MoleditPy-linux 2.6.2__tar.gz → 2.6.3__tar.gz

{moleditpy_linux-2.6.2 → moleditpy_linux-2.6.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: MoleditPy-linux
-Version: 2.6.2
+Version: 2.6.3
 Summary: A cross-platform, simple, and intuitive molecular structure editor built in Python. It allows 2D molecular drawing and 3D structure visualization. It supports exporting structure files for input to DFT calculation software.
 Author-email: HiroYokoyama <titech.yoko.hiro@gmail.com>
 License:                     GNU GENERAL PUBLIC LICENSE

{moleditpy_linux-2.6.2 → moleditpy_linux-2.6.3}/pyproject.toml

@@ -5,7 +5,7 @@ build-backend = "setuptools.build_meta"
 [project]
 name = "MoleditPy-linux"
 
-version = "2.6.2"
+version = "2.6.3"
 
 license = {file = "LICENSE"}
 

{moleditpy_linux-2.6.2 → moleditpy_linux-2.6.3}/src/MoleditPy_linux.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: MoleditPy-linux
-Version: 2.6.2
+Version: 2.6.3
 Summary: A cross-platform, simple, and intuitive molecular structure editor built in Python. It allows 2D molecular drawing and 3D structure visualization. It supports exporting structure files for input to DFT calculation software.
 Author-email: HiroYokoyama <titech.yoko.hiro@gmail.com>
 License:                     GNU GENERAL PUBLIC LICENSE

{moleditpy_linux-2.6.2 → moleditpy_linux-2.6.3}/src/moleditpy_linux/modules/analysis_window.py

@@ -20,6 +20,7 @@ from PyQt6.QtWidgets import (
     QPushButton,
     QVBoxLayout,
 )
+
 from rdkit import Chem
 from rdkit.Chem import Descriptors, rdMolDescriptors
 from rdkit.Chem import inchi as rd_inchi

{moleditpy_linux-2.6.2 → moleditpy_linux-2.6.3}/src/moleditpy_linux/modules/calculation_worker.py

@@ -82,7 +82,7 @@ class CalculationWorker(QObject):
                 if _check_halted():
                     return
                 self.status_update.emit(msg)
-            except Exception:  # pragma: no cover
+            except Exception:
                 # Swallow any signal-emission errors to avoid crashing the worker
                 pass
 

{moleditpy_linux-2.6.2 → moleditpy_linux-2.6.3}/src/moleditpy_linux/modules/constants.py

@@ -16,7 +16,7 @@ from PyQt6.QtGui import QColor, QFont
 from rdkit import Chem
 
 # Version
-VERSION = "2.6.2"
+VERSION = "2.6.3"
 
 ATOM_RADIUS = 18
 BOND_OFFSET = 3.5

{moleditpy_linux-2.6.2 → moleditpy_linux-2.6.3}/src/moleditpy_linux/modules/custom_interactor_style.py

@@ -599,11 +599,11 @@ class CustomInteractorStyle(vtkInteractorStyleTrackballCamera):
                             try:
                                 pos = mw.atom_positions_3d[i]
                                 conf.SetAtomPosition(i, pos.tolist())
-                            except Exception:  # pragma: no cover
+                            except Exception:
                                 # Skip individual failures but continue applying
                                 # other atom positions.
                                 pass
-                    except Exception:  # pragma: no cover
+                    except Exception:
                         # If applying positions fails, continue to redraw from
                         # whatever authoritative state is available.
                         pass
@@ -640,9 +640,6 @@ class CustomInteractorStyle(vtkInteractorStyleTrackballCamera):
             except Exception:  # pragma: no cover
                 import traceback
                 traceback.print_exc()
-            except Exception:  # pragma: no cover
-                # Do not allow a failure here to interrupt release flow
-                pass
         else:
             # カメラ回転の後始末を親クラスに任せます
             super().OnLeftButtonUp()

{moleditpy_linux-2.6.2 → moleditpy_linux-2.6.3}/src/moleditpy_linux/modules/main_window.py

