Finish up the Cython revolution

[camillescott]

I'm a little exhausted on converting code to Cython, and have other things to do, though the revolution is nearly complete. If somebody would like to make a final push (maybe @luizirber ;)), there's a PR up at #1774 which removes the floating functions and finishes up a lot of the ReadParser conversion.

To-do's there:

• Strip out the rest of the CPython code
• Convert sandbox from ReadParser
• Something broke with a couple (but not all) of the streaming tests, making them hang. Not sure if this is something with Threads and FIFO (some of the tests are a bit janky) or with the seqan stream.