lint repo with ruff, update pyproject.toml and pre-commit for linting

[jGaboardi]

lint repo with ruff, update pyproject.toml and pre-commit for linting.

• __init__ in all levels – begin the repo linting  #597
• top level .py files – begin the repo linting  #597
• cg
  • ./cg/*.py – ./cg/*.py – format, lint, & remove docstring spaces #608
  • ./cg/ops/*.py – format, lint, numpydoc – cg/ops/*.py #610
  • ./cg/ops/tests/*.py – format & lint – cg/ops/tests*.py #611
  • ./cg/tests/*.py – format & lint – cg/tests/*.py #614
• examples – lint ./examples/* #607
• graph
  • ./graph/base.py – lint graph/base.py #615
  • ./graph/_*.py – lint graph/_*.py #618
  • ./graph/tests/*.py – lint & format graph/tests/*.py #619
• io
  • ./io/*.py – lint & format io/*.py #620
  • ./io/geotable/* – lint & format – io/geotable/* #622
  • ./io/iohandlers/* – (lint & format – io/iohandlers/* #630)
    • lint & format io/iohandlers{a-d}.py #637
    • lint & format io/iohandlers{g-m}.py #638
    • lint & format io/iohandlers{p-s}.py #641
    • lint & format io/iohandlers{t-w}.py #642
    • lint & format io/iohandlers/tests/*.py #643
  • ./io/{tests,util}/*
    • lint & format io/{tests, util}/*.py part 1 #644
    • lint & format io/{tests, util}/*.py part 2 #645
    • lint & format io/{tests, util}/*.py part 3 #646
• weights
  • lint & format weights/*.py part 1 #648
  • lint & format weights/*.py part 2 #650
  • lint & format weights/*.py part 3 #651
  • lint & format weights/*.py part 4 #652
  • lint & format weights/*.py part 5 #653
  • lint & format weights/*.py part 6 #654
  • lint & format weights/*.py part 7 #655
  • lint & format weights/*.py part 8 #658
• review and final pass
  • convert # noqa <CODE> --> # noqa: <CODE> – correct in-line ruff syntax #660
    • Without that colon, any violation is skipped, not only the one from <CODE>
  • other rough edges? – final lint/format run through & update pre-commit #661
• update infra
  • pyproject.toml– final lint/format run through & update pre-commit #661
  • .pre-commit-config.yaml– final lint/format run through & update pre-commit #661
  • enable pre-commit on triggered GHA – https://results.pre-commit.ci

[jGaboardi]

xref #594

[jGaboardi]

All files formatted and listed; pre-commit hook for CI/PRs is enabled.