
         if app:

finalcif/equip_property/properties.py

@@ -1,3 +1,4 @@
+from __future__ import annotations
 import threading
 import time
 from contextlib import suppress
@@ -15,15 +16,14 @@
 from finalcif.tools.settings import FinalCifSettings
 from finalcif.tools import misc
 
-
 from typing import TYPE_CHECKING
 
 if TYPE_CHECKING:
     from finalcif.appwindow import AppWindow
 
 
 class Properties(QtCore.QObject):
-    def __init__(self, parent: 'AppWindow', settings: FinalCifSettings):
+    def __init__(self, parent: AppWindow, settings: FinalCifSettings):
         super().__init__(parent=parent)
         self.app = parent
         self.settings = settings

finalcif/equip_property/tools.py

@@ -1,4 +1,3 @@
-from pathlib import Path
 from typing import Union
 
 import gemmi.cif

finalcif/finalcif_start.py

@@ -5,15 +5,12 @@
 #  and you think this stuff is worth it, you can buy me a beer in return.
 #  Dr. Daniel Kratzert
 #  ----------------------------------------------------------------------------
-import os
 import sys
 import time
 import traceback
 from pathlib import Path
 from typing import Type
 
-from PyQt5.QtGui import QIcon
-
 from finalcif import VERSION
 from finalcif.app_path import application_path
 from finalcif.appwindow import AppWindow, DEBUG, app
@@ -62,6 +59,7 @@ def main():
             file = None
     app.setQuitOnLastWindowClosed(True)
     w = AppWindow(file=file)
+    from PyQt5.QtGui import QIcon
     app.setWindowIcon(QIcon(os.path.join(application_path, r'icon/finalcif2.png')))
     w.setWindowTitle('FinalCif v{}'.format(VERSION))
     # w.showMaximized()  # For full screen view

finalcif/gui/custom_classes.py

@@ -11,7 +11,6 @@
 from finalcif.cif.text import retranslate_delimiter
 from finalcif.gui.combobox import MyComboBox
 from finalcif.gui.dialogs import show_keyword_help
-from finalcif.gui.edit_button import FloatingButtonWidget
 from finalcif.gui.mixins import ItemTextMixin
 from finalcif.gui.plaintextedit import MyQPlainTextEdit
 

finalcif/gui/dialogs.py

@@ -5,7 +5,7 @@
 
 from PyQt5.QtCore import Qt
 from PyQt5.QtWidgets import QMessageBox, QMainWindow, QFileDialog, QVBoxLayout, QTextEdit, \
-    QPushButton, QFrame, QApplication
+    QPushButton, QFrame
 
 from finalcif import VERSION
 
@@ -226,6 +226,7 @@ def cif_file_save_dialog(filename: str) -> str:
 
 if __name__ == '__main__':
     from PyQt5 import QtWidgets
+    from PyQt5.QtWidgets import QApplication
 
     app = QApplication.instance()
     if app is None:

finalcif/report/report_text.py

@@ -268,8 +268,8 @@ def __init__(self, cif: CifContainer, paragraph: Paragraph, ref: ReferenceList):
             refineref = SHELXLReference()
         if 'OLEX' in refined.upper():
             refineref = Olex2Reference()
-        if 'NOSPHERA2' in solution_prog.upper() or 'NOSPHERA2' in cif['_refine_special_details'].upper() \
-            or 'NOSPHERA2' in cif['_olex2_refine_details'].upper():
+        if ('NOSPHERA2' in solution_prog.upper() or 'NOSPHERA2' in cif['_refine_special_details'].upper()
+                or 'NOSPHERA2' in cif['_olex2_refine_details'].upper()):
             refineref = [Olex2Reference(), Nosphera2Reference()]
         refine_coef = gstr(cif['_refine_ls_structure_factor_coef'])
         if manual_method:

finalcif/report/templated_report.py

@@ -444,6 +444,21 @@ def get_integration_program(self, cif: CifContainer) -> str:
 
