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PyQt frontend (chemical signaling and neuronal simulations) for MOOSE

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dilawar neurord jccsanabria hrani mahdise

moose-gui's Issues

<?xml version='1.0' encoding='utf-8' standalone='yes' ?>

150 UTF-8 1 0 1 3 Unicode/UTF-8-character table 2

Originally posted by @Zssn101 in #16 (comment)

Undefined `Info`

This Exception is not defined. Even if this code is unreachable, it will create problem during packaging with Py3.

moose-gui/objectedit.py

Line 282 in 31e493c

raise Info('No more redo information')

Import error with new matplotib which uses `PyQt5`

If python-matplotlib-qt5 or python-matplotlib-qtshared package is installed, moosegui won't launch. The trace-back is following:

Traceback (most recent call last):
  File "mgui.py", line 1194, in <module>
    main()
  File "mgui.py", line 1178, in main
    mWindow =  MWindow()
  File "mgui.py", line 177, in __init__
    self.setPlugin('default', '/')
  File "mgui.py", line 460, in setPlugin
    self.plugin = self.loadPluginClass(str(name))(str(root), self)
  File "mgui.py", line 412, in loadPluginClass
    pluginModule = self.loadPluginModule(name, re=re)
  File "mgui.py", line 364, in loadPluginModule
    module = imp.load_module(name, fp, pathname, description)
  File "/usr/lib/moose/gui/plugins/default.py", line 89, in <module>
    from matplotlib.backends.backend_qt4agg import NavigationToolbar2QT as NavigationToolbar
  File "/usr/lib64/python2.7/site-packages/matplotlib/backends/backend_qt4agg.py", line 18, in <module>
    from .backend_qt5agg import FigureCanvasQTAggBase as _FigureCanvasQTAggBase
  File "/usr/lib64/python2.7/site-packages/matplotlib/backends/backend_qt5agg.py", line 15, in <module>
    from .backend_qt5 import QtCore
  File "/usr/lib64/python2.7/site-packages/matplotlib/backends/backend_qt5.py", line 27, in <module>
    import matplotlib.backends.qt_editor.figureoptions as figureoptions
  File "/usr/lib64/python2.7/site-packages/matplotlib/backends/qt_editor/figureoptions.py", line 17, in <module>
    import matplotlib.backends.qt_editor.formlayout as formlayout
  File "/usr/lib64/python2.7/site-packages/matplotlib/backends/qt_editor/formlayout.py", line 58, in <module>
    from matplotlib.backends.qt_compat import QtGui, QtWidgets, QtCore
  File "/usr/lib64/python2.7/site-packages/matplotlib/backends/qt_compat.py", line 114, in <module>
    from PyQt5 import QtCore, QtGui, QtWidgets
RuntimeError: the PyQt5.QtCore module failed to register with the sip module

To fix it, make sure that matplotlib uses PyQt4 and an appropriate back-end is initialized. Otherwise you might run into following:

/usr/lib/python2.7/site-packages/moose/utils.py:35: UserWarning: Failed to importing plotting utilities: No module named backend_qt5agg
  warnings.warn("Failed to importing plotting utilities: %s" % e)
Traceback (most recent call last):
  File "mgui.py", line 1194, in <module>
    main()
  File "mgui.py", line 1178, in main
    mWindow =  MWindow()
  File "mgui.py", line 177, in __init__
    self.setPlugin('default', '/')
  File "mgui.py", line 460, in setPlugin
    self.plugin = self.loadPluginClass(str(name))(str(root), self)
  File "mgui.py", line 412, in loadPluginClass
    pluginModule = self.loadPluginModule(name, re=re)
  File "mgui.py", line 364, in loadPluginModule
    module = imp.load_module(name, fp, pathname, description)
  File "/usr/lib/moose/gui/plugins/default.py", line 89, in <module>
    from matplotlib.backends.backend_qt4agg import NavigationToolbar2QT as NavigationToolbar
ImportError: No module named backend_qt4agg

It might need some attention before next release.

OS: OpenSuSE-Leap_42.1

`moose-gui` does not launch on MacOSX

This ticket is here to track the status of moose-gui on MacOSX.

Run launch GUI, one needs to install PyQt using brew.

  $ brew install pyqt

Currently, pyqt-5.8.2 is available on homebrew. The moose-gui does not launch with this version.

