This is a somewhat lengthy process - a progress dialog should be shown to inform the user of this and to prevent the UI from blocking.

Should provide an option again to update PyXRD automatically. Tricky bit would be to solve numpy and scipy updates as well...

Traceback:
Traceback (most recent call last):

  File "/usr/lib/python3/dist-packages/gi/overrides/Gtk.py", line 103, _builder_connect_callback(builder=<Gtk.Builder object at 0x7f0a8bd7dca8 (GtkBuilder at 0x5787570)>, gobj=<Gtk.TreeView object at 0x7f0a8bc62438 (GtkTreeView at 0x7249370)>, signal_name='focus-in-event', handler_name='on_focusin', connect_obj=None, flags=<flags 0 of type GObject.ConnectFlags>, obj_or_map={'_Controller__autoconnect_signals': <bound method Controller.__autoconnect_signals o...arker_controllers.MatchMineralController object>>, '_Observer__original_observe': <bound method good_decorator_accepting_args.<loc...lers.marker_controllers.MatchMineralController'>>, '_Observer__register_notification': <bound method Observer.__register_notification o...arker_controllers.MatchMineralController object>>, '__class__': <class 'pyxrd.specimen.controllers.marker_controllers.MatchMineralController'>, '__create_adapters__': <bound method Controller.__create_adapters__ of ...arker_controllers.MatchMineralController object>>, '__delattr__': <method-wrapper '__delattr__' of MatchMineralController object>, '__dir__': <built-in method __dir__ of MatchMineralController object>, '__eq__': <method-wrapper '__eq__' of MatchMineralController object>, '__format__': <built-in method __format__ of MatchMineralController object>, '__ge__': <method-wrapper '__ge__' of MatchMineralController object>, ...})
    def _builder_connect_callback(builder, gobj, signal_name, handler_name, connect_obj, flags, obj_or_map):
        handler, args = _extract_handler_and_args(obj_or_map, handler_name)
  variables: {'handler': (None, []), '_extract_handler_and_args': ('global', <function _extract_handler_and_args at 0x7f0abf212950>), 'obj_or_map': ('local', {'on_keypress': <bound method DialogController.on_keypress of <pyxrd.specimen.controllers.marker_controllers.MatchMineralController object at 0x7f0a8bd8b7b8>>, '_Observer__register_notification': <bound method Observer.__register_notification of <pyxrd.specimen.controllers.marker_controllers.MatchMineralController object at 0x7f0a8bd8b7b8>>, '__subclasshook__': <built-in method __subclasshook__ of type object at 0x3b94fb8>, 'get_observing_method_kwargs': <bound method Observer.get_observing_method_kwargs of <pyxrd.specimen.controllers.marker_controllers.MatchMineralController object at 0x7f0a8bd8b7b8>>, '__gt__': <method-wrapper '__gt__' of MatchMineralController object at 0x7f0a8bd8b7b8>, 'pop_status_msg': <bound method StatusBarMixin.pop_status_msg of <pyxrd.specimen.controllers.marker_controllers.MatchMineralController object at 0x7f0a8bd8b7b8>>, '__setattr__': <method-wrapper '__setattr__' of MatchMineralController object at 0x7f0a8bd8b7b8>, '__le__': <method-wrapper '__le__' of MatchMineralController object at 0x7f0a8bd8b7b8>, 'register_adapters': <bound method MatchMineralController.register_adapters of <pyxrd.specimen.controllers.marker_controllers.MatchMineralController object at 0x7f0a8bd8b7b8>>, '__repr__': <method-wrapper '__repr__' of MatchMineralController object at 0x7f0a8bd8b7b8>, 'selection_changed': <bound method MatchMineralController.selection_changed of <pyxrd.specimen.controllers.marker_controllers.MatchMineralController object at 0x7f0a8bd8b7b8>>, 'reload_minerals': <bound method MatchMineralController.reload_minerals of <pyxrd.specimen.controllers.marker_controllers.MatchMineralController object at 0x7f0a8bd8b7b8>>, 'register_view': <bound method MatchMineralController.register_view of <pyxrd.specimen.controllers.marker_controllers.MatchMineralController object at 0x7f0a8bd8b7b8>>, 'observe': <function Observer.__init__.<locals>.