AddH not installable into ChimeraX 1.1 due to "py38" in wheel name

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Darwin-19.6.0-x86_64-i386-64bit
ChimeraX Version: 1.1 (2020-09-09 22:22:27 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.1 (2020-09-09)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  
Looking in indexes: https://pypi.org/simple,
https://cxtoolshed.rbvi.ucsf.edu/pypi/  
ERROR: Could not find a version that satisfies the requirement ChimeraX-
AddH==2.1.3  
ERROR: No matching distribution found for ChimeraX-AddH==2.1.3  
WARNING: You are using pip version 20.2.2; however, version 20.3.1 is
available.  
You should consider upgrading via the
'/Applications/ChimeraX-1.1.app/Contents/MacOS/ChimeraX -m pip install
--upgrade pip' command.  
  
Looking in indexes: https://pypi.org/simple,
https://cxtoolshed.rbvi.ucsf.edu/pypi/  
ERROR: Could not find a version that satisfies the requirement ChimeraX-
AddH==2.1.3  
ERROR: No matching distribution found for ChimeraX-AddH==2.1.3  
WARNING: You are using pip version 20.2.2; however, version 20.3.1 is
available.  
You should consider upgrading via the
'/Applications/ChimeraX-1.1.app/Contents/MacOS/ChimeraX -m pip install
--upgrade pip' command.  
  

> open 7k

'7k' has no suffix  

> open 7k5w

Summary of feedback from opening 7k5w fetched from pdb  
---  
note | Fetching compressed mmCIF 7k5w from
http://files.rcsb.org/download/7k5w.cif  
  
7k5w title:  
Cryo-EM structure of heterologous protein complex loaded Thermotoga maritima
encapsulin capsid [more info...]  
  
Chain information for 7k5w #1  
---  
Chain | Description  
A | Maritimacin  
  
7k5w mmCIF Assemblies  
---  
1| complete icosahedral assembly  
2| icosahedral asymmetric unit  
3| icosahedral pentamer  
4| icosahedral 23 hexamer  
5| icosahedral asymmetric unit, std point frame  
  

> close session

> open 4pt2

Summary of feedback from opening 4pt2 fetched from pdb  
---  
note | Fetching compressed mmCIF 4pt2 from
http://files.rcsb.org/download/4pt2.cif  
  
4pt2 title:  
Myxococcus xanthus encapsulin protein (EncA) [more info...]  
  
Chain information for 4pt2 #1  
---  
Chain | Description  
A B P | Encapsulin protein  
  
4pt2 mmCIF Assemblies  
---  
1| complete icosahedral assembly  
2| icosahedral asymmetric unit  
3| icosahedral pentamer  
4| icosahedral 23 hexamer  
5| icosahedral asymmetric unit, std point frame  
  

> close session

> open 3dkt

Summary of feedback from opening 3dkt fetched from pdb  
---  
note | Fetching compressed mmCIF 3dkt from
http://files.rcsb.org/download/3dkt.cif  
  
3dkt title:  
Crystal structure of Thermotoga maritima encapsulin [more info...]  
  
Chain information for 3dkt #1  
---  
Chain | Description  
A B C D E F G H I J | Maritimacin  
K L M N O P Q R S T | Putative uncharacterized protein  
  
3dkt mmCIF Assemblies  
---  
1| author_defined_assembly  
  

> hide atoms

> show cartoons

> color cyan

> select /K/L/M/N/O/P/Q/R/S/T

560 atoms, 550 bonds, 80 residues, 1 model selected  

> select sel @< 5

1507 atoms, 1290 bonds, 280 residues, 1 model selected  

> color sel red

> select /K/L/M/N/O/P/Q/R/S/T

560 atoms, 550 bonds, 80 residues, 1 model selected  

> color sel orange

> show sel surfaces

> hide sel surfaces

> select

22070 atoms, 22370 bonds, 2820 residues, 1 model selected  

> show sel surfaces

> transparency (#!1 & sel) 50

> hide sel surfaces

> select /K/L/M/N/O/P/Q/R/S/T

560 atoms, 550 bonds, 80 residues, 1 model selected  
Alignment identifier is 1  

> select sel @< 5

1507 atoms, 1290 bonds, 280 residues, 1 model selected  
Alignment identifier is 1  
Alignment identifier is 2  