$ python mgui.py 
Traceback (most recent call last):
  File "mgui.py", line 57, in <module>
    from PyQt4 import QtGui, QtCore, Qt
ImportError: cannot import name QtGui

It is unlikely that old version of pyqt are tapped somewhere on homebrew (though I am not sure about this). See the their transition status to (https://github.com/Homebrew/homebrew-science/issues/4595). Until moose-gui run with pyqt5, gui will not be available on MacOSX via homebrew.

Tag required to build with homebrew

Bugfix releases needs to be tagged. It has to be added to brew script with sha256sum. Create a tag branch and close this issue.

`action` undefined

The variable action is undefined. Packaing will be an issue later.

moose-gui/mgui.py

Line 615 in b375e56

action.menu().addSeparator()

dependency `python-suds` does not work on MacOSX

I've install suds using pip yet the moosegui does not launch: (On MacOSX).

File "/opt/local/lib/moose/gui/biomodelsclient.py", line 49, in <module>
    from suds.client import Client
ImportError: No module named suds.client

This is probably related to this http://stackoverflow.com/questions/14973852/suds-install-error-no-module-named-client

/cc @hrani @subhacom @aviralg

Import error when button Fig5BCD is pressed

Here is trace-back

Traceback (most recent call last):
  File "mgui.py", line 271, in <lambda>
    button.clicked.connect(lambda x, script = k[1]: self.run_python_script(script))
  File "mgui.py", line 308, in run_python_script
    p = subprocess.Popen(["python", filename], cwd=directory)
  File "/usr/lib64/python2.7/subprocess.py", line 710, in __init__
    errread, errwrite)
  File "/usr/lib64/python2.7/subprocess.py", line 1335, in _execute_child
    raise child_exception
OSError: [Errno 2] No such file or directory: '/usr/lib/moose/moose-examples/paper-2015/Fig6_CellMultiscale'

Tested on MacOSX/OpenSUSE. The directory structure in package is following:

gui/mgui.py 
moose-examples/*

On MacOSX, create new model does not work

Here is the issue:

QPixmap::scaled: Pixmap is a null pixmap
2015-11-07 22:32:33.146 Python[1852:5401535] modalSession has been exited prematurely - check for a reentrant call to endModalSession:
/Volumes/Moose_3.0.2/lib/python2.7/site-packages/matplotlib/backends/backend_qt5agg.py:210: MatplotlibDeprecationWarning: This class has been deprecated in 1.4 as it has no additional functionality over `NavigationToolbar2QT`.  Please change your code to use `NavigationToolbar2QT` instead
  mplDeprecation)
QPixmap::scaled: Pixmap is a null pixmap
/Volumes/Moose_3.0.2/lib/python2.7/site-packages/matplotlib/axes/_axes.py:475: UserWarning: No labelled objects found. Use label='...' kwarg on individual plots.
  warnings.warn("No labelled objects found. "
QPixmap::scaled: Pixmap is a null pixmap
QPixmap::scaled: Pixmap is a null pixmap
QPixmap::scaled: Pixmap is a null pixmap
QPixmap::scaled: Pixmap is a null pixmap

Missing `PlotView`

Either it has been removed/deprecated or some import is missing.

moose-gui/plugins/default.py

Line 137 in 44b53bc

self.plotView = PlotView(self)

GUI crashes, can't save models

Current gui is crashing on Ubuntu-16.04. It also freezes when I try to save the model. I am getting the following in terminal.

