Merge pull request #21 from EBjerrum/pyside6

Pyside6

DEVELOPER.md

@@ -4,7 +4,7 @@
 
 ### Prerequisites
 
-rdkit, numpy, pyside2 are installed by default.
+rdkit, numpy, pyside and pqtdarktheme are installed by default.
 ruff is installed using the dev tag as described below
 
 ### Installation Steps

README.md

@@ -1,27 +1,22 @@
 # rdeditor
 
-Simple RDKit molecule editor GUI using PySide2
+Simple RDKit molecule editor GUI using PySide6
 ![rdeditor, the RDKit molecule editor](./Screenshots/Main_window.png)
 
 ## Installation
 
 - requirements
 
-RDKit, NumPy and PySide2 should be automatically pip installed by the setup.py script.
+RDKit, NumPy, PySide6 and pyqtdarktheme should be automatically pip installed by the setup.py script.
 
 - installation
 
 ```bash
-python setup.py install
+pip install rdeditor
 
 ```
 
-A launch script will also be added so that it can be started from the command line via the rdEditor command.
-
-## Alternative install
-
-Install PySide and RDKit yourself, save the content of rdeditor folder to somewhere you like and start it with
-`python rdEditor.py`
+A launch script will also be added so that it can be started from the command line via the `rdEditor` command.
 
 ## Usage
 
@@ -59,6 +54,17 @@ Most commonly used bond types, and atom types can be selected. A Periodic table
 
 Access to all standard operations as well as less used atom types and bond-types.
 
+#### Settings
+
+Themes can be selected from the ones available on your platform (Mac/Linux/Windows)
+
+The debug level can be selected
+
+## Development
+
+Instructions to set it up in editable modes and instructions for eventual contributions can be found in the [DEVELOPER.md](./DEVELOPER.md) file.
+Please reach out first, there may be a relevant development branch.
+
 ## Additional Reading
 
 I wrote a blog post with an overview of the structure of the code.
@@ -70,3 +76,5 @@ We also published a preprint on ChemRxiv: [https://chemrxiv.org/engage/chemrxiv/
 
 - Not possible to distinguish undefined and trans when editing cis/trans double bonds
 - Aromaticity perception hides double-single bonds (kekulization can do likewise)
+
+please report issues at GitHub, it's tough getting all corners of a GUI tested.

pyproject.toml

@@ -0,0 +1,55 @@
+[build-system]
+requires = ["setuptools>=45", "setuptools_scm[toml]>=6.2"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "rdeditor"
+description = "An RDKit based molecule editor using PySide"
+readme = "README.md"
+requires-python = ">=3.8"
+license = {text = "LGPL"}
+authors = [
+    {name = "Esben Jannik Bjerrum", email = "[email protected]"},
+]
+keywords = ["RDKit", "molecule", "editor", "pyside"]
+
+dependencies = [
+    "PySide6",
+    "numpy",
+    "rdkit",
+    "pyqtdarktheme",
+]
+dynamic = ["version"]
+
+[project.urls]
+Homepage = "http://github.com/ebjerrum/rdeditor"
+"Bug Tracker" = "https://github.com/ebjerrum/rdeditor/issues"
+Documentation = "https://github.com/ebjerrum/rdeditor/blob/master/README.md"
+"Source Code" = "https://github.com/ebjerrum/rdeditor"
+"Citation" = "https://github.com/ebjerrum/rdeditor/blob/master/CITATION.md"
+"ChemRxiv Preprint" = "https://chemrxiv.org/engage/chemrxiv/article-details/65e6dcfa9138d23161b2979c"
+"Developer Guide" = "https://github.com/ebjerrum/rdeditor/blob/master/DEVELOPER.md"
+
+[project.optional-dependencies]
+dev = ["ruff", "wheel", "twine", "setuptools_scm"]
+
+[project.scripts]
+rdEditor = "rdeditor.rdEditor:launch"
+
+[tool.setuptools]
+packages = ["rdeditor"]
+zip-safe = false
+
+[tool.setuptools.package-data]
+rdeditor = [
+    "icon_themes/dark/*",
+    "icon_themes/dark/application/*",
+    "icon_themes/light/*",
+    "icon_themes/light/application/*",
+]
+
+[tool.setuptools_scm]
+write_to = "rdeditor/_version.py"
+
+[tool.ruff]
+extend = "ruff.toml"

rdeditor/molEditWidget.py

@@ -1,7 +1,6 @@
 #!/usr/bin/python
 # Import required modules
-from __future__ import print_function
-from PySide2 import QtCore, QtGui, QtSvg, QtWidgets
+from PySide6 import QtCore, QtGui, QtSvg, QtWidgets
 import sys
 import logging
 from warnings import warn
@@ -19,7 +18,7 @@
 
 from rdeditor.molViewWidget import MolWidget
 
-from types import *
+# from types import *
 
 from rdeditor.ptable import symboltoint
 
@@ -159,7 +158,7 @@ def setRing(self, ringtype):
             self.logger.error(f"Currently only {self.available_rings} are supported.")
 