__observe at 0x7f0a8bc63400>, '__reduce__': <built-in method __reduce__ of MatchMineralController object at 0x7f0a8bd8b7b8>, 'on_add_match_clicked': <bound method MatchMineralController.on_add_match_clicked of <pyxrd.specimen.controllers.marker_controllers.MatchMineralController object at 0x7f0a8bd8b7b8>>, 'get_custom_observing_methods': <bound method Observer.get_observing_methods of <pyxrd.specimen.controllers.marker_controllers.MatchMineralController object at 0x7f0a8bd8b7b8>>, 'observe_model': <bound method Observer.observe_model of <pyxrd.specimen.controllers.marker_controllers.MatchMineralController object at 0x7f0a8bd8b7b8>>, 'close_callback': <function MarkersController.on_match_minerals_clicked.<locals>.close_cb at 0x7f0a8bc63488>, '_del_view': <bound method Controller._del_view of <pyxrd.specimen.controllers.marker_controllers.MatchMineralController object at 0x7f0a8bd8b7b8>>, '_Observer__original_observe': <bound method good_decorator_accepting_args.<locals>.new_decorator of <class 'pyxrd.specimen.controllers.marker_controllers.MatchMineralController'>>, '__lt__': <method-wrapper '__lt__' of MatchMineralController object at 0x7f0a8bd8b7b8>, '__format__': <built-in method __format__ of MatchMineralController object at 0x7f0a8bd8b7b8>, '_del_model': <bound method Controller._del_model of <pyxrd.specimen.controllers.marker_controllers.MatchMineralController object at 0x7f0a8bd8b7b8>>, 'relieve_model': <bound method Observer.relieve_model of <pyxrd.specimen.controllers.marker_controllers.MatchMineralController object at 0x7f0a8bd8b7b8>>, 'remove_observing_method': <bound method Observer.remove_observing_method of <pyxrd.specimen.controllers.marker_controllers.MatchMineralController object at 0x7f0a8bd8b7b8>>, '_find_widget_match': <bound method Controller._find_widget_match of <pyxrd.specimen.controllers.marker_controllers.MatchMineralController object at 0x7f0a8bd8b7b8>>, '__ge__': <method-wrapper '__ge__' of MatchMineralController object at 0x7f0a8bd8b7b8>, 'is_observing_method': <bound method Observer.is_observing_method of <pyxrd.specimen.controllers.marker_controllers.MatchMineralController object at 0x7f0a8bd8b7b8>>, '_idle_register_view': <bound method Controller._idle_register_view of <pyxrd.specimen.controllers.marker_controllers.MatchMineralController object at 0x7f0a8bd8b7b8>>, '__init__': <bound method MatchMineralController.__init__ of <pyxrd.specimen.controllers.marker_controllers.MatchMineralController object at 0x7f0a8bd8b7b8>>, '_set_view': <bound method Controller._set_view of <pyxrd.specimen.controllers.marker_controllers.MatchMineralController object at 0x7f0a8bd8b7b8>>, '__eq__': <method-wrapper '__eq__' of MatchMineralController object at 0x7f0a8bd8b7b8>, '_set_model': <bound method Controller._set_model of <pyxrd.specimen.controllers.marker_controllers.MatchMineralController object at 0x7f0a8bd8b7b8>>, '_get_handler_list': <bound method Controller._get_handler_list of <pyxrd.specimen.controllers.marker_controllers.MatchMineralController object at 0x7f0a8bd8b7b8>>, 'adapt': <bound method Controller.adapt of <pyxrd.specimen.controllers.marker_controllers.MatchMineralController object at 0x7f0a8bd8b7b8>>, 'notif_parameter_changed': <bound method MatchMineralController.notif_parameter_changed of <pyxrd.specimen.controllers.marker_controllers.MatchMineralController object at 0x7f0a8bd8b7b8>>, '__weakref__': <weakref at 0x7f0a8bc5cdb8; to 'MatchMineralController' at 0x7f0a8bd8b7b8>, '__getattribute__': <method-wrapper '__getattribute__' of MatchMineralController object at 0x7f0a8bd8b7b8>, '__delattr__': <method-wrapper '__delattr__' of MatchMineralController object at 0x7f0a8bd8b7b8>, 'on_window_edit_dialog_delete_event': <bound method DialogController.on_window_edit_dialog_delete_event of <pyxrd.specimen.controllers.marker_controllers.MatchMineralController object at 0x7f0a8bd8b7b8>>, 'status_message': <function StatusBarMixin.status_message at 0x7f0a91003378>, 'accepts_spurious_change': <bound method Observer.accepts_spurious_change of <pyxrd.specimen.controllers.marker_controllers.MatchMineralController object at 0x7f0a8bd8b7b8>>, '_get_view': <bound method Controller._get_view of <pyxrd.specimen.controllers.marker_controllers.MatchMineralController object at 0x7f0a8bd8b7b8>>, '__create_adapters__': <bound method Controller.