General dependency updates

[trevorb1]

Description

In this PR I have fixed installation issues that are in the format of:

ERROR: Could not build wheels for pandas, which is required to install pyproject.toml-based projects

Changes made:

• Update pyscaffold to version 4.5
• Update flake8 to version 7.1.0
• Update mypy to 1.10.1

Issue Ticket Number

Closes #229

Documentation

na