moleditpy 5.0.0a2__tar.gz → 5.0.2__tar.gz

{moleditpy-5.0.0a2 → moleditpy-5.0.2}/LICENSING.md

@@ -1,11 +1,9 @@
 # Licensing and independently developed plugins
 
-MoleditPy 5.0.0a1 and later is licensed under the GNU Lesser General Public License, version 3 or (at your option) any later version (LGPL-3.0-or-later). `LICENSE` contains LGPLv3's additional permissions; `COPYING` contains the incorporated GPLv3 terms. Earlier releases keep their original license.
+MoleditPy 5.0.0 and later is licensed under the GNU Lesser General Public License, version 3 or (at your option) any later version (LGPL-3.0-or-later). `LICENSE` contains LGPLv3's additional permissions; `COPYING` contains the incorporated GPLv3 terms. Earlier releases keep their original license.
 
 Copyright holder permission: independently developed plugins that use MoleditPy's documented plugin API may be distributed under any license, including proprietary licenses. Their authors choose their license and retain their copyright. This permission does not relicense copied or modified MoleditPy code, or code/libraries belonging to third parties. Those components retain their own licenses and obligations. Existing plugins retain their current licenses unless their authors explicitly change them.
 
 Modifications to MoleditPy itself remain subject to the LGPL. Distribution terms must allow users to modify the covered components and reverse engineer for debugging their modifications as required by LGPLv3. No separate activation, signature check, or plugin restriction blocks modified builds.
 
-This migration was authorized by the project owner. The repository attribution audit (`git shortlog -sne`) identifies Hiromichi Yokoyama/HiroYokoyama identities, automation bots, and CodexSandboxOffline under the owner's email. Third-party code is excluded from the relicensing grant.
-
 See [distribution and library replacement instructions](DISTRIBUTION.md) and [third-party notices](THIRD_PARTY_NOTICES.md).

{moleditpy-5.0.0a2 → moleditpy-5.0.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: MoleditPy
-Version: 5.0.0a2
+Version: 5.0.2
 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-Expression: LGPL-3.0-or-later
@@ -92,6 +92,6 @@ Please also cite the plugins you used; see [Citation in the plugin collection](h
 
 ## License & Disclaimer
 
-This project is licensed under the GNU Lesser General Public License v3.0 or later (LGPL-3.0-or-later) - see the [LICENSE](https://github.com/HiroYokoyama/python_molecular_editor/blob/v5.0.0a1/LICENSE) file for details. As open-source software, it is provided 'as is' without warranty of any kind, and the author assumes no responsibility or liability for the results. Although outputs have been carefully verified, users are strongly encouraged to independently check and validate them for critical applications (such as publications). If you encounter any bugs, please open an issue.
+This project is licensed under the GNU Lesser General Public License v3.0 or later (LGPL-3.0-or-later) - see the [LICENSE](https://github.com/HiroYokoyama/python_molecular_editor/blob/main/LICENSE) file for details. As open-source software, it is provided 'as is' without warranty of any kind, and the author assumes no responsibility or liability for the results. Although outputs have been carefully verified, users are strongly encouraged to independently check and validate them for critical applications (such as publications). If you encounter any bugs, please open an issue.
 
-Independently developed plugins may use any license, including proprietary licenses. Existing plugins retain their licenses. See [licensing policy](https://github.com/HiroYokoyama/python_molecular_editor/blob/v5.0.0a1/LICENSING.md) and [binary distribution instructions](https://github.com/HiroYokoyama/python_molecular_editor/blob/v5.0.0a1/DISTRIBUTION.md).
+Independently developed plugins may use any license, including proprietary licenses. Existing plugins retain their licenses. See [licensing policy](https://github.com/HiroYokoyama/python_molecular_editor/blob/main/LICENSING.md) and [binary distribution instructions](https://github.com/HiroYokoyama/python_molecular_editor/blob/main/DISTRIBUTION.md).

{moleditpy-5.0.0a2 → moleditpy-5.0.2}/README.md

@@ -59,6 +59,6 @@ Please also cite the plugins you used; see [Citation in the plugin collection](h
 
 ## License & Disclaimer
 
-This project is licensed under the GNU Lesser General Public License v3.0 or later (LGPL-3.0-or-later) - see the [LICENSE](https://github.com/HiroYokoyama/python_molecular_editor/blob/v5.0.0a1/LICENSE) file for details. As open-source software, it is provided 'as is' without warranty of any kind, and the author assumes no responsibility or liability for the results. Although outputs have been carefully verified, users are strongly encouraged to independently check and validate them for critical applications (such as publications). If you encounter any bugs, please open an issue.
+This project is licensed under the GNU Lesser General Public License v3.0 or later (LGPL-3.0-or-later) - see the [LICENSE](https://github.com/HiroYokoyama/python_molecular_editor/blob/main/LICENSE) file for details. As open-source software, it is provided 'as is' without warranty of any kind, and the author assumes no responsibility or liability for the results. Although outputs have been carefully verified, users are strongly encouraged to independently check and validate them for critical applications (such as publications). If you encounter any bugs, please open an issue.
 