__create_adapters__ of <pyxrd.specimen.controllers.marker_controllers.MatchMineralController object at 0x7f0a8bd8b7b8>>, 'on_del_match_clicked': <bound method MatchMineralController.on_del_match_clicked of <pyxrd.specimen.controllers.marker_controllers.MatchMineralController object at 0x7f0a8bd8b7b8>>, 'apply_callback': <function MarkersController.on_match_minerals_clicked.<locals>.apply_cb at 0x7f0a8bc63598>, 'get_observing_methods': <bound method Observer.get_observing_methods of <pyxrd.specimen.controllers.marker_controllers.MatchMineralController object at 0x7f0a8bd8b7b8>>, '__reduce_ex__': <built-in method __reduce_ex__ of MatchMineralController object at 0x7f0a8bd8b7b8>, 'reload_matches': <bound method MatchMineralController.reload_matches of <pyxrd.specimen.controllers.marker_controllers.MatchMineralController object at 0x7f0a8bd8b7b8>>, '_Controller__autoconnect_signals': <bound method Controller.__autoconnect_signals of <pyxrd.specimen.controllers.marker_controllers.MatchMineralController object at 0x7f0a8bd8b7b8>>, '__dir__': <built-in method __dir__ of MatchMineralController object at 0x7f0a8bd8b7b8>, '__class__': <class 'pyxrd.specimen.controllers.marker_controllers.MatchMineralController'>, 'on_auto_match_clicked': <bound method MatchMineralController.on_auto_match_clicked of <pyxrd.specimen.controllers.marker_controllers.MatchMineralController object at 0x7f0a8bd8b7b8>>, 'on_cancel': <bound method MatchMineralController.on_cancel of <pyxrd.specimen.controllers.marker_controllers.MatchMineralController object at 0x7f0a8bd8b7b8>>, 'on_btn_ok_clicked': <bound method DialogController.on_btn_ok_clicked of <pyxrd.specimen.controllers.marker_controllers.MatchMineralController object at 0x7f0a8bd8b7b8>>, '__sizeof__': <built-in method __sizeof__ of MatchMineralController object at 0x7f0a8bd8b7b8>, '__str__': <method-wrapper '__str__' of MatchMineralController object at 0x7f0a8bd8b7b8>, '_get_model': <bound method Controller._get_model of <pyxrd.specimen.controllers.marker_controllers.MatchMineralController object at 0x7f0a8bd8b7b8>>, 'on_apply_clicked': <bound method MatchMineralController.on_apply_clicked of <pyxrd.specimen.controllers.marker_controllers.MatchMineralController object at 0x7f0a8bd8b7b8>>, '__hash__': <method-wrapper '__hash__' of MatchMineralController object at 0x7f0a8bd8b7b8>, '_clear_adapters': <bound method Controller._clear_adapters of <pyxrd.specimen.controllers.marker_controllers.MatchMineralController object at 0x7f0a8bd8b7b8>>, '__new__': <built-in method __new__ of type object at 0xa3ec60>, 'push_status_msg': <bound method StatusBarMixin.push_status_msg of <pyxrd.specimen.controllers.marker_controllers.MatchMineralController object at 0x7f0a8bd8b7b8>>, '__ne__': <method-wrapper '__ne__' of MatchMineralController object at 0x7f0a8bd8b7b8>}), 'handler_name': ('local', 'on_focusin'), 'args': (None, [])}
  File "/usr/lib/python3/dist-packages/gi/overrides/Gtk.py", line 83, _extract_handler_and_args(obj_or_map={'_Controller__autoconnect_signals': <bound method Controller.__autoconnect_signals o...arker_controllers.MatchMineralController object>>, '_Observer__original_observe': <bound method good_decorator_accepting_args.<loc...lers.marker_controllers.MatchMineralController'>>, '_Observer__register_notification': <bound method Observer.__register_notification o...arker_controllers.MatchMineralController object>>, '__class__': <class 'pyxrd.specimen.controllers.marker_controllers.MatchMineralController'>, '__create_adapters__': <bound method Controller.__create_adapters__ of ...arker_controllers.MatchMineralController object>>, '__delattr__': <method-wrapper '__delattr__' of MatchMineralController object>, '__dir__': <built-in method __dir__ of MatchMineralController object>, '__eq__': <method-wrapper '__eq__' of MatchMineralController object>, '__format__': <built-in method __format__ of MatchMineralController object>, '__ge__': <method-wrapper '__ge__' of MatchMineralController object>, ...}, handler_name='on_focusin')
        if handler is None:
            raise AttributeError('Handler %s not found' % handler_name)
  variables: {'AttributeError': ('builtin', <class 'AttributeError'>), 'handler_name': ('local', 'on_focusin')}
AttributeError: Handler on_focusin not found

