Add pre-commit configuration and pyproject.toml and update gitignore

[stellaprins]

pyproject toml and pre-commit config

Adds:

• very lightweight pyproject.toml to make it easy for potential users to install the correct environment
• a pre-commit-config.yaml
• ran pre-commit hooks on all files and fixed linting and formatting errors

pre-commit hooks exclude tellurium/simple.py, files with .xml, .sedml, .sbml and .omex, 'json', and 'md' extensions, and files in the following folders:

• LEMS
• Brian
• NEURON
• NeuroML2