Update to SQLAlchemy 2.0

[alexhad6]

The Painter Lab would like to use the newest version of SQLAlchemy, version 2.0, in our software. Since SQLAlchemy 2.0 introduces breaking changes from version 1.4, I had to make the following changes in order to pass the EntropyLab test suite:

• Using with engine.connect() as connection: and connection.execute() instead of engine.execute().
• Wrapping SQL statements in text().
• Session.close_all() was replaced with sqlalchemy.orm.close_all_sessions() in version 2.0.
• Branched connections are removed from SQLAlchemy 2.0, so I simplified code in the env.py files to just assume that config.attributes["connection"] is a connection, and to use that connection directly instead of branching. I am not very familiar with Alembic though, so this may have unintended consequences even though it passed the tests.
• Pandas 1.x uses SQLAlchemy 1.4 for pandas.read_sql(), so I refactored the code to make the SQL request separately and convert it using pandas.DataFrame.
• SQLAlchemy 2.0 appears to handle UUIDs differently (internally using UUID.hex to convert them to strings), so some changes needed to be made to UUIDs.
• A few import paths changed in version 2.0, including for contextmanager and declarative_base.

[github-actions[bot]]

Unit Test Results

328 tests   322 :heavy_check_mark:  53s :stopwatch:     1 suites      6 :zzz:     1 files        0 :x:

Results for commit b1e68de5.

[nikolaqm]

Hi @alexhad6

Thank you for your work on this PR! This has been merged and is released now as v0.15.9