MoleditPy-linux 4.5.1__tar.gz → 4.5.2__tar.gz

{moleditpy_linux-4.5.1 → moleditpy_linux-4.5.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: MoleditPy-linux
-Version: 4.5.1
+Version: 4.5.2
 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
@@ -697,7 +697,7 @@ Requires-Dist: numpy
 Requires-Dist: pyqt6<6.10; python_version == "3.9"
 Requires-Dist: pyqt6<6.12; python_version != "3.9"
 Requires-Dist: pyvista<0.49
-Requires-Dist: pyvistaqt<0.12
+Requires-Dist: pyvistaqt<0.13
 Requires-Dist: rdkit<2026.4
 Dynamic: license-file
 

{moleditpy_linux-4.5.1 → moleditpy_linux-4.5.2}/pyproject.toml

@@ -5,7 +5,7 @@ build-backend = "setuptools.build_meta"
 [project]
 name = "MoleditPy-linux"
 
-version = "4.5.1"
+version = "4.5.2"
 
 license = {file = "LICENSE"}
 
@@ -37,7 +37,7 @@ dependencies = [
     "pyqt6 < 6.10; python_version == '3.9'",
     "pyqt6 < 6.12; python_version != '3.9'",
     "pyvista < 0.49",
-    "pyvistaqt < 0.12",
+    "pyvistaqt < 0.13",
     "rdkit < 2026.4",
 ]
 

{moleditpy_linux-4.5.1 → moleditpy_linux-4.5.2}/src/MoleditPy_linux.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: MoleditPy-linux
-Version: 4.5.1
+Version: 4.5.2
 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
@@ -697,7 +697,7 @@ Requires-Dist: numpy
 Requires-Dist: pyqt6<6.10; python_version == "3.9"
 Requires-Dist: pyqt6<6.12; python_version != "3.9"
 Requires-Dist: pyvista<0.49
-Requires-Dist: pyvistaqt<0.12
+Requires-Dist: pyvistaqt<0.13
 Requires-Dist: rdkit<2026.4
 Dynamic: license-file
 

{moleditpy_linux-4.5.1 → moleditpy_linux-4.5.2}/src/MoleditPy_linux.egg-info/requires.txt

@@ -1,6 +1,6 @@
 numpy
 pyvista<0.49
-pyvistaqt<0.12
+pyvistaqt<0.13
 rdkit<2026.4
 
 [:python_version != "3.9"]

{moleditpy_linux-4.5.1 → moleditpy_linux-4.5.2}/src/moleditpy_linux/ui/atom_item.py

@@ -43,6 +43,34 @@ from ..utils.sip_isdeleted_safe import sip_isdeleted_safe
 if TYPE_CHECKING:
     from .bond_item import BondItem
 
+SUBSCRIPT_MAP = str.maketrans("0123456789", "₀₁₂₃₄₅₆₇₈₉")
+
+# Every subscript digit, so one warm-up covers any implicit-H count.
+_WARM_UP_TEXT = "CH" + "0123456789".translate(SUBSCRIPT_MAP)
+
+
+def warm_font_cache(font: Optional[QFont] = None) -> None:
+    """Pay Qt's one-off font costs up front instead of on the first heteroatom.
+
+    Two process-wide costs hide in QFontMetricsF: the first text shaping in a
+    family (~10-120 ms, worse on a cold Windows font cache) and the first
+    lookup of a subscript digit, which Arial lacks — Qt answers that by walking
+    the whole system font database (~200-330 ms, measured).
+
+    Drawing a carbon skeleton pays neither: a bonded neutral carbon is
+    invisible, so it renders no glyph at all. The first O or N a user places
+    gets "OH₂" and pays both at once, mid-click, as a visible freeze.
+
+    Call once on the GUI thread after the window is up. QFontMetricsF is not
+    usable off the GUI thread, so this cannot move to a worker.
+    """
+    try:
+        QFontMetricsF(font or QFont(FONT_FAMILY, 20, FONT_WEIGHT_BOLD)).boundingRect(
+            _WARM_UP_TEXT
+        )
+    except (RuntimeError, TypeError, ValueError):
+        logging.debug("Font cache warm-up skipped", exc_info=True)
+
 