Click catcher broke due to the changes in the MainPlotController

When colour is inherited from the 'based on' phase, it is not changed accordingly.

Module works fine in recent Linux (Debian derivatives) distros. Matplotlib must be <=3.2.0!

Dear Mathijs,
when generating phases the program (Linux version) crashes saying a programming error was detected.
Here I copied the error message.
Thanks a lot

Traceback (most recent call last):
File "/home/labcrescita/.local/lib/python3.8/site-packages/mvc/controller.py", line 157, _idle_register_view(self=<pyxrd.phases.controllers.CSDS_controllers.EditCSDSDistributionController object>, view=<pyxrd.phases.views.EditCSDSDistributionView object>)
self.register_view(self.view)
self.register_adapters()
variables: {'self.register_view': ('local', <bound method EditCSDSDistributionController.register_view of <pyxrd.phases.controllers.CSDS_controllers.EditCSDSDistributionController object at 0x7f36f7309cd0>>), 'self.view': ('local', <pyxrd.phases.views.EditCSDSDistributionView object at 0x7f3721f5c490>)}
File "/home/labcrescita/.local/lib/python3.8/site-packages/pyxrd/phases/controllers/CSDS_controllers.py", line 107, register_view(self=<pyxrd.phases.controllers.CSDS_controllers.EditCSDSDistributionController object>, view=<pyxrd.phases.views.EditCSDSDistributionView object>)
if self.model is not None:
self.reset_view()
variables: {'self.reset_view': ('local', <bound method EditCSDSDistributionController.reset_view of <pyxrd.phases.controllers.CSDS_controllers.EditCSDSDistributionController object at 0x7f36f7309cd0>>)}
File "/home/labcrescita/.local/lib/python3.8/site-packages/pyxrd/phases/controllers/CSDS_controllers.py", line 101, reset_view(self=<pyxrd.phases.controllers.CSDS_controllers.EditCSDSDistributionController object>)
)
self.view.update_figure(self.model.distrib[0])
self.register_adapters()
variables: {'self.view.update_figure': ('local', <bound method EditCSDSDistributionView.update_figure of <pyxrd.phases.views.EditCSDSDistributionView object at 0x7f3721f5c490>>), 'self.model.distrib': ('local', (array([0.00000000e+00, 4.22798362e-05, 4.14794680e-03, 2.40761188e-02,
5.54406161e-02, 8.35815096e-02, 1.00271239e-01, 1.05026084e-01,
1.00952692e-01, 9.16846847e-02, 8.01134260e-02, 6.81509294e-02,
5.68933190e-02, 4.68688067e-02, 3.82521482e-02, 3.10186349e-02,
2.50439457e-02, 2.01642327e-02, 1.62097649e-02, 1.30221002e-02,
1.04615344e-02, 8.40912194e-03, 6.76588131e-03, 5.45070933e-03,
4.39785745e-03, 3.55441673e-03]), 9.670586370099196))}
File "/home/labcrescita/.local/lib/python3.8/site-packages/pyxrd/phases/views.py", line 179, update_figure(self=<pyxrd.phases.views.EditCSDSDistributionView object>, distr=array([0.00000000e+00, 4.22798362e-05, 4.1479468...0933e-03,
4.39785745e-03, 3.55441673e-03]))
self.plot.cla()
self.plot.hist(list(range(len(distr))), len(distr), weights=distr, normed=1, ec='b', histtype='stepfilled')
self.plot.set_ylabel('')
variables: {'self.plot.hist': ('local', <bound method Axes.hist of AxesSubplot:>), 'list': ('builtin', <class 'list'>), 'range': ('builtin', <class 'range'>), 'len': ('builtin', ), 'distr': ('local', array([0.00000000e+00, 4.22798362e-05, 4.14794680e-03, 2.40761188e-02,
