Create virtual 4C tool

[Phlya]

API and CLI for virtual 4C.
No support for expected (for now?).

[Phlya]

Example how to use. Notice that using a viewpoint larger than binsize averages all bins within it, and masks out interactions inside the viewpoint.

[gfudenberg]

nice!
Couple q's:

• would it make sense to add an option to smooth via

  cooltools/cooltools/lib/numutils.py

  Line 994 in 51cc542

  def smooth(y, box_pts):

• should this go through sandbox first? or have a test?

[Phlya]

Can try to see what smoothing does to this! But I'm not sure there really is a reason to smooth this, idk...

Don't mind putting into sandbox first!

[Phlya]

For sandbox, is there a way to make the CLI accessible somehow?..

Instead of sandbox, add a note to the docstring that this is new and experimental

[Phlya]

And is there an example how to use the smooth function somewhere? I'm not sure what it does exactly, and how it works...

[Phlya]

For CLI tests to pass I had to add an empty return in the end, and assert that exit code==0, not ==1, any idea why? Otherwise the code was 2. In geneal, some of out tests assert code==0, and some==1. Why is that?

[agalitsyna]

Exit codes seems like a serious issue, e.g. see here (exit_code==1, but not 0 for no reason):

cooltools/tests/test_insulation.py

Line 23 in a86fbec

assert result.exit_code == 1

This is dangerous for the tests, because if it's actual mistake it can also naturally have exit_code 1 and it will be never captured by our tests.

One of the ways to debug it is to output stderr and stdout alongside with exit_code while creating tests: pallets/click#737

[Phlya]

I think in this case it's not an issue, since with an empty return statement at the end the code is 0. And I assume if there is an actual error it won't get to the return statement and will give an error-y code. So perhaps this should be a broader discussion in a separate issue? @agalitsyna

[Phlya]

@gfudenberg added a note that it's new and experimental, do you think it's enough?

[gfudenberg]

sounds good!

one question though: would these functions make more sense as part of cooler, if they don't modify/process in any way other than querying/balancing ?
cc @nvictus

[Phlya]

It's also averaging bins within the viewpoint...

[gfudenberg]

indeed!

[Phlya]

@gfudenberg any more comments?

[gfudenberg]

nope!

[Phlya]

Ok to merge?

[gfudenberg]

fine by me!