process_subways.py and stop_areas/serve.py are independent applications, so separate the requirements.
shapely package is needed only if scripts/process_subways.sh is used which is not always the case.
Also update package versions to the latest stable.
process_subways.pyandstop_areas/serve.pyare independent applications, so separate the requirements.shapelypackage is needed only ifscripts/process_subways.shis used which is not always the case. Also update package versions to the latest stable.