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[DOC, MRG] Minor documentation improvements and remove glossary entry for array-like#11207

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drammock merged 7 commits intomne-tools:mainfrom
mscheltienne:doc-format
Sep 27, 2022
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[DOC, MRG] Minor documentation improvements and remove glossary entry for array-like#11207
drammock merged 7 commits intomne-tools:mainfrom
mscheltienne:doc-format

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@mscheltienne mscheltienne commented Sep 26, 2022

A couple of minor formatting fixes, and I removed the entry for array-like in favor of the one defined in the numpy glossary.

Also looking if I can figure out which CSS variable to override to format terms in the same way as py:obj.

Screenshot 2022-09-26 at 13 59 10

agramfort
agramfort reviewed Sep 26, 2022
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@mscheltienne can you share a link to the rendered doc for us to see how it impacts doc? 🙏

mne/utils/docs.py
)
docdict['method_psd'] = _method_psd.format('', '')
docdict['method_psd_auto'] = _method_psd.format(" | 'auto'", '')
docdict['method_psd_auto'] = _method_psd.format(" | ``'auto'``", '')
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@agramfort agramfort Sep 26, 2022

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are these changes consistent with the rest of the docstrings?

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@mscheltienne mscheltienne Sep 26, 2022

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They are, if I did not make a mistake. I'll check and share the links to the render doc as soon as it's built.

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in fact we're not systematic about using double-backticks in docstrings when specifying specific strings allowed as parameter values. In a few cases they are mandatory (I think if it's a tuple maybe?). But in most cases we don't include the double backticks (see, for example, outlines : 'head' | 'skirt' | dict | None or ch_type : ‘mag’ | ‘grad’ | ‘planar1’ | ‘planar2’ | ‘eeg’ | None

However, it does look better the way you've done it here, so maybe we should slowly move toward including double-backticks.

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mscheltienne commented Sep 26, 2022

Spectrum class: removes the whitespace before the [k] reference, add the missing footbibliography directives, and format the argument method with double backticks.

Same for EpochsSpectrum class.

Add references and footbiliography to psd_array_welch and psd_array_multitaper functions:

Good to merge on my end, I haven't figured out which CSS variable had to be changed to format the terms in the same way as py:obj. I'll look into it again in another PR.

@mscheltienne mscheltienne changed the title [DOC] Minor documentation improvements and remove glossary entry for array-like [DOC, MRG] Minor documentation improvements and remove glossary entry for array-like Sep 26, 2022
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agramfort approved these changes Sep 26, 2022
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@drammock ok for you?

@drammock drammock merged commit e10b1da into mne-tools:main Sep 27, 2022
@mscheltienne mscheltienne deleted the doc-format branch September 27, 2022 14:22
larsoner added a commit to drammock/mne-python that referenced this pull request Sep 28, 2022
@larsoner
Merge remote-tracking branch 'upstream/main' into fix-mesh-display
c5b4198 
* upstream/main:
  MAINT: Fix CircleCI error (mne-tools#11205) [circle deploy]
  Add regression-based approach to removing EOG artifacts (mne-tools#11046)
  [DOC, MRG] Minor documentation improvements and remove glossary entry for array-like (mne-tools#11207)
  Fix `include_tmax` not considered in `mne.io.Raw.crop` to check `tmax` in bounds (mne-tools#11204)
  MAINT: Fix notebook backend (mne-tools#11206)
  MRG: Fix displayed Raw duration in Jupyter notebook (mne-tools#11203)
  add EpochsSpectrum.average() (mne-tools#11198)
larsoner added a commit to alexrockhill/mne-python that referenced this pull request Sep 28, 2022
@larsoner
Merge remote-tracking branch 'upstream/main' into stc
e1414ad 
* upstream/main:
  MAINT: Fix CircleCI error (mne-tools#11205) [circle deploy]
  Add regression-based approach to removing EOG artifacts (mne-tools#11046)
  [DOC, MRG] Minor documentation improvements and remove glossary entry for array-like (mne-tools#11207)
  Fix `include_tmax` not considered in `mne.io.Raw.crop` to check `tmax` in bounds (mne-tools#11204)
  MAINT: Fix notebook backend (mne-tools#11206)
  MRG: Fix displayed Raw duration in Jupyter notebook (mne-tools#11203)
  add EpochsSpectrum.average() (mne-tools#11198)
  reduce memory [circle deploy] (mne-tools#11199)
  [BUG, MRG] Fix bug in find_bads_muscle (mne-tools#11197)
  BUG: Fix bug with long legend labels (mne-tools#11181)
larsoner added a commit to drammock/mne-python that referenced this pull request Sep 28, 2022
@larsoner
Merge remote-tracking branch 'upstream/main' into standardize-topomap…
0267853 
…-args

* upstream/main:
  Fix mesh display in tutorial (mne-tools#11200)
  MAINT: Add arm64 CI using CirrusCI (mne-tools#11209)
  Fix spatial colors (mne-tools#11201)
  MAINT: Fix CircleCI error (mne-tools#11205) [circle deploy]
  Add regression-based approach to removing EOG artifacts (mne-tools#11046)
  [DOC, MRG] Minor documentation improvements and remove glossary entry for array-like (mne-tools#11207)
  Fix `include_tmax` not considered in `mne.io.Raw.crop` to check `tmax` in bounds (mne-tools#11204)
  MAINT: Fix notebook backend (mne-tools#11206)
  MRG: Fix displayed Raw duration in Jupyter notebook (mne-tools#11203)
  add EpochsSpectrum.average() (mne-tools#11198)
@sappelhoff sappelhoff mentioned this pull request Sep 29, 2022
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larsoner added a commit to larsoner/mne-python that referenced this pull request Oct 11, 2022
@larsoner
Merge remote-tracking branch 'upstream/main' into fix_fnirschannelmerge
6f62a9d 
* upstream/main: (64 commits)
  MAINT: Better check (mne-tools#11229)
  MAINT: Fix link and update instantiation note (mne-tools#11228)
  BUG: Add estimated fiducials when missing / assumed head coords (mne-tools#11212)
  Fix tfr db (mne-tools#11223)
  MAINT: Update link (mne-tools#11222)
  add CPGRL doc section (mne-tools#11216)
  Don't insert superfluous newlines in subprocess log messages (mne-tools#11219)
  purge _get_args helper func (mne-tools#11215)
  Standardize topomap args (mne-tools#11123)
  MAINT: Ensure no datasets are downloaded in tests (mne-tools#11213)
  MAINT: Fix Cirrus caching (mne-tools#11211)
  Fix mesh display in tutorial (mne-tools#11200)
  MAINT: Add arm64 CI using CirrusCI (mne-tools#11209)
  Fix spatial colors (mne-tools#11201)
  MAINT: Fix CircleCI error (mne-tools#11205) [circle deploy]
  Add regression-based approach to removing EOG artifacts (mne-tools#11046)
  [DOC, MRG] Minor documentation improvements and remove glossary entry for array-like (mne-tools#11207)
  Fix `include_tmax` not considered in `mne.io.Raw.crop` to check `tmax` in bounds (mne-tools#11204)
  MAINT: Fix notebook backend (mne-tools#11206)
  MRG: Fix displayed Raw duration in Jupyter notebook (mne-tools#11203)
  ...
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@mscheltienne @agramfort @drammock