Codecov Report

Merging #1279 (dbc4f26) into latest (63f545b) will increase coverage by 5.26%.
The diff coverage is 93.10%.

@@            Coverage Diff             @@
##           latest    #1279      +/-   ##
==========================================
+ Coverage   88.69%   93.96%   +5.26%     
==========================================
  Files         125       98      -27     
  Lines       18281    14677    -3604     
  Branches     1440     1438       -2     
==========================================
- Hits        16215    13791    -2424     
+ Misses       1819      640    -1179     
+ Partials      247      246       -1     

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sourmash.sourmash_args docstring says:
"Utility functions for dealing with input args to the sourmash command line."

At this point, shouldn't we actually move functions like sourmash_args.load_file_as_signatures and sourmash_args.load_database into the sourmash module instead, since they are useful in general (especially when using notebooks) and move any remaining functions in sourmash.sourmash_args into sourmash.cli?

sourmash.sourmash_args docstring says:
"Utility functions for dealing with input args to the sourmash command line."

At this point, shouldn't we actually move functions like sourmash_args.load_file_as_signatures and sourmash_args.load_database into the sourmash module instead, since they are useful in general (especially when using notebooks) and move any remaining functions in sourmash.sourmash_args into sourmash.cli?

hmm, I am making load_file_as_signatures and load_database available at the top level, yes, but I wasn't planning on defining them in __init__.py because I like keeping that short. I'm amenable to moving them away from sourmash_args but not sure where?

The cli submodule closely mirrors the actual CLI in structure, which I like. The functions in sourmash_args, by contrast, are used extensively by the sourmash.commands module (and related), and would seem to fit better in a command_utils module than under cli. (I seem to recall we have an issue somewhere about making sourmash more usable via the Python API and providing a way to use the commands in a notebook-friendly way, but I can't find that issue now; my memory is that it's relevant here because it talks about where to put Python-usable functions.)

It's also worth noting that sourmash_args is a bit of a dogs breakfast of odds and ends...

I think this is ready for review, @luizirber