MoleditPy 4.10.1__tar.gz → 4.10.3__tar.gz

{moleditpy-4.10.1 → moleditpy-4.10.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: MoleditPy
-Version: 4.10.1
+Version: 4.10.3
 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
@@ -705,9 +705,10 @@ Dynamic: license-file
 # MoleditPy — A Python Molecular Editor
 
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.17268532.svg)](https://doi.org/10.5281/zenodo.17268532)
+![MoleditPy](https://img.shields.io/badge/MoleditPy-v4-3577F7)
 [![Powered by RDKit](https://img.shields.io/badge/Powered%20by-RDKit-3838ff.svg?logo=data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAABAAAAAQBAMAAADt3eJSAAAABGdBTUEAALGPC/xhBQAAACBjSFJNAAB6JgAAgIQAAPoAAACA6AAAdTAAAOpgAAA6mAAAF3CculE8AAAAFVBMVEXc3NwUFP8UPP9kZP+MjP+0tP////9ZXZotAAAAAXRSTlMAQObYZgAAAAFiS0dEBmFmuH0AAAAHdElNRQfmAwsPGi+MyC9RAAAAQElEQVQI12NgQABGQUEBMENISUkRLKBsbGwEEhIyBgJFsICLC0iIUdnExcUZwnANQWfApKCK4doRBsKtQFgKAQC5Ww1JEHSEkAAAACV0RVh0ZGF0ZTpjcmVhdGUAMjAyMi0wMy0xMVQxNToyNjo0NyswMDowMDzr2J4AAAAldEVYdGRhdGU6bW9kaWZ5ADIwMjItMDMtMTFUMTU6MjY6NDcrMDA6MDBNtmAiAAAAAElFTkSuQmCC)](https://www.rdkit.org/)
 [![PyPI version](https://badge.fury.io/py/MoleditPy.svg)](https://badge.fury.io/py/MoleditPy)
-[![Python Versions](https://img.shields.io/pypi/pyversions/MoleditPy.svg)](https://pypi.org/project/MoleditPy/)
+[![Python Versions](https://img.shields.io/badge/python-3.9--3.14-blue.svg)](https://pypi.org/project/MoleditPy/)
 [![License: GPL v3](https://img.shields.io/badge/License-GPLv3-blue.svg)](https://www.gnu.org/licenses/gpl-3.0)
 [![Build Status](https://github.com/HiroYokoyama/python_molecular_editor/actions/workflows/tests.yml/badge.svg)](https://github.com/HiroYokoyama/python_molecular_editor/actions)
 [![codecov](https://codecov.io/gh/HiroYokoyama/python_molecular_editor/graph/badge.svg)](https://codecov.io/gh/HiroYokoyama/python_molecular_editor)
@@ -727,7 +728,10 @@ Dynamic: license-file
 **Repository**: [https://github.com/HiroYokoyama/python\_molecular\_editor](https://github.com/HiroYokoyama/python_molecular_editor)
 
 -----
-![](img/icon.png)
+<p align="center">
+  <img src="img/icon.png" width="500" alt="MoleditPy Icon">
+</p>
+
 ![](img/screenshot.png)
 
 

