MDANSE-GUI 2.0.0__tar.gz → 2.0.2__tar.gz

mdanse_gui-2.0.2/PKG-INFO

@@ -0,0 +1,203 @@
+Metadata-Version: 2.4
+Name: MDANSE_GUI
+Version: 2.0.2
+Summary: MDANSE GUI package - the graphical interface for MDANSE
+Maintainer-email: Maciej Bartkowiak <maciej.bartkowiak@stfc.ac.uk>, "Chi Y. Cheng" <chi.cheng@stfc.ac.uk>, Jacob Wilkins <jacob.wilkins@stfc.ac.uk>
+License-Expression: GPL-3.0-or-later
+Project-URL: homepage, https://pypi.org/project/MDANSE
+Project-URL: documentation, https://mdanse.readthedocs.io/
+Project-URL: repository, https://github.com/ISISNeutronMuon/MDANSE
+Keywords: molecular dynamics,science,simulation,analysis
+Classifier: Development Status :: 5 - Production/Stable
+Classifier: Intended Audience :: Science/Research
+Classifier: Topic :: Scientific/Engineering :: Chemistry
+Classifier: Topic :: Scientific/Engineering :: Physics
+Classifier: Topic :: Scientific/Engineering :: Visualization
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Programming Language :: Python :: 3.14
+Classifier: Programming Language :: Python :: 3 :: Only
+Classifier: Operating System :: OS Independent
+Requires-Python: >=3.11
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: MDANSE
+Requires-Dist: matplotlib
+Requires-Dist: qtpy
+Requires-Dist: vtk>=9.4.0
+Requires-Dist: PyQt6
+Requires-Dist: PyYAML
+Requires-Dist: tomlkit
+Requires-Dist: setuptools-git-versioning<4,>=3.0
+Provides-Extra: pymixbox
+Requires-Dist: pymixbox; extra == "pymixbox"
+Provides-Extra: shortcuts
+Requires-Dist: pyshortcuts>=1.9.11; extra == "shortcuts"
+Provides-Extra: all
+Requires-Dist: MDANSE_GUI[pymixbox,shortcuts]; extra == "all"
+Dynamic: license-file
+
+# MDANSE_GUI 
+
+## MDANSE_GUI Python Module
+
+This is the module containing the Graphical User Interface (GUI) of the
+Molecular Dynamics Analysis for Neutron Scattering Experiments (MDANSE) software package.
+
+The GUI depends on the [MDANSE package](https://pypi.org/project/MDANSE).
+
+> [!NOTE]
+> The default behaviour of MDANSE_GUI has changed in version 2.0.2
+> where the system tray icon has been added to the interface.
+> When the system tray icon of the MDANSE GUI is present, closing
+> the main window does not close the software, and the main window
+> can be shown again. The system tray icon can be disabled in the
+> GUI in Settings -> User Settings, in the 'startup' group.
+
+## Quick start: installation
+
+We recommend that you install MDANSE in a Python virtual environment.
+You can create a virtual environment named mdanse_env by typing
+```
+python3 -m venv mdanse_env
+```
+
+To activate your virtual environment, type
+```
+source mdanse_env/bin/activate
+```
+in a bash console, or
+```
+mdanse_env\Scripts\activate.bat
+```
+if you are using cmd.exe on Windows.
+
+While your virtual environment is active, you can install MDANSE:
+```
+pip install MDANSE_GUI
+```
+and start the GUI by typing
+```
+mdanse_gui
+```
+
+If you are using a virtual environment in which you had installed
+MDANSE in the past, you can upgrade MDANSE to the current version
+by typing:
+```
+pip install --upgrade MDANSE
+```
+
+If you experience problems with the installation, you may want to upgrade pip
+```
+pip install --upgrade pip
+```
+and try again.
+
+Please remember to activate your virtual environment when you start a new
+shell before you run `mdanse_gui`.
+
+## Additional installation options
+
+MDANSE_GUI has optional dependencies, which are not installed unless they are
+requested by the user. It is possible to install all the optional dependencies
