moleditpy 2.5.1__tar.gz → 2.5.2__tar.gz

{moleditpy-2.5.1 → moleditpy-2.5.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: MoleditPy
-Version: 2.5.1
+Version: 2.5.2
 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-2.5.1 → moleditpy-2.5.2}/pyproject.toml

@@ -5,7 +5,7 @@ build-backend = "setuptools.build_meta"
 [project]
 name = "MoleditPy"
 
-version = "2.5.1"
+version = "2.5.2"
 
 license = {file = "LICENSE"}
 

{moleditpy-2.5.1 → moleditpy-2.5.2}/src/MoleditPy.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: MoleditPy
-Version: 2.5.1
+Version: 2.5.2
 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-2.5.1 → moleditpy-2.5.2}/src/moleditpy/__main__.py

@@ -16,11 +16,8 @@ print("MoleditPy — A Python-based molecular editing software")
 print("-----------------------------------------------------\n")
 
 try:
-    # Preferred when running as a package: python -m moleditpy
     from .main import main
 except Exception:
-    # Fallback when running the file directly: python __main__.py
-    # This will import the top-level `main` module in the same folder.
     from main import main
 
 # --- Application Execution ---

{moleditpy-2.5.1 → moleditpy-2.5.2}/src/moleditpy/main.py

@@ -17,11 +17,8 @@ import ctypes
 from PyQt6.QtWidgets import QApplication
 
 try:
-    # When executed as part of the package (python -m moleditpy)
     from .modules.main_window import MainWindow
 except Exception:
-    # When executed as a standalone script (python main.py) the package-relative
-    # import won't work; fall back to absolute import that works with sys.path
     from modules.main_window import MainWindow
 
 def main():

{moleditpy-2.5.1 → moleditpy-2.5.2}/src/moleditpy/modules/__init__.py

@@ -15,7 +15,7 @@ DOI: 10.5281/zenodo.17268532
 # Do not import `pybel` at module import time. Only expose the presence
 # of Open Babel via `OBABEL_AVAILABLE`. Modules should import `pybel`
 # lazily if and when they need it.
-try:
+try: # pragma: no cover
     import importlib.util
     OBABEL_AVAILABLE = importlib.util.find_spec("openbabel") is not None
 except Exception:
@@ -26,7 +26,7 @@ except Exception:
 # it once at module import time and expose a small, robust wrapper so callers
 # can avoid re-importing sip repeatedly and so we centralize exception
 # handling (this reduces crash risk during teardown and deletion operations).
-try:
+try: # pragma: no cover
     import sip as _sip  # type: ignore
     _sip_isdeleted = getattr(_sip, 'isdeleted', None)
 except Exception:
@@ -40,7 +40,7 @@ def sip_isdeleted_safe(obj) -> bool:
     occurs while checking, it returns False (i.e. not deleted) so that the
     caller can continue other lightweight guards (like checking scene()).
     """
-    try:
+    try: # pragma: no cover
         if _sip_isdeleted is None:
             return False
         return bool(_sip_isdeleted(obj))

{moleditpy-2.5.1 → moleditpy-2.5.2}/src/moleditpy/modules/about_dialog.py

@@ -21,7 +21,7 @@ try:
 except Exception:
     from modules.constants import VERSION
 
-class AboutDialog(QDialog):
+class AboutDialog(QDialog): # pragma: no cover
     def __init__(self, main_window, parent=None):
         super().__init__(parent)
         self.main_window = main_window

{moleditpy-2.5.1 → moleditpy-2.5.2}/src/moleditpy/modules/align_plane_dialog.py

@@ -21,7 +21,7 @@ try:
 except Exception:
     from modules.dialog3_d_picking_mixin import Dialog3DPickingMixin
 