{moleditpy-4.10.1 → moleditpy-4.10.3}/README.md

@@ -1,9 +1,10 @@
 # MoleditPy — A Python Molecular Editor
 
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.17268532.svg)](https://doi.org/10.5281/zenodo.17268532)
+![MoleditPy](https://img.shields.io/badge/MoleditPy-v4-3577F7)
 [![Powered by RDKit](https://img.shields.io/badge/Powered%20by-RDKit-3838ff.svg?logo=data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAABAAAAAQBAMAAADt3eJSAAAABGdBTUEAALGPC/xhBQAAACBjSFJNAAB6JgAAgIQAAPoAAACA6AAAdTAAAOpgAAA6mAAAF3CculE8AAAAFVBMVEXc3NwUFP8UPP9kZP+MjP+0tP////9ZXZotAAAAAXRSTlMAQObYZgAAAAFiS0dEBmFmuH0AAAAHdElNRQfmAwsPGi+MyC9RAAAAQElEQVQI12NgQABGQUEBMENISUkRLKBsbGwEEhIyBgJFsICLC0iIUdnExcUZwnANQWfApKCK4doRBsKtQFgKAQC5Ww1JEHSEkAAAACV0RVh0ZGF0ZTpjcmVhdGUAMjAyMi0wMy0xMVQxNToyNjo0NyswMDowMDzr2J4AAAAldEVYdGRhdGU6bW9kaWZ5ADIwMjItMDMtMTFUMTU6MjY6NDcrMDA6MDBNtmAiAAAAAElFTkSuQmCC)](https://www.rdkit.org/)
 [![PyPI version](https://badge.fury.io/py/MoleditPy.svg)](https://badge.fury.io/py/MoleditPy)
-[![Python Versions](https://img.shields.io/pypi/pyversions/MoleditPy.svg)](https://pypi.org/project/MoleditPy/)
+[![Python Versions](https://img.shields.io/badge/python-3.9--3.14-blue.svg)](https://pypi.org/project/MoleditPy/)
 [![License: GPL v3](https://img.shields.io/badge/License-GPLv3-blue.svg)](https://www.gnu.org/licenses/gpl-3.0)
 [![Build Status](https://github.com/HiroYokoyama/python_molecular_editor/actions/workflows/tests.yml/badge.svg)](https://github.com/HiroYokoyama/python_molecular_editor/actions)
 [![codecov](https://codecov.io/gh/HiroYokoyama/python_molecular_editor/graph/badge.svg)](https://codecov.io/gh/HiroYokoyama/python_molecular_editor)
@@ -23,7 +24,10 @@
 **Repository**: [https://github.com/HiroYokoyama/python\_molecular\_editor](https://github.com/HiroYokoyama/python_molecular_editor)
 
 -----
-![](img/icon.png)
+<p align="center">
+  <img src="img/icon.png" width="500" alt="MoleditPy Icon">
+</p>
+
 ![](img/screenshot.png)
 
 

{moleditpy-4.10.1 → moleditpy-4.10.3}/pyproject.toml

@@ -5,7 +5,7 @@ build-backend = "setuptools.build_meta"
 [project]
 name = "MoleditPy"
 
-version = "4.10.1"
+version = "4.10.3"
 
 license = {file = "LICENSE"}
 

{moleditpy-4.10.1 → moleditpy-4.10.3}/src/MoleditPy.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: MoleditPy
-Version: 4.10.1
+Version: 4.10.3
 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
@@ -705,9 +705,10 @@ Dynamic: license-file
 # MoleditPy — A Python Molecular Editor
 
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.17268532.svg)](https://doi.org/10.5281/zenodo.17268532)
+![MoleditPy](https://img.shields.io/badge/MoleditPy-v4-3577F7)
 [![Powered by RDKit](https://img.shields.io/badge/Powered%20by-RDKit-3838ff.svg?logo=data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAABAAAAAQBAMAAADt3eJSAAAABGdBTUEAALGPC/xhBQAAACBjSFJNAAB6JgAAgIQAAPoAAACA6AAAdTAAAOpgAAA6mAAAF3CculE8AAAAFVBMVEXc3NwUFP8UPP9kZP+MjP+0tP////9ZXZotAAAAAXRSTlMAQObYZgAAAAFiS0dEBmFmuH0AAAAHdElNRQfmAwsPGi+MyC9RAAAAQElEQVQI12NgQABGQUEBMENISUkRLKBsbGwEEhIyBgJFsICLC0iIUdnExcUZwnANQWfApKCK4doRBsKtQFgKAQC5Ww1JEHSEkAAAACV0RVh0ZGF0ZTpjcmVhdGUAMjAyMi0wMy0xMVQxNToyNjo0NyswMDowMDzr2J4AAAAldEVYdGRhdGU6bW9kaWZ5ADIwMjItMDMtMTFUMTU6MjY6NDcrMDA6MDBNtmAiAAAAAElFTkSuQmCC)](https://www.rdkit.org/)
 [![PyPI version](https://badge.fury.io/py/MoleditPy.svg)](https://badge.fury.io/py/MoleditPy)
-[![Python Versions](https://img.shields.io/pypi/pyversions/MoleditPy.svg)](https://pypi.org/project/MoleditPy/)
+[![Python Versions](https://img.shields.io/badge/python-3.9--3.14-blue.svg)](https://pypi.org/project/MoleditPy/)
 [![License: GPL v3](https://img.shields.io/badge/License-GPLv3-blue.svg)](https://www.gnu.org/licenses/gpl-3.0)
 [![Build Status](https://github.com/HiroYokoyama/python_molecular_editor/actions/workflows/tests.yml/badge.svg)](https://github.com/HiroYokoyama/python_molecular_editor/actions)
 [![codecov](https://codecov.io/gh/HiroYokoyama/python_molecular_editor/graph/badge.svg)](https://codecov.io/gh/HiroYokoyama/python_molecular_editor)
@@ -727,7 +728,10 @@ Dynamic: license-file
 **Repository**: [https://github.com/HiroYokoyama/python\_molecular\_editor](https://github.com/HiroYokoyama/python_molecular_editor)
 