5.54406161e-02, 8.35815096e-02, 1.00271239e-01, 1.05026084e-01,
1.00952692e-01, 9.16846847e-02, 8.01134260e-02, 6.81509294e-02,
5.68933190e-02, 4.68688067e-02, 3.82521482e-02, 3.10186349e-02,
2.50439457e-02, 2.01642327e-02, 1.62097649e-02, 1.30221002e-02,
1.04615344e-02, 8.40912194e-03, 6.76588131e-03, 5.45070933e-03,
4.39785745e-03, 3.55441673e-03])), 'weights': (None, []), 'normed': (None, []), 'ec': (None, []), 'histtype': (None, [])}
File "/home/labcrescita/.local/lib/python3.8/site-packages/matplotlib/init.py", line 1361, inner(ax=AxesSubplot:, data=None, *args=([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, ...], 26), **kwargs={'ec': 'b', 'histtype': 'stepfilled', 'normed': 1, 'weights': array([0.00000000e+00, 4.22798362e-05, 4.1479468...0933e-03,
4.39785745e-03, 3.55441673e-03])})
if data is None:
return func(ax, *map(sanitize_sequence, args), **kwargs)
variables: {'func': ('local', <function Axes.hist at 0x7f3729a004c0>), 'ax': ('local', AxesSubplot:), 'map': ('builtin', <class 'map'>), 'sanitize_sequence': ('global', <function sanitize_sequence at 0x7f3751b5b790>), 'args': ('local', ([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25], 26)), 'kwargs': ('local', {'weights': array([0.00000000e+00, 4.22798362e-05, 4.14794680e-03, 2.40761188e-02,
5.54406161e-02, 8.35815096e-02, 1.00271239e-01, 1.05026084e-01,
1.00952692e-01, 9.16846847e-02, 8.01134260e-02, 6.81509294e-02,
5.68933190e-02, 4.68688067e-02, 3.82521482e-02, 3.10186349e-02,
2.50439457e-02, 2.01642327e-02, 1.62097649e-02, 1.30221002e-02,
1.04615344e-02, 8.40912194e-03, 6.76588131e-03, 5.45070933e-03,
4.39785745e-03, 3.55441673e-03]), 'normed': 1, 'ec': 'b', 'histtype': 'stepfilled'})}
File "/home/labcrescita/.local/lib/python3.8/site-packages/matplotlib/axes/_axes.py", line 6911, hist(self=AxesSubplot:, x=array([ 0. , 0. , 0.96153846, 0...92307692, 0.96153846, 0.96153846, 0. ]), bins=array([ 0. , 0.96153846, 1.92307692, 2...2, 23.07692308,
24.03846154, 25. ]), range=<class 'range'>, density=False, weights=array([0.00000000e+00, 4.22798362e-05, 4.1479468...0933e-03,
4.39785745e-03, 3.55441673e-03]), cumulative=False, bottom=0, histtype='stepfilled', align='mid', orientation='vertical', rwidth=None, log=False, color=['#1f77b4'], label=None, stacked=False, **kwargs={'ec': 'b', 'normed': 1})
p = patch[0]
p.update(kwargs)
if lbl is not None:
variables: {'p.update': ('local', <bound method Artist.update of <matplotlib.patches.Polygon object at 0x7f3726d67820>>), 'kwargs': ('local', {'normed': 1, 'ec': 'b'})}
File "/home/labcrescita/.local/lib/python3.8/site-packages/matplotlib/artist.py", line 1062, update(self=<matplotlib.patches.Polygon object>, props={'ec': 'b', 'normed': 1})
if not callable(func):
raise AttributeError(f"{type(self).name!r} object "
f"has no property {k!r}")
variables: {'AttributeError': ('builtin', <class 'AttributeError'>)}
AttributeError: 'Polygon' object has no property 'normed'

Annoying when saving multiple plots.

