Extend pre-commit configuration

[skosukhin]

This PR:

• extends the pre-commit configuration:
  • isort, black and pyproject-flake8 for Python code (all three tools are configured via pyproject.toml);
  • check-yaml for yaml files;
  • actionlint for GitHub workflows;
  • end-of-file-fixer and trailing-whitespace for all text files in the repo;
  • ci entry with the configuration for pre-commit ci;
• updates .git-blame-ignore-revs with the changes from Format entire codebase #337;
• addresses issues identified by flake8 and actionlint.

Depends on #337.

[RobertPincus]

@skosukhin This seems a good set of automation. We've discussed linting/formatting the Fortran code too but there's no strong consensus on how to do this; I'd be inclined to leave it for now.

[RobertPincus]

Thanks so much for this @skosukhin