@@ -12,19 +12,12 @@ DOI: 10.5281/zenodo.17268532
 
 import traceback
 
-# RDKit imports (explicit to satisfy flake8 and used features)
-try:
-    pass
-except Exception:  # pragma: no cover
-    traceback.print_exc()
-
 # PyQt6 Modules
 from PyQt6.QtCore import pyqtSignal, pyqtSlot
 from PyQt6.QtWidgets import QMainWindow
 
 try:
     from PyQt6 import sip as _sip  # type: ignore
-
     _sip_isdeleted = getattr(_sip, "isdeleted", None)
 except Exception:
     _sip = None

{moleditpy_linux-2.6.2 → moleditpy_linux-2.6.3}/src/moleditpy_linux/modules/main_window_app_state.py

@@ -16,27 +16,22 @@ MainWindow (main_window.py) から分離されたモジュール
 機能クラス: MainWindowAppState
 """
 
-
 import base64
 import copy
 import os
 import traceback
-
 import numpy as np
 
 # RDKit imports (explicit to satisfy flake8 and used features)
 from rdkit import Chem
 from rdkit.Chem import Descriptors, rdMolDescriptors
 
-
-
 # PyQt6 Modules
 from PyQt6.QtCore import QDateTime, QPointF, Qt
 from PyQt6.QtWidgets import QMessageBox
 
 try:
     from PyQt6 import sip as _sip  # type: ignore
-
     _sip_isdeleted = getattr(_sip, "isdeleted", None)
 except Exception:
     _sip = None
@@ -860,7 +855,7 @@ class MainWindowAppState(object):
                                 except Exception:  # pragma: no cover
                                     import traceback
                                     traceback.print_exc()
-                            except Exception:  # pragma: no cover
+                            except Exception:
                                 # non-fatal if mapping creation fails
                                 pass
 

{moleditpy_linux-2.6.2 → moleditpy_linux-2.6.3}/src/moleditpy_linux/modules/main_window_compute.py

@@ -33,7 +33,6 @@ except Exception:
 
 try:
     from PyQt6 import sip as _sip  # type: ignore
-
     _sip_isdeleted = getattr(_sip, "isdeleted", None)
 except Exception:
     _sip = None
@@ -397,7 +396,7 @@ class MainWindowCompute(object):
         # Keep a reference so we can reliably remove the text actor later
         try:
             self._calculating_text_actor = text_actor
-        except Exception:  # pragma: no cover
+        except Exception:
             # Best-effort: if storing fails, ignore — cleanup will still attempt renderer removal
             pass
         text_actor.GetTextProperty().SetOpacity(1)  # pragma: no cover
@@ -1005,7 +1004,7 @@ class MainWindowCompute(object):
                     try:
                         if mol.HasProp("_pme_optimization_method"):
                             opt_method = mol.GetProp("_pme_optimization_method")
-                    except Exception:  # pragma: no cover
+                    except Exception:
                         # not all Mol objects support HasProp/GetProp safely
                         pass
             except Exception:  # pragma: no cover
@@ -1025,7 +1024,7 @@ class MainWindowCompute(object):
                 else:
                     # store raw value otherwise
                     self.last_successful_optimization_method = opt_method
-        except Exception:  # pragma: no cover
+        except Exception:
             # non-fatal
             pass
 
@@ -1054,8 +1053,8 @@ class MainWindowCompute(object):
 
             self.update_chiral_labels()
         except Exception:  # pragma: no cover
-            # 念のためエラーを握り潰して UI を壊さない
-            pass
+            import traceback
+            traceback.print_exc()
 
         self.draw_molecule_3d(mol)
 

{moleditpy_linux-2.6.2 → moleditpy_linux-2.6.3}/src/moleditpy_linux/modules/main_window_dialog_manager.py

@@ -19,21 +19,12 @@ MainWindow (main_window.py) から分離されたモジュール
 import json
 import os
 
-# RDKit imports (explicit to satisfy flake8 and used features)
-try:
-    pass
-except Exception:  # pragma: no cover
-    import traceback
-
-    pass
-
 # PyQt6 Modules
 from PyQt6.QtCore import QDateTime
 from PyQt6.QtWidgets import QInputDialog, QMessageBox
 
 try:
     from PyQt6 import sip as _sip  # type: ignore
-
     _sip_isdeleted = getattr(_sip, "isdeleted", None)
 except Exception:
     _sip = None

