Add local Pylint rule ignore directives for E1130 false positives

[matt-graham]

Part of #1181.

Adds a series of local Pylint rule ignores / disables for rule E1130 (invalid-unary-operand-type) to avoid false positives on using ~ bitwise inversion / not operator with pandas Series objects or numpy.int64 data, which both seem to be incorrectly identified by Pylint as not support the ~ operator. Also removes the global E1130 rule ignore in pyproject.toml.