> save "/Users/jessejones/Documents/ChimeraX/Sessions/T1 TP 5A Zone.cxs"

> close session

> open "/Users/jessejones/Documents/ChimeraX/Sessions/T4 TP 5A Zone.cxs"
> format session

Unable to restore session, resetting.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 683, in restore  
obj = sm.restore_snapshot(self, data)  
File
"/Applications/ChimeraX-1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/seq-view/tool.py", line 646, in restore_snapshot  
inst._finalize_init(data['alignment'])  
File
"/Applications/ChimeraX-1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/seq-view/tool.py", line 174, in _finalize_init  
self.seq_canvas = SeqCanvas(parent, self, self.alignment)  
File
"/Applications/ChimeraX-1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/seq-view/seq_canvas.py", line 186, in __init__  
self.layout_alignment()  
File
"/Applications/ChimeraX-1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/seq-view/seq_canvas.py", line 744, in layout_alignment  
self.label_width, self.font_pixels, self.numbering_widths, self.letter_gaps())  
File
"/Applications/ChimeraX-1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/seq-view/seq_canvas.py", line 1546, in __init__  
self.layout_lines(alignment.seqs, self.normal_label_color)  
File
"/Applications/ChimeraX-1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/seq-view/seq_canvas.py", line 2185, in layout_lines  
self._layout_line(line, label_color, bli, end)  
File
"/Applications/ChimeraX-1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/seq-view/seq_canvas.py", line 2135, in _layout_line  
font=self._label_font(line))  
File
"/Applications/ChimeraX-1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/seq-view/seq_canvas.py", line 2074, in _label_font  
if self.has_associated_structures(line):  
File
"/Applications/ChimeraX-1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/seq-view/seq_canvas.py", line 2018, in
has_associated_structures  
and [chain for chain in line.match_maps.keys() if not
chain.structure.deleted]:  
File
"/Applications/ChimeraX-1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/seq-view/seq_canvas.py", line 2018, in <listcomp>  
and [chain for chain in line.match_maps.keys() if not
chain.structure.deleted]:  
File
"/Applications/ChimeraX-1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 39, in _getattr_  
return look_in_class._attr_registration.get_attr(attr_name)  
File
"/Applications/ChimeraX-1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 69, in get_attr  
raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None  
AttributeError: 'Sequence' object has no attribute 'structure'  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 683, in restore  
obj = sm.restore_snapshot(self, data)  
File
"/Applications/ChimeraX-1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/seq-view/tool.py", line 646, in restore_snapshot  
inst._finalize_init(data['alignment'])  
File
"/Applications/ChimeraX-1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/seq-view/tool.py", line 174, in _finalize_init  
self.seq_canvas = SeqCanvas(parent, self, self.alignment)  
File
"/Applications/ChimeraX-1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/seq-view/seq_canvas.py", line 186, in __init__  
self.layout_alignment()  
File
"/Applications/ChimeraX-1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/seq-view/seq_canvas.py", line 744, in layout_alignment  
self.label_width, self.font_pixels, self.numbering_widths, self.letter_gaps())  
File
"/Applications/ChimeraX-1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/seq-view/seq_canvas.py", line 1546, in __init__  
self.layout_lines(alignment.seqs, self.normal_label_color)  
File
"/Applications/ChimeraX-1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/seq-view/seq_canvas.py", line 2185, in layout_lines  
self._layout_line(line, label_color, bli, end)  
File
"/Applications/ChimeraX-1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/seq-view/seq_canvas.py", line 2135, in _layout_line  
font=self._label_font(line))  
File
"/Applications/ChimeraX-1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/seq-view/seq_canvas.py", line 2074, in _label_font  
if self.has_associated_structures(line):  
File
"/Applications/ChimeraX-1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/seq-view/seq_canvas.py", line 2018, in
has_associated_structures  
and [chain for chain in line.match_maps.keys() if not
chain.structure.deleted]:  
File
"/Applications/ChimeraX-1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/seq-view/seq_canvas.py", line 2018, in <listcomp>  
and [chain for chain in line.match_maps.keys() if not
chain.structure.deleted]:  
File
"/Applications/ChimeraX-1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 39, in _getattr_  
return look_in_class._attr_registration.get_attr(attr_name)  
File
"/Applications/ChimeraX-1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 69, in get_attr  
raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None  
AttributeError: 'Sequence' object has no attribute 'structure'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/gui.py", line 629, in customEvent  
func(*args, **kw)  
File
"/Applications/ChimeraX-1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/widgets/htmlview.py", line 440, in defer  
cxcmd(session, topic)  
File
"/Applications/ChimeraX-1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/widgets/htmlview.py", line 456, in cxcmd  
run(session, cmd)  
File
"/Applications/ChimeraX-1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/run.py", line 31, in run  
results = command.run(text, log=log)  
File
"/Applications/ChimeraX-1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2805, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX-1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/open_command/cmd.py", line 100, in cmd_open  
return Command(session, registry=registry).run(provider_cmd_text, log=log)  
File
"/Applications/ChimeraX-1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2805, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX-1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/open_command/cmd.py", line 154, in provider_open  
name or model_name_from_path(fi.file_name)), provider_kw)  
File
"/Applications/ChimeraX-1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/open_command/cmd.py", line 390, in collated_open  
return func(*func_args, **func_kw)  
File
"/Applications/ChimeraX-1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core_formats/__init__.py", line 26, in open  
return cxs_open(session, data, **kw)  
File
"/Applications/ChimeraX-1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 925, in open  
session.restore(stream, path=path, resize_window=resize_window)  
File
"/Applications/ChimeraX-1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 691, in restore  
self.reset()  
File
"/Applications/ChimeraX-1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 502, in reset  
sm.reset_state(container, self)  
File
"/Applications/ChimeraX-1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/seqalign/manager.py", line 259, in reset_state  
alignment._destroy()  
File
"/Applications/ChimeraX-1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/seqalign/alignment.py", line 587, in _destroy  
self._notify_observers(self.NOTE_DESTROYED, None)  
File
"/Applications/ChimeraX-1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/seqalign/alignment.py", line 636, in _notify_observers  
recipient.alignment_notification(note_name, note_data)  
File
"/Applications/ChimeraX-1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/seq-view/tool.py", line 464, in alignment_notification  
self.delete()  
File
"/Applications/ChimeraX-1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/seq-view/tool.py", line 495, in delete  
self.region_browser.destroy()  
AttributeError: 'SequenceViewer' object has no attribute 'region_browser'  
  