-class AlignPlaneDialog(Dialog3DPickingMixin, QDialog):
+class AlignPlaneDialog(Dialog3DPickingMixin, QDialog): # pragma: no cover
     def __init__(self, mol, main_window, plane, preselected_atoms=None, parent=None):
         QDialog.__init__(self, parent)
         Dialog3DPickingMixin.__init__(self)
@@ -44,7 +44,7 @@ class AlignPlaneDialog(Dialog3DPickingMixin, QDialog):
     def init_ui(self):
         plane_names = {'xy': 'XY', 'xz': 'XZ', 'yz': 'YZ'}
         self.setWindowTitle(f"Align to {plane_names[self.plane]} Plane")
-        self.setModal(False)  # モードレスにしてクリックを阻害しない
+        self.setModal(False)
         layout = QVBoxLayout(self)
         
         # Instructions

{moleditpy-2.5.1 → moleditpy-2.5.2}/src/moleditpy/modules/alignment_dialog.py

@@ -22,7 +22,7 @@ try:
 except Exception:
     from modules.dialog3_d_picking_mixin import Dialog3DPickingMixin
 
-class AlignmentDialog(Dialog3DPickingMixin, QDialog):
+class AlignmentDialog(Dialog3DPickingMixin, QDialog): # pragma: no cover
     def __init__(self, mol, main_window, axis, preselected_atoms=None, parent=None):
         QDialog.__init__(self, parent)
         Dialog3DPickingMixin.__init__(self)
@@ -46,7 +46,7 @@ class AlignmentDialog(Dialog3DPickingMixin, QDialog):
     def init_ui(self):
         axis_names = {'x': 'X-axis', 'y': 'Y-axis', 'z': 'Z-axis'}
         self.setWindowTitle(f"Align to {axis_names[self.axis]}")
-        self.setModal(False)  # モードレスにしてクリックを阻害しない
+        self.setModal(False)
         layout = QVBoxLayout(self)
         
         # Instructions

{moleditpy-2.5.1 → moleditpy-2.5.2}/src/moleditpy/modules/angle_dialog.py

@@ -24,7 +24,7 @@ from PyQt6.QtWidgets import QMessageBox
 import numpy as np
 
 
-class AngleDialog(Dialog3DPickingMixin, QDialog):
+class AngleDialog(Dialog3DPickingMixin, QDialog): # pragma: no cover
     def __init__(self, mol, main_window, preselected_atoms=None, parent=None):
         QDialog.__init__(self, parent)
         Dialog3DPickingMixin.__init__(self)
@@ -44,8 +44,7 @@ class AngleDialog(Dialog3DPickingMixin, QDialog):
     
     def init_ui(self):
         self.setWindowTitle("Adjust Angle")
-        self.setModal(False)  # モードレスにしてクリックを阻害しない
-  # 常に前面表示
+        self.setModal(False)
         layout = QVBoxLayout(self)
         
         # Instructions

{moleditpy-2.5.1 → moleditpy-2.5.2}/src/moleditpy/modules/bond_item.py

@@ -34,6 +34,8 @@ except Exception:
         HOVER_PEN_WIDTH, DESIRED_BOND_PIXEL_WIDTH,
     )
 
+from rdkit import Chem
+
 class BondItem(QGraphicsItem):
 
     def get_ez_label_rect(self):
@@ -206,9 +208,6 @@ class BondItem(QGraphicsItem):
         except Exception:
             return None
 
-
-
-
     def paint(self, painter, option, widget):
         if self.atom1 is None or self.atom2 is None:
             return
@@ -341,7 +340,6 @@ class BondItem(QGraphicsItem):
                                     if bond and bond.IsInRing():
                                         is_in_ring = True
                                         # 環の中心を計算（この結合を含む最小環）
-                                        from rdkit import Chem
                                         ring_info = mol.GetRingInfo()
                                         for ring in ring_info.AtomRings():
                                             if rdkit_idx1 in ring and rdkit_idx2 in ring:

{moleditpy-2.5.1 → moleditpy-2.5.2}/src/moleditpy/modules/bond_length_dialog.py

@@ -19,7 +19,7 @@ from .dialog3_d_picking_mixin import Dialog3DPickingMixin
 from PyQt6.QtCore import Qt
 import numpy as np
 
