[MAINT] Expose standardize parameter in function signatures to allow handling of deprecation

[ymzayek]

• Closes Silence standardize deprecation warnings not possible with functions that set parameter internally  #3825

Changes proposed in this pull request:

• Add standardize parameter to plot_carpet and ConnectivityMeasure so users can deal with "zscore" deprecation
• Update examples
• Update/add tests that warnings are not raised with new input

[github-actions]

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[codecov]

Codecov Report

Merging #3927 (44b71df) into main (457c79e) will decrease coverage by 0.02%.
Report is 6 commits behind head on main.
The diff coverage is 100.00%.

@@            Coverage Diff             @@
##             main    #3927      +/-   ##
==========================================
- Coverage   91.76%   91.75%   -0.02%     
==========================================
  Files         134      134              
  Lines       15747    15751       +4     
  Branches     3283     3283              
==========================================
+ Hits        14451    14453       +2     
- Misses        752      753       +1     
- Partials      544      545       +1     

Flag	Coverage Δ
macos-latest_3.10	91.68% <100.00%> (?)
macos-latest_3.11	91.68% <100.00%> (?)
macos-latest_3.8	91.64% <100.00%> (?)
macos-latest_3.9	91.64% <100.00%> (?)
ubuntu-latest_3.10	91.68% <100.00%> (+<0.01%)	⬆️
ubuntu-latest_3.11	91.68% <100.00%> (+<0.01%)	⬆️
ubuntu-latest_3.8	91.64% <100.00%> (?)
ubuntu-latest_3.9	91.64% <100.00%> (+<0.01%)	⬆️
windows-latest_3.10	91.62% <100.00%> (?)
windows-latest_3.11	?
windows-latest_3.8	?

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

Files Changed	Coverage Δ
nilearn/regions/region_extractor.py	97.94% <ø> (ø)
nilearn/connectome/connectivity_matrices.py	94.44% <100.00%> (+0.03%)	⬆️
nilearn/plotting/img_plotting.py	89.13% <100.00%> (-0.41%)	⬇️

... and 4 files with indirect coverage changes

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[bthirion]

LGTM so far, but we need to check that the behavior of the examples is still fine.

[ymzayek]

Showing main branch build versus changes in this PR for affected examples:

plot_carpet: main version vs this pr

plot_atlas_comparison: main version vs this pr

plot_extract_regions_dictlearning_maps: main version vs this pr

plot_group_level_connectivity: main version vs this pr

plot_probabilistic_atlas_extraction: main version vs this pr

plot_signal_extraction: main version vs this pr

plot_sphere_based_connectome: main version vs this pr

plot_age_group_prediction_cross_val: main version vs this pr

[ymzayek]

Is there a reason that standardize_confounds was not passed to RegionExtractor?

[bthirion]

Thx ! LGTM

[bthirion]

No, I think it was simply forgotten.

[Remi-Gau]

had a look yesterday and it LGTM
let me know if something else needs reviewing otherwise I think this can be merged

[ymzayek]

Ok should be good to go once the CI passes