pre-commit hook causes unexpected problems on existing codebase

[theferrit32]

Describe the bug
When I take existing code in main and run the pre-commit checks installed by make devready, it fails, which means contributors cannot commit code to many existing files without disabling the pre-commit hook or fixing things unrelated to their change.

To Reproduce

Add a trivial edit to an existing git-tracked file which should be committable and not cause lint failures.

$ git clone  git@github.com:biocommons/biocommons.seqrepo.git biocommons.seqrepo-clean
$ cd biocommons.seqrepo-clean
$ make devready
$ source venv/bin/activate
$ echo "# blah" >> src/biocommons/seqrepo/cli.py
$ git add ./src/biocommons/seqrepo/cli.py
$ git commit -m "throwaway"

This fails on main.

Actual behavior

(venv) ➜  biocommons.seqrepo-clean git:(main) ✗ echo "# blah" >> src/biocommons/seqrepo/cli.py
(venv) ➜  biocommons.seqrepo-clean git:(main) ✗ git add ./src/biocommons/seqrepo/cli.py
(venv) ➜  biocommons.seqrepo-clean git:(main) ✗ git commit -m "throwaway"
flake8...................................................................Passed
pyright..................................................................Failed
- hook id: pyright
- exit code: 1

/Users/kferrite/dev/biocommons.seqrepo-clean/src/biocommons/seqrepo/cli.py
  /Users/kferrite/dev/biocommons.seqrepo-clean/src/biocommons/seqrepo/cli.py:331:37 - error: "execute" is not a known member of "None" (reportOptionalMemberAccess)
  /Users/kferrite/dev/biocommons.seqrepo-clean/src/biocommons/seqrepo/cli.py:399:13 - error: Function declaration "_rec_iterator" is obscured by a declaration of the same name (reportRedeclaration)
  /Users/kferrite/dev/biocommons.seqrepo-clean/src/biocommons/seqrepo/cli.py:411:13 - error: Function declaration "_rec_iterator" is obscured by a declaration of the same name (reportRedeclaration)
  /Users/kferrite/dev/biocommons.seqrepo-clean/src/biocommons/seqrepo/cli.py:466:24 - error: Cannot access member "fetchone" for type "Generator[dict[Any, Any] | Unknown, Any, None]"
    Member "fetchone" is unknown (reportAttributeAccessIssue)
  /Users/kferrite/dev/biocommons.seqrepo-clean/src/biocommons/seqrepo/cli.py:697:53 - error: Cannot access member "seqinfo" for type "SeqRepo"
    Member "seqinfo" is unknown (reportAttributeAccessIssue)
5 errors, 0 warnings, 0 informations

isort....................................................................Passed
black....................................................................Passed
(venv) ➜  biocommons.seqrepo-clean git:(main) ✗  echo $?
1

Expected behavior
The git commit should succeed with exit code 0.

[jsstevenson]

Fwiw there's also a pre commit command that will run hooks against every file regardless of staging status: I think it's --all?