MoleditPy 1.16.0a1__tar.gz → 1.16.0a2__tar.gz

{moleditpy-1.16.0a1 → moleditpy-1.16.0a2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: MoleditPy
-Version: 1.16.0a1
+Version: 1.16.0a2
 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>
 Project-URL: Homepage, https://github.com/HiroYokoyama/python_molecular_editor

{moleditpy-1.16.0a1 → moleditpy-1.16.0a2}/pyproject.toml

@@ -5,7 +5,7 @@ build-backend = "setuptools.build_meta"
 [project]
 name = "MoleditPy"
 
-version = "1.16.0a1"
+version = "1.16.0a2"
 
 authors = [
   { name="HiroYokoyama", email="titech.yoko.hiro@gmail.com" },

{moleditpy-1.16.0a1 → moleditpy-1.16.0a2}/src/MoleditPy.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: MoleditPy
-Version: 1.16.0a1
+Version: 1.16.0a2
 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>
 Project-URL: Homepage, https://github.com/HiroYokoyama/python_molecular_editor

{moleditpy-1.16.0a1 → moleditpy-1.16.0a2}/src/MoleditPy.egg-info/SOURCES.txt

@@ -60,4 +60,5 @@ src/moleditpy/modules/user_template_dialog.py
 src/moleditpy/modules/zoomable_view.py
 src/moleditpy/modules/assets/icon.icns
 src/moleditpy/modules/assets/icon.ico
-src/moleditpy/modules/assets/icon.png
+src/moleditpy/modules/assets/icon.png
+tests/test_project_io_wrappers.py

{moleditpy-1.16.0a1 → moleditpy-1.16.0a2}/src/moleditpy/main.py

@@ -22,10 +22,7 @@ try:
 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
-    try:
-        from .modules.main_window import MainWindow
-    except Exception:
-        from modules.main_window import MainWindow
+    from modules.main_window import MainWindow
 
 def main():
     # --- Windows タスクバーアイコンのための追加処理 ---

{moleditpy-1.16.0a1 → moleditpy-1.16.0a2}/src/moleditpy/modules/constants.py

@@ -4,7 +4,7 @@ from PyQt6.QtGui import QFont, QColor
 from rdkit import Chem
 
 #Version
-VERSION = '1.16.0a1'
+VERSION = '1.16.0a2'
 
 ATOM_RADIUS = 18
 BOND_OFFSET = 3.5

{moleditpy-1.16.0a1 → moleditpy-1.16.0a2}/src/moleditpy/modules/main_window.py

@@ -109,6 +109,9 @@ class MainWindow(QMainWindow):
         # 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:
             """Bind a feature-class method calls to the MainWindow.
@@ -395,7 +398,7 @@ class MainWindow(QMainWindow):
 
     def load_mol_file(self, file_path=None):
         # --- MOVED TO main_window_molecular_parsers.py ---
-        return self.main_window_molecular_parsers.load_mol_file(file_path=None)
+        return self.main_window_molecular_parsers.load_mol_file(file_path)
 
     def load_mol_for_3d_viewing(self):
         # --- MOVED TO main_window_view_loaders.py ---
@@ -403,9 +406,9 @@ class MainWindow(QMainWindow):
 
     def load_xyz_for_3d_viewing(self, file_path=None):
         # --- MOVED TO main_window_view_loaders.py ---
-        return self.main_window_view_loaders.load_xyz_for_3d_viewing(file_path=None)
+        return self.main_window_view_loaders.load_xyz_for_3d_viewing(file_path)
 
-    def load_xyz_file(self, file_path):
+    def load_xyz_file(self, file_path=None):
         # --- MOVED TO main_window_molecular_parsers.py ---
         return self.main_window_molecular_parsers.load_xyz_file(file_path)
 
