Move notebooks to separate directory; enhance makefile

[dominikmn]

• Moving the notebooks to a separate directory (Issue #18 and #139)
  • Move the notebook files to ./notebooks
  • Adapt the paths in the notebook files (like ../data)
  • Adapt scripts in ./utils/
  • Adding setup.py (by which the utils are loaded as local package)
  • Adapt requirements.txt
  • Adapt README.md
• Minor improvements on the makefile
  • Issue #140 (remove setup.sh)
  • Issue #141 (ask user to install pytorch manually)