-class BondLengthDialog(Dialog3DPickingMixin, QDialog):
+class BondLengthDialog(Dialog3DPickingMixin, QDialog): # pragma: no cover
     def __init__(self, mol, main_window, preselected_atoms=None, parent=None):
         QDialog.__init__(self, parent)
         Dialog3DPickingMixin.__init__(self)
@@ -37,8 +37,8 @@ class BondLengthDialog(Dialog3DPickingMixin, QDialog):
     
     def init_ui(self):
         self.setWindowTitle("Adjust Bond Length")
-        self.setModal(False)  # モードレスにしてクリックを阻害しない
-  # 常に前面表示
+        self.setModal(False)
+
         layout = QVBoxLayout(self)
         
         # Instructions

{moleditpy-2.5.1 → moleditpy-2.5.2}/src/moleditpy/modules/calculation_worker.py

@@ -22,12 +22,6 @@ from rdkit.DistanceGeometry import DoTriangleSmoothing
 import math
 import re
 
-
-# Use centralized Open Babel availability from package-level __init__
-# Use per-package modules availability (local __init__).
-# Prefer package-relative import when running as `python -m moleditpy` and
-# fall back to a top-level import when running as a script. This mirrors the
-# import style used in other modules and keeps the package robust.
 try:
     from . import OBABEL_AVAILABLE
 except Exception:
@@ -47,22 +41,14 @@ else:
 class CalculationWorker(QObject):
     status_update = pyqtSignal(str)
     finished = pyqtSignal(object)
-    error = pyqtSignal(object)  # emit (worker_id, msg) tuples for robustness
-    # Per-worker start signal to avoid sharing a single MainWindow signal
-    # among many worker instances (which causes race conditions and stale
-    # workers being started on a single emission).
+    error = pyqtSignal(object) 
     start_work = pyqtSignal(str, object)
 
     def __init__(self, parent=None):
         super().__init__(parent)
-        # Connect the worker's own start signal to its run slot. This
-        # guarantees that only this worker will respond when start_work
-        # is emitted (prevents cross-talk between workers).
         try:
             self.start_work.connect(self.run_calculation)
         except Exception:
-            # Be defensive: if connection fails, continue; the caller may
-            # fallback to emitting directly.
             pass
 
     @pyqtSlot(str, object)
@@ -75,11 +61,7 @@ class CalculationWorker(QObject):
                 worker_id = options.get('worker_id') if options else None
             except Exception:
                 worker_id = None
-
-            # If a caller starts a worker without providing a worker_id, treat
-            # it as a "global" worker that can still be halted via a global
-            # halt flag. Emit a single status warning so callers know that
-            # the worker was started without an identifier.
+                
             _warned_no_worker_id = False
             if worker_id is None:
                 try:
@@ -92,9 +74,6 @@ class CalculationWorker(QObject):
             def _check_halted():
                 try:
                     halt_ids = getattr(self, 'halt_ids', None)
-                    # If worker_id is None, allow halting via a global mechanism:
-                    #  - an explicit attribute `halt_all` set to True on the worker
-                    #  - the shared `halt_ids` set containing None or the sentinel 'ALL'
                     if worker_id is None:
                         if getattr(self, 'halt_all', False):
                             return True
@@ -115,11 +94,11 @@ class CalculationWorker(QObject):
                     if _check_halted():
                         return
                     self.status_update.emit(msg)
-                except Exception:
+                except Exception: # pragma: no cover
                     # Swallow any signal-emission errors to avoid crashing the worker
                     pass
 
-            def _safe_finished(payload):
+            def _safe_finished(payload): # pragma: no cover
                 try:
                     # Attempt to emit the payload; preserve existing fallback behavior
                     try:
@@ -137,7 +116,7 @@ class CalculationWorker(QObject):
                 except Exception:
                     pass
 