AttributeError: 'SequenceViewer' object has no attribute 'region_browser'  
  
File
"/Applications/ChimeraX-1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/seq-view/tool.py", line 495, in delete  
self.region_browser.destroy()  
  
See log for complete Python traceback.  
  

> open "/Users/jessejones/Documents/ChimeraX/Sessions/T4 TP 5A Zone.cxs"
> format session

Unable to restore session, resetting.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 649, in restore  
self.reset()  
File
"/Applications/ChimeraX-1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 502, in reset  
sm.reset_state(container, self)  
File
"/Applications/ChimeraX-1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/seqalign/manager.py", line 259, in reset_state  
alignment._destroy()  
File
"/Applications/ChimeraX-1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/seqalign/alignment.py", line 587, in _destroy  
self._notify_observers(self.NOTE_DESTROYED, None)  
File
"/Applications/ChimeraX-1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/seqalign/alignment.py", line 636, in _notify_observers  
recipient.alignment_notification(note_name, note_data)  
File
"/Applications/ChimeraX-1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/seq-view/tool.py", line 464, in alignment_notification  
self.delete()  
File
"/Applications/ChimeraX-1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/seq-view/tool.py", line 495, in delete  
self.region_browser.destroy()  
AttributeError: 'SequenceViewer' object has no attribute 'region_browser'  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 649, in restore  
self.reset()  
File
"/Applications/ChimeraX-1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 502, in reset  
sm.reset_state(container, self)  
File
"/Applications/ChimeraX-1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/seqalign/manager.py", line 259, in reset_state  
alignment._destroy()  
File
"/Applications/ChimeraX-1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/seqalign/alignment.py", line 587, in _destroy  
self._notify_observers(self.NOTE_DESTROYED, None)  
File
"/Applications/ChimeraX-1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/seqalign/alignment.py", line 636, in _notify_observers  
recipient.alignment_notification(note_name, note_data)  
File
"/Applications/ChimeraX-1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/seq-view/tool.py", line 464, in alignment_notification  
self.delete()  
File
"/Applications/ChimeraX-1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/seq-view/tool.py", line 495, in delete  
self.region_browser.destroy()  
AttributeError: 'SequenceViewer' object has no attribute 'region_browser'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/gui.py", line 629, in customEvent  
func(*args, **kw)  
File
"/Applications/ChimeraX-1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/widgets/htmlview.py", line 440, in defer  
cxcmd(session, topic)  
File
"/Applications/ChimeraX-1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/widgets/htmlview.py", line 456, in cxcmd  
run(session, cmd)  
File
"/Applications/ChimeraX-1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/run.py", line 31, in run  
results = command.run(text, log=log)  
File
"/Applications/ChimeraX-1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2805, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX-1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/open_command/cmd.py", line 100, in cmd_open  
return Command(session, registry=registry).run(provider_cmd_text, log=log)  
File
"/Applications/ChimeraX-1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2805, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX-1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/open_command/cmd.py", line 154, in provider_open  
name or model_name_from_path(fi.file_name)), provider_kw)  
File
"/Applications/ChimeraX-1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/open_command/cmd.py", line 390, in collated_open  
return func(*func_args, **func_kw)  
File
"/Applications/ChimeraX-1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core_formats/__init__.py", line 26, in open  
return cxs_open(session, data, **kw)  
File
"/Applications/ChimeraX-1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 925, in open  
session.restore(stream, path=path, resize_window=resize_window)  
File
"/Applications/ChimeraX-1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 691, in restore  
self.reset()  
File
"/Applications/ChimeraX-1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 502, in reset  
sm.reset_state(container, self)  
File
"/Applications/ChimeraX-1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/seqalign/manager.py", line 259, in reset_state  
alignment._destroy()  
File
"/Applications/ChimeraX-1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/seqalign/alignment.py", line 587, in _destroy  
self._notify_observers(self.NOTE_DESTROYED, None)  
File
"/Applications/ChimeraX-1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/seqalign/alignment.py", line 636, in _notify_observers  
recipient.alignment_notification(note_name, note_data)  
File
"/Applications/ChimeraX-1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/seq-view/tool.py", line 464, in alignment_notification  
self.delete()  
File
"/Applications/ChimeraX-1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/seq-view/tool.py", line 495, in delete  
self.region_browser.destroy()  
AttributeError: 'SequenceViewer' object has no attribute 'region_browser'  
  
AttributeError: 'SequenceViewer' object has no attribute 'region_browser'  
  
File
"/Applications/ChimeraX-1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/seq-view/tool.py", line 495, in delete  
self.region_browser.destroy()  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 INTEL-14.7.8
OpenGL renderer: Intel(R) Iris(TM) Plus Graphics OpenGL Engine
OpenGL vendor: Intel Inc.Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro16,2
      Processor Name: Quad-Core Intel Core i5
      Processor Speed: 2 GHz
      Number of Processors: 1
      Total Number of Cores: 4
      L2 Cache (per Core): 512 KB
      L3 Cache: 6 MB
      Hyper-Threading Technology: Enabled
      Memory: 16 GB
      Boot ROM Version: 1037.147.4.0.0 (iBridge: 17.16.16610.0.0,0)

Software:

    System Software Overview:

      System Version: macOS 10.15.7 (19H2)
      Kernel Version: Darwin 19.6.0
      Time since boot: 7 days 21:49

Graphics/Displays:

