Opened 6 years ago

Closed 6 years ago

#2375 closed defect (nonchimerax)

Shell tab-completion attempts import of non-Python libs

Reported by: Tristan Croll Owned by: pett
Priority: normal Milestone:
Component: General Controls Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Linux-3.10.0-957.12.2.el7.x86_64-x86_64-with-centos-7.6.1810-Core
ChimeraX Version: 0.91 (2019-08-27)
Description
A bit weird... tab-completing "from chimerax.clipper." in the shell seems to have led to it trying to import all the non-python compiled libraries in the Clipper directory (lib_symmetry, libccp4, libclipper etc. are all C++-only libraries). 

Log:
UCSF ChimeraX version: 0.91 (2019-08-27)  
© 2016-2019 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 6cdx structureFactors true

Summary of feedback from opening 6cdx fetched from pdb  
---  
notes | Fetching compressed mmCIF 6cdx from
http://files.rcsb.org/download/6cdx.cif  
Fetching CCD 4LT from http://ligand-expo.rcsb.org/reports/4/4LT/4LT.cif  
Fetching compressed 6cdx structure factors from
http://files.rcsb.org/download/6cdx-sf.cif  
Resolution: 1.000002419435916  
  
6cdx title:  
High-resolution crystal structure of fluoropropylated cystine knot, binding to
alpha-5 beta-6 integrin [more info...]  
  
Chain information for 6cdx  
---  
Chain | Description  
1.3/A 1.3/B | cystine knot (fluoropropylated)  
  
Non-standard residues in 6cdx #1.3  
---  
4LT — (2R)-2-fluoropropanoic acid  
  
6cdx mmCIF Assemblies  
---  
1| author_defined_assembly  
2| author_defined_assembly  
  
  