+by running
+```
+pip install mdanse_gui[all]
+```
+
+The alternative is to install specific dependencies individually. This is described
+in the subsections below.
+
+### pymixbox
+
+An optional dependency, [pymixbox](https://github.com/scrtwpns/mixbox) can be
+installed to enable an alternative mechanism of colour mixing. It will be used
+in the MDANSE_GUI plotter when plotting a 2D data set as a series of 1D curves.
+The colours of consecutive curves will be generated from the initial and final
+colour values using pymixbox. (If pymixbox is not installed, the colours of
+intermediate curves will be generated by linear interpolation.)
+
+To install MDANSE_GUI with pymixbox, replace the normal installation command with
+```
+pip install mdanse_gui[pymixbox]
+```
+
+### pyshortcuts
+
+Users who want to create a desktop shortcut and a start menu entry for MDANSE_GUI
+can install MDANSE_GUI with [pyshortcuts](https://github.com/newville/pyshortcuts).
+It can be done by replacing the normal installation command with
+```
+pip install mdanse_gui[shortcuts]
+```
+
+Once MDANSE_GUI and its dependencies have been installed, run the script
+```
+create_mdanse_link
+```
+to create a desktop icon and a start menu entry for MDANSE_GUI (or just
+one of the two, depending on the operating system you are running.)
+
+
+## Quick start: workflow
+
+The typical workflow of MDANSE:
+
+1. Convert a trajectory from the file format generated by an MD simulation
+   software into the MDANSE trajectory format,
+2. Load the converted trajectory into MDANSE,
+3. Perform an analysis,
+4. Check the results with the plotter.
+
+Each one of these operations has its own dedicated tab in the GUI.
+The plotter consists of two tabs, one for selecting the data for plotting,
+and the other for viewing and customising the plot.
+
+The most complete user documentation of MDANSE can be found on
+[our Read the Docs page](https://mdanse.readthedocs.io).
+
+Other information, including tutorials, can be found in the
+[MDANSE-Examples repository](https://github.com/ISISNeutronMuon/MDANSE-Examples).
+
+## Citing MDANSE
+
+If you used MDANSE in your research, please cite it according to the CITATION.cff file
+in the [MDANSE GitHub repository](https://github.com/ISISNeutronMuon/MDANSE).
+On GitHub, you can use the "cite this repository" link to generate the citation.
+
+## License
+
+MDANSE_GUI is licensed under GPL-3.0. See
+[LICENSE](https://github.com/ISISNeutronMuon/MDANSE/blob/protos/LICENSE)
+for more information.
+
+## Acknowledgements
+
+The VTK-based 3D viewer was taken and adapted from another software project
+authored by Eric Pellegrini. We would like to thank Eric for making
+his code available.
+
+## Joining the project
+
+MDANSE_GUI is currently maintained and developed by software developers
+from ISIS and ILL, but we are fully open to new collaborators who would
+like to contribute code, documentation, tutorials or usage examples.
+If you want to join the project contact:
+
+>Dr. Sanghamitra Mukhopadhyay (sanghamitra.mukhopadhyay@stfc.ac.uk) \
+ISIS Neutron and Muon Source \
+Rutherford Appleton Laboratory \
+Didcot, UK
+
+## Software Inquiries
+
+You are welcome to use the
+[issue tracker](https://github.com/ISISNeutronMuon/MDANSE/issues)
+to submit ideas for
+extending the MDANSE code or to report problems you encountered.
+However, if you prefer to contact the MDANSE developers directly,
+you can send us a message:
+>MDANSE Help (MDANSE-help@stfc.ac.uk)