-            def _safe_error(msg):
+            def _safe_error(msg): # pragma: no cover
                 try:
                     # Emit a tuple containing the worker_id (may be None) and the message
                     try:
@@ -155,10 +134,6 @@ class CalculationWorker(QObject):
             if options is None:
                 options = {}
             conversion_mode = options.get('conversion_mode', 'fallback')
-            # Ensure params exists in all code paths (some RDKit calls below
-            # reference `params` and earlier editing introduced a path where
-            # it might not be defined). Initialize to None here and assign
-            # a proper ETKDG params object later where needed.
             params = None
             if not mol_block:
                 raise ValueError("No atoms to convert.")
@@ -173,8 +148,6 @@ class CalculationWorker(QObject):
             if _check_halted():
                 raise RuntimeError("Halted")
 
-            # CRITICAL FIX: Extract and restore explicit E/Z labels from MOL block
-            # Parse M CFG lines to get explicit stereo labels
             explicit_stereo = {}
             mol_lines = mol_block.split('\n')
             for line in mol_lines:
@@ -552,10 +525,6 @@ class CalculationWorker(QObject):
                     stereo_atoms = bond.GetStereoAtoms()
                     original_stereo_info.append((bond.GetIdx(), bond.GetStereo(), stereo_atoms))
             
-            # Only report RDKit-specific messages when RDKit embedding will be
-            # attempted. For other conversion modes, emit clearer, non-misleading
-            # status messages so the UI doesn't show "RDKit" when e.g. direct
-            # coordinates or Open Babel will be used.
             if conversion_mode in ('fallback', 'rdkit'):
                 _safe_status("RDKit: Embedding 3D coordinates...")
             elif conversion_mode == 'obabel':

{moleditpy-2.5.1 → moleditpy-2.5.2}/src/moleditpy/modules/color_settings_dialog.py

@@ -20,7 +20,7 @@ try:
 except Exception:
     from modules.constants import CPK_COLORS, DEFAULT_CPK_COLORS
 
-class ColorSettingsDialog(QDialog):
+class ColorSettingsDialog(QDialog): # pragma: no cover
     """Dialog to customize CPK element colors.
 
     - Click an element to pick a new color for the element (CPK colors).
@@ -126,11 +126,6 @@ class ColorSettingsDialog(QDialog):
         h.addWidget(apply_button); h.addWidget(ok_button); h.addWidget(cancel_button)
         layout.addLayout(h)
 
-        # initialize
-        # No 2D bond color control here
-
-    # 2D bond color picker removed — 2D bond color is fixed and not configurable here
-
     def on_element_clicked(self):
         b = self.sender()
         symbol = b.text()

{moleditpy-2.5.1 → moleditpy-2.5.2}/src/moleditpy/modules/constants.py

@@ -16,7 +16,7 @@ from PyQt6.QtGui import QFont, QColor
 from rdkit import Chem
 
 #Version
-VERSION = '2.5.1'
+VERSION = '2.5.2'
 
 ATOM_RADIUS = 18
 BOND_OFFSET = 3.5

{moleditpy-2.5.1 → moleditpy-2.5.2}/src/moleditpy/modules/constrained_optimization_dialog.py

@@ -21,7 +21,7 @@ from PyQt6.QtCore import Qt
 from rdkit.Chem import AllChem, rdMolTransforms
 
 
-class ConstrainedOptimizationDialog(Dialog3DPickingMixin, QDialog):
+class ConstrainedOptimizationDialog(Dialog3DPickingMixin, QDialog): # pragma: no cover
     """制約付き最適化ダイアログ"""
     
     def __init__(self, mol, main_window, parent=None):
@@ -90,8 +90,6 @@ class ConstrainedOptimizationDialog(Dialog3DPickingMixin, QDialog):
             current_method_str = self.main_window.optimization_method or "MMFF_RDKIT"
             current_method = current_method_str.upper()
             
-            # (修正) 比較順序を厳密化
-            
             # 1. UFF_RDKIT
             if current_method == "UFF_RDKIT":
                 self.ff_combo.setCurrentText("UFF")
@@ -278,8 +276,7 @@ class ConstrainedOptimizationDialog(Dialog3DPickingMixin, QDialog):
                 return
 
         self.constraints.append((constraint_type, atom_indices, value, force_const))
-        
-        # 表を更新
+
         # 表を更新
         row_count = self.constraint_table.rowCount()
         self.constraint_table.insertRow(row_count)