nisha@nisha-LIFEBOOK-A555:~/Work/moose/moose-gui$ python mgui.py 
void DBusMenuExporterPrivate::addAction(QAction*, int): Already tracking action "Python" under id 24 
void DBusMenuExporterPrivate::addAction(QAction*, int): Already tracking action "Edit: /" under id 25 
void DBusMenuExporterPrivate::addAction(QAction*, int): Already tracking action "&Tabbed view" under id 27 
void DBusMenuExporterPrivate::addAction(QAction*, int): Already tracking action "&SubWindow view" under id 28 
void DBusMenuExporterPrivate::addAction(QAction*, int): Already tracking action "Ti&le subwindows" under id 29 
void DBusMenuExporterPrivate::addAction(QAction*, int): Already tracking action "&Cascade subwindows" under id 30 
void DBusMenuExporterPrivate::addAction(QAction*, int): Already tracking action "Python" under id 24 
void DBusMenuExporterPrivate::addAction(QAction*, int): Already tracking action "Edit: /" under id 25 
void DBusMenuExporterPrivate::addAction(QAction*, int): Already tracking action "&Tabbed view" under id 27 
void DBusMenuExporterPrivate::addAction(QAction*, int): Already tracking action "&SubWindow view" under id 28 
void DBusMenuExporterPrivate::addAction(QAction*, int): Already tracking action "Ti&le subwindows" under id 29 
void DBusMenuExporterPrivate::addAction(QAction*, int): Already tracking action "&Cascade subwindows" under id 30 
void DBusMenuExporterPrivate::addAction(QAction*, int): Already tracking action "Python" under id 24 
void DBusMenuExporterPrivate::addAction(QAction*, int): Already tracking action "Edit: /" under id 25 
void DBusMenuExporterPrivate::addAction(QAction*, int): Already tracking action "&Tabbed view" under id 27 
void DBusMenuExporterPrivate::addAction(QAction*, int): Already tracking action "&SubWindow view" under id 28 
void DBusMenuExporterPrivate::addAction(QAction*, int): Already tracking action "Ti&le subwindows" under id 29 
void DBusMenuExporterPrivate::addAction(QAction*, int): Already tracking action "&Cascade subwindows" under id 30 
void DBusMenuExporterPrivate::addAction(QAction*, int): Already tracking action "Python" under id 24 
void DBusMenuExporterPrivate::addAction(QAction*, int): Already tracking action "Edit: /" under id 25 
void DBusMenuExporterPrivate::addAction(QAction*, int): Already tracking action "&Tabbed view" under id 27 
void DBusMenuExporterPrivate::addAction(QAction*, int): Already tracking action "&SubWindow view" under id 28 
void DBusMenuExporterPrivate::addAction(QAction*, int): Already tracking action "Ti&le subwindows" under id 29 
void DBusMenuExporterPrivate::addAction(QAction*, int): Already tracking action "&Cascade subwindows" under id 30 
/usr/lib/python2.7/dist-packages/matplotlib/axes/_axes.py:519: UserWarning: No labelled objects found. Use label='...' kwarg on individual plots.
  warnings.warn("No labelled objects found. "
void DBusMenuExporterPrivate::addAction(QAction*, int): Already tracking action "Python" under id 24 
void DBusMenuExporterPrivate::addAction(QAction*, int): Already tracking action "Edit: /" under id 25 
void DBusMenuExporterPrivate::addAction(QAction*, int): Already tracking action "&Tabbed view" under id 27 
void DBusMenuExporterPrivate::addAction(QAction*, int): Already tracking action "&SubWindow view" under id 28 
void DBusMenuExporterPrivate::addAction(QAction*, int): Already tracking action "Ti&le subwindows" under id 29 
void DBusMenuExporterPrivate::addAction(QAction*, int): Already tracking action "&Cascade subwindows" under id 30 
void DBusMenuExporterPrivate::addAction(QAction*, int): Already tracking action "Python" under id 24 
void DBusMenuExporterPrivate::addAction(QAction*, int): Already tracking action "Edit: /" under id 25 
void DBusMenuExporterPrivate::addAction(QAction*, int): Already tracking action "&Tabbed view" under id 27 
void DBusMenuExporterPrivate::addAction(QAction*, int): Already tracking action "&SubWindow view" under id 28 