{mdanse_gui-2.0.0 → mdanse_gui-2.0.2}/README.md

@@ -7,18 +7,13 @@ Molecular Dynamics Analysis for Neutron Scattering Experiments (MDANSE) software
 
 The GUI depends on the [MDANSE package](https://pypi.org/project/MDANSE).
 
-## Version information
-
-This is the first release of MDANSE_GUI 2.0.0.
-
 > [!NOTE]
-> Considering the large number of different MD engines and analysis types,
-> it is still possible that some conversion or analysis runs will not
-> produce the expected results. Please report any problems
-> you experience while using MDANSE by adding them to the
-> [GitHub issue tracker](https://github.com/ISISNeutronMuon/MDANSE/issues).
-> You can also send a message to MDANSE-help@stfc.ac.uk to get in touch
-> with MDANSE developers.
+> The default behaviour of MDANSE_GUI has changed in version 2.0.2
+> where the system tray icon has been added to the interface.
+> When the system tray icon of the MDANSE GUI is present, closing
+> the main window does not close the software, and the main window
+> can be shown again. The system tray icon can be disabled in the
+> GUI in Settings -> User Settings, in the 'startup' group.
 
 ## Quick start: installation
 
@@ -63,6 +58,49 @@ and try again.
 Please remember to activate your virtual environment when you start a new
 shell before you run `mdanse_gui`.
 
+## Additional installation options
+
+MDANSE_GUI has optional dependencies, which are not installed unless they are
+requested by the user. It is possible to install all the optional dependencies
+by running
+```
+pip install mdanse_gui[all]
+```
+
+The alternative is to install specific dependencies individually. This is described
+in the subsections below.
+
+### pymixbox
+
+An optional dependency, [pymixbox](https://github.com/scrtwpns/mixbox) can be
+installed to enable an alternative mechanism of colour mixing. It will be used
+in the MDANSE_GUI plotter when plotting a 2D data set as a series of 1D curves.
+The colours of consecutive curves will be generated from the initial and final
+colour values using pymixbox. (If pymixbox is not installed, the colours of
+intermediate curves will be generated by linear interpolation.)
+
+To install MDANSE_GUI with pymixbox, replace the normal installation command with
+```
+pip install mdanse_gui[pymixbox]
+```
+
+### pyshortcuts
+
+Users who want to create a desktop shortcut and a start menu entry for MDANSE_GUI
+can install MDANSE_GUI with [pyshortcuts](https://github.com/newville/pyshortcuts).
+It can be done by replacing the normal installation command with
+```
+pip install mdanse_gui[shortcuts]
+```
+
+Once MDANSE_GUI and its dependencies have been installed, run the script
+```
+create_mdanse_link
+```
+to create a desktop icon and a start menu entry for MDANSE_GUI (or just
+one of the two, depending on the operating system you are running.)
+
+
 ## Quick start: workflow
 
 The typical workflow of MDANSE:

{mdanse_gui-2.0.0 → mdanse_gui-2.0.2}/Src/MDANSE_GUI/ElementsDatabaseEditor.py

@@ -38,7 +38,8 @@ from qtpy.QtWidgets import (
 )
 
 from MDANSE.Chemistry import ATOMS_DATABASE
-from MDANSE.Chemistry.Databases import AtomsDatabaseError
+from MDANSE.Chemistry.AtomsDatabase import AtomsDatabase, AtomsDatabaseError
+from MDANSE.IO.IOUtils import get_next_name
 from MDANSE.MLogging import LOG
 from MDANSE_GUI.Tabs.Views.Delegates import ColourPicker
 from MDANSE_GUI.Widgets.GeneralWidgets import (
@@ -246,14 +247,14 @@ class ElementView(QTableView):
     def contextMenuEvent(self, event):
         menu = QMenu(self)
 
-        Action1 = menu.addAction("New Custom Atom")
-        Action2 = menu.addAction("Copy Atoms")
-        Action3 = menu.addAction("Rename Custom Atom")
-        Action4 = menu.addAction("Delete Custom Atoms")
-        Action5 = menu.addAction("New Custom Property")
-        Action6 = menu.addAction("Copy Properties")
-        Action7 = menu.addAction("Rename Custom Property")
-        Action8 = menu.addAction("Delete Custom Properties")
+        NewAtom = menu.addAction("New Custom Atom")
+        CopyAtom = menu.addAction("Copy Atoms")
+        RenameAtom = menu.addAction("Rename Custom Atom")
+        DeleteAtom = menu.addAction("Delete Custom Atoms")
+        NewProp = menu.addAction("New Custom Property")
+        CopyProp = menu.addAction("Copy Properties")
+        RenameProp = menu.addAction("Rename Custom Property")
+        DeleteProp = menu.addAction("Delete Custom Properties")
 
         data_model = self.parent().data_model
 
@@ -292,26 +293,26 @@ class ElementView(QTableView):
 
