adding cli.py for command line app use

[MrSqually]

This PR addresses #198 , by adding a "cli.py" template to the clams SDK. This script iterates over the "parameters" in a new app's metadata and parses them into argparse arguments. From here, it collects those arguments and stdin, runs app._annotate() , and produces the result to stdout

Review

Generally, I think the areas that I'm least sure about:

• Safer / more idiomatic access to stdin / stdout
• I didn't add the template to any scripts, if that's something needed

[keighrim]

I left some in-line comments. Also, for commit logs don't seem to be very informative anyway. If the commits are small, incremental changes, how about squash them during we're working in the PR, before merge the history into the main?

[codecov]

Codecov Report

Attention: Patch coverage is 26.53061% with 36 lines in your changes missing coverage. Please review.

Project coverage is 72.65%. Comparing base (392b4c8) to head (75a5be5).

Files	Patch %	Lines
clams/develop/__init__.py	12.82%	34 Missing ⚠️
clams/mmif_utils/rewind.py	50.00%	2 Missing ⚠️

Additional details and impacted files

@@             Coverage Diff             @@
##           develop     #217      +/-   ##
===========================================
- Coverage    73.94%   72.65%   -1.29%     
===========================================
  Files            9        9              
  Lines          756      779      +23     
===========================================
+ Hits           559      566       +7     
- Misses         197      213      +16     

Flag	Coverage Δ
unittests	72.65% <26.53%> (-1.29%)	⬇️

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[keighrim]

requesting review from @marcverhagen . Particularly regarding the documentation at https://github.com/clamsproject/clams-python/blob/a8ae2afc1e589976cf837f108ae85f60999092fe/documentation/clamsapp.md#using-clams-app-as-a-cli-program