void DBusMenuExporterPrivate::addAction(QAction*, int): Already tracking action "Ti&le subwindows" under id 29 
void DBusMenuExporterPrivate::addAction(QAction*, int): Already tracking action "&Cascade subwindows" under id 30 
void DBusMenuExporterPrivate::addAction(QAction*, int): Already tracking action "Python" under id 24 
void DBusMenuExporterPrivate::addAction(QAction*, int): Already tracking action "Edit: /" under id 25 
void DBusMenuExporterPrivate::addAction(QAction*, int): Already tracking action "&Tabbed view" under id 27 
void DBusMenuExporterPrivate::addAction(QAction*, int): Already tracking action "&SubWindow view" under id 28 
void DBusMenuExporterPrivate::addAction(QAction*, int): Already tracking action "Ti&le subwindows" under id 29 
void DBusMenuExporterPrivate::addAction(QAction*, int): Already tracking action "&Cascade subwindows" under id 30 
void DBusMenuExporterPrivate::addAction(QAction*, int): Already tracking action "Python" under id 24 
void DBusMenuExporterPrivate::addAction(QAction*, int): Already tracking action "Edit: /" under id 25 
void DBusMenuExporterPrivate::addAction(QAction*, int): Already tracking action "&Tabbed view" under id 27 
void DBusMenuExporterPrivate::addAction(QAction*, int): Already tracking action "&SubWindow view" under id 28 
void DBusMenuExporterPrivate::addAction(QAction*, int): Already tracking action "Ti&le subwindows" under id 29 
void DBusMenuExporterPrivate::addAction(QAction*, int): Already tracking action "&Cascade subwindows" under id 30 
uint DBusMenuExporterDBus::GetLayout(int, int, const QStringList&, DBusMenuLayoutItem&): Condition failed: menu 
uint DBusMenuExporterDBus::GetLayout(int, int, const QStringList&, DBusMenuLayoutItem&): Condition failed: menu 
uint DBusMenuExporterDBus::GetLayout(int, int, const QStringList&, DBusMenuLayoutItem&): Condition failed: menu 
uint DBusMenuExporterDBus::GetLayout(int, int, const QStringList&, DBusMenuLayoutItem&): Condition failed: menu 
uint DBusMenuExporterDBus::GetLayout(int, int, const QStringList&, DBusMenuLayoutItem&): Condition failed: menu 
uint DBusMenuExporterDBus::GetLayout(int, int, const QStringList&, DBusMenuLayoutItem&): Condition failed: menu 
uint DBusMenuExporterDBus::GetLayout(int, int, const QStringList&, DBusMenuLayoutItem&): Condition failed: menu 
uint DBusMenuExporterDBus::GetLayout(int, int, const QStringList&, DBusMenuLayoutItem&): Condition failed: menu 
uint DBusMenuExporterDBus::GetLayout(int, int, const QStringList&, DBusMenuLayoutItem&): Condition failed: menu 
uint DBusMenuExporterDBus::GetLayout(int, int, const QStringList&, DBusMenuLayoutItem&): Condition failed: menu 
uint DBusMenuExporterDBus::GetLayout(int, int, const QStringList&, DBusMenuLayoutItem&): Condition failed: menu 
QGraphicsView::dragLeaveEvent: drag leave received before drag enter
QGraphicsView::dragLeaveEvent: drag leave received before drag enter
QGraphicsView::dragLeaveEvent: drag leave received before drag enter
QGraphicsView::dragLeaveEvent: drag leave received before drag enter
void DBusMenuExporterPrivate::addAction(QAction*, int): Already tracking action "Python" under id 24 
void DBusMenuExporterPrivate::addAction(QAction*, int): Already tracking action "Edit: /" under id 25 
void DBusMenuExporterPrivate::addAction(QAction*, int): Already tracking action "&Tabbed view" under id 27 
void DBusMenuExporterPrivate::addAction(QAction*, int): Already tracking action "&SubWindow view" under id 28 
void DBusMenuExporterPrivate::addAction(QAction*, int): Already tracking action "Ti&le subwindows" under id 29 
void DBusMenuExporterPrivate::addAction(QAction*, int): Already tracking action "&Cascade subwindows" under id 30 
uint DBusMenuExporterDBus::GetLayout(int, int, const QStringList&, DBusMenuLayoutItem&): Condition failed: menu 
uint DBusMenuExporterDBus::GetLayout(int, int, const QStringList&, DBusMenuLayoutItem&): Condition failed: menu 
uint DBusMenuExporterDBus::GetLayout(int, int, const QStringList&, DBusMenuLayoutItem&): Condition failed: menu 