{moleditpy-2.5.1 → moleditpy-2.5.2}/src/moleditpy/modules/custom_interactor_style.py

@@ -171,9 +171,7 @@ class CustomInteractorStyle(vtkInteractorStyleTrackballCamera):
         # 測定モードが有効な場合の処理
         if mw.measurement_mode and mw.current_mol:
             click_pos = self.GetInteractor().GetEventPosition()
-            # Note: We do NOT set _mouse_press_pos here initially.
-            # We only set it if we confirm it's a background click (see below).
-            self._mouse_moved_during_drag = False  # Reset drag flag
+            self._mouse_moved_during_drag = False
             
             picker = mw.plotter.picker
             
@@ -212,10 +210,6 @@ class CustomInteractorStyle(vtkInteractorStyleTrackballCamera):
             super().OnLeftButtonDown()
             return
         
-        # Ctrl+クリックの原子選択機能は無効化（Move Group機能で代替）
-        # if is_ctrl_click and mw.current_mol:
-        #     ... (無効化)
-
         # 3D分子(mw.current_mol)が存在する場合のみ、原子の選択処理を実行
         if is_edit_active and mw.current_mol:
             click_pos = self.GetInteractor().GetEventPosition()
@@ -372,14 +366,6 @@ class CustomInteractorStyle(vtkInteractorStyleTrackballCamera):
             # カスタムの原子ドラッグ処理
             self.is_dragging = True
             atom_id = mw.dragged_atom_info['id']
-            # We intentionally do NOT update visible coordinates or the
-            # authoritative atom position during mouse-move while dragging.
-            # The UX requirement here is that atoms need not visibly move
-            # while the mouse is being dragged. Compute and apply the final
-            # world-coordinate only once on mouse release (on_left_button_up).
-            # Keep minimal state: mark that a drag occurred (is_dragging)
-            # and allow the release handler to compute the final position.
-            # This avoids duplicate updates and simplifies event ordering.
         else:
             # カメラ回転処理を親クラスに任せます
             super().OnMouseMove()
@@ -502,13 +488,6 @@ class CustomInteractorStyle(vtkInteractorStyleTrackballCamera):
             if self.is_dragging:
                 if mw.current_mol and mw.current_mol.GetNumConformers() > 0:
                     try:
-                        # Before applying conformer updates, compute the final
-                        # world coordinates for the dragged atom based on the
-                        # release pointer position. During the drag we did not
-                        # update mw.atom_positions_3d (to keep the visuals
-                        # static). Now compute the final position for the
-                        # dragged atom and store it into mw.atom_positions_3d
-                        # so the conformer update loop below will pick it up.
                         atom_id = None
                         try:
                             atom_id = mw.dragged_atom_info.get('id') if mw.dragged_atom_info else None
@@ -521,10 +500,6 @@ class CustomInteractorStyle(vtkInteractorStyleTrackballCamera):
                                 renderer = mw.plotter.renderer
                                 current_display_pos = interactor.GetEventPosition()
                                 conf = mw.current_mol.GetConformer()
-                                # Use the atom's current 3D position to obtain a
-                                # display-space depth (z) value, then replace the
-                                # x/y with the pointer position to project back to
-                                # world coordinates at that depth.
                                 pos_3d = conf.GetAtomPosition(atom_id)
                                 renderer.SetWorldPoint(pos_3d.x, pos_3d.y, pos_3d.z, 1.0)
                                 renderer.WorldToDisplay()
@@ -538,8 +513,6 @@ class CustomInteractorStyle(vtkInteractorStyleTrackballCamera):
                                 try:
                                     mw.atom_positions_3d[atom_id] = new_world_coords
                                 except Exception:
-                                    # If atom_positions_3d is immutable or shaped
-                                    # differently, attempt a safe conversion.
                                     try:
                                         ap = list(mw.atom_positions_3d)
                                         ap[atom_id] = new_world_coords
@@ -547,13 +520,8 @@ class CustomInteractorStyle(vtkInteractorStyleTrackballCamera):
                                     except Exception:
                                         pass
                             except Exception:
-                                # If final-position computation fails, continue
-                                # and apply whatever state is available.
                                 pass
 