@@ -427,7 +430,7 @@ class MainWindow(QMainWindow):
 
     def load_raw_data(self, file_path=None):
         # --- MOVED TO main_window_project_io.py ---
-        return self.main_window_project_io.load_raw_data(file_path=None)
+        return self.main_window_project_io.load_raw_data(file_path)
 
     def save_as_json(self):
         # --- MOVED TO main_window_project_io.py ---
@@ -439,11 +442,11 @@ class MainWindow(QMainWindow):
 
     def load_json_data(self, file_path=None):
         # --- MOVED TO main_window_project_io.py ---
-        return self.main_window_project_io.load_json_data(file_path=None)
+        return self.main_window_project_io.load_json_data(file_path)
 
     def open_project_file(self, file_path=None):
         # --- MOVED TO main_window_project_io.py ---
-        return self.main_window_project_io.open_project_file(file_path=None)
+        return self.main_window_project_io.open_project_file(file_path)
 
     def load_from_json_data(self, json_data):
         # --- MOVED TO main_window_app_state.py ---
@@ -611,7 +614,7 @@ class MainWindow(QMainWindow):
 
     def load_mol_file_for_3d_viewing(self, file_path=None):
         # --- MOVED TO main_window_view_loaders.py ---
-        return self.main_window_view_loaders.load_mol_file_for_3d_viewing(file_path=None)
+        return self.main_window_view_loaders.load_mol_file_for_3d_viewing(file_path)
 
     def load_command_line_file(self, file_path):
         # --- MOVED TO main_window_main_init.py ---

{moleditpy-1.16.0a1 → moleditpy-1.16.0a2}/src/moleditpy/modules/main_window_app_state.py

@@ -80,9 +80,13 @@ except Exception:
 class MainWindowAppState(object):
     """ main_window.py から分離された機能クラス """
 
-    def __init__(self, main_window):
-        """ クラスの初期化 """
-        self.mw = main_window
+    def __init__(self):
+        """
+        クラスの初期化
+        BoundFeature経由で呼ばれるため、'self' には MainWindow インスタンスが渡されます。
+        """
+        self.DEBUG_UNDO = False
+
 
 
     def get_current_state(self):
@@ -234,6 +238,9 @@ class MainWindowAppState(object):
 
 
     def push_undo_state(self):
+        if self._is_restoring_state:
+            return
+            
         current_state_for_comparison = {
             'atoms': {k: (v['symbol'], v['item'].pos().x(), v['item'].pos().y(), v.get('charge', 0), v.get('radical', 0)) for k, v in self.data.atoms.items()},
             'bonds': {k: (v['order'], v.get('stereo', 0)) for k, v in self.data.bonds.items()},
@@ -254,8 +261,15 @@ class MainWindowAppState(object):
             }
 
         if not last_state_for_comparison or current_state_for_comparison != last_state_for_comparison:
-            state = self.get_current_state()
+            # Deepcopy state to ensure saved states are immutable and not affected
+            # by later modifications to objects referenced from the state.
+            state = copy.deepcopy(self.get_current_state())
             self.undo_stack.append(state)
+            if getattr(self, 'DEBUG_UNDO', False):
+                try:
+                    print(f"DEBUG_UNDO: push_undo_state -> new stack size: {len(self.undo_stack)}")
+                except Exception:
+                    pass
             self.redo_stack.clear()
             # 初期化完了後のみ変更があったことを記録
             if self.initialization_complete:
@@ -320,6 +334,11 @@ class MainWindowAppState(object):
         self.undo_stack.clear()
         self.redo_stack.clear()
         self.push_undo_state()
+        if getattr(self, 'DEBUG_UNDO', False):
+            try:
+                print(f"DEBUG_UNDO: reset_undo_stack -> undo={len(self.undo_stack)} redo={len(self.redo_stack)}")
+            except Exception:
+                pass
 
 
 
@@ -327,7 +346,12 @@ class MainWindowAppState(object):
         if len(self.undo_stack) > 1:
             self.redo_stack.append(self.undo_stack.pop())
             state = self.undo_stack[-1]
-            self.set_state_from_data(state)
+            self._is_restoring_state = True
+            try:
+                self.set_state_from_data(state)
+            finally:
+                self._is_restoring_state = False
+
             
             # Undo後に3D構造の状態に基づいてメニューを再評価
             if self.current_mol and self.current_mol.GetNumAtoms() > 0:
@@ -337,6 +361,11 @@ class MainWindowAppState(object):
                 # 3D構造がない場合は3D編集機能を無効化
                 self._enable_3d_edit_actions(False)
                     