 class AtomItem(QGraphicsItem):
     """2D scene item representing a single atom in the molecule editor."""
@@ -138,8 +166,7 @@ class AtomItem(QGraphicsItem):
             if not is_skeletal_carbon:
                 hydrogen_part = "H"
                 if self.implicit_h_count > 1:
-                    subscript_map = str.maketrans("0123456789", "₀₁₂₃₄₅₆₇₈₉")
-                    hydrogen_part += str(self.implicit_h_count).translate(subscript_map)
+                    hydrogen_part += str(self.implicit_h_count).translate(SUBSCRIPT_MAP)
 
         flip_text = False
         if hydrogen_part and self.bonds:
@@ -261,8 +288,7 @@ class AtomItem(QGraphicsItem):
             if not is_skeletal_carbon:
                 hydrogen_part = "H"
                 if self.implicit_h_count > 1:
-                    subscript_map = str.maketrans("0123456789", "₀₁₂₃₄₅₆₇₈₉")
-                    hydrogen_part += str(self.implicit_h_count).translate(subscript_map)
+                    hydrogen_part += str(self.implicit_h_count).translate(SUBSCRIPT_MAP)
 
         flip_text = False
         if hydrogen_part and self.bonds:
@@ -361,9 +387,8 @@ class AtomItem(QGraphicsItem):
                 if not is_skeletal_carbon:
                     hydrogen_part = "H"
                     if self.implicit_h_count > 1:
-                        subscript_map = str.maketrans("0123456789", "₀₁₂₃₄₅₆₇₈₉")
                         hydrogen_part += str(self.implicit_h_count).translate(
-                            subscript_map
+                            SUBSCRIPT_MAP
                         )
 
             # --- Determine if the text should be flipped ---

{moleditpy_linux-4.5.1 → moleditpy_linux-4.5.2}/src/moleditpy_linux/ui/main_window_init.py

@@ -20,9 +20,6 @@ import os
 import sys
 from typing import Any, Dict, Optional
 
-# RDKit imports (explicit to satisfy flake8 and used features)
-from rdkit import Chem
-
 # PyQt6 Modules
 from PyQt6.QtCore import QLineF, QPointF, QRectF, Qt, QTimer, QUrl
 from PyQt6.QtGui import (
@@ -65,7 +62,8 @@ except ImportError:
     winreg = None  # type: ignore[assignment]
 
 
-from ..utils.constants import DEFAULT_CPK_COLORS, NUM_DASHES, VERSION
+from ..utils.constants import DEFAULT_CPK_COLORS, FONT_FAMILY, NUM_DASHES, VERSION
+from .atom_item import warm_font_cache
 from .custom_qt_interactor import CustomQtInteractor
 from ..core.molecular_data import MolecularData
 from .molecule_scene import MoleculeScene
@@ -74,6 +72,10 @@ from .settings_dialog import SettingsDialog
 from .zoomable_view import ZoomableView
 
 
+# Distinct from None, which is a real answer meaning "OS preference unknown".
+_UNQUERIED = object()
+
+
 class MainInitManager:
     """Feature class separated from main_window.py"""
 
@@ -82,6 +84,7 @@ class MainInitManager:
     ) -> None:
         self.host = host
         # Explicit declarations for Mypy
+        self._os_dark_pref: Any = _UNQUERIED
         self.scene: Any = None  # MoleculeScene, created during init
         self.data: Optional[MolecularData] = None
         self.formula_label: Optional[QLabel] = None
@@ -179,18 +182,6 @@ class MainInitManager:
         # Install event filter to capture window close events (handled in UIManager)
         self.host.installEventFilter(self.host.ui_manager)
 
-        # RDKit Warm-up (initial execution cost)
-        try:
-            # Create a molecule with a variety of common atoms to ensure
-            # the valence/H-count machinery is fully initialized.
-            warmup_smiles = "OC(N)C(S)P"
-            warmup_mol = Chem.MolFromSmiles(warmup_smiles)
-            if warmup_mol:
-                for atom in warmup_mol.GetAtoms():
-                    atom.GetNumImplicitHs()
-        except (AttributeError, RuntimeError, ValueError) as e:
-            logging.warning(f"RDKit warm-up failed: {e}")
-
         self.host.state_manager.reset_undo_stack()
         self.scene.selectionChanged.connect(  # type: ignore[attr-defined]
             self.host.edit_actions_manager.update_edit_menu_actions
@@ -206,6 +197,8 @@ class MainInitManager:
             QTimer.singleShot(0, lambda: self.load_command_line_file(initial_file))
 
