Python 3 update and installation improvements

[conchoecia]

Summary

• Updates dip-c for Python 3 compatibility, easier installation of dependencies, and adds "getting started" documentation.

Changes

• Python 3 Compatibility (commits: 51de989, ff32f80, d231dd4)
  • iterator formatting
  • print statements
  • file read/write differences between python2 and python3
• Easier install with "git clone / cd / make " pattern common in bioinformatics
• Updated Python 2 syntax to Python 3
• Fixed some whitespace and formatting
• Verified all dependencies work with Python 3

Added "Getting Started" section with installation commands:

Testing

• Tested with Python 3.10 on Stanford Sherlock
• No breaking changes to API or CLI
• Backward compatible with existing workflows. Works with calls to the containing ${folder}/dip-c align, et cetera.

Requesting a PR now because the next major changes will enable dip-c to be installed with the conda and pypi package managers.

CAVEAT:

• pymol command code needs testing