+        if getattr(self, 'DEBUG_UNDO', False):
+            try:
+                print(f"DEBUG_UNDO: undo -> undo_stack size: {len(self.undo_stack)}, redo_stack size: {len(self.redo_stack)}")
+            except Exception:
+                pass
         self.update_undo_redo_actions()
         self.update_realtime_info()
         self.view_2d.setFocus() 
@@ -347,7 +376,11 @@ class MainWindowAppState(object):
         if self.redo_stack:
             state = self.redo_stack.pop()
             self.undo_stack.append(state)
-            self.set_state_from_data(state)
+            self._is_restoring_state = True
+            try:
+                self.set_state_from_data(state)
+            finally:
+                self._is_restoring_state = False
             
             # Redo後に3D構造の状態に基づいてメニューを再評価
             if self.current_mol and self.current_mol.GetNumAtoms() > 0:
@@ -357,6 +390,11 @@ class MainWindowAppState(object):
                 # 3D構造がない場合は3D編集機能を無効化
                 self._enable_3d_edit_actions(False)
                     
+        if getattr(self, 'DEBUG_UNDO', False):
+            try:
+                print(f"DEBUG_UNDO: redo -> undo_stack size: {len(self.undo_stack)}, redo_stack size: {len(self.redo_stack)}")
+            except Exception:
+                pass
         self.update_undo_redo_actions()
         self.update_realtime_info()
         self.view_2d.setFocus() 

{moleditpy-1.16.0a1 → moleditpy-1.16.0a2}/src/moleditpy/modules/main_window_main_init.py

@@ -36,6 +36,65 @@ from PyQt6.QtGui import (
 from PyQt6.QtCore import (
     Qt, QPointF, QRectF, QLineF, QUrl, QTimer
 )
+import platform
+import subprocess
+try:
+    import winreg
+except Exception:
+    winreg = None
+
+
+def detect_system_dark_mode():
+    """Return True if the OS prefers dark app theme, False if light, or None if unknown.
+
+    This is a best-effort, cross-platform check supporting Windows (registry),
+    macOS (defaults read), and GNOME/GTK-based Linux (gsettings). Return
+    None if no reliable information is available.
+    """
+    try:
+        # Windows: read registry AppsUseLightTheme (0 = dark, 1 = light)
+        if platform.system() == 'Windows' and winreg is not None:
+            try:
+                with winreg.OpenKey(winreg.HKEY_CURRENT_USER,
+                                    r'Software\Microsoft\Windows\CurrentVersion\Themes\Personalize') as k:
+                    val, _ = winreg.QueryValueEx(k, 'AppsUseLightTheme')
+                    return False if int(val) == 0 else True
+            except Exception:
+                pass
+
+        # macOS: 'defaults read -g AppleInterfaceStyle' returns 'Dark' in dark mode
+        if platform.system() == 'Darwin':
+            try:
+                p = subprocess.run(['defaults', 'read', '-g', 'AppleInterfaceStyle'], capture_output=True, text=True)
+                if p.returncode == 0 and p.stdout.strip().lower() == 'dark':
+                    return True
+                # Key absence implies light mode
+                return False
+            except Exception:
+                pass
+
+        # Linux / GNOME: try color-scheme gsetting; fallback to gtk-theme detection
+        if platform.system() == 'Linux':
+            try:
+                p = subprocess.run(['gsettings', 'get', 'org.gnome.desktop.interface', 'color-scheme'], capture_output=True, text=True)
+                if p.returncode == 0:
+                    out = p.stdout.strip().strip("'\n ")
+                    if 'dark' in out.lower():
+                        return True
+                    if 'light' in out.lower():
+                        return False
+            except Exception:
+                pass
+
+            try:
+                p = subprocess.run(['gsettings', 'get', 'org.gnome.desktop.interface', 'gtk-theme'], capture_output=True, text=True)
+                if p.returncode == 0 and '-dark' in p.stdout.lower():
+                    return True
+            except Exception:
+                pass
+    except Exception:
+        pass
+    return None
 
 
 # Use centralized Open Babel availability from package-level __init__
@@ -406,10 +465,19 @@ class MainWindowMainInit(object):
         toolbar.addSeparator()
 
