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

[codecov-commenter]

Codecov Report

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Flag	Coverage Δ
unittests	91.48% <0.00%> (?)

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[sfarrens]

Thanks for the feedback @paquiteau, I am still playing around with this PR, but I like these suggestions. I will play around some more this week and ping you when the PR is ready for final review.