Ignore .venv* when using multiple virtualenvs
Move the C files into /lib
Move count code into codonpdx module
Disable pretty print json formatting by default

This commit adds a -p and --pretty flag to enable pretty print
json. By default pretty printing is disabled to avoid a performance
penalty.

Fixes #5
Merge pull request #10 from PDX-Flamingo/refactor_into_pyproject

Refactor to use standard py project layout