> toolshed show Shell

/opt/UCSF/ChimeraX-daily/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")  
Module chimerax.clipper.lib_symmetry not importable in path
['/run/media/tic20/storage/structure_dump/3io0',
'/home/tic20/.local/share/ChimeraX/0.91/site-packages', '/opt/UCSF/ChimeraX-
daily/lib/python37.zip', '/opt/UCSF/ChimeraX-daily/lib/python3.7',
'/opt/UCSF/ChimeraX-daily/lib/python3.7/lib-dynload', '/opt/UCSF/ChimeraX-
daily/lib/python3.7/site-packages', '/opt/UCSF/ChimeraX-
daily/lib/python3.7/site-packages/PyOpenGL-3.1.3b2-py3.7.egg',
'/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/PyOpenGL_accelerate-3.1.3b1-py3.7-linux-x86_64.egg',
'/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/tables-3.4.4-py3.7-linux-x86_64.egg', '/opt/UCSF/ChimeraX-
daily/lib/python3.7/site-packages/numexpr-2.7.0-py3.7-linux-x86_64.egg',
'/home/tic20/chimerax_start', '/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/IPython/extensions'].  
Module chimerax.clipper.libccp4 not importable in path
['/run/media/tic20/storage/structure_dump/3io0',
'/home/tic20/.local/share/ChimeraX/0.91/site-packages', '/opt/UCSF/ChimeraX-
daily/lib/python37.zip', '/opt/UCSF/ChimeraX-daily/lib/python3.7',
'/opt/UCSF/ChimeraX-daily/lib/python3.7/lib-dynload', '/opt/UCSF/ChimeraX-
daily/lib/python3.7/site-packages', '/opt/UCSF/ChimeraX-
daily/lib/python3.7/site-packages/PyOpenGL-3.1.3b2-py3.7.egg',
'/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/PyOpenGL_accelerate-3.1.3b1-py3.7-linux-x86_64.egg',
'/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/tables-3.4.4-py3.7-linux-x86_64.egg', '/opt/UCSF/ChimeraX-
daily/lib/python3.7/site-packages/numexpr-2.7.0-py3.7-linux-x86_64.egg',
'/home/tic20/chimerax_start', '/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/IPython/extensions'].  
Module chimerax.clipper.libclipper not importable in path
['/run/media/tic20/storage/structure_dump/3io0',
'/home/tic20/.local/share/ChimeraX/0.91/site-packages', '/opt/UCSF/ChimeraX-
daily/lib/python37.zip', '/opt/UCSF/ChimeraX-daily/lib/python3.7',
'/opt/UCSF/ChimeraX-daily/lib/python3.7/lib-dynload', '/opt/UCSF/ChimeraX-
daily/lib/python3.7/site-packages', '/opt/UCSF/ChimeraX-
daily/lib/python3.7/site-packages/PyOpenGL-3.1.3b2-py3.7.egg',
'/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/PyOpenGL_accelerate-3.1.3b1-py3.7-linux-x86_64.egg',
'/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/tables-3.4.4-py3.7-linux-x86_64.egg', '/opt/UCSF/ChimeraX-
daily/lib/python3.7/site-packages/numexpr-2.7.0-py3.7-linux-x86_64.egg',
'/home/tic20/chimerax_start', '/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/IPython/extensions'].  
Module chimerax.clipper.libclipper_cx not importable in path
['/run/media/tic20/storage/structure_dump/3io0',
'/home/tic20/.local/share/ChimeraX/0.91/site-packages', '/opt/UCSF/ChimeraX-
daily/lib/python37.zip', '/opt/UCSF/ChimeraX-daily/lib/python3.7',
'/opt/UCSF/ChimeraX-daily/lib/python3.7/lib-dynload', '/opt/UCSF/ChimeraX-
daily/lib/python3.7/site-packages', '/opt/UCSF/ChimeraX-
daily/lib/python3.7/site-packages/PyOpenGL-3.1.3b2-py3.7.egg',
'/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/PyOpenGL_accelerate-3.1.3b1-py3.7-linux-x86_64.egg',
'/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/tables-3.4.4-py3.7-linux-x86_64.egg', '/opt/UCSF/ChimeraX-
daily/lib/python3.7/site-packages/numexpr-2.7.0-py3.7-linux-x86_64.egg',
'/home/tic20/chimerax_start', '/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/IPython/extensions'].  
Module chimerax.clipper.libfftw2xc not importable in path
['/run/media/tic20/storage/structure_dump/3io0',
'/home/tic20/.local/share/ChimeraX/0.91/site-packages', '/opt/UCSF/ChimeraX-
daily/lib/python37.zip', '/opt/UCSF/ChimeraX-daily/lib/python3.7',
'/opt/UCSF/ChimeraX-daily/lib/python3.7/lib-dynload', '/opt/UCSF/ChimeraX-
daily/lib/python3.7/site-packages', '/opt/UCSF/ChimeraX-
daily/lib/python3.7/site-packages/PyOpenGL-3.1.3b2-py3.7.egg',
'/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/PyOpenGL_accelerate-3.1.3b1-py3.7-linux-x86_64.egg',
'/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/tables-3.4.4-py3.7-linux-x86_64.egg', '/opt/UCSF/ChimeraX-
daily/lib/python3.7/site-packages/numexpr-2.7.0-py3.7-linux-x86_64.egg',
'/home/tic20/chimerax_start', '/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/IPython/extensions'].  
Module chimerax.clipper.libfftw_mkl_core not importable in path
['/run/media/tic20/storage/structure_dump/3io0',
'/home/tic20/.local/share/ChimeraX/0.91/site-packages', '/opt/UCSF/ChimeraX-
daily/lib/python37.zip', '/opt/UCSF/ChimeraX-daily/lib/python3.7',
'/opt/UCSF/ChimeraX-daily/lib/python3.7/lib-dynload', '/opt/UCSF/ChimeraX-
daily/lib/python3.7/site-packages', '/opt/UCSF/ChimeraX-
daily/lib/python3.7/site-packages/PyOpenGL-3.1.3b2-py3.7.egg',
'/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/PyOpenGL_accelerate-3.1.3b1-py3.7-linux-x86_64.egg',
'/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/tables-3.4.4-py3.7-linux-x86_64.egg', '/opt/UCSF/ChimeraX-
daily/lib/python3.7/site-packages/numexpr-2.7.0-py3.7-linux-x86_64.egg',
'/home/tic20/chimerax_start', '/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/IPython/extensions'].  
Module chimerax.clipper.libmmdb2 not importable in path
['/run/media/tic20/storage/structure_dump/3io0',
'/home/tic20/.local/share/ChimeraX/0.91/site-packages', '/opt/UCSF/ChimeraX-
daily/lib/python37.zip', '/opt/UCSF/ChimeraX-daily/lib/python3.7',
'/opt/UCSF/ChimeraX-daily/lib/python3.7/lib-dynload', '/opt/UCSF/ChimeraX-
daily/lib/python3.7/site-packages', '/opt/UCSF/ChimeraX-
daily/lib/python3.7/site-packages/PyOpenGL-3.1.3b2-py3.7.egg',
'/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/PyOpenGL_accelerate-3.1.3b1-py3.7-linux-x86_64.egg',
'/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/tables-3.4.4-py3.7-linux-x86_64.egg', '/opt/UCSF/ChimeraX-
daily/lib/python3.7/site-packages/numexpr-2.7.0-py3.7-linux-x86_64.egg',
'/home/tic20/chimerax_start', '/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/IPython/extensions'].  




OpenGL version: 3.3.0 NVIDIA 415.27
OpenGL renderer: TITAN Xp/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Change History (5)

comment:1 by pett, 6 years ago

Component: Unassigned → General Controls
Owner: set to pett
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → Shell tab-completion attempts import of non-Python libs

comment:2 by pett, 6 years ago

Status: accepted → feedback

They are libraries with the same extension (.so) as importable Python libraries, in a directory in the Python path. I don't know how the shell would be able to tell they're _not_ Python libs without trying to import them. Do you have some kind of suggestion here?

in reply to:  3 ; comment:3 by Tristan Croll, 6 years ago 

Not really... I guess I could see about moving them into a dedicated directory off the Python search path. I’ve just never seen this message printed to the log before.

comment:4 by Conrad Huang, 6 years ago

I just saw in the "tables" package where they put the hdf libraries in a ".libs" subdirectory, so the non-Python stuff is not actually on sys.path.

comment:5 by pett, 6 years ago

Resolution: → nonchimerax
Status: feedback → closed

I don't think there's anything I can do about this.

Note: See TracTickets for help on using tickets.