    Intel Iris Plus Graphics:

      Chipset Model: Intel Iris Plus Graphics
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x8a53
      Revision ID: 0x0007
      Metal: Supported, feature set macOS GPUFamily2 v1
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 2560 x 1600 Retina
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: No
          Connection Type: Internal

PyQt version: 5.12.3
Compiled Qt version: 5.12.4
Runtime Qt version: 5.12.9
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    appnope: 0.1.0
    Babel: 2.8.0
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2020.6.20
    chardet: 3.0.4
    ChimeraX-AddH: 2.1.1
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.1
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.6.1
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 1.0.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.0
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.0
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.1
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.0
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-CommandLine: 1.1.3
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.1
    ChimeraX-CoreFormats: 1.0
    ChimeraX-coulombic: 1.0.1
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-DataFormats: 1.0
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1
    ChimeraX-DistUI: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.1
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.0
    ChimeraX-Hbonds: 2.0
    ChimeraX-Help: 1.0
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.0
    ChimeraX-ImageFormats: 1.0
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0
    ChimeraX-Label: 1.0
    ChimeraX-ListInfo: 1.0
    ChimeraX-Log: 1.1.1
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Map: 1.0.1
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.0
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 1.1
    ChimeraX-MDcrds: 2.0
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.0
    ChimeraX-mmCIF: 2.2
    ChimeraX-MMTF: 2.0
    ChimeraX-Modeller: 1.0
    ChimeraX-ModelPanel: 1.0
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.0
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0
    ChimeraX-OpenCommand: 1.2.1
    ChimeraX-PDB: 2.1
    ChimeraX-PDBBio: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0
    ChimeraX-PubChem: 2.0
    ChimeraX-Read-Pbonds: 1.0
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.0
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.2
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SeqView: 2.2
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.0
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.0
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.0.4
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-Struts: 1.0
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.0
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.0
    ChimeraX-ToolshedUtils: 1.0
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.2.3
    ChimeraX-uniprot: 2.0
    ChimeraX-ViewDockX: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0
    ChimeraX-WebServices: 1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.3
    comtypes: 1.1.7
    cxservices: 1.0
    cycler: 0.10.0
    Cython: 0.29.20
    decorator: 4.4.2
    distlib: 0.3.1
    docutils: 0.16
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 2.10.0
    html2text: 2020.1.16
    idna: 2.10
    ihm: 0.16
    imagecodecs: 2020.5.30
    imagecodecs-lite: 2020.1.31
    imagesize: 1.2.0
    ipykernel: 5.3.0
    ipython: 7.15.0
    ipython-genutils: 0.2.0
    jedi: 0.17.2
    Jinja2: 2.11.2
    jupyter-client: 6.1.3
    jupyter-core: 4.6.3
    kiwisolver: 1.2.0
    line-profiler: 2.1.2
    lxml: 4.5.1
    MarkupSafe: 1.1.1
    matplotlib: 3.2.1
    msgpack: 1.0.0
    netifaces: 0.10.9
    networkx: 2.4
    numexpr: 2.7.1
    numpy: 1.18.5
    numpydoc: 1.0.0
    openvr: 1.12.501
    packaging: 20.4
    parso: 0.7.1
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 7.1.2
    pip: 20.2.2
    pkginfo: 1.5.0.1
    prompt-toolkit: 3.0.7
    psutil: 5.7.0
    ptyprocess: 0.6.0
    pycollada: 0.7.1
    pydicom: 2.0.0
    Pygments: 2.6.1
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 2.4.7
    PyQt5-commercial: 5.12.3
    PyQt5-sip: 4.19.19
    PyQtWebEngine-commercial: 5.12.1
    python-dateutil: 2.8.1
    pytz: 2020.1
    pyzmq: 19.0.2
    qtconsole: 4.7.4
    QtPy: 1.9.0
    RandomWords: 0.3.0
    requests: 2.24.0
    scipy: 1.4.1
    setuptools: 49.4.0
    sfftk-rw: 0.6.6.dev0
    six: 1.15.0
    snowballstemmer: 2.0.0
    sortedcontainers: 2.2.2
    Sphinx: 3.1.1
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 2.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 1.0.3
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.4
    suds-jurko: 0.6
    tables: 3.6.1
    tifffile: 2020.6.3
    tinyarray: 1.2.2
    tornado: 6.0.4
    traitlets: 5.0.4
    urllib3: 1.25.10
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.34.2