 -----
-![](img/icon.png)
+<p align="center">
+  <img src="img/icon.png" width="500" alt="MoleditPy Icon">
+</p>
+
 ![](img/screenshot.png)
 
 

{moleditpy-4.10.1 → moleditpy-4.10.3}/src/MoleditPy.egg-info/SOURCES.txt

@@ -53,6 +53,7 @@ src/moleditpy/ui/main_window_init.py
 src/moleditpy/ui/mirror_dialog.py
 src/moleditpy/ui/molecular_scene_handler.py
 src/moleditpy/ui/molecule_scene.py
+src/moleditpy/ui/move_dialog_mixin.py
 src/moleditpy/ui/move_group_dialog.py
 src/moleditpy/ui/move_selected_atoms_dialog.py
 src/moleditpy/ui/periodic_table_dialog.py

{moleditpy-4.10.1 → moleditpy-4.10.3}/src/moleditpy/main.py

@@ -280,7 +280,9 @@ def main() -> None:
                 metadata_file = init_py
 
         info = (
-            pm.get_plugin_info_safe(metadata_file)
+            pm.get_plugin_info_safe(
+                metadata_file, fallback_name=os.path.basename(plugin_path)
+            )
             if metadata_file.endswith(".py")
             else {}
         )

{moleditpy-4.10.1 → moleditpy-4.10.3}/src/moleditpy/plugins/plugin_manager.py

@@ -348,10 +348,11 @@ class PluginManager:
         self, filepath: str, module_name: str, category: str
     ) -> None:
         """Add a disabled plugin without importing or initializing its code."""
-        info = self.get_plugin_info_safe(filepath)
+        # Same fallback as _load_single_plugin's getattr(..., module_name).
+        info = self.get_plugin_info_safe(filepath, fallback_name=module_name)
         self.plugins.append(
             {
-                "name": info.get("name", module_name),
+                "name": info["name"],
                 "version": info.get("version", "Unknown"),
                 "author": info.get("author", "Unknown"),
                 "description": info.get("description", ""),
@@ -800,10 +801,13 @@ class PluginManager:
             logging.debug("Suppressed non-critical error", exc_info=True)
         return False
 
-    def get_plugin_info_safe(self, file_path: str) -> Dict[str, str]:
-        """Extracts plugin metadata using AST parsing (safe, no execution)."""
+    def get_plugin_info_safe(
+        self, file_path: str, fallback_name: Optional[str] = None
+    ) -> Dict[str, str]:
+        """Extract plugin metadata by AST parsing; ``fallback_name`` stands in
+        for a missing PLUGIN_NAME, defaulting to the file's basename."""
         info = {
-            "name": os.path.basename(file_path),
+            "name": fallback_name or os.path.basename(file_path),
             "version": "Unknown",
             "author": "Unknown",
             "description": "",

{moleditpy-4.10.1 → moleditpy-4.10.3}/src/moleditpy/plugins/plugin_manager_window.py

@@ -13,7 +13,7 @@ DOI: 10.5281/zenodo.17268532
 import logging
 import os
 import shutil
-from typing import Any, Optional
+from typing import Any, Optional, cast
 
 
 from PyQt6.QtCore import Qt, QUrl
@@ -25,6 +25,7 @@ from PyQt6.QtWidgets import (
     QHBoxLayout,
     QHeaderView,
     QLabel,
+    QLineEdit,
     QMessageBox,
     QPushButton,
     QTableWidget,
@@ -42,42 +43,68 @@ class PluginManagerWindow(QDialog):
         super().__init__(parent)
         self.btn_remove: Any = None
         self.table: Any = None
+        self.search_input: Any = None
         self.plugin_manager = plugin_manager
         self._preferences_applied = False
         self.setWindowTitle("Plugin Manager")
-        self.resize(800, 500)
+        self.resize(850, 520)
         self.setAcceptDrops(True)  # Enable drag & drop for the whole window
 
         self.init_ui()
         self.refresh_plugin_list()
 
     def init_ui(self) -> None:
-        """Build the plugin manager UI with table, buttons, and drag-and-drop support."""
+        """Build plugin manager UI with table, buttons, search box, and drop support."""
         layout = QVBoxLayout(self)
 
         lbl_info = QLabel(
-            "Drag & Drop .py or .zip files here to install plugins. Use the checkbox to enable/disable plugins."
+            "Drag & Drop .py or .zip files to install plugins. Use checkboxes to enable/disable."
         )
         lbl_info.setStyleSheet("color: gray; font-style: italic;")
         layout.addWidget(lbl_info)
 
+        # Search Box
+        search_layout = QHBoxLayout()
+        search_label = QLabel("Search:")
+        self.search_input = QLineEdit()
+        self.search_input.setPlaceholderText(
+            "Search plugins by name, author, location, or description..."
+        )
+        self.search_input.setClearButtonEnabled(True)
+        self.search_input.textChanged.connect(self.filter_plugins)
+        search_layout.addWidget(search_label)
+        search_layout.addWidget(self.search_input)
+        layout.addLayout(search_layout)
+
         # Plugin Table
         self.table = QTableWidget()
-        self.table.setColumnCount(6)
+        self.table.setColumnCount(7)
         self.table.setHorizontalHeaderLabels(
-            ["Status", "Name", "Version", "Author", "Location", "Description"]
+            [
+                "Enabled",
+                "Status",
+                "Name",
+                "Version",
+                "Author",
+                "Location",
+                "Description",
+            ]
         )
         self.table.horizontalHeader().setSectionResizeMode(
             QHeaderView.ResizeMode.Interactive
         )
         self.table.horizontalHeader().setSectionResizeMode(
-            4, QHeaderView.ResizeMode.Interactive
+            0, QHeaderView.ResizeMode.ResizeToContents
+        )
+        self.table.horizontalHeader().setSectionResizeMode(
+            5, QHeaderView.ResizeMode.Interactive
         )
         self.table.horizontalHeader().setSectionResizeMode(
-            5, QHeaderView.ResizeMode.Stretch
+            6, QHeaderView.ResizeMode.Stretch
         )  # Description stretches
-        self.table.setColumnWidth(1, 200)  # Make Name column wider
-        self.table.setColumnWidth(0, 120)  # Keep the status checkbox on one line
+        self.table.setColumnWidth(0, 70)  # Enabled checkbox
+        self.table.setColumnWidth(1, 100)  # Status
+        self.table.setColumnWidth(2, 180)  # Name
         self.table.setSelectionBehavior(QAbstractItemView.SelectionBehavior.SelectRows)
         self.table.setEditTriggers(QAbstractItemView.EditTrigger.NoEditTriggers)
         self.table.itemSelectionChanged.connect(self.update_button_state)
@@ -88,7 +115,8 @@ class PluginManagerWindow(QDialog):
         btn_layout = QHBoxLayout()
 
         btn_reload = QPushButton("Reload Plugins")
-        btn_reload.clicked.connect(self.on_reload)
+        # Not connect(self.on_reload): clicked(bool) would land in *silent*.
+        btn_reload.clicked.connect(lambda: self.on_reload())
         btn_layout.addWidget(btn_reload)
 
         btn_folder = QPushButton("Open Plugin Folder")
@@ -115,6 +143,20 @@ class PluginManagerWindow(QDialog):
 
         layout.addLayout(btn_layout)
 
+    def _create_checkbox_container(
+        self, checked: bool, tooltip: str = "Enable or disable this plugin"
+    ) -> QWidget:
+        """Create a centered QCheckBox container; read it back via _status_checkbox."""
+        container = QWidget()
+        box_layout = QHBoxLayout(container)
+        box_layout.setContentsMargins(0, 0, 0, 0)
+        box_layout.setAlignment(Qt.AlignmentFlag.AlignCenter)
+        checkbox = QCheckBox()
+        checkbox.setChecked(checked)
+        checkbox.setToolTip(tooltip)
+        box_layout.addWidget(checkbox)
+        return container
+
     def refresh_plugin_list(self) -> None:
         """Repopulate the plugin table from the current plugin registry."""
         self.table.setRowCount(0)
@@ -122,22 +164,35 @@ class PluginManagerWindow(QDialog):
 
