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[DOC] link terms to glossary #4038

Merged
merged 19 commits into from Oct 13, 2023
Merged

[DOC] link terms to glossary #4038

merged 19 commits into from Oct 13, 2023

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Remi-Gau
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@Remi-Gau Remi-Gau commented Oct 7, 2023 •
edited

Changes proposed in this pull request:

  • add script to help the terms are properly linked
  • link terms to glossary in doc
  • link terms to glossary in example
  • link terms to glossary in doc string of public functions

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github-actions bot commented Oct 7, 2023

👋 @Remi-Gau Thanks for creating a PR!

Until this PR is ready for review, you can include the [WIP] tag in its title, or leave it as a github draft.

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codecov bot commented Oct 7, 2023 •
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Codecov Report

Merging #4038 (552d49a) into main (00fcbae) will not change coverage.
Report is 3 commits behind head on main.
The diff coverage is n/a.

@@           Coverage Diff           @@
##             main    #4038   +/-   ##
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Flags with carried forward coverage won't be shown. Click here to find out more.

Files Coverage Δ
nilearn/_utils/data_gen.py 95.52% <ø> (ø)
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@Remi-Gau Remi-Gau marked this pull request as ready for review October 8, 2023 17:03
ymzayek
ymzayek reviewed Oct 9, 2023
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examples/02_decoding/plot_mixed_gambles_frem.py Outdated Show resolved Hide resolved
examples/04_glm_first_level/plot_first_level_details.py Outdated Show resolved Hide resolved
nilearn/datasets/func.py Outdated Show resolved Hide resolved
nilearn/datasets/func.py Outdated Show resolved Hide resolved
nilearn/datasets/neurovault.py Outdated Show resolved Hide resolved
examples/04_glm_first_level/plot_hrf.py Outdated Show resolved Hide resolved
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Remi-Gau commented Oct 9, 2023

oh that's one funky list of merge conflicts

image

Remi-Gau and others added 3 commits October 9, 2023 23:09
@Remi-Gau @ymzayek
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71caf82 
Co-authored-by: Yasmin <63292494+ymzayek@users.noreply.github.com>
@Remi-Gau @ymzayek
Update nilearn/datasets/func.py
80d0a72 
Co-authored-by: Yasmin <63292494+ymzayek@users.noreply.github.com>
@Remi-Gau @ymzayek
Update nilearn/datasets/func.py
b8cff52 
Co-authored-by: Yasmin <63292494+ymzayek@users.noreply.github.com>
@Remi-Gau
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Remi-Gau commented Oct 9, 2023

And of course I messed that conflict resolution... Well... Will reset and try again...

ymzayek
ymzayek approved these changes Oct 10, 2023
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Thanks for resolving that, I know it came from my PR :) LGTM!

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Thanks for resolving that, I know it came from my PR :) LGTM!

Yeah I think I actually need to redo the merge conflict resolution.

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ymzayek commented Oct 10, 2023

Ah ok, the diff and merge look fine to me but given all the affected files it's hard to tell so I'll let you handle it

bthirion
bthirion reviewed Oct 10, 2023
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Looks great. Just outline a few occurrences that may have been forgotten.

doc/glm/glm_intro.rst Outdated Show resolved Hide resolved
doc/glm/glm_intro.rst
@@ -141,7 +141,7 @@ i.e. values of ``z`` larger than the :math:`(1-\alpha)`-quantile of the standard
The first idea that one might think of is to take a much smaller :math:`\alpha`:
for instance, if we take, :math:`\alpha=\frac{0.05}{n\_voxels}`
then the expected number of false discoveries is only about 0.05, meaning
that there is a 5% chance that a truly inactive voxel is declared active.
that there is a 5% chance that a truly inactive :term:`voxel` is declared active.
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Unsure whether we really need to track all occurrences of 'voxels' ;-)

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Trust me: I left some out. 😉

doc/glm/second_level_model.rst Outdated Show resolved Hide resolved
examples/01_plotting/plot_overlay.py Show resolved Hide resolved
examples/02_decoding/plot_haxby_glm_decoding.py Show resolved Hide resolved
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nilearn/_utils/data_gen.py Show resolved Hide resolved
nilearn/interfaces/bids/glm.py Outdated Show resolved Hide resolved
bthirion
bthirion approved these changes Oct 12, 2023
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LGTM, thx.

@Remi-Gau @bthirion
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Co-authored-by: bthirion <bertrand.thirion@inria.fr>
@Remi-Gau Remi-Gau merged commit b6f4ff0 into nilearn:main Oct 13, 2023
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@Remi-Gau Remi-Gau deleted the glossary branch October 13, 2023 10:22
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@ymzayek ymzayek ymzayek approved these changes

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Add link to glossary terms in doc strings of public functions
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@Remi-Gau @ymzayek @bthirion