ISOLDE not longer compatible with 0.9

[madhan@…]

The following bug report has been submitted:
Platform:        Linux-3.10.0-1062.9.1.el7.x86_64-x86_64-with-redhat-7.7-Nitrogen
ChimeraX Version: 0.9 (2019-06-06)
Description
Dear ISOLDE, 
I am just trying to install ISOLDE program embedded in my chimerax but it fails with this message. Please could help me out? 

Log:
UCSF ChimeraX version: 0.9 (2019-06-06)  
© 2016-2019 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  
Successfully installed 'ChimeraX_ISOLDE-1.0b3-cp37-cp37m-linux_x86_64.whl'  
Looking in indexes: https://pypi.org/simple,
https://cxtoolshed.rbvi.ucsf.edu/pypi/  
Processing
/lmb/home/madhan/.cache/ChimeraX/0.9/installers/ChimeraX_ISOLDE-1.0b3-cp37-cp37m-linux_x86_64.whl  
Requirement already satisfied, skipping upgrade: ChimeraX-Atomic>=0.7 in
/net/nfs1/public/chimerax_public/opt/UCSF/ChimeraX/lib/python3.7/site-packages
(from ChimeraX-ISOLDE==1.0b3) (1.0)  
Requirement already satisfied, skipping upgrade: ChimeraX-Core==0.9 in
/net/nfs1/public/chimerax_public/opt/UCSF/ChimeraX/lib/python3.7/site-packages
(from ChimeraX-ISOLDE==1.0b3) (0.9)  
Requirement already satisfied, skipping upgrade: ChimeraX-Clipper>=0.9.4 in
/lmb/home/madhan/.local/share/ChimeraX/0.9/site-packages (from ChimeraX-
ISOLDE==1.0b3) (0.10.0)  
Installing collected packages: ChimeraX-ISOLDE  
Found existing installation: ChimeraX-ISOLDE 1.0b3  
Uninstalling ChimeraX-ISOLDE-1.0b3:  
Successfully uninstalled ChimeraX-ISOLDE-1.0b3  
Successfully installed ChimeraX-ISOLDE-1.0b3  
Lock 47273222118144 acquired on
/lmb/home/madhan/.cache/ChimeraX/0.9/toolshed/bundle_info.cache.lock  
Lock 47273222118144 released on
/lmb/home/madhan/.cache/ChimeraX/0.9/toolshed/bundle_info.cache.lock  
  

You are using pip version 19.0.3, however version 19.3.1 is available.  
You should consider upgrading via the 'pip install --upgrade pip' command.  
  

> toolshed show ISOLDE

Traceback (most recent call last):  
File "/public/chimerax_public/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/core/toolshed/info.py", line 627, in start_tool  
ti = api._api_caller.start_tool(api, session, self, tool_info)  
File "/public/chimerax_public/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/core/toolshed/__init__.py", line 1435, in start_tool  
return cls._get_func(api, "start_tool")(session, ti.name)  
File "/lmb/home/madhan/.local/share/ChimeraX/0.9/site-
packages/chimerax/isolde/__init__.py", line 31, in start_tool  
return tools.get_singleton(session, ISOLDE_ToolUI, 'ISOLDE', create=True)  
File "/public/chimerax_public/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/core/tools.py", line 214, in get_singleton  
tinst = tool_class(session, tool_name, **kw)  
File "/lmb/home/madhan/.local/share/ChimeraX/0.9/site-
packages/chimerax/isolde/tool.py", line 167, in __init__  
from . import isolde  
File "/lmb/home/madhan/.local/share/ChimeraX/0.9/site-
packages/chimerax/isolde/isolde.py", line 35, in <module>  
from chimerax import clipper  
File "/lmb/home/madhan/.local/share/ChimeraX/0.9/site-
packages/chimerax/clipper/__init__.py", line 26, in <module>  
__version__ = _version()  
File "/lmb/home/madhan/.local/share/ChimeraX/0.9/site-
packages/chimerax/clipper/__init__.py", line 24, in _version  
return pkg_resources.require('ChimeraX-Clipper')[0].version  
File "/public/chimerax_public/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/pkg_resources/__init__.py", line 900, in require  
needed = self.resolve(parse_requirements(requirements))  
File "/public/chimerax_public/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/pkg_resources/__init__.py", line 791, in resolve  
raise VersionConflict(dist, req).with_context(dependent_req)  
pkg_resources.ContextualVersionConflict: (ChimeraX-Core 0.9
(/net/nfs1/public/chimerax_public/opt/UCSF/ChimeraX/lib/python3.7/site-
packages), Requirement.parse('ChimeraX-Core==0.91'), {'ChimeraX-Clipper'})  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/public/chimerax_public/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/ui/gui.py", line 1137, in <lambda>  
run(ses, "toolshed show %s" % quote_if_necessary(tool_name)))  
File "/public/chimerax_public/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/core/commands/run.py", line 31, in run  
results = command.run(text, log=log)  
File "/public/chimerax_public/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2632, in run  
result = ci.function(session, **kw_args)  
File "/public/chimerax_public/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/core/commands/toolshed.py", line 337, in toolshed_show  
bi.start_tool(session, tool_name)  
File "/public/chimerax_public/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/core/toolshed/info.py", line 633, 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 ISOLDE in
bundle ChimeraX-ISOLDE:  
(ChimeraX-Core 0.9
(/net/nfs1/public/chimerax_public/opt/UCSF/ChimeraX/lib/python3.7/site-
packages), Requirement.parse('ChimeraX-Core==0.91'), {'ChimeraX-Clipper'})  
  
chimerax.core.toolshed.ToolshedError: start_tool() failed for tool ISOLDE in
bundle ChimeraX-ISOLDE:  
(ChimeraX-Core 0.9
(/net/nfs1/public/chimerax_public/opt/UCSF/ChimeraX/lib/python3.7/site-
packages), Requirement.parse('ChimeraX-Core==0.91'), {'ChimeraX-Clipper'})  
  
File "/public/chimerax_public/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/core/toolshed/info.py", line 633, 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 418.56
OpenGL renderer: GeForce GTX 1080/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

[Eric Pettersen]

I believe you now need to use the 0.91 version of ChimeraX to install ISOLDE, not the 0.9 version that you are currently using.

[Tristan Croll]

Doing some spring cleaning, closing out obsolete old tickets.