     def setBond(self, bondtype):
-        if type(bondtype) == Chem.rdchem.BondType:
+        if isinstance(bondtype, Chem.rdchem.BondType):
             self._chementitytype = "bond"
             self._chementity = bondtype
 
@@ -286,21 +285,23 @@ def get_molobject(self, event):
             return self.SVG_to_coord(x_svg, y_svg)
 
     def mousePressEvent(self, event):
-        if event.button() == QtCore.Qt.LeftButton:
+        if event.button() is QtCore.Qt.LeftButton:
             clicked = self.get_molobject(event)
-            if type(clicked) == Chem.rdchem.Atom:
+            if isinstance(clicked, Chem.rdchem.Atom):
                 self.logger.debug(
                     "You clicked atom %i, with atomic number %i" % (clicked.GetIdx(), clicked.GetAtomicNum())
                 )
                 # Call the atom_click function
                 self.atom_click(clicked)
                 # self.add_atom(self.pen, clicked)
-            elif type(clicked) == Chem.rdchem.Bond:
+            elif isinstance(clicked, Chem.rdchem.Bond):
                 self.logger.debug("You clicked bond %i with type %s" % (clicked.GetIdx(), clicked.GetBondType()))
                 self.bond_click(clicked)
-            elif type(clicked) == Point2D:
+            elif isinstance(clicked, Point2D):
                 self.logger.debug("Canvas Click")
                 self.canvas_click(clicked)
+            else:
+                self.logger.error(f"Clicked entity, {clicked} of unknown type {type(clicked)}")
 
     # Lookup tables to relate actions to context type with action type #TODO more clean to use Dictionaries??
     def atom_click(self, atom):
@@ -654,4 +655,4 @@ def backupMol(self):
     myApp = QtWidgets.QApplication(sys.argv)
     molblockview = MolWidget(mol)
     molblockview.show()
-    myApp.exec_()
+    myApp.exec()

rdeditor/molViewWidget.py

@@ -1,9 +1,10 @@
 #!/usr/bin/python
 # Import required modules
 from __future__ import print_function
-from PySide2 import QtCore, QtGui, QtSvg, QtWidgets
+from PySide6 import QtCore, QtGui, QtSvg, QtWidgets, QtSvgWidgets
 import sys
-from types import *
+
+# from types import *
 import logging
 
 import numpy as np
@@ -18,7 +19,7 @@
 
 
 # The Viewer Class
-class MolWidget(QtSvg.QSvgWidget):
+class MolWidget(QtSvgWidgets.QSvgWidget):
     def __init__(self, mol=None, parent=None):
         # Also init the super class
         super(MolWidget, self).__init__(parent)
@@ -286,4 +287,4 @@ def getMolSvg(self):
     molview.selectAtom(1)
     molview.selectedAtoms = [1, 2, 3]
     molview.show()
-    myApp.exec_()
+    myApp.exec()

rdeditor/ptable_widget.py

@@ -1,10 +1,9 @@
 #!/usr/bin/python
 # -*- coding: utf-8 -*-
-from __future__ import print_function
 import sys
 import logging
 
-from PySide2 import QtGui, QtCore, QtWidgets
+from PySide6 import QtGui, QtCore, QtWidgets
 
 from rdeditor.ptable import ptable
 
@@ -25,7 +24,7 @@ def initUI(self, actionGroup):
         # for atomname in self.editor.atomtypes.keys(): Gives unsorted list
         for key in self.ptable.keys():
             atomname = self.ptable[key]["Symbol"]
-            action = QtWidgets.QAction(
+            action = QtGui.QAction(
                 "%s" % atomname,
                 self,
                 statusTip="Set atomtype to %s" % atomname,
@@ -75,7 +74,7 @@ def main():
     pt = PTable()
     pt.selectAtomtype("N")
     pt.show()
-    sys.exit(app.exec_())
+    sys.exit(app.exec())
 
 
 if __name__ == "__main__":

rdeditor/rdEditor.py

@@ -1,19 +1,19 @@
 #!/usr/bin/env python
-from __future__ import print_function
-
 
 # Import required modules
 import sys
 import time
 import os
-from PySide2.QtGui import *
-from PySide2.QtWidgets import *
-from PySide2.QtCore import QByteArray
-from PySide2.QtCore import QSettings
-from PySide2 import QtCore, QtGui, QtWidgets
-from PySide2 import QtSvg
-from PySide2.QtCore import QUrl
-from PySide2.QtGui import QDesktopServices
+
+from PySide6.QtWidgets import QMenu, QApplication, QStatusBar, QMessageBox, QFileDialog
+from PySide6.QtCore import QByteArray
+from PySide6.QtCore import QSettings
+from PySide6 import QtCore, QtGui, QtWidgets
+from PySide6 import QtSvg
+from PySide6.QtCore import QUrl
+from PySide6.QtGui import QDesktopServices, QIcon, QAction, QKeySequence
+
+import darkdetect
 import qdarktheme
 