         self.table.setRowCount(len(plugins))
         for row, p in enumerate(plugins):
-            # Keep an empty item for row selection; the checkbox owns visible status text.
-            status_item = QTableWidgetItem()
-            self.table.setItem(row, 0, status_item)
-
-            # Use an explicit widget so macOS keeps the checkbox and status text
-            # in a stable horizontal layout instead of stacking the item indicator.
-            status_checkbox = QCheckBox(str(p.get("status", "Unknown")))
-            status_checkbox.setChecked(not p.get("disabled", False))
-            status_checkbox.setToolTip("Enable or disable this plugin")
-            status_checkbox.setStyleSheet("QCheckBox { padding-left: 4px; }")
-            self.table.setCellWidget(row, 0, status_checkbox)
-            self.table.setItem(row, 1, QTableWidgetItem(str(p.get("name", "Unknown"))))
-            self.table.setItem(row, 2, QTableWidgetItem(str(p.get("version", ""))))
-            self.table.setItem(row, 3, QTableWidgetItem(str(p.get("author", ""))))
-
-            # Location (Relative Path)
+            # Column 0: Enabled Checkbox (Clean native check, centered)
+            is_enabled = not p.get("disabled", False)
+            self.table.setCellWidget(
+                row, 0, self._create_checkbox_container(is_enabled)
+            )
+
+            # Empty item behind the widget so the column still selects the row.
+            self.table.setItem(row, 0, QTableWidgetItem())
+
+            # Column 1: Status (colored text)
+            status = str(p.get("status", "Unknown"))
+            status_item = QTableWidgetItem(status)
+            status_item.setTextAlignment(Qt.AlignmentFlag.AlignCenter)
+            if status.startswith("Error"):
+                status_item.setForeground(Qt.GlobalColor.red)
+            elif status == "Loaded":
+                status_item.setForeground(Qt.GlobalColor.darkGreen)
+            elif status in ("No Entry Point", "Disabled"):
+                status_item.setForeground(Qt.GlobalColor.gray)
+            self.table.setItem(row, 1, status_item)
+
+            # Column 2: Name
+            self.table.setItem(row, 2, QTableWidgetItem(str(p.get("name", "Unknown"))))
+            # Column 3: Version
+            self.table.setItem(row, 3, QTableWidgetItem(str(p.get("version", ""))))
+            # Column 4: Author
+            self.table.setItem(row, 4, QTableWidgetItem(str(p.get("author", ""))))
+
+            # Column 5: Location (Relative Path)
             full_path = p.get("filepath", "")
             rel_path = ""
             if full_path:
@@ -147,38 +202,85 @@ class PluginManagerWindow(QDialog):
                     )
                 except (AttributeError, RuntimeError, ValueError, TypeError):
                     rel_path = os.path.basename(full_path)
-            self.table.setItem(row, 4, QTableWidgetItem(str(rel_path)))
+            self.table.setItem(row, 5, QTableWidgetItem(str(rel_path)))
+
+            # Column 6: Description
+            self.table.setItem(row, 6, QTableWidgetItem(str(p.get("description", ""))))
+
+        if self.search_input and self.search_input.text():
+            self.filter_plugins(self.search_input.text())
+
+    def filter_plugins(self, text: str) -> None:
+        """Filter table rows based on search text."""
+        query = text.strip().lower()
+        for row in range(self.table.rowCount()):
+            if not query:
+                self.table.setRowHidden(row, False)
+                continue
+
+            # Check status, name, author, location, and description
+            status = (
+                self.table.item(row, 1).text().lower()
+                if self.table.item(row, 1)
+                else ""
+            )
+            name = (
+                self.table.item(row, 2).text().lower()
+                if self.table.item(row, 2)
+                else ""
+            )
+            author = (
+                self.table.item(row, 4).text().lower()
+                if self.table.item(row, 4)
+                else ""
+            )
+            location = (
+                self.table.item(row, 5).text().lower()
+                if self.table.item(row, 5)
+                else ""
+            )
+            description = (
+                self.table.item(row, 6).text().lower()
+                if self.table.item(row, 6)
+                else ""
+            )
 
-            self.table.setItem(row, 5, QTableWidgetItem(str(p.get("description", ""))))
+            match = (
+                query in name
+                or query in author
+                or query in location
+                or query in description
+                or query in status
+            )
+            self.table.setRowHidden(row, not match)
 
