Bump sqlalchemy to 1.4 and database-related dependencies

[psrok1]

Your checklist for this pull request

• I've read the contributing guideline.
• I've tested my changes by building and running the project, and testing changed functionality (if applicable)
• I've added automated tests for my change (if applicable, optional)
• I've updated documentation to reflect my change (if applicable)

What is the current behaviour?

I'm missing some features in 1.3.x branch. The 1.3.x branch is also from 2021 and it's good time to switch to something with better support.

What is the new behaviour?

This PR upgrades sqlalchemy to 1.4 and all related dependencies to newer versions. Flask-SQLAlchemy is pinned on 3.0.5, because 3.1.0 requires sqlalchemy 2.0. I think this needs a bit more work.

[psrok1]

Fixed warnings:

• implicit scalar_subquery in Object.upload_count
• viewonly relationships Object.comment_authors and User.commented_objects that were declared as passive_deletes only while it's only a view used by search and real relationship is represented by Comment.object and Comment.user.

Checked if everything works without warnings both on empty database, e2e tests and production-like database.