Python shell scripts refer to wrong install location

[tic20@…]

The Python shell script included in Linux ChimeraX in the bin directory point to the wrong install location. For example, the "pip" executable shell script starts with

#!/var/tmp/chimerax_build/develop/chimerax/ChimeraX.app/bin/python3.5

I guess it require a Linux installer to fix all of these paths when ChimeraX is installed. Currently the Linux build is simply a tar.gz file with no installer. I don't know which of the shell scripts that use Python (there are more than 30 of them) are needed.

Begin forwarded message:

From: Tristan Croll
Subject: Re: Fix to depth cueing
Date: October 7, 2016 at 2:47:33 AM PDT
To: Tom Goddard

Another ~bug I should mention: in the Linux build, at the moment all the python-dependent executables in .../chimerax/bin have the path to python hard-coded as /var/tmp/chimerax_build/develop/chimerax/ChimeraX.app/bin/python3.5. I just replaced it with the path I decompressed to, and everything (well, at least pyuic5...) seems to be happy.

[Tom Goddard]

Tristan, I'm curious which ChimeraX bin shell script were you trying to use? pip for installing a new package in Python?

[tic20@…]

Just pyuic5, to generate Python code from a Qt Designer .ui file. It worked happily after I updated the path to the python executable.

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

 

[Greg Couch]

I see that there are many scripts in ChimeraX.app/bin that have this problem.

The solution in most (all?) cases is to use 'ChimeraX.app/bin/ChimeraX -m module' instead of the shell script, in this case it would be:

ChimeraX -m PyQt5.uic.pyuic

And the fix will be to remove all of those shell scripts.

-- Greg

[Greg Couch]

Python scripts are now removed from the application to avoid them appearing as if they should work.