uint DBusMenuExporterDBus::GetLayout(int, int, const QStringList&, DBusMenuLayoutItem&): Condition failed: menu 
void DBusMenuExporterPrivate::addAction(QAction*, int): Already tracking action "Python" under id 24 
void DBusMenuExporterPrivate::addAction(QAction*, int): Already tracking action "Edit: /" under id 25 
void DBusMenuExporterPrivate::addAction(QAction*, int): Already tracking action "&Tabbed view" under id 27 
void DBusMenuExporterPrivate::addAction(QAction*, int): Already tracking action "&SubWindow view" under id 28 
void DBusMenuExporterPrivate::addAction(QAction*, int): Already tracking action "Ti&le subwindows" under id 29 
void DBusMenuExporterPrivate::addAction(QAction*, int): Already tracking action "&Cascade subwindows" under id 30 
uint DBusMenuExporterDBus::GetLayout(int, int, const QStringList&, DBusMenuLayoutItem&): Condition failed: menu 
uint DBusMenuExporterDBus::GetLayout(int, int, const QStringList&, DBusMenuLayoutItem&): Condition failed: menu 
uint DBusMenuExporterDBus::GetLayout(int, int, const QStringList&, DBusMenuLayoutItem&): Condition failed: menu 
void DBusMenuExporterPrivate::addAction(QAction*, int): Already tracking action "Python" under id 24 
void DBusMenuExporterPrivate::addAction(QAction*, int): Already tracking action "Edit: /" under id 25 
void DBusMenuExporterPrivate::addAction(QAction*, int): Already tracking action "&Tabbed view" under id 27 
void DBusMenuExporterPrivate::addAction(QAction*, int): Already tracking action "&SubWindow view" under id 28 
void DBusMenuExporterPrivate::addAction(QAction*, int): Already tracking action "Ti&le subwindows" under id 29 
void DBusMenuExporterPrivate::addAction(QAction*, int): Already tracking action "&Cascade subwindows" under id 30 
uint DBusMenuExporterDBus::GetLayout(int, int, const QStringList&, DBusMenuLayoutItem&): Condition failed: menu 
uint DBusMenuExporterDBus::GetLayout(int, int, const QStringList&, DBusMenuLayoutItem&): Condition failed: menu 
uint DBusMenuExporterDBus::GetLayout(int, int, const QStringList&, DBusMenuLayoutItem&): Condition failed: menu 
uint DBusMenuExporterDBus::GetLayout(int, int, const QStringList&, DBusMenuLayoutItem&): Condition failed: menu 
QGraphicsView::dragLeaveEvent: drag leave received before drag enter
void DBusMenuExporterPrivate::addAction(QAction*, int): Already tracking action "Python" under id 24 
void DBusMenuExporterPrivate::addAction(QAction*, int): Already tracking action "Edit: /" under id 25 
void DBusMenuExporterPrivate::addAction(QAction*, int): Already tracking action "&Tabbed view" under id 27 
void DBusMenuExporterPrivate::addAction(QAction*, int): Already tracking action "&SubWindow view" under id 28 
void DBusMenuExporterPrivate::addAction(QAction*, int): Already tracking action "Ti&le subwindows" under id 29 
void DBusMenuExporterPrivate::addAction(QAction*, int): Already tracking action "&Cascade subwindows" under id 30 
uint DBusMenuExporterDBus::GetLayout(int, int, const QStringList&, DBusMenuLayoutItem&): Condition failed: menu 
uint DBusMenuExporterDBus::GetLayout(int, int, const QStringList&, DBusMenuLayoutItem&): Condition failed: menu 
uint DBusMenuExporterDBus::GetLayout(int, int, const QStringList&, DBusMenuLayoutItem&): Condition failed: menu 
uint DBusMenuExporterDBus::GetLayout(int, int, const QStringList&, DBusMenuLayoutItem&): Condition failed: menu 
QGraphicsView::dragLeaveEvent: drag leave received before drag enter
void DBusMenuExporterPrivate::addAction(QAction*, int): Already tracking action "Python" under id 24 
void DBusMenuExporterPrivate::addAction(QAction*, int): Already tracking action "Edit: /eIF4E_MNK1[0]/model[0]/Compartment[0]/MNK1[0]/Enz[0]" under id 25 
void DBusMenuExporterPrivate::addAction(QAction*, int): Already tracking action "&Tabbed view" under id 27 
void DBusMenuExporterPrivate::addAction(QAction*, int): Already tracking action "&SubWindow view" under id 28 
void DBusMenuExporterPrivate::addAction(QAction*, int): Already tracking action "Ti&le subwindows" under id 29 
void DBusMenuExporterPrivate::addAction(QAction*, int): Already tracking action "&Cascade subwindows" under id 30 
uint DBusMenuExporterDBus::GetLayout(int, int, const QStringList&, DBusMenuLayoutItem&): Condition failed: menu 
uint DBusMenuExporterDBus::GetLayout(int, int, const QStringList&, DBusMenuLayoutItem&): Condition failed: menu 
uint DBusMenuExporterDBus::GetLayout(int, int, const QStringList&, DBusMenuLayoutItem&): Condition failed: menu 
uint DBusMenuExporterDBus::GetLayout(int, int, const QStringList&, DBusMenuLayoutItem&): Condition failed: menu 
void DBusMenuExporterPrivate::addAction(QAction*, int): Already tracking action "Python" under id 24 
void DBusMenuExporterPrivate::addAction(QAction*, int): Already tracking action "Edit: /" under id 25 
void DBusMenuExporterPrivate::addAction(QAction*, int): Already tracking action "&Tabbed view" under id 27 
void DBusMenuExporterPrivate::addAction(QAction*, int): Already tracking action "&SubWindow view" under id 28 
void DBusMenuExporterPrivate::addAction(QAction*, int): Already tracking action "Ti&le subwindows" under id 29 
void DBusMenuExporterPrivate::addAction(QAction*, int): Already tracking action "&Cascade subwindows" under id 30 
uint DBusMenuExporterDBus::GetLayout(int, int, const QStringList&, DBusMenuLayoutItem&): Condition failed: menu 
uint DBusMenuExporterDBus::GetLayout(int, int, const QStringList&, DBusMenuLayoutItem&): Condition failed: menu 
uint DBusMenuExporterDBus::GetLayout(int, int, const QStringList&, DBusMenuLayoutItem&): Condition failed: menu 
uint DBusMenuExporterDBus::GetLayout(int, int, const QStringList&, DBusMenuLayoutItem&): Condition failed: menu 
void DBusMenuExporterPrivate::addAction(QAction*, int): Already tracking action "Python" under id 24 
void DBusMenuExporterPrivate::addAction(QAction*, int): Already tracking action "Edit: /" under id 25 
void DBusMenuExporterPrivate::addAction(QAction*, int): Already tracking action "&Tabbed view" under id 27 
void DBusMenuExporterPrivate::addAction(QAction*, int): Already tracking action "&SubWindow view" under id 28 
void DBusMenuExporterPrivate::addAction(QAction*, int): Already tracking action "Ti&le subwindows" under id 29 
void DBusMenuExporterPrivate::addAction(QAction*, int): Already tracking action "&Cascade subwindows" under id 30 
uint DBusMenuExporterDBus::GetLayout(int, int, const QStringList&, DBusMenuLayoutItem&): Condition failed: menu 
uint DBusMenuExporterDBus::GetLayout(int, int, const QStringList&, DBusMenuLayoutItem&): Condition failed: menu 
uint DBusMenuExporterDBus::GetLayout(int, int, const QStringList&, DBusMenuLayoutItem&): Condition failed: menu 
uint DBusMenuExporterDBus::GetLayout(int, int, const QStringList&, DBusMenuLayoutItem&): Condition failed: menu 
void DBusMenuExporterPrivate::addAction(QAction*, int): Already tracking action "Python" under id 24 
void DBusMenuExporterPrivate::addAction(QAction*, int): Already tracking action "Edit: /" under id 25 
void DBusMenuExporterPrivate::addAction(QAction*, int): Already tracking action "&Tabbed view" under id 27 
void DBusMenuExporterPrivate::addAction(QAction*, int): Already tracking action "&SubWindow view" under id 28 
void DBusMenuExporterPrivate::addAction(QAction*, int): Already tracking action "Ti&le subwindows" under id 29 
void DBusMenuExporterPrivate::addAction(QAction*, int): Already tracking action "&Cascade subwindows" under id 30 
uint DBusMenuExporterDBus::GetLayout(int, int, const QStringList&, DBusMenuLayoutItem&): Condition failed: menu 
uint DBusMenuExporterDBus::GetLayout(int, int, const QStringList&, DBusMenuLayoutItem&): Condition failed: menu 
uint DBusMenuExporterDBus::GetLayout(int, int, const QStringList&, DBusMenuLayoutItem&): Condition failed: menu 
uint DBusMenuExporterDBus::GetLayout(int, int, const QStringList&, DBusMenuLayoutItem&): Condition failed: menu

