Add linting and formatting to linkml-runtime

[sneakers-the-rat]

Builds on: #345

The non-modular PR is because the changes to update to 3.9 use the linting rules we're implementing here.

This sets us up with

• The existing rules in linkml
• UP - pyupgrade with an override for X | Y types until 3.9 gets dropped
• T100 - no pdb imports or uses (i am guilty of this a lot)

I punted on a handful of rules for the tests module because there are a lot of violations and it's just in tests, those are mostly assigned values that aren't used, which are fine in tests if a little implicit.

Bigass diff, i'm aware, but that's why we add the linter rules, so future diffs are smaller :)

Review spots

To help out review, all the changes here are linter fixes with no functional change except:

• linkml_runtime.utils.metamodelcore - There were a handful of invalid error handling blocks that looked like this:

  try:
      # something
  except TypeError:
      pass
  except ValueError:
      pass
  if not is_strict():
      return str(value)
  raise e

  And that isn't valid because e is undefined. It's also ambiguous whether or not those values should always pass, and we raise on any other error, or whether we raise those errors if in strict mode. I assumed the latter, so i changed that to

  try:
      # something
  except (TypeError, ValueError):
      if is_strict():
          raise
  
  return str(value)

• linkml_runtime.loaders.rdf_loader - there's a reference to pyld_jsonld_from_rdflib_graph and i'm not sure what that is, can't find it anywhere. so i marked it noqa

• linkml_runtime.utils.permissiblevalueimpl:PvFormulaOptions has a default value that uses EnumDefinition. That would make a pretty nasty dependency loop if we fixed it, so i just commented it out. This prevented the module from being imported at all, so i suspect this is deprecated.

• tests.__init__.py used an eval call to get a log level, using eval that should basically never be done, so i switched it to getattr

[sneakers-the-rat]

looks like we need to add a parameter to the upstream tests that lets us specify which branch to test against.