[MAINT] Update some missed tests and examples to use new standardize strategy to silence warnings

[ymzayek]

Follow-up to #3720 and Closes #3719 .

Changes proposed in this pull request:

[github-actions]

👋 @ymzayek 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.

Please make sure it is compliant with our contributing guidelines. In particular, be sure it checks the boxes listed below.

• PR has an interpretable title.
• PR links to Github issue with mention Closes #XXXX (see our documentation on PR structure)
• Code is PEP8-compliant (see our documentation on coding style)
• Changelog or what's new entry in doc/changes/latest.rst (see our documentation on PR structure)

For new features:

• There is at least one unit test per new function / class (see our documentation on testing)
• The new feature is demoed in at least one relevant example.

For bug fixes:

• There is at least one test that would fail under the original bug conditions.

We will review it as quick as possible, feel free to ping us with questions if needed.

[codecov]

Codecov Report

Merging #3821 (ef983f4) into main (787d662) will increase coverage by 0.00%.
The diff coverage is n/a.

@@           Coverage Diff           @@
##             main    #3821   +/-   ##
=======================================
  Coverage   91.53%   91.53%           
=======================================
  Files         133      133           
  Lines       15600    15623   +23     
  Branches     3246     3250    +4     
=======================================
+ Hits        14279    14301   +22     
  Misses        774      774           
- Partials      547      548    +1     

Flag	Coverage Δ
macos-latest_3.10	91.46% <ø> (+<0.01%)	⬆️
macos-latest_3.11	?
macos-latest_3.8	?
macos-latest_3.9	?
ubuntu-latest_3.10	91.46% <ø> (+<0.01%)	⬆️
ubuntu-latest_3.11	91.46% <ø> (+<0.01%)	⬆️
ubuntu-latest_3.8	91.42% <ø> (+<0.01%)	⬆️
ubuntu-latest_3.9	91.42% <ø> (+<0.01%)	⬆️
windows-latest_3.10	?
windows-latest_3.11	91.40% <ø> (+<0.01%)	⬆️
windows-latest_3.8	91.36% <ø> (+<0.01%)	⬆️
windows-latest_3.9	91.36% <ø> (+<0.01%)	⬆️

Flags with carried forward coverage won't be shown. Click here to find out more.

see 13 files with indirect coverage changes

📣 We’re building smart automated test selection to slash your CI/CD build times. Learn more

[ymzayek]

One issue with silencing all instances of this warning in our examples gallery is that the ones that are still throwing the warning come from the functions plot_carpet and ConnectivityMeasure.fit_transform which call signal.clean with the parameter standardize equal to True or "zscore" internally so these are not exposed to the user. Hence the warning doesn't make sense for these cases as the user has no control and cannot call the new behavior. Probably best to open a new issue to see how to resolve this. Might need to add a deprecated parameter to allow the user to access the new behavior with these functions.

The relevant lines are:

nilearn/nilearn/connectome/connectivity_matrices.py

Line 497 in bce754b

signal._standardize(x, detrend=False, standardize=True)

and

nilearn/nilearn/plotting/img_plotting.py

Line 1430 in bce754b

data = clean(data, t_r=t_r, detrend=True, standardize='zscore')

[Remi-Gau]

One issue with silencing all instances of this warning in our examples gallery is that the ones that are still throwing the warning come from the functions plot_carpet and ConnectivityMeasure.fit_transform which call signal.clean with the parameter standardize equal to True or "zscore" internally so these are not exposed to the user. Hence the warning doesn't make sense for these cases as the user has no control and cannot call the new behavior. Probably best to open a new issue to see how to resolve this. Might need to add a deprecated parameter to allow the user to access the new behavior with these functions.

Sounds good to me and thanks for tracking the source of all those warnings!

[bthirion]

LGTM overall.

[bthirion]

LGTM, thx.