Resolve "Upgrade dependencies"

Description

• alembic (1.12.0 -> 1.13.2)
• annotated-types (0.6.0 -> 0.7.0)
• attrs (23.1.0 -> 23.2.0)
• bcrypt (4.0.1 -> 4.1.3)
• coverage (7.3.3 -> 7.5.4)
• cyvcf2 (0.30.25 -> 0.31.1)
• greenlet (3.0.2 -> 3.0.3)
• gunicorn (21.2.0 -> 22.0.0)
• hypothesis (6.92.0 -> 6.104.2)
• jsonschema (4.19.1 -> 4.22.0)
• jsonschema-specifications (2023.11.2 -> 2023.12.1)
• mako (1.3.0 -> 1.3.5)
• mypy (1.7.1 -> 1.10.1)
• numpy (1.26.2 -> 2.0.0)
• packaging (23.2 -> 24.1)
• pluggy (1.3.0 -> 1.5.0)
• pydantic (2.4.2 -> 2.8.2)
• pydantic-core (2.10.1 -> 2.20.1)
• pytest (7.4.3 -> 7.4.4)
• pytz (2023.3.post1 -> 2024.1)
• referencing (0.32.0 -> 0.35.1)
• rpds-py (0.13.2 -> 0.18.1)
• ruff (0.1.8 -> 0.1.15)
• sqlalchemy (2.0.21 -> 2.0.31)
• sqlalchemy-searchable (2.0.0 -> 2.1.0)
• sqlalchemy-utils (0.41.1 -> 0.41.2)
• types-pytz (2023.3.1.1 -> 2024.1.0.20240417)
• types-pyyaml (6.0.12.12 -> 6.0.12.20240311)
• types-requests (2.31.0.10 -> 2.32.0.20240622)
• typing-extensions (4.9.0 -> 4.12.2)
• urllib3 (2.1.0 -> 2.2.2)

Notes to review (code/docs/QA)

Related issues

Closes #2290