User installed tools should take precedence over app-included tools

[goddard@…]

The following bug report has been submitted:
Platform:        Darwin-18.6.0-x86_64-i386-64bit
ChimeraX Version: 0.91 (2019-06-25)
Description
It seems that tools installed for this user only do not take precedence over tools in the ChimeraX app.  I installed the Segger tool using the ChimeraX "devel install" command with the default "user true" and it put it in 

~/Library/Application Support/ChimeraX/0.91/site-packages/chimerax/segger

but the system path has this location after the ChimeraX app site-packages.  In order to allow a newer Segger to be installed from the toolshed and replace the ChimeraX built in version the user installed tools need to take precedence over the app installed tools.


Here is what ChimeraX reports at the system path.

import sys
sys.path

['/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python37.zip',
 '/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7',
 '/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/lib-dynload',
 '/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages',
 '/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/PyOpenGL-3.1.3b2-py3.7.egg',
 '/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/PyOpenGL_accelerate-3.1.3b1-py3.7-macosx-10.14-x86_64.egg',
 '/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/tables-3.4.4-py3.7-macosx-10.14-x86_64.egg',
 '/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/numexpr-2.6.9-py3.7-macosx-10.14-x86_64.egg',
 '/Users/goddard/Library/Application Support/ChimeraX/0.91/site-packages',
 '/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/IPython/extensions']

Log:
UCSF ChimeraX version: 0.91 (2019-06-25)  
© 2016-2019 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/goddard/ucsf/chimerax/src/bundles/segger/test.cxs format session

Summary of feedback from opening
/Users/goddard/ucsf/chimerax/src/bundles/segger/test.cxs  
---  
note | Showing 1080.seg - 14 regions, 14 surfaces  
  
opened ChimeraX session  

> toolshed show sh

/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/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")  




OpenGL version: 4.1 ATI-2.9.26
OpenGL renderer: AMD Radeon Pro 580 OpenGL Engine
OpenGL vendor: ATI Technologies Inc.

[Conrad Huang]

Should be fixed by 359b54eb0.

Before calling site.addsitedir insert user site directory at the front of sys.path. addsitedir will not add it a second time but will still do the .pth processing.

Tom, can you please confirm it works for Segger?

[goddard@…]

Yep, with the fix the user-only Segger bundle is found instead of the Segger that came with ChimeraX.