Hi Latif, 

Sorry for the trouble.  As Mauro said, some of the packages needed (and pymatgen is one of these) are not super-well supported for installing with pip. 

FWIW, I agree that the needed combination of conda and pip is sort of unfortunate.  But most of the "problem packages" are either Windowing systems (wxPython: that have been challenging to have consistent binary support on Linux is very challenging) or packages of scientific code written by and for scientists, some with excellent engineering support and some (like us!) with "less" support.   Conda is a popular option for many of these.  We try to support the simpler / more ubiquitous pip where we can. 

Anyway, that's basically why we have the binary installers and installation scripts.  But also: thanks for the report and we are trying to clean up or at least document some of these kinds of issues where we can: https://github.com/xraypy/xraylarch/issues/333

--Matt