handle sub packages split between user and app install areas

[pett@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.18362
ChimeraX Version: 0.91 (2019-12-23)
Description
(Describe the actions that caused this problem to occur here) try to launch a matchmaker alignment 

Log:
UCSF ChimeraX version: 0.91 (2019-12-23)  
© 2016-2019 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  
Successfully installed 'ChimeraX_Alignments-1.0-py3-none-any.whl'  
Looking in indexes: https://pypi.org/simple,
https://cxtoolshed.rbvi.ucsf.edu/pypi/  
Processing
c:\users\adele\appdata\local\ucsf\chimerax\cache\0.91\installers\chimerax_alignments-1.0-py3-none-
any.whl  
Requirement already satisfied, skipping upgrade: ChimeraX-Core>=0.9 in
c:\program files\chimerax\bin\lib\site-packages (from ChimeraX-
Alignments==1.0) (0.91)  
Requirement already satisfied, skipping upgrade: ChimeraX-UI>=1.0 in
c:\program files\chimerax\bin\lib\site-packages (from ChimeraX-
Alignments==1.0) (1.0)  
Requirement already satisfied, skipping upgrade: ChimeraX-Atomic>=1.0 in
c:\program files\chimerax\bin\lib\site-packages (from ChimeraX-
Alignments==1.0) (1.0)  
Requirement already satisfied, skipping upgrade: ChimeraX-MouseModes>=1.0 in
c:\program files\chimerax\bin\lib\site-packages (from ChimeraX-
UI>=1.0->ChimeraX-Alignments==1.0) (1.0)  
Installing collected packages: ChimeraX-Alignments  
Successfully installed ChimeraX-Alignments-1.0  
Lock 2942254612104 acquired on
C:\Users\adele\AppData\Local\UCSF\ChimeraX\Cache\0.91\toolshed\bundle_info.cache.lock  
Lock 2942254612104 released on
C:\Users\adele\AppData\Local\UCSF\ChimeraX\Cache\0.91\toolshed\bundle_info.cache.lock  
  

> open C:/Users/adele/Desktop/MesArticles/InProgress/Docking/pdb2vla.ent

pdb2vla.ent title:  
Crystal structure of restriction endonuclease bpuji recognition domain In
complex with cognate DNA [more info...]  
  
Chain information for pdb2vla.ent #1  
---  
Chain | Description  
A | BPUJI  
L | 5'-D(*GP*GP*TP*ap*CP*CP*CP*GP*TP*GP *GP*A)-3'  
M | 5'-D(*TP*CP*CP*ap*CP*GP*GP*GP*TP*ap *CP*C)-3'  
  
Non-standard residues in pdb2vla.ent #1  
---  
NA — sodium ion  
PG6 — 1-(2-methoxy-ethoxy)-2-{2-[2-(2-methoxy-ethoxy]-ethoxy}-ethane  
  

> open
> C:\Users\adele\Desktop\MesArticles\InProgress\Docking\NBI_modelchoisi.pdb

Chain information for NBI_modelchoisi.pdb #2  
---  
Chain | Description  
| No description available  
  

> open
> C:\Users\adele\Desktop\MesArticles\InProgress\Docking\v11plus_unbound.pdb

Summary of feedback from opening
C:\Users\adele\Desktop\MesArticles\InProgress\Docking\v11plus_unbound.pdb  
---  
warning | CONECT record for nonexistent atom: 313  
  
Chain information for v11plus_unbound.pdb #3  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> mmaker #2 to #1 showAlignment true

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 258, in execute  
cmd.run(cmd_text)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2854, in run  
_used_aliases=used_aliases, log=log)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 3400, in __call__  
return self.cmd.run(text, _used_aliases=_used_aliases, log=log)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2837, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\match_maker\match.py", line 603, in cmd_match  
from chimerax.seqalign import sim_matrices  
ImportError: cannot import name 'sim_matrices' from 'chimerax.seqalign'
(C:\Users\adele\AppData\Local\UCSF\ChimeraX\0.91\site-
packages\chimerax\seqalign\\__init__.py)  
  
ImportError: cannot import name 'sim_matrices' from 'chimerax.seqalign'
(C:\Users\adele\AppData\Local\UCSF\ChimeraX\0.91\site-
packages\chimerax\seqalign\\__init__.py)  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\match_maker\match.py", line 603, in cmd_match  
from chimerax.seqalign import sim_matrices  
  
See log for complete Python traceback.  
  

> mmaker #2 to #1 showAlignment true

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 258, in execute  
cmd.run(cmd_text)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2854, in run  
_used_aliases=used_aliases, log=log)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 3400, in __call__  
return self.cmd.run(text, _used_aliases=_used_aliases, log=log)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2837, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\match_maker\match.py", line 603, in cmd_match  
from chimerax.seqalign import sim_matrices  
ImportError: cannot import name 'sim_matrices' from 'chimerax.seqalign'
(C:\Users\adele\AppData\Local\UCSF\ChimeraX\0.91\site-
packages\chimerax\seqalign\\__init__.py)  
  
ImportError: cannot import name 'sim_matrices' from 'chimerax.seqalign'
(C:\Users\adele\AppData\Local\UCSF\ChimeraX\0.91\site-
packages\chimerax\seqalign\\__init__.py)  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\match_maker\match.py", line 603, in cmd_match  
from chimerax.seqalign import sim_matrices  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 - Build 24.20.100.6299
OpenGL renderer: Intel(R) HD Graphics 520
OpenGL vendor: Intel

[Eric Pettersen]

Hi Adele,

Sorry about this, but _don't_ install the Alignments bundle from the Toolshed. ChimeraX ships with the alignment capabilities pre-installed, and they work. Clearly, the bundle on the Toolshed doesn't work. To remove the installed bad bundle is a little tricky but not too hard. Do this:

1) In ChimeraX type "into path". That will list several folders and what they're for. Look for the one labeled "user versioned config directory"
2) Go to that folder. Go into the subfolder named "site-packages". Remove the folder named "ChimeraX_Alignments-1.0.dist-info". Go into the subfolder named "chimera". Remove the folder named "seqalign".
3) Restart ChimeraX. Things should work now.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

[Eric Pettersen]

The plan is to add a meta-importer that can cover this scenario. Whoever gets to this first between me and Conrad will implement it.

[Eric Pettersen]

Since it is no longer easy to into the app, this is less important

[Eric Pettersen]

I am de-milestoning this, since it seems very low priority at this point.

[Eric Pettersen]

This is still an issue for a package such as atomic, where an update to the main bundle/package can put it in the user area, but sub packages are still only in the app.

[Eric Pettersen]

This is now covered by ticket #3353