New bug on UBUNTU

Traceback (most recent call last):
File "/home/labcrescita/.local/lib/python3.9/site-packages/pyxrd/refinement/controllers/refinement_controller.py", line 59, get_pb(column=<treeview_tools.PyXRDTreeViewColumn object at 0x...treeview_tools+PyXRDTreeViewColumn at 0xa8d71a0)>, cell=<Gtk.CellRendererPixbuf object at 0x7fdbb7abecc0 (GtkCellRendererPixbuf at 0xa4ef590)>, model=<object_tree_store.ObjectTreeStore object at 0x7...+object_tree_store+ObjectTreeStore at 0xa8b8120)>, itr=<Gtk.TreeIter object at 0x7fdbb7e1ae20 (GtkTreeIter at 0xa8b8b00)>, user_data=())
if not hasattr(ref_prop, "pb") or not ref_prop.pb:
ref_prop.pb = create_pb_from_mathtext(
ref_prop.title,
File "/home/labcrescita/.local/lib/python3.9/site-packages/pyxrd/generic/mathtext_support.py", line 44, create_pb_from_mathtext(text='Chlorite', align='left', weight='medium', color='b', style='normal')
parts, fontsize = _handle_customs(text)
variables: {'parts': (None, []), 'fontsize': (None, []), '_handle_customs': ('global', <function _handle_customs at 0x7fdbe91a54c0>), 'text': ('local', 'Chlorite')}
File "/home/labcrescita/.local/lib/python3.9/site-packages/pyxrd/generic/mathtext_support.py", line 113, _handle_customs(text='Chlorite')
def _handle_customs(text):
text = text.decode('utf-8')
variables: {'text': ('local', 'Chlorite')}
AttributeError: 'str' object has no attribute 'decode'

Dear Mathijs,
I tried to install PyXRD but I encountered some errors reported in this mail as you suggest. Unfortunately, I’m not expert of python and I’m not able to resolve them also if they, probably, are very simple problems to fix.
Thank for your help
Best whishes
Paolo

C:\Users\pmazz_j36fco8>"C:\Program Files (x86)\PyXRD\bin\python3.exe" -m pyxrd
C:\Program Files (x86)\PyXRD\lib\python3.8\site-packages\pyxrd\generic\outdated_init_.py:103: OutdatedPackageWarning: The package outdated is out of date. Your version is 0.1.2, the latest is 0.2.1.
warn('The package %s is out of date. Your version is %s, the latest is %s.'
pyxrd.generic.asynchronous.providers - INFO: Loading async server provider
pyxrd.generic.asynchronous.providers - INFO: Trying to load async server provider at pyxrd.server.provider.Pyro4AsyncServerProvider
pyxrd.generic.asynchronous.providers - INFO: Loaded async server provider '<class 'pyxrd.server.provider.Pyro4AsyncServerProvider'>'
root - INFO: Pyro4 PyXRD server not (yet) running!
root - INFO: Starting server using script: 'C:\Program Files (x86)\PyXRD\lib\python3.8\site-packages\pyxrd\server\run_server.py', logging to 'C:\Users\pmazz_j36fco8\AppData\Local\PyXRD\PyXRD\Logs\server.log'
root - INFO: Pyro4 PyXRD server not (yet) running!
root - INFO: Pyro4 PyXRD server not (yet) running!
root - INFO: Pyro4 PyXRD server not (yet) running!

Currently default is 3° which is too low. 12 would be more realistic.

add monochromator polarization factor into the goniometer settings

Can't get the parameter names to show up in the refinement dialogue (running on win10)

To be investigated - probably files are missing from the installer

When creating a NEW AtomRatio, the first atom can be set without a problem, second atom raises this error:

Traceback (most recent call last):
File "/media/mathijs/LacieDocs/Projects/PyXRD/pyxrd/phases/controllers/atom_relation_controllers.py", line 76, in on_changed
setattr(self.model, combo.get_data('model_prop'), val)
NameError: free variable 'self' referenced before assignment in enclosing scope

After this error is raised, the dialog will no longer respond and cannot be closed. However, when creating the AtomRatio, changing its name and then setting the atoms does not raise the error. The dialog can then still not be closed.
Probably a reference issue (the main program losing reference to the controller or the view causing Gtk-Python to fail or something like that...)

Currently (v0.6.9) when running a refinement in windows, there will be a considerable memory leak. This is most notable when using the evolutionary algorithms. This problem does not occur on Linux. I have a gut feeling this might be due to some PyGTK issue, maybe this one https://bugzilla.gnome.org/show_bug.cgi?id=685959

matplotlib 2.0 changed some the way artists are rendered, need to verify our current implementation does not try to solve a non-existent problem.

