mne-tools / mne-connectivity

Connectivity algorithms that leverage the MNE-Python API.
https://mne.tools/mne-connectivity/dev/index.html
BSD 3-Clause "New" or "Revised" License
68 stars 34 forks source link

[MRG] Fix docs and numpydoc #41

Closed adam2392 closed 3 years ago

adam2392 commented 3 years ago

PR Description

Closes: #38

Adds numpydoc to circleCI sphinx build and fixes numpydoc errors/warnings.

Merge checklist

Maintainer, please confirm the following before merging:

larsoner commented 3 years ago

CircleCI failure is fixed by #36. I fixed a conflict there, will then merge that and rerun here after fixing the verbose stuff I mention above

adam2392 commented 3 years ago

I'm not sure why but adding the verbose decorator from MNE and then the fill_doc from MNE-connectivity gives these additional weird errors that are not fixable?

reading sources... [100%] whats_new_previous_releases                                                                              
WARNING: [numpydoc] Validation warnings while processing docstring for 'mne_connectivity.phase_slope_index':
  PR09: Parameter "mt_low_bias" description should finish with "."

WARNING: [numpydoc] Validation warnings while processing docstring for 'mne_connectivity.phase_slope_index':
  PR09: Parameter "mt_low_bias" description should finish with "."

/Users/adam2392/Documents/mne-connectivity/mne_connectivity/effective.py:docstring of mne_connectivity.effective.phase_slope_index:83: WARNING: Inline substitution_reference start-string without end-string.
/Users/adam2392/Documents/mne-connectivity/mne_connectivity/effective.py:docstring of mne_connectivity.effective.phase_slope_index:83: WARNING: Inline substitution_reference start-string without end-string.
/Users/adam2392/Documents/mne-connectivity/mne_connectivity/effective.py:docstring of mne_connectivity.effective.phase_slope_index:83: WARNING: Inline substitution_reference start-string without end-string.
/Users/adam2392/Documents/mne-connectivity/mne_connectivity/effective.py:docstring of mne_connectivity.effective.phase_slope_index:83: WARNING: Inline substitution_reference start-string without end-string.
/Users/adam2392/Documents/mne-connectivity/mne_connectivity/effective.py:docstring of mne_connectivity.effective.phase_slope_index:83: WARNING: Inline substitution_reference start-string without end-string.
/Users/adam2392/Documents/mne-connectivity/mne_connectivity/effective.py:docstring of mne_connectivity.effective.phase_slope_index:83: WARNING: Inline substitution_reference start-string without end-string.
/Users/adam2392/Documents/mne-connectivity/mne_connectivity/effective.py:docstring of mne_connectivity.effective.phase_slope_index:83: WARNING: Inline substitution_reference start-string without end-string.
/Users/adam2392/Documents/mne-connectivity/mne_connectivity/effective.py:docstring of mne_connectivity.effective.phase_slope_index:83: WARNING: Inline substitution_reference start-string without end-string.
/Users/adam2392/Documents/mne-connectivity/mne_connectivity/effective.py:docstring of mne_connectivity.effective.phase_slope_index:83: WARNING: Inline substitution_reference start-string without end-string.
looking for now-outdated files... none found
pickling environment... done
checking consistency... done
preparing documents... done
writing output... [100%] whats_new_previous_releases                                                                               
/Users/adam2392/Documents/mne-connectivity/mne_connectivity/effective.py:docstring of mne_connectivity.effective.phase_slope_index:83: WARNING: py:obj reference target not found: mne.stats.{}
/Users/adam2392/Documents/mne-connectivity/mne_connectivity/effective.py:docstring of mne_connectivity.effective.phase_slope_index:83: WARNING: py:obj reference target not found: EpochsTFR
/Users/adam2392/Documents/mne-connectivity/mne_connectivity/effective.py:docstring of mne_connectivity.effective.phase_slope_index:83: WARNING: py:obj reference target not found: AverageTFR
/Users/adam2392/Documents/mne-connectivity/mne_connectivity/effective.py:docstring of mne_connectivity.effective.phase_slope_index:83: WARNING: py:func reference target not found: eeglabio.utils.cart_to_eeglab
/Users/adam2392/Documents/mne-connectivity/mne_connectivity/effective.py:docstring of mne_connectivity.effective.phase_slope_index:83: WARNING: py:func reference target not found: dipy.align._public.affine_registration
larsoner commented 3 years ago

Some of those are %-related issues, others are intersphinx. Will push a commit...

larsoner commented 3 years ago

Also fixed a bug where the maint/0.2 and here had the drop-down link to mne-bids instead of mne-connectivity versions, and also the v0.2 linked to a non-existent directory (v0.2 rather than stable)

adam2392 commented 3 years ago

Thanks @larsoner for the catches