Add initialization of line_number to zero

- Add initialization of line_number to zero in the parse_file function
  because if the parsed file is empty, line_number is not initialized by
  the for loop which leads to a crash.
- Tidy some whitespace.
Add __init__.py for bin folder

- Add __init__.py for bin folder so modules can be imported for testing.
Add bin folder to tests and coverage
Add empty file parsing test for bin/parser.py