[MAINT] follow several recommendations from the Scientific Python Library Development Guide

[Remi-Gau]

• apply several recommendations mentioned in
  NMIND checklist #44 (comment)

[codecov-commenter]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 92.40%. Comparing base (0595d0c) to head (e37b96e).

Additional details and impacted files

@@           Coverage Diff           @@
##             main      #58   +/-   ##
=======================================
  Coverage   92.40%   92.40%           
=======================================
  Files          11       11           
  Lines         487      487           
=======================================
  Hits          450      450           
  Misses         37       37           

Files	Coverage Δ
giga_connectome/methods.py	100.00% <ø> (ø)
giga_connectome/utils.py	94.66% <ø> (ø)

[htwangtw]

okay adding those extra options has raised some issues and revealed some very hacky things I did for good -

• test_load_atlas_setting, test_generate_group_mask: i manually override the templateflow home to load customised atlas. this is not a typical use case of templateflow
• test_calculate_intranetwork_correlation: we used the niftimasker to flatten label atlas (3D); solvable
• test_get_bids_images: this is from a hack to force pybids to index fmriprep outputs, you are a better person to judge if i am doing the right thing here

[Remi-Gau]

Oh I thought I was breaking things... OK will probably move the problematic things in a separate PR so that the things that are 'trivial' in this one can go through

[htwangtw]

We can move the warnings into separate issues since they need fixing eventually

[htwangtw]

commenting this line out should do the trick for now.

[htwangtw]

LGTM thanks!