-            # Simple color coding for status
-            status = str(p.get("status", ""))
-            color = None
-            checkbox_color = None
-            if status.startswith("Error"):
-                color = Qt.GlobalColor.red
-                checkbox_color = "red"
-            elif status == "Loaded":
-                color = Qt.GlobalColor.darkGreen
-                checkbox_color = "darkgreen"
-            elif status in ("No Entry Point", "Disabled"):
-                color = Qt.GlobalColor.gray
-                checkbox_color = "gray"
+        self._drop_hidden_selection()
 
-            if color:
-                status_checkbox.setStyleSheet(
-                    f"QCheckBox {{ padding-left: 4px; color: {checkbox_color}; }}"
-                )
+    def _drop_hidden_selection(self) -> None:
+        """Clear the selection when the filter hides the row it points at."""
+        row = self.table.currentRow()
+        if row >= 0 and self.table.isRowHidden(row):
+            self.table.clearSelection()
+            self.table.setCurrentCell(-1, -1)
+            self.update_button_state()
 
     def _status_checkbox(self, row: int) -> Optional[QCheckBox]:
         """Return the visible status checkbox for a plugin table row."""
-        checkbox = self.table.cellWidget(row, 0)
-        return checkbox if isinstance(checkbox, QCheckBox) else None
+        container = self.table.cellWidget(row, 0)
+        if isinstance(container, QCheckBox):
+            return container
+        if isinstance(container, QWidget):
+            checkbox = container.findChild(QCheckBox)
+            return checkbox
+        return None
 
     def _save_checkbox_preferences(self) -> set[str]:
-        """Collect and persist checkbox choices."""
+        """Collect and persist checkbox choices, hidden rows included."""
         disabled_paths = set()
-        for row, plugin in enumerate(self.plugin_manager.plugins):
+        for row in range(self.table.rowCount()):
+            plugin = self._plugin_for_row(row)
+            if plugin is None:
+                continue
             status_checkbox = self._status_checkbox(row)
             if status_checkbox is not None and not status_checkbox.isChecked():
                 filepath = plugin.get("filepath")
@@ -202,9 +304,12 @@ class PluginManagerWindow(QDialog):
             self.plugin_manager.discover_plugins()
 
     def done(self, result: int) -> None:
-        """Apply plugin preferences for every way the dialog can close."""
-        self._apply_plugin_preferences()
+        """Apply plugin preferences for every way the dialog can close.
+
+        Close first: applying them re-runs every plugin's ``initialize()``.
+        """
         super().done(result)
+        self._apply_plugin_preferences()
 
     def update_button_state(self) -> None:
         """Enable or disable the Remove button based on table selection."""
@@ -226,6 +331,17 @@ class PluginManagerWindow(QDialog):
             self.plugin_manager.discover_plugins()
             self.refresh_plugin_list()
 
+    def _plugin_for_row(self, row: int) -> Optional[dict[str, Any]]:
+        """Retrieve the plugin dict a table row was built from.
+
+        Row index is the plugin index; filtering hides rows, never reorders.
+        """
+        if row < 0 or row >= min(
+            self.table.rowCount(), len(self.plugin_manager.plugins)
+        ):
+            return None
+        return cast(dict[str, Any], self.plugin_manager.plugins[row])
+
     def on_remove_plugin(self) -> None:
         """Delete the selected plugin file or folder and reload."""
         row = self.table.currentRow()
@@ -233,9 +349,8 @@ class PluginManagerWindow(QDialog):
             QMessageBox.warning(self, "Warning", "Please select a plugin to remove.")
             return
 
-        # Assuming table row index matches plugins list index (confirmed in refresh_plugin_list)
-        if row < len(self.plugin_manager.plugins):
-            plugin = self.plugin_manager.plugins[row]
+        plugin = self._plugin_for_row(row)
+        if plugin is not None:
             filepath = plugin.get("filepath")
 
