Consolidate configuration files to `pyproject.toml` file

[fernando-aristizabal]

Where appropriate, we should consolidate configuration files to pyproject.toml unless some other use is required for the file. Some examples include:

• setup.cfg
• .coveragerc
• config.py: this file may not be necessary at all.
• requirements.txt: this file could be used directly by pip so possible argument to keep as-is. It could possibly serve a future conda yaml file.