     def get_absortion_correction_program(self, cif: CifContainer) -> str:
         absdetails = cif['_exptl_absorpt_process_details'].replace('-', ' ').replace(':', '')
+        bruker_scaling = cif['_computing_bruker_data_scaling'].replace('-', ' ').replace(':', '')
+        scale_prog, version = self._get_scaling_program(absdetails)
+        if not scale_prog:
+            scale_prog, version = self._get_scaling_program(bruker_scaling)
+        if 'SORTAV' in absdetails.upper():
+            scale_prog = 'SORTAV'
+            self.literature['absorption'] = SORTAVReference()
+        if 'crysalis' in absdetails.lower():
+            scale_prog = 'SCALE3 ABSPACK'
+            # see above also
+        scale_prog += " " + version
+
+        return scale_prog
+
+    def _get_scaling_program(self, absdetails: str) -> tuple[str, str]:
         scale_prog = ''
         version = ''
         if 'SADABS' in absdetails.upper() or 'TWINABS' in absdetails.upper():
@@ -456,15 +471,7 @@ def get_absortion_correction_program(self, cif: CifContainer) -> str:
             else:
                 scale_prog = 'TWINABS'
             self.literature['absorption'] = SadabsTwinabsReference()
-        if 'SORTAV' in absdetails.upper():
-            scale_prog = 'SORTAV'
-            self.literature['absorption'] = SORTAVReference()
-        if 'crysalis' in absdetails.lower():
-            scale_prog = 'SCALE3 ABSPACK'
-            # see above also
-        scale_prog += " " + version
-
-        return scale_prog
+        return scale_prog, version
 
     def solution_method(self, cif: CifContainer) -> str:
         solution_method = gstr(cif['_atom_sites_solution_primary']) or '??'
@@ -487,7 +494,7 @@ def refinement_prog(self, cif: CifContainer) -> str:
         if 'OLEX' in refined.upper():
             self.literature['refinement'] = Olex2Reference()
         if ('NOSPHERA2' in refined.upper() or 'NOSPHERA2' in cif['_refine_special_details'].upper() or
-            'NOSPHERAT2' in cif['_olex2_refine_details'].upper()):
+                'NOSPHERAT2' in cif['_olex2_refine_details'].upper()):
             self.literature['refinement'] = Nosphera2Reference()
         return refined.split()[0]
 

finalcif/tools/settings.py

@@ -191,7 +191,9 @@ def _load_settings(self, property: str, item_name: str):
             self.settings.beginGroup(property)
             try:
                 v = self.settings.value(item_name)
-            except TypeError:
+            except TypeError as e:
+                print(f"DBG> Item name '{item_name}' could not be loaded from settings.")
+                print(e)
                 v = None
             self.settings.endGroup()
             return v

tests/test_loops.py

@@ -6,8 +6,6 @@
 #   ----------------------------------------------------------------------------
 import os
 
-import gemmi.cif
-
 os.environ["RUNNING_TEST"] = 'True'
 import unittest
 from pathlib import Path
@@ -244,4 +242,4 @@ def test_move_row_up_from_start_save_and_load_again(self):
         except AttributeError:
             self.assertEqual('C', as_string(c.loops[3][0, 0]))
             self.assertEqual('H', as_string(c.loops[3][1, 0]))
-            self.assertEqual('O', as_string(c.loops[3][2, 0]))
+            self.assertEqual('O', as_string(c.loops[3][2, 0]))

tests/test_main_table.py

@@ -10,7 +10,6 @@
 import unittest
 from pathlib import Path
 
-import pytest
 from PyQt5.QtCore import Qt
 from PyQt5.QtGui import QColor
 

tests/test_saint.py

@@ -4,7 +4,6 @@
 #   this notice you can do whatever you want with this stuff. If we meet some day,
 #   and you think this stuff is worth it, you can buy me a beer in return.
 #   ----------------------------------------------------------------------------
-import os
 import unittest
 from pathlib import Path
 
@@ -13,6 +12,7 @@
 
 data = Path('.')
 
+
 class MyTestCase(unittest.TestCase):
 
     def test_saint_repr(self):

tests/test_templated_report.py

@@ -95,7 +95,7 @@ def test_ccdc_num_in_table(self):
         t = TemplatedReport()
         ok = t.make_templated_report(options=self.options,
                                      cif=CifContainer(self.testcif),
-                                     output_filename=self.reportdoc,
+                                     output_filename=str(self.reportdoc),
                                      picfile=self.report_pic,
                                      template_path=self.text_template)
         self.assertTrue(ok)

tests/test_workfolder.py

@@ -34,12 +34,12 @@ def setUp(self) -> None:
     def tearDown(self) -> None:
         Path('foo.cif').unlink(missing_ok=True)
         Path('tests/examples/work/cu_BruecknerJK_153F40_0m-finalcif.cif').unlink(missing_ok=True)
+        self.myapp.ui.trackChangesCifCheckBox.setChecked(False)
         self.myapp.close()
 
     def test_save_action(self):
         self.myapp.save_current_cif_file()
         self.assertEqual(True, (data / 'examples/work/cu_BruecknerJK_153F40_0m-finalcif.cif').exists())
-        self.myapp.ui.trackChangesCifCheckBox.setChecked(False)
 
 
 class TestWorkfolder(unittest.TestCase):