Enable doctests

[tsalo]

Closes none.

Changes proposed in this pull request

• Create a separate CircleCI job to run doctests, which should improve test coverage.

[tsalo]

The only failing doctests now are ones we want to pass, so I think I can transition from getting the workflow configured to fixing up the actual tests.

[tsalo]

There is a mismatch between the expected behavior of the doctest in get_highest_priority_fieldmap and its actual behavior:

https://github.com/PennLINC/qsiprep/blob/317828fe70ea8be7a6fe7b5f86bb521902c5f503/qsiprep/utils/grouping.py#L257-L259

Expected:
    {'suffix': 'epi', 'epi': ['/data/sub-1/fmap/sub-1_dir-AP_run-1_epi.nii.gz']}
Got:
    {'suffix': 'dwi', 'dwi': ['/data/sub-1/dwi/sub-1_dir-AP_run-1_dwi.nii.gz', '/data/sub-1/dwi/sub-1_dir-AP_run-2_dwi.nii.gz', '/data/sub-1/dwi/sub-1_dir-AP_run-3_dwi.nii.gz']}

We expect the EPI field map to be used, but the rpe DWI file is selected instead. @mattcieslak any ideas?

[mattcieslak]

I think we would want to use the dwi instead of the epi if there is a dwi available that can be used for distortion correction

[tsalo]

Sounds good. I changed the documentation and test to reflect that.

[tsalo]

doctests are now passing 🎉

[codecov-commenter]

Codecov Report

:white_check_mark: All modified and coverable lines are covered by tests. :white_check_mark: Project coverage is 48.27%. Comparing base (317828f) to head (db2306e).

Additional details and impacted files

@@            Coverage Diff             @@
##           master     #926      +/-   ##
==========================================
+ Coverage   46.02%   48.27%   +2.25%     
==========================================
  Files          65       65              
  Lines        9764     9764              
  Branches     1074     1074              
==========================================
+ Hits         4494     4714     +220     
+ Misses       5044     4831     -213     
+ Partials      226      219       -7     

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[tsalo]

nice little coverage bump too

[tsalo]

I'm not sure why tests were passing before TBH. The current failure is due to missing datasets, which makes sense.