-Independently developed plugins may use any license, including proprietary licenses. Existing plugins retain their licenses. See [licensing policy](https://github.com/HiroYokoyama/python_molecular_editor/blob/v5.0.0a1/LICENSING.md) and [binary distribution instructions](https://github.com/HiroYokoyama/python_molecular_editor/blob/v5.0.0a1/DISTRIBUTION.md).
+Independently developed plugins may use any license, including proprietary licenses. Existing plugins retain their licenses. See [licensing policy](https://github.com/HiroYokoyama/python_molecular_editor/blob/main/LICENSING.md) and [binary distribution instructions](https://github.com/HiroYokoyama/python_molecular_editor/blob/main/DISTRIBUTION.md).

{moleditpy-5.0.0a2 → moleditpy-5.0.2}/pyproject.toml

@@ -5,7 +5,7 @@ build-backend = "setuptools.build_meta"
 [project]
 name = "MoleditPy"
 
-version = "5.0.0a2"
+version = "5.0.2"
 
 license = "LGPL-3.0-or-later"
 license-files = ["LICENSE", "COPYING", "THIRD_PARTY_NOTICES.md", "DISTRIBUTION.md", "LICENSING.md"]

{moleditpy-5.0.0a2 → moleditpy-5.0.2}/src/MoleditPy.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: MoleditPy
-Version: 5.0.0a2
+Version: 5.0.2
 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-Expression: LGPL-3.0-or-later
@@ -92,6 +92,6 @@ Please also cite the plugins you used; see [Citation in the plugin collection](h
 
 ## License & Disclaimer
 
-This project is licensed under the GNU Lesser General Public License v3.0 or later (LGPL-3.0-or-later) - see the [LICENSE](https://github.com/HiroYokoyama/python_molecular_editor/blob/v5.0.0a1/LICENSE) file for details. As open-source software, it is provided 'as is' without warranty of any kind, and the author assumes no responsibility or liability for the results. Although outputs have been carefully verified, users are strongly encouraged to independently check and validate them for critical applications (such as publications). If you encounter any bugs, please open an issue.
+This project is licensed under the GNU Lesser General Public License v3.0 or later (LGPL-3.0-or-later) - see the [LICENSE](https://github.com/HiroYokoyama/python_molecular_editor/blob/main/LICENSE) file for details. As open-source software, it is provided 'as is' without warranty of any kind, and the author assumes no responsibility or liability for the results. Although outputs have been carefully verified, users are strongly encouraged to independently check and validate them for critical applications (such as publications). If you encounter any bugs, please open an issue.
 
-Independently developed plugins may use any license, including proprietary licenses. Existing plugins retain their licenses. See [licensing policy](https://github.com/HiroYokoyama/python_molecular_editor/blob/v5.0.0a1/LICENSING.md) and [binary distribution instructions](https://github.com/HiroYokoyama/python_molecular_editor/blob/v5.0.0a1/DISTRIBUTION.md).
+Independently developed plugins may use any license, including proprietary licenses. Existing plugins retain their licenses. See [licensing policy](https://github.com/HiroYokoyama/python_molecular_editor/blob/main/LICENSING.md) and [binary distribution instructions](https://github.com/HiroYokoyama/python_molecular_editor/blob/main/DISTRIBUTION.md).

{moleditpy-5.0.0a2 → moleditpy-5.0.2}/src/moleditpy/plugins/plugin_interface.py

@@ -65,7 +65,7 @@ class PluginContext:
                 Anything else is ignored, so unknown values stay forward
                 compatible. Added in 4.8.1 — passing it to an older MoleditPy
                 raises TypeError, so guard the call if your plugin supports
-                both (see PLUGIN_DEVELOPMENT_MANUAL_V4.md).
+                both (see PLUGIN_DEVELOPMENT_MANUAL_V5.md).
         """
         self._manager.register_menu_action(
             self._plugin_name, path, callback, text, icon, shortcut, pin

{moleditpy-5.0.0a2 → moleditpy-5.0.2}/src/moleditpy/ui/compute_logic.py

@@ -86,7 +86,9 @@ class _CalculationReceiver(QObject):
     def cleanup(self) -> None:
         with suppress_log(ValueError):
             self.manager._active_calc_threads.remove(self.calculation_thread)
-            self.manager._calc_receivers.remove(self)
+        # The Python reference goes when Qt has deleted the object (see
+        # _retain_until_destroyed). Releasing it here would let shiboken
+        # delete this receiver inside its own queued slot call.
         self.deleteLater()
 
 
@@ -101,7 +103,8 @@ class ComputeManager:
         self.host = host
         self.last_successful_optimization_method: Optional[str] = None
         self._active_calc_threads: List[QThread] = []
-        self._calc_receivers: List[_CalculationReceiver] = []
+        # id(QObject) -> Python objects kept alive until that QObject is destroyed.
+        self._calc_objects: Dict[int, Tuple[Any, ...]] = {}
         self.halt_ids: Set[int] = set()
         self.next_conversion_id: int = 1
         self.active_worker_ids: Set[int] = set()
@@ -590,6 +593,19 @@ class ComputeManager:
             mol_block, mol, self.host.state_manager.data.bonds
         )
 