New bug on UBUNTU

Traceback (most recent call last):
File "/home/labcrescita/.local/lib/python3.9/site-packages/mvc/controller.py", line 157, _idle_register_view(self=<pyxrd.phases.controllers.CSDS_controllers.EditCSDSDistributionController object>, view=<pyxrd.phases.views.EditCSDSDistributionView object>)
self.register_view(self.view)
self.register_adapters()
variables: {'self.register_view': ('local', <bound method EditCSDSDistributionController.register_view of <pyxrd.phases.controllers.CSDS_controllers.EditCSDSDistributionController object at 0x7fdc1ae951c0>>), 'self.view': ('local', <pyxrd.phases.views.EditCSDSDistributionView object at 0x7fdc1ac8ea60>)}
File "/home/labcrescita/.local/lib/python3.9/site-packages/pyxrd/phases/controllers/CSDS_controllers.py", line 107, register_view(self=<pyxrd.phases.controllers.CSDS_controllers.EditCSDSDistributionController object>, view=<pyxrd.phases.views.EditCSDSDistributionView object>)
if self.model is not None:
self.reset_view()
variables: {'self.reset_view': ('local', <bound method EditCSDSDistributionController.reset_view of <pyxrd.phases.controllers.CSDS_controllers.EditCSDSDistributionController object at 0x7fdc1ae951c0>>)}
File "/home/labcrescita/.local/lib/python3.9/site-packages/pyxrd/phases/controllers/CSDS_controllers.py", line 101, reset_view(self=<pyxrd.phases.controllers.CSDS_controllers.EditCSDSDistributionController object>)
)
self.view.update_figure(self.model.distrib[0])
self.register_adapters()
variables: {'self.view.update_figure': ('local', <bound method EditCSDSDistributionView.update_figure of <pyxrd.phases.views.EditCSDSDistributionView object at 0x7fdc1ac8ea60>>), 'self.model.distrib': ('local', (array([0.00000000e+00, 4.22798362e-05, 4.14794680e-03, 2.40761188e-02,
5.54406161e-02, 8.35815096e-02, 1.00271239e-01, 1.05026084e-01,
1.00952692e-01, 9.16846847e-02, 8.01134260e-02, 6.81509294e-02,
5.68933190e-02, 4.68688067e-02, 3.82521482e-02, 3.10186349e-02,
2.50439457e-02, 2.01642327e-02, 1.62097649e-02, 1.30221002e-02,
1.04615344e-02, 8.40912194e-03, 6.76588131e-03, 5.45070933e-03,
4.39785745e-03, 3.55441673e-03]), 9.670586370099196))}
File "/home/labcrescita/.local/lib/python3.9/site-packages/pyxrd/phases/views.py", line 179, update_figure(self=<pyxrd.phases.views.EditCSDSDistributionView object>, distr=array([0.00000000e+00, 4.22798362e-05, 4.1479468...0933e-03,
4.39785745e-03, 3.55441673e-03]))
self.plot.cla()
self.plot.hist(list(range(len(distr))), len(distr), weights=distr, normed=1, ec='b', histtype='stepfilled')
self.plot.set_ylabel('')
variables: {'self.plot.hist': ('local', <bound method Axes.hist of AxesSubplot:>), 'list': ('builtin', <class 'list'>), 'range': ('builtin', <class 'range'>), 'len': ('builtin', ), 'distr': ('local', array([0.00000000e+00, 4.22798362e-05, 4.14794680e-03, 2.40761188e-02,
5.54406161e-02, 8.35815096e-02, 1.00271239e-01, 1.05026084e-01,
1.00952692e-01, 9.16846847e-02, 8.01134260e-02, 6.81509294e-02,
5.68933190e-02, 4.68688067e-02, 3.82521482e-02, 3.10186349e-02,
2.50439457e-02, 2.01642327e-02, 1.62097649e-02, 1.30221002e-02,
1.04615344e-02, 8.40912194e-03, 6.76588131e-03, 5.45070933e-03,
4.39785745e-03, 3.55441673e-03])), 'weights': (None, []), 'normed': (None, []), 'ec': (None, []), 'histtype': (None, [])}
File "/home/labcrescita/.local/lib/python3.9/site-packages/matplotlib/init.py", line 1361, inner(ax=AxesSubplot:, data=None, *args=([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, ...], 26), **kwargs={'ec': 'b', 'histtype': 'stepfilled', 'normed': 1, 'weights': array([0.00000000e+00, 4.22798362e-05, 4.1479468...0933e-03,
4.39785745e-03, 3.55441673e-03])})
if data is None:
return func(ax, *map(sanitize_sequence, args), **kwargs)
variables: {'func': ('local', <function Axes.hist at 0x7fdbe8855790>), 'ax': ('local', AxesSubplot:), 'map': ('builtin', <class 'map'>), 'sanitize_sequence': ('global', <function sanitize_sequence at 0x7fdc11b5f940>), 'args': ('local', ([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25], 26)), 'kwargs': ('local', {'weights': array([0.00000000e+00, 4.22798362e-05, 4.14794680e-03, 2.40761188e-02,
5.54406161e-02, 8.35815096e-02, 1.00271239e-01, 1.05026084e-01,
1.00952692e-01, 9.16846847e-02, 8.01134260e-02, 6.81509294e-02,
5.68933190e-02, 4.68688067e-02, 3.82521482e-02, 3.10186349e-02,
2.50439457e-02, 2.01642327e-02, 1.62097649e-02, 1.30221002e-02,
1.04615344e-02, 8.40912194e-03, 6.76588131e-03, 5.45070933e-03,
4.39785745e-03, 3.55441673e-03]), 'normed': 1, 'ec': 'b', 'histtype': 'stepfilled'})}
File "/home/labcrescita/.local/lib/python3.9/site-packages/matplotlib/axes/_axes.py", line 6911, hist(self=AxesSubplot:, x=array([ 0. , 0. , 0.96153846, 0...92307692, 0.96153846, 0.96153846, 0. ]), bins=array([ 0. , 0.96153846, 1.92307692, 2...2, 23.07692308,
24.03846154, 25. ]), range=<class 'range'>, density=False, weights=array([0.00000000e+00, 4.22798362e-05, 4.1479468...0933e-03,
4.39785745e-03, 3.55441673e-03]), cumulative=False, bottom=0, histtype='stepfilled', align='mid', orientation='vertical', rwidth=None, log=False, color=['#1f77b4'], label=None, stacked=False, **kwargs={'ec': 'b', 'normed': 1})
p = patch[0]
p.update(kwargs)
if lbl is not None:
variables: {'p.update': ('local', <bound method Artist.update of <matplotlib.patches.Polygon object at 0x7fdc1ae8fe50>>), 'kwargs': ('local', {'normed': 1, 'ec': 'b'})}
File "/home/labcrescita/.local/lib/python3.9/site-packages/matplotlib/artist.py", line 1062, update(self=<matplotlib.patches.Polygon object>, props={'ec': 'b', 'normed': 1})
if not callable(func):
raise AttributeError(f"{type(self).name!r} object "
f"has no property {k!r}")
variables: {'AttributeError': ('builtin', <class 'AttributeError'>)}
AttributeError: 'Polygon' object has no property 'normed'

