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Fix toml parsing and bump toml from 0.10.0 to 0.10.1 (#1501)

* Bump toml from 0.10.0 to 0.10.1 to fix a bug

* Add tests for TOML parsing and reading

* Fix configuration bug affecting vim plugin

The vim plugin directly calls parse_pyproject and skips the Click processing
, but parse_pyproject assumed that it would only be used before Click processing
and therefore made the config values click friendly. This moves the "make the values
click friendly processing" into read_pyproject_toml which is only called by a Click
callback.

* Please mypy and flake8

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