final lint/format run through & update pre-commit

[jGaboardi]

This PR:

• cleans up several lingering formatting & linting spots
• updates .pre-commit for for black and ruff
• xref lint repo with ruff, update pyproject.toml and pre-commit for linting #589

To decide:

• Within pyproject.toml, I am more leaning towards the mindset of omitting [tool.ruff.ignore] in pyproject.toml altogether and handling 99.9% of cases within files themselves (everything in the PR passes that way). However, I know others may think this is too strict. So yay or nay for keeping [tool.ruff.ignore]?

Once the PR is reviewed and merged the last step in #589 will be to enable pre-commit on triggered GHA

[codecov]

Codecov Report

Merging #661 (074004b) into main (9e45960) will not change coverage.
The diff coverage is 100.0%.

Additional details and impacted files

@@          Coverage Diff          @@
##            main    #661   +/-   ##
=====================================
  Coverage   85.0%   85.0%           
=====================================
  Files        139     139           
  Lines      14889   14889           
=====================================
  Hits       12663   12663           
  Misses      2226    2226           

Files	Coverage Δ
libpysal/cg/standalone.py	91.3% <100.0%> (ø)
libpysal/graph/_kernel.py	88.8% <100.0%> (ø)
libpysal/io/fileio.py	60.5% <100.0%> (ø)

[martinfleis]

I am more leaning towards the mindset of omitting

If there are no global rules we want to disable then there's no reason to keep that section. But there is some minor compatibility issue with black I think. Some rules go against black, that is why they're disallowed. Otherwise you get to a dance between ruff and black with one making a change and the other reverting it.

[jGaboardi]

This PR passes both black and ruff with no global rules (confirmed locally). But yes, I have experience in the past where black and ruff seem to countermand each other. Though recently, no.

[martinfleis]

Okay. Let's give it a go without.