Toolshed allows very old ISOLDE/Clipper to install

[Scooter Morris]

The following bug report has been submitted:
Platform:        Darwin-18.2.0-x86_64-i386-64bit
ChimeraX Version: 0.9 (2019-06-06)
Description
Tried to start ISOLDE after a fresh install of both ISOLDE and clipper

Log:
Startup Messages  
---  
warning | 'clip' is a prefix of an existing command 'clipper'  
  
UCSF ChimeraX version: 0.9 (2019-06-06)  
© 2016-2019 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> toolshed show ISOLDE

Traceback (most recent call last):  
File
"/Applications/ChimeraX-0.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/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
"/Applications/ChimeraX-0.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/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 "/Users/scooter/Library/Application Support/ChimeraX/0.9/site-
packages/chimerax/isolde/__init__.py", line 23, in start_tool  
return tools.get_singleton(session, ISOLDE_ToolUI, 'ISOLDE', create=True)  
File
"/Applications/ChimeraX-0.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/tools.py", line 214, in get_singleton  
tinst = tool_class(session, tool_name, **kw)  
File "/Users/scooter/Library/Application Support/ChimeraX/0.9/site-
packages/chimerax/isolde/tool.py", line 157, in __init__  
self.isolde = isolde.Isolde(self)  
File "/Users/scooter/Library/Application Support/ChimeraX/0.9/site-
packages/chimerax/isolde/isolde.py", line 251, in __init__  
from . import mousemodes  
File "/Users/scooter/Library/Application Support/ChimeraX/0.9/site-
packages/chimerax/isolde/mousemodes.py", line 5, in <module>  
from chimerax.core.ui import MouseMode  
ImportError: cannot import name 'MouseMode' from 'chimerax.ui'
(/Applications/ChimeraX-0.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/__init__.py)  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-0.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/gui.py", line 1137, in <lambda>  
run(ses, "toolshed show %s" % quote_if_necessary(tool_name)))  
File
"/Applications/ChimeraX-0.9.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-0.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2632, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX-0.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/toolshed.py", line 337, in toolshed_show  
bi.start_tool(session, tool_name)  
File
"/Applications/ChimeraX-0.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/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:  
cannot import name 'MouseMode' from 'chimerax.ui'
(/Applications/ChimeraX-0.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/__init__.py)  
  
chimerax.core.toolshed.ToolshedError: start_tool() failed for tool ISOLDE in
bundle ChimeraX-ISOLDE:  
cannot import name 'MouseMode' from 'chimerax.ui'
(/Applications/ChimeraX-0.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/__init__.py)  
  
File
"/Applications/ChimeraX-0.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/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: 4.1 ATI-2.4.10
OpenGL renderer: AMD Radeon Pro 555X OpenGL Engine
OpenGL vendor: ATI Technologies Inc.

[Tristan Croll]

Yep - I haven't put a new version of ISOLDE up on the Tool Shed yet (still doing a little polishing). The problem is that there are some (very) old versions of both ISOLDE and Clipper up there that had the required ChimeraX version string set to ">=" rather than "==". Probably the best thing to do would be to remove all offending versions of both plugins from the Tool Shed database.

[tic20@…]

I’m afraid I don’t have the power to fix this - the Tool Shed only lets me submit new bundles, not delete old ones. I’m quite happy for the offending versions to be removed, but it will have to happen at your end.

 
 
Tristan Croll
Research Fellow
Cambridge Institute for Medical Research
University of Cambridge CB2 0XY
 

 

[Tristan Croll]

Looks like for ISOLDE, everything up to and including 0.9.24 will have to go, and Clipper up to and including 0.1.9. There's very little reason to keep these other than historical interest - they're built for ChimeraX 0.5 and 0.1 respectively and tens of thousands of lines of code out of date.

[Conrad Huang]

All versions of ISOLDE 0.9.24 and prior, and Clipper 0.1.9 and prior have been deleted. Unfortunately, I was unable to save the download history for those releases.

[tic20@…]

No problem by me. Most of the downloads from that period were just me 
and bots anyway. 1.0b1 was the first version I announced publicly.

On 2019-06-13 18:41, ChimeraX wrote: