Pyproject code refactor

[sfarrens]

Summary

This PR refactors the codebase to simplify maintenance and development.

• Removed setup.py and setup.cfg and added pyproject.toml
• Removed redundant files/directories: .pylintrc, .pyup.yml, develop.txt, docs/requirements.txt, notebooks
• Ran Black on modopt (i.e. only style changes, no changes to code or tests)
• Updated docs: removed redundant notebook tools, cleaned up
• Updated manifest
• Simplified CI tests: several tests can now be run manually rather that being triggered for each commit, only the latest version of Python will run automatically

To Do

• [ ] Update README.md and installation instructions
• [ ] Check that new CI/CD works correctly
• [ ] Additional checks