Missing paths on gui launch

These paths are redundant on Mac. The installation scheme is

/path/to/gui
/path/to/moose-examples

/Volumes/Moose_3.0.2/bin/moosegui 
Could not access D/Volumes/Moose_3.0.2/bin/moosegui 
Could not access Demos directory: /usr/share/doc/moose
[Errno 13] Cannot access /usr/share/doc/moose

Seg fault if ksolve is deleted before stoich

Seg fault if ksolve is removed before stoich

import moose
moose.loadModel('~/acc27.g','/acc27',"gsl")
compts = moose.wildcardFind('/acc27/##[ISA=ChemCompt]')
for compt in compts:
if moose.exists(compt.path+'/stoich'):
st = moose.element(compt.path+'/stoich')
st_ksolve = st.ksolve
moose.delete(st)
#print st_ksolve.path
if moose.exists((st_ksolve).path):
moose.delete(st_ksolve)
print " stoich is removed first and then ksolve, works fine\n"

print " If ksolve is removed first and then stoich then gives seg fault\n"

moose.loadModel('~/acc27.g','/acc27_1',"gsl")
compts = moose.wildcardFind('/acc27_1/##[ISA=ChemCompt]')
for compt in compts:
if moose.exists(compt.path+'/stoich'):
st = moose.element(compt.path+'/stoich')
#print " stoich ksolve ",st.ksolve.path
if moose.exists((st.ksolve).path):
moose.delete(st.ksolve)
moose.delete(st)

Error loading SBML model.

I was trying to load sbml model in moose-examples/genesis/00001-sbml-l3v1.xml. It failed with following error. This is from branch chamcham. If this work fine on master branch, it has to be merged with chamcham branch as well which is released.

Before launching I installed python-libsbml
$ pip install python-libsbml

AttributeError: 'NoneType' object has no attribute 'path'

Traceback (most recent call last):
  File "mgui.py", line 1130, in loadModelDialogSlot
    ret,pluginName = self.checkPlugin(dialog)
  File "mgui.py", line 1183, in checkPlugin
    print 'Loaded model', ret['model'].path
AttributeError: 'NoneType' object has no attribute 'path'

Same with the other XML files in this folder.

Installing gui using setup.py

It would be great if GUI can be installed as a python package using setup.py file. Currently we copy and paste the whole directory.

In packages, it is copied to <prefix>/share/moose/gui and a shell script moosegui is installed in /usr/bin to launch the gui.

Naming inconsistencies

There is an inconsistency in the object names when a model is converted from SBML to genesis. I notice a change in object names with special characters such as 'space', '-' has been removed and replaced with '_'. There is no warning when the changes are made.

The widget with demo list hides behind main window

moose-gui/mgui.py

Line 289 in e7786c7

 self.menuitems = OrderedDict([("Fig2C" , "../moose-examples/paper-2015/Fig2_elecModels/Fig2C.py"), 

To fix it: see https://dilawarnotes.wordpress.com/2019/06/13/how-to-make-pyqt-widget-stays-on-top/

Todo for Chamcham release

@hrani To keep the track of upcoming release:

SBML support. Either python-sbml or libSBML-5.9.0. OSX home-brew does not have support for libsbml-5.9.0.
Other fixes/todo in developer list. Expand this list.

Once this issue is closed, tag the branch with chamcham-3.1.0, I'll use the commit for packaging.

PyQt4 version on CentOS does not support moosegui

File "mgui.py", line 66, in <module>
    from objectedit import ObjectEditDockWidget
  File "/usr/lib/moose/gui/objectedit.py", line 70, in <module>
    from PyQt4.QtCore import QMargins
ImportError: cannot import name QMargins

Although the dependency PyQt4 is available on CentOS, it is not the correct version. The module QMargins is not available. Either a user warning can be emitted to install the correct version of PyQt4.

Python3 incompible lambda

In python3, lambda can not use print. More here https://stackoverflow.com/questions/2970858/why-doesnt-print-work-in-a-lambda

moose-gui/sidebar.py

Line 93 in a82842f

, callback = (lambda event: print("Delete Graph Clicked!"))

MacOSX: On startup, large logo windows hides the smaller option window with examples

On startup, The larger windows completely hides the smaller windows on MacOSX. Check if this is not the intended behaviour (after the DMG) file is uploaded.

Keyboard Shortcuts Widget

Put a little bar at the bottom of the edit window to indicate keyboard shortcuts.

migrated from sourceforge, Reported by: aviralg

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