This patch moves the `--allow-redefinition` into the `.mypi.ini` file.
Centralizing our mypy config in a single file makes sense, and this way,
if people want to run mypy locally, they don't need to remember to
supply this command-line argument.
Our package doesn't have type annotations everywhere, so we can't use
mypy in strict mode just yet. Still, adding type checking in CI is
valuable, so we don't have unchecked annotations in our code.
This patch includes basic fixes to make type checking pass, including
switching the incorrect `np.array` type annotation for `np.ndarray` and
adding some assertions for flow-sensitive typing.
Ulyana