The current pymol sources don't appear to compile the python scripts in the modules directory (at least as we are installing them under MacPorts https://github.com/macports/macports-ports/blob/master/science/pymol/Portfile ). Oddly all the python scropts outside of the modules subdirectory are properly compiled. Any idea why this is happening?
FYI, the current 2.1.0 release with PyQt support can be built under MacPorts with the proposed packaging changes at https://trac.macports.org/ticket/56139 .
Last edit: Jack Howarth 2018-04-19
The actual problem stems from setup.py not installing the modules directory. Is there a reason why we have to manually install that directory?
what do you mean by it's not installed? What's your manual step?
This is using the MacPorts python packaging for the 2.7 and 3.x series using the Python port group for installing python packages.
https://guide.macports.org/chunked/reference.portgroup.html
which should be installing pymol with....
${python.bin} setup.py install --no-user-cfg --prefix=${python.prefix} --root=${destroot}
Note that the fink packaging system sees the same issue...
https://github.com/fink/fink-distributions/blob/master/10.9-libcxx/stable/main/finkinfo/sci/pymol-py.info
and the modules subdirectory has to be explicitly copied over there as well. So it seems that the install method in setup.py doesn't consider the modules subdirectory.
Last edit: Jack Howarth 2018-04-20
Does the incentive build install the modules subdirectory? I don't recall it having APBS Tools plugin. Perhaps it has been omitted by accident because of that.
The problem is in the fink and macports packaging which was based on a much earlier behavior of PYMOL_PATH. Setting it to
PYMOL_PATH=/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/pymol/pymol_path
instead of
PYMOL_PATH=/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/pymol
eliminated the need for the redundant installation of the subdirectories associated with pymol_path.
is this issue resolved for you? It works fine in my hands, doing "/opt/local/bin/python setup.py --no-user-cfg install --prefix=... --root=..." installs everything.