update bbknn arguments and docstring

[ktpolanski]

Updated sc.external.pp.bbknn() to match current arguments and docstring.

[codecov]

Codecov Report

Merging #1868 (7526663) into master (4dd8de9) will not change coverage.
The diff coverage is 100.00%.

@@           Coverage Diff           @@
##           master    #1868   +/-   ##
=======================================
  Coverage   71.22%   71.22%           
=======================================
  Files          92       92           
  Lines       11181    11181           
=======================================
  Hits         7964     7964           
  Misses       3217     3217           

Impacted Files	Coverage Δ
scanpy/external/pp/_bbknn.py	58.33% <100.00%> (ø)

[ktpolanski]

It seems this is of some relevance to users, as shown by it showing up twice independently over the course of the past week.

For some reason, my tweaks have killed off ReadTheDocs, and I can't check why as upon pressing the "details" button I get the 404 equivalent :) I am now importing types so I can correctly define metric as also including types.FunctionType. This is probably what is causing whatever hiccup is happening.

@giovp , some assistance with getting the ball rolling on this? The changes are a result of me expanding BBKNN with pynndescent on your recommendation.

[pinin4fjords]

@ktpolanski following from https://scanpy.readthedocs.io/en/stable/dev/code.html#code-style and building the docs locally gives me (among some errors that were not relevant):

...
/path/to/scanpy/scanpy/external/pp/_bbknn.py:docstring of scanpy.external.pp._bbknn.bbknn:28: WARNING: py:class reference target not found: function
/path/to/scanpy/scanpy/external/pp/_bbknn.py:docstring of scanpy.external.pp._bbknn.bbknn:28: WARNING: py:class reference target not found: function
...

Maybe that gives you some pointers?

[ktpolanski]

I ran pip3 install scanpy[doc], as instructed by that page, and the doc seems to have built fine locally.

The only fishy thing is the function is not clickable, while the other two are, but it built.

Also, line 28 is trim: Optional[int] = None,, which was there previously already. It's the metric change that's causing this - your argument renaming PR did not hiccup.

[pinin4fjords]

Hmm, I'm stumped. @ivirshup ?

[ivirshup]

The only fishy thing is the function is not clickable, while the other two are, but it built

I think this is it. The error I see is:

sphinx.errors.SphinxWarning: /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1868/scanpy/external/pp/_bbknn.py:docstring of scanpy.external.pp._bbknn.bbknn:28:py:class reference target not found: function

Warning, treated as error:
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1868/scanpy/external/pp/_bbknn.py:docstring of scanpy.external.pp._bbknn.bbknn:28:py:class reference target not found: function

I don't think the 'types.FunctionType' needs to be quoted, but we've used collections.abc.Callable in other places without issue.

[ivirshup]

Could the representation be chosen with keywords like obsm, layers? You can use the helper functions sc.get._get_obs_rep and sc .get._set_obs_rep.

[ktpolanski]

I can't get it to work. I have unquoted types.FunctionType, and function remains unclickable. I have tried to switch to an collections.abc.Callable, and instead of anything helping the entire argument support vanishes:

Please help?

[ivirshup]

I think that should do it. I believe the types module isn't actually meant to be used for type annotations, that's what the typing module is for (which is always confusing to me).

and instead of anything helping the entire argument support vanishes:

I got this behaviour too, but running make clean and building from scratch got things working again. ¯_(ツ)_/¯

[ktpolanski]

Thanks a lot for the help, assuming things are in order then that's it for me.

[ivirshup]

Thanks for the update!