Update pre-commit-config.yaml + pyproject.toml + ceil rerun & transformer dependencies version (#1520)

* chore: update .gitignore

* chore: update pre-commit

* chore(deps): update pyproject

* fix(ci): multiple fixes

* chore: pre-commit apply

* chore: address review comments

* Update pyproject.toml

Co-authored-by: Ben Zhang <5977478+ben-z@users.noreply.github.com>
Signed-off-by: Steven Palma <imstevenpmwork@ieee.org>

* chore(deps): add todo

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Signed-off-by: Steven Palma <imstevenpmwork@ieee.org>
Co-authored-by: Ben Zhang <5977478+ben-z@users.noreply.github.com>