Py39 upgrade

[mr-c]

please MERGE not SQUASH, so that the noisy commits can be ignored

Changelog Entry

To be copied to the draft changelog by merger:

• Code was updated to be more idiomatic Python 3.9, and reformatted using black.

Reviewer Checklist

• [ ] Make sure it is coming from issues/XXXX-fix-the-thing in the Toil repo, or from an external repo.
  • [ ] If it is coming from an external repo, make sure to pull it in for CI with:

    contrib/admin/test-pr otheruser theirbranchname issues/XXXX-fix-the-thing

  • [ ] If there is no associated issue, create one.
  • [ ] Read through the code changes. Make sure that it doesn't have:
  • [ ] Addition of trailing whitespace.
  • [ ] New variable or member names in camelCase that want to be in snake_case.
  • [ ] New functions without type hints.
  • [ ] New functions or classes without informative docstrings.
  • [ ] Changes to semantics not reflected in the relevant docstrings.
  • [ ] New or changed command line options for Toil workflows that are not reflected in docs/running/{cliOptions,cwl,wdl}.rst
  • [ ] New features without tests.
  • [ ] Comment on the lines of code where problems exist with a review comment. You can shift-click the line numbers in the diff to select multiple lines.
  • [ ] Finish the review with an overall description of your opinion.

Merger Checklist

• [ ] Make sure the PR passes tests.
• [ ] Make sure the PR has been reviewed since its last modification. If not, review it.
• [ ] Merge with the Github "Squash and merge" feature.
  • [ ] If there are multiple authors' commits, add Co-authored-by to give credit to all contributing authors.
• [ ] Copy its recommended changelog entry to the Draft Changelog.
• [ ] Append the issue number in parentheses to the changelog entry.