         QTimer.singleShot(0, self.apply_initial_settings)
+        # After apply_initial_settings, so the user's own font family is warmed.
+        QTimer.singleShot(0, self._warm_font_cache)
         # Camera initialization flag (permits reset only during the first draw)
         self._camera_initialized = False
 
@@ -226,6 +219,19 @@ class MainInitManager:
                 f"Suppressed exception: {e}"
             )  # Suppress non-critical UI/menu initialization errors
 
+    def _warm_font_cache(self) -> None:
+        """Resolve the atom-label font now, in the user's configured family."""
+        scene = getattr(self, "scene", None)
+        font = None
+        if scene is not None and hasattr(scene, "get_setting"):
+            family = scene.get_setting("atom_font_family_2d", FONT_FAMILY)
+            size = scene.get_setting("atom_font_size_2d", 20)
+            bold = scene.get_setting("atom_font_bold_2d", True)
+            font = QFont(
+                family, size, QFont.Weight.Bold if bold else QFont.Weight.Normal
+            )
+        warm_font_cache(font)
+
     def init_ui(self) -> None:
         """Set the window icon and initialize main layout, toolbars, and menu bar."""
         script_dir = os.path.dirname(os.path.abspath(__file__))
@@ -1076,7 +1082,11 @@ class MainInitManager:
                 return QColor(fg)
 
         with suppress_log(Exception):
-            os_pref = detect_system_dark_mode()
+            # Cached: this forks `defaults`/`gsettings` on macOS and Linux, and
+            # icon painting asks once per icon (15+ during startup).
+            if self._os_dark_pref is _UNQUERIED:
+                self._os_dark_pref = detect_system_dark_mode()
+            os_pref = self._os_dark_pref
             if os_pref is not None:
                 return QColor("#FFFFFF") if os_pref else QColor("#000000")
 

{moleditpy_linux-4.5.1 → moleditpy_linux-4.5.2}/src/moleditpy_linux/utils/system_utils.py

@@ -21,6 +21,9 @@ try:
 except ImportError:
     winreg = None  # type: ignore[assignment]
 
+# A wedged `defaults`/`gsettings` must not take the app's startup with it.
+_THEME_QUERY_TIMEOUT_S = 5.0
+
 
 def detect_system_dark_mode() -> Optional[bool]:
     """Return True if the OS prefers dark app theme, False if light, or None if unknown."""
@@ -33,8 +36,18 @@ def detect_system_dark_mode() -> Optional[bool]:
 
 
 def detect_system_theme() -> Optional[str]:
-    """Return the OS's preferred theme setting as 'dark', 'light', or None."""
-    with suppress_log(AttributeError, RuntimeError, OSError, FileNotFoundError):
+    """Return the OS's preferred theme setting as 'dark', 'light', or None.
+
+    Forks a helper process on macOS and Linux, so callers that ask repeatedly
+    should hold on to the answer rather than re-querying.
+    """
+    with suppress_log(
+        AttributeError,
+        RuntimeError,
+        OSError,
+        FileNotFoundError,
+        subprocess.SubprocessError,
+    ):
         # Windows
         if platform.system() == "Windows" and winreg is not None:
             with winreg.OpenKey(
@@ -50,6 +63,7 @@ def detect_system_theme() -> Optional[str]:
                 ["defaults", "read", "-g", "AppleInterfaceStyle"],
                 capture_output=True,
                 text=True,
+                timeout=_THEME_QUERY_TIMEOUT_S,
             )
             if p.returncode == 0 and "dark" in p.stdout.strip().lower():
                 return "dark"
@@ -61,6 +75,7 @@ def detect_system_theme() -> Optional[str]:
                 ["gsettings", "get", "org.gnome.desktop.interface", "color-scheme"],
                 capture_output=True,
                 text=True,
+                timeout=_THEME_QUERY_TIMEOUT_S,
             )
             if p.returncode == 0:
                 out = p.stdout.strip().strip("'\n ")
@@ -73,6 +88,7 @@ def detect_system_theme() -> Optional[str]:
                 ["gsettings", "get", "org.gnome.desktop.interface", "gtk-theme"],
                 capture_output=True,
                 text=True,
+                timeout=_THEME_QUERY_TIMEOUT_S,
             )
             if p.returncode == 0 and "-dark" in p.stdout.lower():
                 return "dark"