Resolve "Update python packages"

Description

Packages not updated:

Part of API v1 - won't bother to upgrade:

• apispec
• flask
• flask-swagger-ui
• gunicorn
• itsdangerous
• jinja2
• markupsafe
• marshmallow
• werkzeug

Part of SQLALchemy upgrade:

• alembic
• psycopg2-binary
• sqlalchemy
• sqlalchemy-searchable
• sqlalchemy-utils

Changes

Removed unused packages:

• beautifulsoup4
• openpyxl
• ptvsd
• XlsxWriter
• python-digitalocean
• scp
• types-paramiko
• Flask-Cors

ptvsd and openpyxl was referenced in the source code, but never used (or tested), so this code has been removed.

Upgraded packages:

• bcrypt
• click
• cyvcf2
• jsonref
• jsonschema
• supervisor
• pydantic
• black
• flake8
• hypothesis
• mypy
• pytest
• pytest-env

Of these, pydantic required by far the most changes. However, if we are to rely on pydantic moving forward, the upgrade to v2 is very valuable.

Some unused code have been removed, in particular the options jsonschema= and field_map= to src/api/util/util.py:request_json, which also triggered removal of json schemas that have not been maintained.

Notes to review (code/docs/QA)

Related issues

Closes #2232 (closed)