-                        # Apply the (now updated) positions to the RDKit conformer
-                        # exactly once. This ensures the conformer is
-                        # authoritative and avoids double-moves.
                         conf = mw.current_mol.GetConformer()
                         for i in range(mw.current_mol.GetNumAtoms()):
                             try:
@@ -575,9 +543,6 @@ class CustomInteractorStyle(vtkInteractorStyleTrackballCamera):
                         pass
                     mw.push_undo_state()
             mw.dragged_atom_info = None
-            # Refresh overlays and labels that depend on atom_positions_3d. Do
-            # not overwrite mw.atom_positions_3d here — it already reflects the
-            # positions the user dragged to. Only update dependent displays.
             try:
                 mw.update_3d_selection_display()
             except Exception:

{moleditpy-2.5.1 → moleditpy-2.5.2}/src/moleditpy/modules/custom_qt_interactor.py

@@ -18,11 +18,6 @@ class CustomQtInteractor(QtInteractor):
     def __init__(self, parent=None, main_window=None, **kwargs):
         super().__init__(parent, **kwargs)
         self.main_window = main_window
-        # Track recent clicks so we can detect and swallow triple-clicks
-        # Triple-clicks are not a distinct Qt event on all platforms, so we
-        # implement a small timing-based counter here and accept the event
-        # when 3 rapid clicks are detected to prevent them from reaching
-        # the VTK interactor and causing unexpected behaviour in the 3D view.
         self._last_click_time = 0.0
         self._click_count = 0
         self._ignore_next_release = False
@@ -91,7 +86,6 @@ class CustomQtInteractor(QtInteractor):
         else:
              self._click_count = 2 # Force sync
         
-        # We must ignore the release event that follows this double-click event
         self._ignore_next_release = True
         
         try:

{moleditpy-2.5.1 → moleditpy-2.5.2}/src/moleditpy/modules/dialog3_d_picking_mixin.py

@@ -62,11 +62,6 @@ class Dialog3DPickingMixin:
                             click_threshold = vdw_radius * 1.5
 
                             if distances[closest_atom_idx] < click_threshold:
-                                # We handled the pick (atom clicked) -> consume the event so
-                                # other UI elements (including the VTK interactor observers)
-                                # don't also process it. Set a flag on the main window so
-                                # the VTK-based handlers can ignore the same logical click
-                                # when it arrives via the VTK event pipeline.
                                 try:
                                     self.main_window._picking_consumed = True
                                 except Exception:

{moleditpy-2.5.1 → moleditpy-2.5.2}/src/moleditpy/modules/dihedral_dialog.py

@@ -24,7 +24,7 @@ import numpy as np
 from PyQt6.QtWidgets import QMessageBox
 
 
-class DihedralDialog(Dialog3DPickingMixin, QDialog):
+class DihedralDialog(Dialog3DPickingMixin, QDialog): # pragma: no cover
     def __init__(self, mol, main_window, preselected_atoms=None, parent=None):
         QDialog.__init__(self, parent)
         Dialog3DPickingMixin.__init__(self)
@@ -46,8 +46,7 @@ class DihedralDialog(Dialog3DPickingMixin, QDialog):
     
     def init_ui(self):
         self.setWindowTitle("Adjust Dihedral Angle")
-        self.setModal(False)  # モードレスにしてクリックを阻害しない
-  # 常に前面表示
+        self.setModal(False)
         layout = QVBoxLayout(self)
         
         # Instructions

{moleditpy-2.5.1 → moleditpy-2.5.2}/src/moleditpy/modules/main_window.py

@@ -24,15 +24,10 @@ from PyQt6.QtWidgets import (
     QMainWindow
 )
 
-
-
 from PyQt6.QtCore import (
     pyqtSignal, pyqtSlot
 )
 
-
-# Use centralized Open Babel availability from package-level __init__
-# Use per-package modules availability (local __init__).
 try:
     from . import OBABEL_AVAILABLE
 except Exception:
@@ -49,11 +44,6 @@ if OBABEL_AVAILABLE:
 else:
     pybel = None
     
