updated build_tree code

[nick-youngblut]

Switched to os.path.join and os.makedirs for paths. Switched to f" " and sys.stderr.write for string formatting and writing updates to the console.

@liaoherui you may want to consider using codon to speed up at least some of the python functions in build_tree and other parts of the codebase.

[liaoherui]

Thanks! I will check the codes and merge them! Also, appreciate for the suggestions about using "codon". I will see whether I can use it to speed up the program!