[Eric Pettersen]

Greg, I need a suggestion as to what to do here before we get a zillion copies of this bug report as users get notified of the "availability" of the AddH 2.1.3 bundle for their ChimeraX 1.1 installation. Do I remove the bundle from the toolshed? Can I rename the "py38" part of the wheel name to "py37"? What? I put up the bundle in the first place because it fixes a crash that happens for some structures.

[Greg Couch]

Yes, it is possible to remove bundles from the toolshed. You have access to the admin interface.

There are a couple of options:

(1) You can build the bundle with ChimeraX 1.0 or 1.1 -- which has the advantage that it's built with the ChimeraX versions it's supposed to work with. This is the recommendation for outside developers. And this works for both binary and Python-only bundles.

(2) In bundle_info.xml, you can set limitedAPI="3.7" and carefully limit anything you code to Python 3.7. But if you test with Python 3.7, that means that you're testing using ChimeraX 1.0 or 1.1, so you might as well do (1).

(3) can't remember :-)

[Eric Pettersen]

Yes, I know I can remove the bundle.  I was asking whether or not that is what I should do.


Okay, I have built the wheel using the 1.1 release.  This produced a wheel named ChimeraX_AddH-2.1.3-py3-none-any.whl (note the "py3" instead of "py38").  How can I get the Toolshed to point to this wheel instead of the original one?  The location for the wheel on plato seems to be /wynton/group/ferrin/usr.local/projects/chimerax/builds/repo.  I have copied the new wheel there but I don't know how to fix up the Toolshed web site to point to the revised wheel.

In the long run this is a bad approach for developers.  It would mean they would need to figure out for themselves what the oldest compatible release is for all their bundle's requirements, download that and build against it.  It's a nightmare.


As per #3898, I feel this is the wrong decision.  99% of pure-Python bundles (including our own) will not be using bleeding-edge Python 3.5+ features.  Forcing all of them to put an esoteric tag in their bundle_info.xml so that their bundle will be known to be compatible with older releases is just a recipe for lots of bundles to be wrongly marked as incompatible with older releases -- including in this case the latest production release.  The small number of developers actually knowingly using the very most recent features of Python should be the ones putting the extra tag in their bundle_info.xml.

[Eric Pettersen]

Of course, the instant I send that reply it occurs to me that I can move the original wheel aside and make a symbolic link to the new wheel.

[Eric Pettersen]

With the symbolic link installed, now run into the problem in ticket #4032, where the tool is "already installed" despite the fact that the installed version is 2.1.1 and the new version is 2.1.3.

[Eric Pettersen]

If there is no way to remedy #4032 in the 1.1 release, I will have to remove the bundle from the Toolshed.

[Tom Goddard]

I agree with Eric's comment 3. Pure Python bundles should by default work with all Python 3 versins, ie have py3 in the wheel name. In the exceedingly rare case that a developer uses Python features only in say Python 3.8, it will be there responsibility to use a bundle_info.xml tag to say that.

[Eric Pettersen]

Tom, you're not on #3898 but Greg changed the behavior for pure Python bundles to what we suggested.

Greg, I fleshed out the description of the limitedAPI tag in the developer documentation to cover its use with pure Python bundles and to offer somewhat more information about its use with binary bundles.

[Eric Pettersen]

I don't think the "symbolic link" trick actually works. The file probably still gets downloaded with "py38" in its name and the installation fails (as per #4037). Greg, how can I get the toolshed to point directly to the "py3" version of the wheel. Do I have to remove the AddH bundle entirely and re-upload it?

[Greg Couch]

That would be the simplest way to do it.

[Eric Pettersen]

_How_ do I access the admin interface? I'm logged into the Toolshed as me and I don't see anything obvious...