Dependencies: Update to sqlalchemy~=2.0

[sphuber]

A number of minor changes were required for the update:

• Queries that use order_by now need to include the property that is
  being ordered on in the list of projections.
• The Session.bulk_update_mappings and Session.bulk_insert_mappings
  are replaced by using Session.execute with the update and insert
  methods.
• The sqlalchemy-utils dependency is no longer used as well as the
  tests/storage/psql_dos/test_utils.py file that used it.
• The future=True is removed from the engine creation. This was a
  temporary flag to enable v2.0 compatibility with v1.4.
• Test of schema equivalence for export archives needed to be updated
  since the casting of UUID columns for PostgreSQL changed.
• Remove the sphinx-sqlalchemy dependency since it is not compatible
  with sqlalchemy~=2.0. Temporarily comment out its usage in docs.

[edan-bainglass]

A few general questions:

1. What's with all the mypy/pylint overrides?
2. Lots of failed tests at the bottom. Plan?

For 1, I see that you also updated the sqlalchemy[mypy] pre-commit dependency? Related?

[sphuber]

Thanks for the review @edan-bainglass

What's with all the mypy/pylint overrides?

Typing changed a lot in v2.0 (see below). There are some issues where these lead to false positives: sqlalchemy/sqlalchemy#7726
There may be solutions, but I don't have time to work on those now and they are not worth the investment frankly.

Lots of failed tests at the bottom. Plan?

Do you mean the red crosses at the end of the changes in the github interface? Those are not failed tests. All tests pass (see bottom of this PR where there is a box of all checks and it says "All checks have passed"). They are just "annotations" that Github adds in scanning the code. They are quite dumb since it just does some static analysis and trips over raise RuntimeErrors in the code, but these are added intentionally in the tests. You can ignore them, they are there in every PR.

For 1, I see that you also updated the sqlalchemy[mypy] pre-commit dependency? Related?

For v2.0, we no longer need a separate sqlalchemy-stubs2 package for typing stubs. Just need mypy installed. This can be installed with the mypy extra of sqlalchemy: https://docs.sqlalchemy.org/en/20/orm/extensions/mypy.html#installation
We already install it ourselves, but I still add, because in this way we are sure that our requirement is compatible with that of sqlalchemy.

[edan-bainglass]

@sphuber Thanks for answering my previous questions.

LGTM!