[MAINT] run isort and flake8 on the whole nilearn code base in CI

[Remi-Gau]

Relates to #2528

Changes proposed in this pull request:

• change CI to run isort and flake on the whole nilearn folder
• simplify isort and flake8 config
• fix remaining issues

This PR should be green once the following have been merged:

• [MAINT] Format nilearn/maskers: apply isort and fix flake8 errors #3650
• [MAINT] Format nilearn/plotting: apply isort and fix flake8 errors #3648
• [MAINT] Format nilearn/interfaces: apply isort and fix flake8 errors #3647
• [MAINT] Format nilearn/surface: apply isort and fix flake8 errors #3645
• [MAINT] Format nilearn/glm: apply isort and fix flake8 errors #3640
• [MAINT] Update config for formatting of nilearn/datasets #3697
• [MAINT] Formatting _utils #3614
• [MAINT] Format reporting #3615

This will then mean that the whole code base is PEP8 compliant and should hopefully stay that way.

[github-actions]

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[codecov]

Codecov Report

Merging #3651 (bb4a42e) into main (2e9344d) will decrease coverage by 0.01%.
The diff coverage is 100.00%.

@@            Coverage Diff             @@
##             main    #3651      +/-   ##
==========================================
- Coverage   91.60%   91.60%   -0.01%     
==========================================
  Files         139      139              
  Lines       16594    16593       -1     
  Branches     3244     3244              
==========================================
- Hits        15201    15200       -1     
  Misses       1390     1390              
  Partials        3        3              

Impacted Files	Coverage Δ
nilearn/_utils/testing.py	68.68% <ø> (ø)
nilearn/decoding/space_net_solvers.py	100.00% <ø> (ø)
nilearn/glm/contrasts.py	94.28% <ø> (ø)
nilearn/glm/first_level/design_matrix.py	96.63% <ø> (ø)
nilearn/interfaces/bids/glm.py	95.58% <ø> (ø)
...ces/fmriprep/tests/test_load_confounds_strategy.py	100.00% <ø> (ø)
...rfaces/fmriprep/tests/test_load_confounds_utils.py	100.00% <ø> (ø)
nilearn/interfaces/fmriprep/tests/utils.py	100.00% <ø> (ø)
nilearn/maskers/multi_nifti_masker.py	97.72% <ø> (ø)
nilearn/maskers/nifti_labels_masker.py	93.64% <ø> (ø)
... and 49 more

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

[Remi-Gau]

• fix any left over flake8 and isort issues

Once that is done, nilearn should be mostly PEP8 compliant and stay that way.

[Remi-Gau]

• add changelog entry to point to all the PRs that have not yet been referenced and concern PEP8 / isort compliance
• update gitblame ignore

will address those in a separate PR

[Remi-Gau]

It seems I had slightly misconfigured isort so that it was not always runnning on the whole codebase: started fixing it here which results in a lot of very minor changes in many files.

I also need to finish running it on all the examples: will do this in a subsquent PR as this one is big enough as it is.

[Remi-Gau]

Getting some install errors for some ci that are unrelated to this PR.
Will try to tackle in a separate PR.

[bthirion]

LGTM otherwise. Thx !

[bthirion]

This is no longer needed ?

[Remi-Gau]

flake8 was flagging them as unnecessary because unused so I removed them thinking "for sure this will break something and this will require a 'noqa' to pacify flake8"

so I am a bit puzzled nothing broke

will try to track down when they became unneeded.

[Remi-Gau]

apparently this was added here: https://github.com/nilearn/nilearn/blame/91039a92982b8f442517a8d552d3dae815d6d33f/nilearn/plotting/img_plotting.py

but it is never used in the whole module

[bthirion]

LGTM, thx.

[emdupre]

It looks like flake8 didn't catch the correct indentation on this 😅

[Remi-Gau]

wait... Does flake8 cover toml files as well?
If not I can at least add a pre-commit hook to help "enforce" some formatting of such support / config files (yaml, json, toml).
There are a couple of options available.
https://pre-commit.com/hooks.html

[Remi-Gau]

turned out this was a double space instead of a tab...

[ymzayek]

LGTM thx!

[Remi-Gau]

Thanks for the reviews y'all.
Will wait for CI to finish and merge if all green.
Will add a single entry in the changelog for all the new PRs that relate to flake8 / isort.