{moleditpy_linux-2.6.2 → moleditpy_linux-2.6.3}/src/moleditpy_linux/modules/main_window_edit_3d.py

@@ -38,7 +38,6 @@ from PyQt6.QtWidgets import QGraphicsTextItem
 
 try:
     from PyQt6 import sip as _sip  # type: ignore
-
     _sip_isdeleted = getattr(_sip, "isdeleted", None)
 except Exception:
     _sip = None

{moleditpy_linux-2.6.2 → moleditpy_linux-2.6.3}/src/moleditpy_linux/modules/main_window_edit_actions.py

@@ -194,8 +194,6 @@ class MainWindowEditActions(object):
 
         except Exception as e:
             print(f"Error during copy operation: {e}")
-
-            pass
             self.statusBar().showMessage(f"Error during copy operation: {e}")
 
     def cut_selection(self):
@@ -214,8 +212,6 @@ class MainWindowEditActions(object):
 
         except Exception as e:
             print(f"Error during cut operation: {e}")
-
-            pass
             self.statusBar().showMessage(f"Error during cut operation: {e}")
 
     def paste_from_clipboard(self):
@@ -270,8 +266,6 @@ class MainWindowEditActions(object):
 
         except Exception as e:
             print(f"Error during paste operation: {e}")
-
-            pass
             self.statusBar().showMessage(f"Error during paste operation: {e}")
         self.statusBar().showMessage(f"Pasted {len(new_atoms)} atoms.", 2000)
         self.activate_select_mode()
@@ -384,8 +378,8 @@ class MainWindowEditActions(object):
                 try:
                     self.push_undo_state()
                 except Exception:  # pragma: no cover
-                    # Do not allow undo stack problems to crash the app
-                    pass
+                    import traceback
+                    traceback.print_exc()
                 self.statusBar().showMessage(
                     f"Removed {removed_count} hydrogen atoms.", 2000
                 )
@@ -404,7 +398,6 @@ class MainWindowEditActions(object):
         except Exception as e:
             # Capture and log unexpected errors but don't let them crash the UI
             print(f"Error during hydrogen removal: {e}")
-            pass
             try:
                 self.statusBar().showMessage(f"Error removing hydrogen atoms: {e}")
             except Exception:  # pragma: no cover
@@ -608,7 +601,6 @@ class MainWindowEditActions(object):
 
         except Exception as e:
             print(f"Error during hydrogen addition: {e}")
-            pass
             self.statusBar().showMessage(f"Error adding hydrogen atoms: {e}")
 
     def update_edit_menu_actions(self):
@@ -697,7 +689,6 @@ class MainWindowEditActions(object):
 
         except Exception as e:
             print(f"Error rotating molecule: {e}")
-            pass
             self.statusBar().showMessage(f"Error rotating: {e}")
 
     def select_all(self):
@@ -911,8 +902,8 @@ class MainWindowEditActions(object):
                             if is_deleted_func and is_deleted_func(item):
                                 continue
                         except Exception:  # pragma: no cover
-                            # If sip check itself fails, continue with other lightweight guards
-                            pass
+                            import traceback
+                            traceback.print_exc()
 
                         # If the item is no longer in a scene, skip updating it to avoid
                         # touching partially-deleted objects during scene teardown.
@@ -950,9 +941,8 @@ class MainWindowEditActions(object):
                             try:
                                 item.implicit_h_count = new_count
                             except Exception:  # pragma: no cover
-                                # If setting the count fails, continue but still
-                                # attempt to set the problem flag below.
-                                pass
+                                import traceback
+                                traceback.print_exc()
 