         temp_model = self.model().sourceModel()
         if temp_model is not None:
-            Action1.triggered.connect(temp_model.new_line_dialog)
-            Action2.triggered.connect(temp_model.copy_rows)
+            NewAtom.triggered.connect(temp_model.new_line_dialog)
+            CopyAtom.triggered.connect(temp_model.copy_rows)
             if self.mouse_atm in custom_atms:
-                Action3.triggered.connect(temp_model.rename_row_dialog)
+                RenameAtom.triggered.connect(temp_model.rename_row_dialog)
             else:
-                Action3.setEnabled(False)
+                RenameAtom.setEnabled(False)
             if enable_delete_atms:
-                Action4.triggered.connect(temp_model.delete_rows)
+                DeleteAtom.triggered.connect(temp_model.delete_rows)
             else:
-                Action4.setEnabled(False)
-            Action5.triggered.connect(temp_model.new_column_dialog)
-            Action6.triggered.connect(temp_model.copy_columns)
+                DeleteAtom.setEnabled(False)
+            NewProp.triggered.connect(temp_model.new_column_dialog)
+            CopyProp.triggered.connect(temp_model.copy_columns)
             if self.mouse_prop in custom_props:
-                Action7.triggered.connect(temp_model.rename_column_dialog)
+                RenameProp.triggered.connect(temp_model.rename_column_dialog)
             else:
-                Action7.setEnabled(False)
+                RenameProp.setEnabled(False)
             if enable_delete_props:
-                Action8.triggered.connect(temp_model.delete_columns)
+                DeleteProp.triggered.connect(temp_model.delete_columns)
             else:
-                Action8.setEnabled(False)
+                DeleteProp.setEnabled(False)
 
         menu.exec_(event.globalPos())
 
@@ -323,6 +324,7 @@ class NewElementDialog(QDialog):
 
     def __init__(self, *args, **kwargs):
         super().__init__(*args, **kwargs)
+        self.setModal(True)
 
         layout = QVBoxLayout(self)
         edit = QLineEdit(self)
@@ -351,7 +353,7 @@ class ElementModel(QStandardItemModel):
     table gets sorted.
     """
 
-    def __init__(self, *args, element_database=None, **kwargs):
+    def __init__(self, *args, element_database: AtomsDatabase, **kwargs):
         super().__init__(*args, **kwargs)
 
         self.custom_header_brush = QBrush(QColor(255, 165, 0))
@@ -410,8 +412,8 @@ class ElementModel(QStandardItemModel):
         column = idx.column()
         row_name = self.verticalHeaderItem(row).text()
         column_name = self.horizontalHeaderItem(column).text()
-        LOG.info(f"data:{data}, text:{text}, row:{row}, column:{column}")
-        LOG.info(f"column name={column_name}, row name={row_name}")
+        LOG.debug(f"data:{data}, text:{text}, row:{row}, column:{column}")
+        LOG.debug(f"column name={column_name}, row name={row_name}")
         self.database.set_value(row_name, column_name, text)
         self.save_changes()
 
@@ -610,7 +612,7 @@ class ElementModel(QStandardItemModel):
         if new_label not in self.database.default_atoms_types:
             item.setForeground(self.custom_header_brush)
         self.setVerticalHeaderItem(self.rowCount() - 1, item)
-        LOG.info(f"self.all_row_names has length: {len(self.all_row_names)}")
+        LOG.debug(f"self.all_row_names has length: {len(self.all_row_names)}")
 
     @Slot()
     def copy_rows(self):
@@ -623,13 +625,13 @@ class ElementModel(QStandardItemModel):
 
         for _, idx in row_idxs:
             atm_sym = self.verticalHeaderItem(idx).text()
-            atm_sym_copy = atm_sym + "(copy)"
-            while True:
-                if atm_sym_copy not in self.database.atoms:
-                    self.database.add_atom(atm_sym_copy)
-                    self.copy_row_in_database(atm_sym_copy, atm_sym)
-                    break
-                atm_sym_copy += "(copy)"
+            atm_sym_copy = get_next_name(
+                f"{atm_sym}(copy{{trial}})",
+                exists=self.database.atoms,
+                default="",
+            )
+            self.database.add_atom(atm_sym_copy)
+            self.copy_row_in_database(atm_sym_copy, atm_sym)
         self.save_changes()
 
     @Slot(dict)
@@ -708,7 +710,7 @@ class ElementModel(QStandardItemModel):
             item.setForeground(self.custom_header_brush)
         self.setHorizontalHeaderItem(self.columnCount() - 1, item)
         self.parent().set_column_delegate(self.columnCount() - 1)
-        LOG.info(f"self.all_column_names has length: {len(self.all_column_names)}")
+        LOG.debug(f"self.all_column_names has length: {len(self.all_column_names)}")
 
