Make the lint and type checks actually run

[rcannood]

The lint job could not fail

tox -e lint ran black . -- which reformats the files in the runner, discards the result and exits 0. Two files were unformatted on main while CI was green. It now runs black --check --diff .; tox -e lint -- . still applies the changes.

The first commit is that reformat on its own, so the rest of the diff stays readable.

The type checks never ran

tox.ini has had a type env since the start, but nothing invoked it: the test job skips every env that is not py<version> (--skip-env '^(?!py310).+') and the lint job only runs lint. It had quietly accumulated 25 errors, so this adds a type job alongside lint and clears them:

• deep_merge() and process_nested_yaml() annotated their arguments as any -- the builtin function -- rather than typing.Any
• process_nested_yaml() did not accept a project_path of None, which is what read_nested_yaml() hands it for a yaml outside a viash project
• check_links() said the values of .links may be lists of urls. They are urls -- see Links in schemas/schema_viash.yaml -- and check_url() would have choked on a list
• anndata, pandas, requests, networkx, spatialdata, urllib3 and yaml have no type information, and are imported inside the function that needs them so a task repo only provides the ones its own components use. They get an ignore_missing_imports override

tox -e lint, tox -e type and tox run -e py310 all pass.