         # --- アイコン前景色を決めるヘルパー（ダーク/ライトモード対応） ---
-        def _icon_foreground_color():
-            """Return a QColor for icon foreground (black on light backgrounds, white on dark backgrounds).
+        # Use module-level detector `detect_system_dark_mode()` so tests and other
+        # modules can reuse the logic.
+
 
-            Priority: explicit setting 'icon_foreground' in settings -> infer from configured background color -> infer from application palette.
+        def _icon_foreground_color():
+            """Return a QColor for icon foreground.
+
+            NOTE: this application inverts the usual foreground mapping so icons
+            will be the *opposite* color to the background (i.e., black on dark
+            backgrounds, white on light backgrounds). This intentionally reverses
+            the previous behavior so button icons don't blend into the 3D-view
+            background. Priority: explicit setting in 'icon_foreground' -> OS
+            theme preference -> configured 3D background -> application palette.
             """
             try:
                 fg_hex = self.settings.get('icon_foreground')
@@ -420,13 +488,25 @@ class MainWindowMainInit(object):
             except Exception:
                 pass
 
+            # 1) Prefer the system/OS dark-mode preference if available.
+            try:
+                os_pref = detect_system_dark_mode()
+                # Invert the color so in dark-pref OS we return black, in light we return white
+                if os_pref is not None:
+                    return QColor('#000000') if os_pref else QColor('#FFFFFF')
+            except Exception:
+                pass
+
             try:
+                # Keep background_color as a fallback: if system preference isn't
+                # available we'll use the configured 3D view background from settings.
                 bg_hex = self.settings.get('background_color')
                 if bg_hex:
                     bg = QColor(bg_hex)
                     if bg.isValid():
                         lum = 0.2126 * bg.redF() + 0.7152 * bg.greenF() + 0.0722 * bg.blueF()
-                        return QColor('#FFFFFF') if lum < 0.5 else QColor('#000000')
+                        # Inverted: return black on dark (lum<0.5), white on light
+                        return QColor('#000000') if lum < 0.5 else QColor('#FFFFFF')
             except Exception:
                 pass
 
@@ -435,7 +515,8 @@ class MainWindowMainInit(object):
                 # palette.window() returns a QBrush; call color()
                 window_bg = pal.window().color()
                 lum = 0.2126 * window_bg.redF() + 0.7152 * window_bg.greenF() + 0.0722 * window_bg.blueF()
-                return QColor('#FFFFFF') if lum < 0.5 else QColor('#000000')
+                # Inverted mapping for palette fallback
+                return QColor('#000000') if lum < 0.5 else QColor('#FFFFFF')
             except Exception:
                 return QColor('#000000')
 

{moleditpy-1.16.0a1 → moleditpy-1.16.0a2}/src/moleditpy/modules/main_window_project_io.py

@@ -164,6 +164,11 @@ class MainWindowProjectIo(object):
             # Replace current file with the newly saved file so subsequent saves go to this path
             self.current_file_path = file_path
             self.update_window_title()
+            # Mark this state as the last saved state for undo tracking
+            try:
+                self._saved_state = copy.deepcopy(self.get_current_state())
+            except Exception:
+                pass
             
             self.statusBar().showMessage(f"Project saved to {file_path}")
             
@@ -217,6 +222,10 @@ class MainWindowProjectIo(object):
             # Update current file to the newly saved raw file
             self.current_file_path = file_path
             self.update_window_title()
+            try:
+                self._saved_state = copy.deepcopy(self.get_current_state())
+            except Exception:
+                pass
             
             self.statusBar().showMessage(f"Project saved to {file_path}")
             
@@ -249,8 +258,12 @@ class MainWindowProjectIo(object):
             self.has_unsaved_changes = False
             self.current_file_path = file_path
             self.update_window_title()
-            
-            self.statusBar().showMessage(f"Project loaded from {file_path}")
+            try:
+                self._saved_state= copy.deepcopy(self.et_current_state())
+            except Exception:
+                pass
+         
+            self.statusBar.showMessage(f"Project loaded from {file_path}")
             
             QTimer.singleShot(0, self.fit_to_view)