     @Slot(dict)
     def add_new_column(self, input_variables: dict):
@@ -786,6 +788,7 @@ class ElementsDatabaseEditor(QDialog):
         super().__init__(*args, **kwargs)
 
         self.setWindowTitle("MDANSE Chemical Elements Database Editor")
+        self.setModal(True)
 
         layout = QVBoxLayout(self)
 

{mdanse_gui-2.0.0 → mdanse_gui-2.0.2}/Src/MDANSE_GUI/Icons/__init__.py

@@ -15,11 +15,14 @@
 #
 from __future__ import annotations
 
-from pathlib import Path
+from typing import TYPE_CHECKING
 
 from qtpy.QtCore import QDir
 from qtpy.QtGui import QIcon
 
+if TYPE_CHECKING:
+    from pathlib import Path
+
 
 class PyQtIcons:
     def __init__(self, path: Path | str):

{mdanse_gui-2.0.0 → mdanse_gui-2.0.2}/Src/MDANSE_GUI/InputWidgets/AseInputFileWidget.py

@@ -16,9 +16,9 @@
 from __future__ import annotations
 
 import os
+from contextlib import suppress
 from pathlib import PurePath
 
-from ase.io.formats import filetype
 from qtpy.QtCore import Slot
 from qtpy.QtWidgets import QComboBox, QFileDialog, QLineEdit, QPushButton
 
@@ -28,6 +28,9 @@ from MDANSE.Framework.Configurators.AseInputFileConfigurator import (
 from MDANSE.MLogging import LOG
 from MDANSE_GUI.InputWidgets.WidgetBase import WidgetBase
 
+with suppress(ImportError):
+    from ase.io.formats import filetype
+
 
 class AseInputFileWidget(WidgetBase):
     def __init__(self, *args, **kwargs):

{mdanse_gui-2.0.0 → mdanse_gui-2.0.2}/Src/MDANSE_GUI/InputWidgets/AtomMappingWidget.py

@@ -58,6 +58,7 @@ class AtomMappingHelperDialog(QDialog):
         """
         super().__init__(parent, *args, **kwargs)
         self.setWindowTitle("Atom mapping helper")
+        self.setModal(True)
         self.min_width = kwargs.get("min_width", 500)
         self.min_height = kwargs.get("min_width", 600)
         self.resize(self.min_width, self.min_height)

{mdanse_gui-2.0.0 → mdanse_gui-2.0.2}/Src/MDANSE_GUI/InputWidgets/AtomSelectionWidget.py

@@ -349,6 +349,7 @@ class SelectionHelper(QDialog):
         super().__init__(parent, *args, **kwargs)
         self.setWindowTitle(self._helper_title)
         self.setWindowFlags(Qt.Window)
+        self.setModal(True)
 
         self.trajectory = traj_data[1]
         self.system = self.trajectory.chemical_system
@@ -408,6 +409,7 @@ class SelectionHelper(QDialog):
         3D viewer when it is closed and then reopened.
         """
         self.selection_model.finalise_manual_selection()
+        self.view_3d.stop_animation()
         a0.ignore()
         self.hide()
 
@@ -445,6 +447,7 @@ class SelectionHelper(QDialog):
         or JSON text files.
         """
         self.selection_model.finalise_manual_selection()
+        self.view_3d.stop_animation()
         fname = QFileDialog.getSaveFileName(
             self,
             "Save current selection to a JSON file",

{mdanse_gui-2.0.0 → mdanse_gui-2.0.2}/Src/MDANSE_GUI/InputWidgets/FloatWidget.py

@@ -15,13 +15,18 @@
 #
 from __future__ import annotations
 
+from typing import TypeVar
+
 from qtpy.QtGui import QDoubleValidator
 from qtpy.QtWidgets import QDoubleSpinBox, QLineEdit
 
+from MDANSE.Framework.Configurators import FloatConfigurator
 from MDANSE_GUI.InputWidgets.WidgetBase import WidgetBase
 
+FloatConfig = TypeVar("FloatConfig", bound=FloatConfigurator)
+
 
-class FloatWidget(WidgetBase):
+class FloatWidget(WidgetBase[FloatConfig]):
     def __init__(self, *args, **kwargs):
         super().__init__(*args, **kwargs)
         try: