Logging + parsing +pep8

[landmanbester]

Just making sure tests pass on CI because this is is turning into a big one. So far:

• basic logging with pyscilog (curtesy of @gijzelaerr)
• pep8 compliance (mostly, haven't added this to the CI checks)
• improved minor cycles (faster version of hogbom + undersizing psf in the backward steps of spotless and sara)

I still need to switch out the parser. I've taken some steps to making things omegaconf compatible but I really don't like that there is no way to add argparse --help style documentation for the options (this is my main form of documentation at this stage). I've been thinking about a hack for this (inspired by https://github.com/facebookresearch/hydra/issues/633) but it looks like something more sophisticated is on the way for omegaconf https://github.com/omry/omegaconf/issues/131

[landmanbester]

superseded by https://github.com/ratt-ru/pfb-clean/pull/53