                             # Apply problem flag (visual red-outline)
                             try:
@@ -984,8 +974,8 @@ class MainWindowEditActions(object):
                             try:
                                 it.update()
                             except Exception:  # pragma: no cover
-                                # ignore update errors for robustness
-                                pass
+                                import traceback
+                                traceback.print_exc()
                     except Exception:
                         # Ignore any unexpected errors when touching the item
                         continue
@@ -1001,8 +991,8 @@ class MainWindowEditActions(object):
                     import traceback
                     traceback.print_exc()
         except Exception:  # pragma: no cover
-            # Make sure update failures never crash the application
-            pass
+            import traceback
+            traceback.print_exc()
 
     def clean_up_2d_structure(self):
         self.statusBar().showMessage("Optimizing 2D structure...")
@@ -1084,8 +1074,8 @@ class MainWindowEditActions(object):
                     if sip_isdeleted_safe(item):
                         continue
                 except Exception:  # pragma: no cover
-                    # If the sip check fails, continue with other lightweight guards
-                    pass
+                    import traceback
+                    traceback.print_exc()
                 try:
                     sc = None
                     try:
@@ -1557,8 +1547,8 @@ class MainWindowEditActions(object):
                     import traceback
                     traceback.print_exc()
         except Exception:  # pragma: no cover
-            # best-effort only
-            pass
+            import traceback
+            traceback.print_exc()
 
         # Reset UI flags
         try:

{moleditpy_linux-2.6.2 → moleditpy_linux-2.6.3}/src/moleditpy_linux/modules/main_window_export.py

@@ -21,14 +21,6 @@ import os
 
 import numpy as np
 
-# RDKit imports (explicit to satisfy flake8 and used features)
-try:
-    pass
-except Exception:  # pragma: no cover
-    import traceback
-
-    pass
-
 # PyQt6 Modules
 import pyvista as pv
 from PyQt6.QtCore import QRectF, QSize, Qt
@@ -38,7 +30,6 @@ from PyQt6.QtWidgets import QApplication, QFileDialog, QMessageBox
 
 try:
     from PyQt6 import sip as _sip  # type: ignore
-
     _sip_isdeleted = getattr(_sip, "isdeleted", None)
 except Exception:
     _sip = None

{moleditpy_linux-2.6.2 → moleditpy_linux-2.6.3}/src/moleditpy_linux/modules/main_window_main_init.py

@@ -26,13 +26,6 @@ import sys
 # RDKit imports (explicit to satisfy flake8 and used features)
 from rdkit import Chem
 
-try:
-    pass
-except Exception:  # pragma: no cover
-    import traceback
-
-    pass
-
 # PyQt6 Modules
 from PyQt6.QtCore import QLineF, QPointF, QRectF, Qt, QTimer, QUrl
 from PyQt6.QtGui import (
@@ -453,7 +446,6 @@ class MainWindowMainInit(object):
         except Exception:  # pragma: no cover
             import traceback
             traceback.print_exc()
-            pass
 
         right_buttons_layout.addWidget(self.optimize_3d_button)
 

{moleditpy_linux-2.6.2 → moleditpy_linux-2.6.3}/src/moleditpy_linux/modules/main_window_molecular_parsers.py

@@ -25,13 +25,6 @@ import traceback
 from rdkit import Chem
 from rdkit.Chem import AllChem, Descriptors, rdGeometry, rdMolTransforms
 
-try:
-    pass
-except Exception:  # pragma: no cover
-    import traceback
-
-    pass
-
 # PyQt6 Modules
 from PyQt6.QtCore import QPointF, QTimer
 from PyQt6.QtWidgets import (
@@ -48,7 +41,6 @@ from PyQt6.QtWidgets import (
 
 try:
     from PyQt6 import sip as _sip  # type: ignore
-
     _sip_isdeleted = getattr(_sip, "isdeleted", None)
 except Exception:
     _sip = None
@@ -194,7 +186,6 @@ class MainWindowMolecularParsers(object):
             self.statusBar().showMessage(f"Invalid MOL file format: {e}")
         except Exception as e:
             self.statusBar().showMessage(f"Error loading file: {e}")
-            pass
 
     def load_xyz_file(self, file_path):
         """XYZファイルを読み込んでRDKitのMolオブジェクトを作成する"""
@@ -971,7 +962,7 @@ class MainWindowMolecularParsers(object):
                     try:
                         mol.AddBond(i, j, Chem.BondType.SINGLE)
                         bonds_added.append((i, j, distance))
-                    except Exception:  # pragma: no cover
+                    except Exception:
                         # 既に結合が存在する場合はスキップ
                         pass
 