             if filepath and os.path.exists(filepath):
@@ -280,15 +395,15 @@ class PluginManagerWindow(QDialog):
     def show_plugin_details(self, item: QTableWidgetItem) -> None:
         """Show a message box with full metadata for the double-clicked plugin."""
         row = item.row()
-        if row < len(self.plugin_manager.plugins):
-            p = self.plugin_manager.plugins[row]
+        plugin = self._plugin_for_row(row)
+        if plugin is not None:
             msg = (
-                f"Name: {p.get('name', 'Unknown')}\n"
-                f"Version: {p.get('version', 'Unknown')}\n"
-                f"Author: {p.get('author', 'Unknown')}\n"
-                f"Status: {p.get('status', 'Unknown')}\n"
-                f"Location: {p.get('filepath', 'Unknown')}\n\n"
-                f"Description:\n{p.get('description', 'No description available.')}"
+                f"Name: {plugin.get('name', 'Unknown')}\n"
+                f"Version: {plugin.get('version', 'Unknown')}\n"
+                f"Author: {plugin.get('author', 'Unknown')}\n"
+                f"Status: {plugin.get('status', 'Unknown')}\n"
+                f"Location: {plugin.get('filepath', 'Unknown')}\n\n"
+                f"Description:\n{plugin.get('description', 'No description available.')}"
             )
             QMessageBox.information(self, "Plugin Details", msg)
 
@@ -316,7 +431,8 @@ class PluginManagerWindow(QDialog):
             is_folder = False
 
             if os.path.isfile(file_path):
-                # Special handling: If user drops __init__.py, assume they want to install the package (folder)
+                # Special handling: If user drops __init__.py,
+                # assume they want to install the package (folder)
                 if os.path.basename(file_path) == "__init__.py":
                     file_path = os.path.dirname(file_path)
                     is_valid = True
@@ -346,8 +462,14 @@ class PluginManagerWindow(QDialog):
                     # Try to parse __init__.py if it exists
                     init_path = os.path.join(file_path, "__init__.py")
                     if os.path.exists(init_path):
-                        info = self.plugin_manager.get_plugin_info_safe(init_path)
-                        info["description"] += f" (Package: {info['name']})"
+                        folder_note = info["description"]
+                        info = self.plugin_manager.get_plugin_info_safe(
+                            init_path, fallback_name=os.path.basename(file_path)
+                        )
+                        declared = info["description"]
+                        info["description"] = f"{folder_note} (Package: {info['name']})"
+                        if declared:
+                            info["description"] += f" - {declared}"
 
                 elif is_zip:
                     info["description"] = "ZIP Package Plugin"

{moleditpy-4.10.1 → moleditpy-4.10.3}/src/moleditpy/ui/compute_logic.py

@@ -66,12 +66,12 @@ class ComputeManager:
         self._active_calc_threads = []
 
     def _safe_disconnect(self, signal: Any) -> None:
-        """Safely disconnect a signal, silently ignoring RuntimeError."""
+        """Disconnect a signal, tolerating one that has nothing connected."""
         try:
             signal.disconnect()
-        except RuntimeError:
-            # Safe defensive fallback catching RuntimeError
-            logging.debug("Suppressed non-critical error", exc_info=True)
+        except (RuntimeError, TypeError):
+            # PyQt raises TypeError, not RuntimeError, when nothing is attached.
+            logging.debug("Nothing to disconnect from %s", signal, exc_info=True)
 
     def _remove_calculating_text(self) -> None:
         """Safely remove the 'Calculating...' text actor from the plotter."""
@@ -90,14 +90,17 @@ class ComputeManager:
         """Restore the Convert and Optimize buttons to their default state."""
         self._safe_disconnect(self.host.init_manager.convert_button.clicked)  # type: ignore[union-attr]
         self.host.init_manager.convert_button.setText("Convert 2D to 3D")  # type: ignore[union-attr]
-        self.host.init_manager.convert_button.clicked.connect(self.trigger_conversion)  # type: ignore[union-attr]
+        # Wrapped: clicked(bool) would otherwise arrive as conversion_mode.
+        self.host.init_manager.convert_button.clicked.connect(  # type: ignore[union-attr]
+            lambda: self.trigger_conversion()
+        )
         self.host.init_manager.convert_button.setEnabled(True)  # type: ignore[union-attr]
 
         if self.host.init_manager.optimize_3d_button:
             self._safe_disconnect(self.host.init_manager.optimize_3d_button.clicked)
             self.host.init_manager.optimize_3d_button.setText("Optimize 3D")
             self.host.init_manager.optimize_3d_button.clicked.connect(
-                self.optimize_3d_structure
+                lambda: self.optimize_3d_structure()
             )
             self.host.init_manager.optimize_3d_button.setEnabled(True)