Shell does not start

[Tristan Croll]

The following bug report has been submitted:
Platform:        Linux-5.4.13-201.fc31.x86_64-x86_64-with-fedora-31-Thirty_One
ChimeraX Version: 0.92 (2020-02-23)
Description
When trying to open the shell via the menu. Also happened in today's Windows build (couldn't report - blocked by firewall).

Log:
Startup Messages  
---  
warning | 'clip' is a prefix of an existing command 'clipper'  
  
UCSF ChimeraX version: 0.92 (2020-02-23)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> toolshed show Shell

/opt/UCSF/chimerax-2020.02.23/lib/python3.7/site-
packages/IPython/core/history.py:226: UserWarning: IPython History requires
SQLite, your history will not be saved  
warn("IPython History requires SQLite, your history will not be saved")  
Traceback (most recent call last):  
File "/opt/UCSF/chimerax-2020.02.23/lib/python3.7/site-
packages/chimerax/core/toolshed/info.py", line 621, in start_tool  
ti = api._api_caller.start_tool(api, session, self, tool_info)  
File "/opt/UCSF/chimerax-2020.02.23/lib/python3.7/site-
packages/chimerax/core/toolshed/__init__.py", line 1612, in start_tool  
return cls._get_func(api, "start_tool")(session, ti.name)  
File "/opt/UCSF/chimerax-2020.02.23/lib/python3.7/site-
packages/chimerax/shell/__init__.py", line 21, in start_tool  
return ShellUI(session, tool_name)  
File "/opt/UCSF/chimerax-2020.02.23/lib/python3.7/site-
packages/chimerax/shell/tool.py", line 39, in __init__  
kernel_client.start_channels()  
File "/opt/UCSF/chimerax-2020.02.23/lib/python3.7/site-
packages/qtconsole/kernel_mixins.py", line 47, in start_channels  
super(QtKernelClientMixin, self).start_channels(*args, **kw)  
File "/opt/UCSF/chimerax-2020.02.23/lib/python3.7/site-
packages/ipykernel/inprocess/client.py", line 64, in start_channels  
super(InProcessKernelClient, self).start_channels()  
File "/opt/UCSF/chimerax-2020.02.23/lib/python3.7/site-
packages/jupyter_client/client.py", line 118, in start_channels  
self.control_channel.start()  
File "/opt/UCSF/chimerax-2020.02.23/lib/python3.7/site-
packages/jupyter_client/client.py", line 200, in control_channel  
socket, self.session, self.ioloop  
TypeError: ChannelABC() takes no arguments  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/opt/UCSF/chimerax-2020.02.23/lib/python3.7/site-
packages/chimerax/ui/gui.py", line 1347, in <lambda>  
run(ses, "toolshed show %s" % StringArg.unparse(tool_name)))  
File "/opt/UCSF/chimerax-2020.02.23/lib/python3.7/site-
packages/chimerax/core/commands/run.py", line 31, in run  
results = command.run(text, log=log)  
File "/opt/UCSF/chimerax-2020.02.23/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2837, in run  
result = ci.function(session, **kw_args)  
File "/opt/UCSF/chimerax-2020.02.23/lib/python3.7/site-
packages/chimerax/core/commands/toolshed.py", line 339, in toolshed_show  
bi.start_tool(session, name)  
File "/opt/UCSF/chimerax-2020.02.23/lib/python3.7/site-
packages/chimerax/core/toolshed/info.py", line 627, in start_tool  
"start_tool() failed for tool %s in bundle %s:\n%s" % (tool_name, self.name,
str(e)))  
chimerax.core.toolshed.ToolshedError: start_tool() failed for tool Shell in
bundle ChimeraX-Shell:  
ChannelABC() takes no arguments  
  
chimerax.core.toolshed.ToolshedError: start_tool() failed for tool Shell in
bundle ChimeraX-Shell:  
ChannelABC() takes no arguments  
  
File "/opt/UCSF/chimerax-2020.02.23/lib/python3.7/site-
packages/chimerax/core/toolshed/info.py", line 627, in start_tool  
"start_tool() failed for tool %s in bundle %s:\n%s" % (tool_name, self.name,
str(e)))  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 440.44
OpenGL renderer: GeForce GTX 1070/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

[Eric Pettersen]

On Feb 23rd, the jupyter-client package went to version 6.0.0, which broke everything. The qtconsole package depends on jupyter-client. We list qtconsole in pips/app-requirements.txt, but not jupyter-client (nor several other qtconsole dependencies). Can we list jupyter-client [5.3.4] explicitly (at least temporarily)?

[Conrad Huang]

Fixed in 6d8525e5c. Added jupyter-client 5.3.4 as explicit dependency in prereq/pips.