@@ -983,7 +974,7 @@ class MainWindowMolecularParsers(object):
     def save_as_mol(self):
         try:
             mol_block = self.data.to_mol_block()
-            if not mol_block:  # pragma: no cover
+            if not mol_block:
                 self.statusBar().showMessage("Error: No 2D data to save.")
                 return
 
@@ -1037,8 +1028,6 @@ class MainWindowMolecularParsers(object):
         except Exception as e:
             self.statusBar().showMessage(f"Error saving file: {e}")
 
-            pass
-
     def save_as_xyz(self):
         if not self.current_mol:  # pragma: no cover
             self.statusBar().showMessage("Error: Please generate a 3D structure first.")

{moleditpy_linux-2.6.2 → moleditpy_linux-2.6.3}/src/moleditpy_linux/modules/main_window_project_io.py

@@ -22,33 +22,17 @@ import os
 import pickle
 import traceback
 
-# RDKit imports (explicit to satisfy flake8 and used features)
-try:
-    pass
-except Exception:  # pragma: no cover
-    import traceback
-
-    pass
-
 # PyQt6 Modules
 from PyQt6.QtCore import QTimer
 from PyQt6.QtWidgets import QFileDialog, QMessageBox
 
 try:
     from PyQt6 import sip as _sip  # type: ignore
-
     _sip_isdeleted = getattr(_sip, "isdeleted", None)
 except Exception:
     _sip = None
     _sip_isdeleted = None
 
-try:
-    # package relative imports (preferred when running as `python -m moleditpy`)
-    pass
-except Exception:  # pragma: no cover
-    # Fallback to absolute imports for script-style execution
-    pass
-
 
 # --- クラス定義 ---
 class MainWindowProjectIo(object):
@@ -93,7 +77,6 @@ class MainWindowProjectIo(object):
                 self.statusBar().showMessage(f"Data serialization error: {e}")
             except Exception as e:
                 self.statusBar().showMessage(f"Error saving project file: {e}")
-                pass
         else:
             # MOL/SDF/XYZなどは上書き保存せず、必ず「名前を付けて保存」にする
             self.save_project_as()
@@ -158,7 +141,6 @@ class MainWindowProjectIo(object):
             self.statusBar().showMessage(f"Data serialization error: {e}")
         except Exception as e:
             self.statusBar().showMessage(f"Error saving project file: {e}")
-            pass
 
     def save_raw_data(self):
         if not self.data.atoms and not self.current_mol:
@@ -218,7 +200,6 @@ class MainWindowProjectIo(object):
             self.statusBar().showMessage(f"Data serialization error: {e}")
         except Exception as e:
             self.statusBar().showMessage(f"Error saving project file: {e}")
-            pass
 
     def load_raw_data(self, file_path=None):
         if not file_path:  # pragma: no cover
@@ -255,7 +236,6 @@ class MainWindowProjectIo(object):
             self.statusBar().showMessage(f"Invalid project file format: {e}")
         except Exception as e:
             self.statusBar().showMessage(f"Error loading project file: {e}")
-            pass
 
     def save_as_json(self):
         """PMEJSONファイル形式で保存 (3D MOL情報含む)"""
@@ -314,7 +294,6 @@ class MainWindowProjectIo(object):
             self.statusBar().showMessage(f"JSON serialization error: {e}")
         except Exception as e:
             self.statusBar().showMessage(f"Error saving PME Project file: {e}")
-            pass
 
     def load_json_data(self, file_path=None):
         """PME Projectファイル形式を読み込み"""
@@ -371,7 +350,6 @@ class MainWindowProjectIo(object):
             self.statusBar().showMessage(f"File I/O error: {e}")
         except Exception as e:
             self.statusBar().showMessage(f"Error loading PME Project file: {e}")
-            pass
 
     def open_project_file(self, file_path=None):
         """プロジェクトファイルを開く（.pmeprjと.pmerawの両方に対応）"""

{moleditpy_linux-2.6.2 → moleditpy_linux-2.6.3}/src/moleditpy_linux/modules/main_window_string_importers.py

@@ -21,32 +21,17 @@ import traceback
 from rdkit import Chem
 from rdkit.Chem import AllChem
 