+    def _retain_until_destroyed(self, owner: QObject, *extra: Any) -> None:
+        """Keep *owner* (and *extra*) referenced until Qt deletes *owner*.
+
+        These objects have no Qt parent, so shiboken deletes the C++ object
+        as soon as the last Python reference goes. Dropping that reference
+        only from ``destroyed`` leaves every deletion to ``deleteLater``.
+        """
+        key = id(owner)
+        self._calc_objects[key] = (owner, *extra)
+        owner.destroyed.connect(
+            lambda *_args, key=key: self._calc_objects.pop(key, None)
+        )
+
     def _start_calculation_worker(
         self, mol_block: str, options: Dict[str, Any], run_id: int
     ) -> None:
@@ -604,7 +620,11 @@ class ComputeManager:
         worker.error.connect(receiver.error)
         thread.finished.connect(receiver.cleanup)
         thread.finished.connect(thread.deleteLater)
-        self._calc_receivers.append(receiver)
+        # The worker is deleted on its own thread before ~QThread returns, so
+        # it is released with the thread rather than by its own destroyed
+        # signal, which would be emitted off the GUI thread.
+        self._retain_until_destroyed(thread, worker)
+        self._retain_until_destroyed(receiver)
         thread.start()
         QTimer.singleShot(10, lambda: worker.start_work.emit(mol_block, options))
         self._active_calc_threads.append(thread)

{moleditpy-5.0.0a2 → moleditpy-5.0.2}/src/moleditpy/ui/main_window_init.py

@@ -99,6 +99,7 @@ class MainInitManager:
         self.toolbar_bottom: Any = None
         self.plugin_toolbar: Optional[QToolBar] = None
         self.tool_group: Optional[QActionGroup] = None
+        self.style_group: Optional[QActionGroup] = None
         self.other_atom_action: Optional[QAction] = None
         self.splitter: Optional[QSplitter] = None
         self.cleanup_button: Optional[QPushButton] = None
@@ -960,7 +961,7 @@ class MainInitManager:
 
         style_menu = QMenu(self.host)
         self.style_button.setMenu(style_menu)
-        style_group = QActionGroup(self.host)
+        self.style_group = style_group = QActionGroup(self.host)
         style_group.setExclusive(True)
 
         for name, key in [
@@ -971,6 +972,7 @@ class MainInitManager:
         ]:
             action = QAction(name, self.host)
             action.setCheckable(True)
+            action.setProperty("moleditpy_3d_style", key)
             if key == "ball_and_stick":
                 action.setChecked(True)
             action.triggered.connect(
@@ -985,6 +987,7 @@ class MainInitManager:
                 if not any(a.text() == style_name for a in style_menu.actions()):
                     action = QAction(style_name, self.host)
                     action.setCheckable(True)
+                    action.setProperty("moleditpy_3d_style", style_name)
                     action.triggered.connect(
                         lambda checked=False, s=style_name: (
                             self.host.view_3d_manager.set_3d_style(s)

{moleditpy-5.0.0a2 → moleditpy-5.0.2}/src/moleditpy/ui/plugin_menu_manager.py

@@ -463,6 +463,7 @@ class PluginMenuManager:
                 if not any(a.text() == style_name for a in style_menu.actions()):
                     action = QAction(style_name, self._im.host)
                     action.setCheckable(True)
+                    action.setProperty("moleditpy_3d_style", style_name)
                     action.triggered.connect(
                         lambda checked=False, s=style_name: (
                             self._im.host.view_3d_manager.set_3d_style(s)

{moleditpy-5.0.0a2 → moleditpy-5.0.2}/src/moleditpy/ui/user_template_dialog.py

@@ -298,7 +298,7 @@ class UserTemplateDialog(QDialog):
         layout = QVBoxLayout(widget)
 
         # Preview graphics - use custom view class for better resize handling
-        preview_scene = QGraphicsScene()
+        preview_scene = QGraphicsScene(widget)
         preview_view = TemplatePreviewView(preview_scene)
         preview_view.setFixedSize(160, 140)
         preview_view.setRenderHint(QPainter.RenderHint.Antialiasing)

{moleditpy-5.0.0a2 → moleditpy-5.0.2}/src/moleditpy/ui/view_3d_logic.py

@@ -116,6 +116,13 @@ class View3DManager:
 
     def set_3d_style(self, style_name: str) -> None:
         """Set 3D display style and update view"""
+        style_button = self.host.init_manager.style_button
+        if style_button is not None and style_button.menu() is not None:
+            for action in style_button.menu().actions():
+                if action.isCheckable():
+                    action.setChecked(
+                        action.property("moleditpy_3d_style") == style_name
+                    )
         current_stored_style = getattr(self, "current_3d_style", None)
         if current_stored_style == style_name:
             return