-# Optional SIP helper: on some PyQt6 builds sip.isdeleted is available and
-# allows safely detecting C++ wrapper objects that have been deleted. Import
-# it once at module import time and expose a small, robust wrapper so callers
-# can avoid re-importing sip repeatedly and so we centralize exception
-# handling (this reduces crash risk during teardown and deletion operations).
 try:
     import sip as _sip  # type: ignore
     _sip_isdeleted = getattr(_sip, 'isdeleted', None)
@@ -96,24 +86,12 @@ class MainWindow(QMainWindow):
 
     # start_calculation carries the MOL block and an options object (second arg)
     start_calculation = pyqtSignal(str, object)
-    def __init__(self, initial_file=None):
-        # Initialize QMainWindow to ensure underlying Qt object is prepared
-        # before helper classes interact with the window (fixes crash when
-        # QMainWindow.__init__ not called).
+    def __init__(self, initial_file=None): # pragma: no cover
         super().__init__()
         # --- MOVED TO main_window_main_init.py ---
-        # The window functionality has been split across several helper
-        # modules (main_window_*). Each helper is implemented as a class
-        # whose methods were originally written to operate on the
-        # MainWindow instance as 'self'. To maintain that behaviour we
-        # create a small proxy (BoundFeature) that will forward call to
-        # the helper class with the MainWindow instance as the first
-        # argument.
-        # Undo/Redo操作中に状態復元中であることを示すフラグ
-        # 他のモジュールが呼び出される前に初期化する
         self._is_restoring_state = False
 
-        class BoundFeature:
+        class BoundFeature: # pragma: no cover
             """Bind a feature-class method calls to the MainWindow.
 
             Usage:
@@ -148,9 +126,6 @@ class MainWindow(QMainWindow):
                     return init_method(self._host, *a, **k)
                 return None
 
-        # Attach bound helpers to the main window; this keeps the
-        # original call sites (e.g. self.main_window_compute.trigger_conversion)
-        # working without changing them.
         self.main_window_main_init = BoundFeature(MainWindowMainInit, self)
         self.main_window_ui_manager = BoundFeature(MainWindowUiManager, self)
         self.main_window_view_3d = BoundFeature(MainWindowView3d, self)
@@ -165,27 +140,11 @@ class MainWindow(QMainWindow):
         self.main_window_dialog_manager = BoundFeature(MainWindowDialogManager, self)
         self.main_window_edit_3d = BoundFeature(MainWindowEdit3d, self)
 
-        # Call the initialization method from main_window_main_init which
-        # sets up the UI and the initial app state. Other helpers may
-        # expect the UI to exist so initialize them after this call.
         try:
-            # The helper's __init__ usually accepts the initial_file
-            # argument and is expected to be invoked with the MainWindow
-            # instance as the host. Because BoundFeature itself defines
-            # __init__, attribute lookup would resolve to BoundFeature.__init__
-            # instead of the helper class method. Call the helper class
-            # __init__ explicitly with the main window instance as the
-            # first argument.
-            # Call the helper's __init__ via helper proxy to ensure the
-            # initial host and arguments are forwarded correctly.
             self.main_window_main_init.init(initial_file)
         except Exception:
-            # If main init fails, still continue so we can attempt
-            # to catch / repair other issues via error messages.
             traceback.print_exc()
 
-        # Initialize other helper modules which implement their own
-        # __init__(self, main_window) if present.
         other_inits = [
             'main_window_view_3d', 'main_window_ui_manager', 'main_window_compute',
             'main_window_edit_actions', 'main_window_string_importers',
@@ -195,12 +154,8 @@ class MainWindow(QMainWindow):
         ]
         for name in other_inits:
             try:
-                # Call the helper's __init__ through the proxy helper to
-                # avoid attribute-resolution issues.
                 getattr(self, name).init()
             except Exception:
-                # Ignore; many helpers only define __init__ when they
-                # actually need it.
                 pass
 
     def init_ui(self):