-try:
-    pass
-except Exception:  # pragma: no cover
-    import traceback
-
-    pass
-
 # PyQt6 Modules
 from PyQt6.QtCore import QPointF, QTimer
 from PyQt6.QtWidgets import QInputDialog
 
 try:
     from PyQt6 import sip as _sip  # type: ignore
-
     _sip_isdeleted = getattr(_sip, "isdeleted", None)
 except Exception:
     _sip = None
     _sip_isdeleted = None
 
-try:
-    # package relative imports (preferred when running as `python -m moleditpy`)
-    pass
-except Exception:  # pragma: no cover
-    # Fallback to absolute imports for script-style execution
-    pass
-
 
 # --- クラス定義 ---
 class MainWindowStringImporters(object):
@@ -158,8 +143,6 @@ class MainWindowStringImporters(object):
         except Exception as e:
             self.statusBar().showMessage(f"Error loading from SMILES: {e}")
 
-            pass
-
     def load_from_inchi(self, inchi_string):
         """InChI文字列から分子を読み込み、2Dエディタに表示する"""
         try:

{moleditpy_linux-2.6.2 → moleditpy_linux-2.6.3}/src/moleditpy_linux/modules/main_window_ui_manager.py

@@ -18,14 +18,6 @@ MainWindow (main_window.py) から分離されたモジュール
 
 import vtk
 
-# RDKit imports (explicit to satisfy flake8 and used features)
-try:
-    pass
-except Exception:  # pragma: no cover
-    import traceback
-
-    pass
-
 # PyQt6 Modules
 from PyQt6.QtCore import QEvent, Qt, QTimer
 from PyQt6.QtWidgets import (
@@ -38,7 +30,6 @@ from PyQt6.QtWidgets import (
 
 try:
     from PyQt6 import sip as _sip  # type: ignore
-
     _sip_isdeleted = getattr(_sip, "isdeleted", None)
 except Exception:
     _sip = None

{moleditpy_linux-2.6.2 → moleditpy_linux-2.6.3}/src/moleditpy_linux/modules/main_window_view_3d.py

@@ -24,13 +24,6 @@ import vtk
 # RDKit imports (explicit to satisfy flake8 and used features)
 from rdkit import Chem
 
-try:
-    pass
-except Exception:  # pragma: no cover
-    import traceback
-
-    pass
-
 # PyQt6 Modules
 import pyvista as pv
 from PyQt6.QtCore import QRectF, Qt
@@ -39,7 +32,6 @@ from PyQt6.QtWidgets import QApplication, QGraphicsView
 
 try:
     from PyQt6 import sip as _sip  # type: ignore
-
     _sip_isdeleted = getattr(_sip, "isdeleted", None)
 except Exception:
     _sip = None

{moleditpy_linux-2.6.2 → moleditpy_linux-2.6.3}/src/moleditpy_linux/modules/main_window_view_loaders.py

@@ -23,19 +23,11 @@ import traceback
 from rdkit import Chem
 from rdkit.Chem import AllChem
 
-try:
-    pass
-except Exception:  # pragma: no cover
-    import traceback
-
-    pass
-
 # PyQt6 Modules
 from PyQt6.QtWidgets import QFileDialog
 
 try:
     from PyQt6 import sip as _sip  # type: ignore
-
     _sip_isdeleted = getattr(_sip, "isdeleted", None)
 except Exception:
     _sip = None
@@ -163,8 +155,6 @@ class MainWindowViewLoaders(object):
             self.statusBar().showMessage(f"Error loading XYZ file: {e}")
             self.restore_ui_for_editing()
 
-            pass
-
     def save_3d_as_mol(self):
         if not self.current_mol:
             self.statusBar().showMessage("Error: Please generate a 3D structure first.")

{moleditpy_linux-2.6.2 → moleditpy_linux-2.6.3}/src/moleditpy_linux/modules/molecule_scene.py

@@ -39,7 +39,6 @@ except Exception:
 
 try:
     from PyQt6 import sip as _sip  # type: ignore
-
     _sip_isdeleted = getattr(_sip, "isdeleted", None)
 except Exception:
     _sip = None