[MAINT] nilearn.interface: make private functions used outside of their module public

[Remi-Gau]

• Relates to Check for inconsistent naming of functions according to PEP8 convention #3319

Changes proposed in this pull request:

• remove nilearn.interface.bids._utils and move functions closer to where they are used or into a new nilearn.interface.bids.utils
• make private functions public if used in nilearn.interface.fmriprep used outside of their module

[Remi-Gau]

Several functions interfaces/fmriprep seem to be unused in the code base.

@htwangtw is this to be expected?

• '_load_motion' mentioned only 1 time in nilearn/interfaces/fmriprep/load_confounds_components.py.
• '_load_high_pass' mentioned only 1 time in nilearn/interfaces/fmriprep/load_confounds_components.py.
• '_load_wm_csf' mentioned only 1 time in nilearn/interfaces/fmriprep/load_confounds_components.py.
• '_load_global_signal' mentioned only 1 time in nilearn/interfaces/fmriprep/load_confounds_components.py.
• '_load_compcor' mentioned only 1 time in nilearn/interfaces/fmriprep/load_confounds_components.py.
• '_load_ica_aroma' mentioned only 1 time in nilearn/interfaces/fmriprep/load_confounds_components.py.
• '_load_scrub' mentioned only 1 time in nilearn/interfaces/fmriprep/load_confounds_components.py.
• '_load_non_steady_state' mentioned only 1 time in nilearn/interfaces/fmriprep/load_confounds_components.py.

[github-actions]

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[codecov]

Codecov Report

Attention: 3 lines in your changes are missing coverage. Please review.

Comparison is base (092c339) 91.97% compared to head (19da3e9) 92.00%.

Files	Patch %	Lines
nilearn/interfaces/bids/utils.py	90.90%	0 Missing and 2 partials ⚠️
nilearn/interfaces/bids/glm.py	97.22%	0 Missing and 1 partial ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #4168      +/-   ##
==========================================
+ Coverage   91.97%   92.00%   +0.02%     
==========================================
  Files         146      145       -1     
  Lines       16382    16378       -4     
  Branches     3431     3431              
==========================================
+ Hits        15068    15069       +1     
+ Misses        771      768       -3     
+ Partials      543      541       -2     

Flag	Coverage Δ
macos-latest_3.10_test_plotting	91.78% <97.45%> (+0.02%)	⬆️
macos-latest_3.11_test_plotting	91.78% <97.45%> (+0.02%)	⬆️
macos-latest_3.12_test_plotting	?
macos-latest_3.8_test_plotting	?
macos-latest_3.9_test_plotting	91.75% <97.45%> (+0.02%)	⬆️
ubuntu-latest_3.10_test_plotting	91.78% <97.45%> (+0.02%)	⬆️
ubuntu-latest_3.11_test_plotting	91.78% <97.45%> (+0.02%)	⬆️
ubuntu-latest_3.12_test_plotting	91.78% <97.45%> (+0.02%)	⬆️
ubuntu-latest_3.12_test_pre	91.78% <97.45%> (+0.02%)	⬆️
ubuntu-latest_3.8_test_min	68.97% <72.88%> (-0.01%)	⬇️
ubuntu-latest_3.8_test_plot_min	91.50% <97.45%> (+0.02%)	⬆️
ubuntu-latest_3.8_test_plotting	91.74% <97.45%> (+0.02%)	⬆️
ubuntu-latest_3.9_test_plotting	91.75% <97.45%> (+0.02%)	⬆️
windows-latest_3.10_test_plotting	91.76% <97.45%> (+0.02%)	⬆️
windows-latest_3.11_test_plotting	91.76% <97.45%> (+0.02%)	⬆️
windows-latest_3.12_test_plotting	?
windows-latest_3.8_test_plotting	91.72% <97.45%> (+0.02%)	⬆️
windows-latest_3.9_test_plotting	91.73% <97.45%> (+0.02%)	⬆️

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[htwangtw]

Several functions interfaces/fmriprep seem to be unused in the code base.

@htwangtw is this to be expected?

• '_load_motion' mentioned only 1 time in nilearn/interfaces/fmriprep/load_confounds_components.py.
• '_load_high_pass' mentioned only 1 time in nilearn/interfaces/fmriprep/load_confounds_components.py.
• '_load_wm_csf' mentioned only 1 time in nilearn/interfaces/fmriprep/load_confounds_components.py.
• '_load_global_signal' mentioned only 1 time in nilearn/interfaces/fmriprep/load_confounds_components.py.
• '_load_compcor' mentioned only 1 time in nilearn/interfaces/fmriprep/load_confounds_components.py.
• '_load_ica_aroma' mentioned only 1 time in nilearn/interfaces/fmriprep/load_confounds_components.py.
• '_load_scrub' mentioned only 1 time in nilearn/interfaces/fmriprep/load_confounds_components.py.
• '_load_non_steady_state' mentioned only 1 time in nilearn/interfaces/fmriprep/load_confounds_components.py.

Yes - here's how these _load_* functions are used in the code:
https://github.com/nilearn/nilearn/blob/main/nilearn%2Finterfaces%2Ffmriprep%2Fload_confounds.py#L485

[Remi-Gau]

Ah yes. Thanks.
Will add a comment at the top of that module in case future me forgets about this.

[bthirion]

LGTM, but there are some codecov complaints...

[Remi-Gau]

LGTM, but there are some codecov complaints...

looks like some of those are "false positive".

will double check but I think that in any case there are couple of lines in the incriminated files that were not hit by the tests so I will to cover them with some new tests

[Remi-Gau]

OK should improve the coverage of those lines: https://app.codecov.io/gh/nilearn/nilearn/blob/master/nilearn%2Finterfaces%2Fbids%2Fglm.py#L98

Had to do some refactoring of the test suite so probably increase the number of line changes

[bthirion]

LGTM, thx.

[htwangtw]

LGTM!