Quoting the main README,

Mac OS X

Currently no support is given for iOS. If anyone is interested in getting this to work feel free to contact me.

Apple's iOS is their phone and tablet touchscreen operating system. I assuming that was a typo?

Apple have since rebranded Mac OS X as macOS, their desktop and laptop operating system.

I expect your tool to work there much like it works on Linux, providing the dependencies can be installed - but pygments and Gtk look like the first hurdles, cross reference conda-forge/pygobject-feedstock#20

Current release is version 0.8.2, https://github.com/PyXRD/PyXRD/blob/master/pyxrd/__version.py

Most prior releases have a git tag with a leading v, e.g. v0.7.5 which is listed first by GitHub.

The recent 0.8.1 and 0.8.2 releases were tagged without the leading v, and therefore sort to the end of the list on GitHub, leaving the current latest release second from bottom.

I suggest re-tagging them as v0.8.1 and v0.8.2 for consistency and to avoid confusion.

Add an indicator in the toolbar when hovering over the main plot showing the intensity values and d-spacing.

https://github.com/PyXRD/PyXRD/blob/master/pyxrd/generic/controllers/line_controllers.py

At dialog.filename for the BG controller.
Needs confirmation if still present.

Now individual traces are hidden when the full calculated trace is hidden. This should be changed so that these can be plotted individually

Need to review how we keep track of these changes and why the needs_saving flags gets triggered.