 # Import model
@@ -37,7 +37,7 @@ def __init__(self, fileName=None, loglevel="WARNING"):
         )
         self.loglevels = ["Critical", "Error", "Warning", "Info", "Debug", "Notset"]
         self.editor = MolEditWidget()
-        self.chemEntityActionGroup = QtWidgets.QActionGroup(self, exclusive=True)
+        self.chemEntityActionGroup = QtGui.QActionGroup(self, exclusive=True)
         self.ptable = PTable(self.chemEntityActionGroup)
         self._fileName = None
         self.initGUI(fileName=fileName)
@@ -71,7 +71,7 @@ def initGUI(self, fileName=None):
 
         self.SetupComponents()
 
-        self.infobar = QLabel("")
+        self.infobar = QtWidgets.QLabel("")
         self.myStatusBar.addPermanentWidget(self.infobar, 0)
 
         if self.fileName is not None:
@@ -217,8 +217,8 @@ def CreateMenus(self):
         # Debug level sub menu
 
     def populateThemeActions(self, menu: QMenu):
-        stylelist = QStyleFactory.keys() + ["Qdt light", "Qdt dark"]
-        self.themeActionGroup = QtWidgets.QActionGroup(self, exclusive=True)
+        stylelist = QtWidgets.QStyleFactory.keys() + ["Qdt light", "Qdt dark"]
+        self.themeActionGroup = QtGui.QActionGroup(self, exclusive=True)
         self.themeActions = {}
         for style_name in stylelist:
             action = QAction(
@@ -434,19 +434,32 @@ def setTheme(self):
         self.settings.setValue("theme_name", theme_name)
         self.settings.sync()
 
+    def is_dark_mode(self):
+        """Hack to detect if we have a dark mode running"""
+        app = QApplication.instance()
+        palette = app.palette()
+        # Get the color of the window background
+        background_color = palette.color(QtGui.QPalette.Window)
+        # Calculate the luminance (brightness) of the color
+        luminance = (
+            0.299 * background_color.red() + 0.587 * background_color.green() + 0.114 * background_color.blue()
+        ) / 255
+        # If the luminance is below a certain threshold, it's considered dark mode
+        return luminance < 0.5
+
     def applyTheme(self, theme_name):
         if "dark" in theme_name:
-            QIcon.setThemeName("dark")
-            self.editor.darkmode = True
-            self.editor.logger.info("Resetting theme for dark theme")
+            self.set_dark()
+        elif "light" in theme_name:
+            self.set_light()
+        elif self.is_dark_mode():
+            self.set_dark()
         else:
-            QIcon.setThemeName("light")
-            self.editor.darkmode = False
-            self.editor.logger.info("Resetting theme for light theme")
+            self.set_light()
 
         app = QApplication.instance()
         app.setStyleSheet("")  # resets style
-        if theme_name in QStyleFactory.keys():
+        if theme_name in QtWidgets.QStyleFactory.keys():
             app.setStyle(theme_name)
         else:
             if theme_name == "Qdt light":
@@ -456,6 +469,16 @@ def applyTheme(self, theme_name):
 
         self.resetActionIcons()
 
+    def set_light(self):
+        QIcon.setThemeName("light")
+        self.editor.darkmode = False
+        self.editor.logger.info("Resetting theme for light theme")
+
+    def set_dark(self):
+        QIcon.setThemeName("dark")
+        self.editor.darkmode = True
+        self.editor.logger.info("Resetting theme for dark theme")
+
     def openUrl(self):
         url = self.sender().data()
         QDesktopServices.openUrl(QUrl(url))
@@ -542,7 +565,7 @@ def CreateActions(self):
         )
 
         # Edit actions
-        self.actionActionGroup = QtWidgets.QActionGroup(self, exclusive=True)
+        self.actionActionGroup = QtGui.QActionGroup(self, exclusive=True)
         self.selectAction = QAction(
             QIcon.fromTheme("icons8-Cursor"),
             "Se&lect",
@@ -653,7 +676,7 @@ def CreateActions(self):
         self.addAction.setChecked(True)
 
         # BondTypeActions
-        self.bondtypeActionGroup = QtWidgets.QActionGroup(self, exclusive=True)
+        self.bondtypeActionGroup = QtGui.QActionGroup(self, exclusive=True)
 
         self.singleBondAction = QAction(
             QIcon.fromTheme("icons8-Single"),
@@ -775,7 +798,7 @@ def CreateActions(self):
             self.atomActions.append(action)
 
         self.loglevelactions = {}
-        self.loglevelActionGroup = QtWidgets.QActionGroup(self, exclusive=True)
+        self.loglevelActionGroup = QtGui.QActionGroup(self, exclusive=True)
         for key in self.loglevels:
             self.loglevelactions[key] = QAction(
                 key,
@@ -817,7 +840,7 @@ def launch(loglevel="WARNING"):
             mainWindow = MainWindow(fileName=sys.argv[1], loglevel=loglevel)
         else:
             mainWindow = MainWindow(loglevel=loglevel)
-        myApp.exec_()
+        myApp.exec()
         sys.exit(0)
     except NameError:
         print("Name Error:", sys.exc_info()[1])