run doctests

[flying-sheep]

This PR adds the --doctest-modules flag to pytest and makes changes necessary to allow the doctests to run.

Those changes include:

• Fixing verbosity
• using pytest-doctestplus to skip doctests entirely or when their dependencies are absent
• fixing broken doctests (the bulk of the changes)

[codecov]

Codecov Report

Merging #2605 (f2c2a52) into master (ec7f925) will increase coverage by 1.01%.
Report is 7 commits behind head on master.
The diff coverage is 82.39%.

❗ Current head f2c2a52 differs from pull request most recent head ad29ca5. Consider uploading reports for the commit ad29ca5 to get more accurate results

Additional details and impacted files

@@            Coverage Diff             @@
##           master    #2605      +/-   ##
==========================================
+ Coverage   71.99%   73.01%   +1.01%     
==========================================
  Files         107      109       +2     
  Lines       11914    12038     +124     
==========================================
+ Hits         8577     8789     +212     
+ Misses       3337     3249      -88     

Files	Coverage Δ
scanpy/cli.py	93.50% <100.00%> (ø)
scanpy/datasets/_datasets.py	85.71% <100.00%> (+16.18%)	⬆️
scanpy/external/pl.py	49.21% <100.00%> (+0.39%)	⬆️
scanpy/external/pp/_harmony_integrate.py	81.81% <100.00%> (ø)
scanpy/external/pp/_hashsolo.py	89.38% <100.00%> (ø)
scanpy/external/pp/_magic.py	86.11% <100.00%> (+0.39%)	⬆️
scanpy/external/pp/_scanorama_integrate.py	86.95% <100.00%> (+0.59%)	⬆️
scanpy/external/tl/_harmony_timeseries.py	28.00% <100.00%> (+3.00%)	⬆️
scanpy/external/tl/_palantir.py	25.00% <100.00%> (+2.41%)	⬆️
scanpy/external/tl/_phate.py	35.00% <100.00%> (+3.42%)	⬆️
... and 33 more

... and 4 files with indirect coverage changes

[flying-sheep]

It’s unblocked again apparently!

[flying-sheep]

@ivirshup any way to force Azure to clear its cache or use a different runner? The “invalid instruction” error here probably comes from using a binary wheel compiled for a newer CPU.

/edit: wow, 9 attempts. Maybe just dropping Python 3.8 will get us there.

[Zethson]

Scientific Python even deprecated Python 3.9 this month. Kill 3.8 please...

[flying-sheep]

For sure, but it won’t help with this issue, I had to merge #2687 for that.

[ivirshup]

Is this ready for review? I think it mostly looks good.

drop 3.8

If our dependencies have dropped support we can too.

---

Have you thought about doctestplus in the context of this PR?

[flying-sheep]

If our dependencies have dropped support we can too.

You mean like anndata? 😆

Is this ready for review? I think it mostly looks good.

yeah!

[flying-sheep]

@ivirshup ping

[flying-sheep]

TODO: check out doctest-plus, if it helps enough, switch to it, then merge

[flying-sheep]

OK, doctest-plus can’t even handle relative imports, and doesn’t respect --import-mode.

It needs quite some work before it works for us.