Make the API layer more conventional

[hrshdhgd]

For e.g.:
parse_file conventionally takes an input and returns object(s) but in our case, it takes a path, converts the data into SSSOM format and exports it (stdout or output file if path provided.).

Ref: Slack conversation with Chris.

[matentzn]

I agree, we should align the design here a bit with pandas.read_csv() etc