Improve log messages

[pluegh]

This pull request changes the way printing status messages is handled.

1. All print functionality is replaced by the logging standard library.
   Messages that were wrapped with if(verbose) are logged as information, or as warnings otherwise.
2. The new function util.log_to_stdout sets up a basic logging handler for easy standalone usage of pypmc.
   This function is called in __init__.py as a drop-in replacement of the current behaviour.

Comments

• Every submodule uses its own logger such that the level of granularity is still high.
  E.g. to only log warnings and errors from PMC, use logging.getLogger('pypmc.mix_adapt.pmc').setLevel(logging.WARNING).
• Note that the default behaviour of logging when no log handler is specified, is to print warnings and errors to stderr.
• Importing pypmc is setting up a log handler (to stdout), which must be removed explicity to use the module as a library.

WIP

• Adding the default StreamHandler creates uncaptured output in the nosetests, as warnings log to stderr. To comply with the previous code, we specify to log only to stdout.
• Emit deprecation notice for optional verbose argument instead of removing the option (breaking change).
• Document logging behaviour and how to use pypmc as a library.
  The wiki page is a good place to document logging after the proposed changes are approved.

Solves #95

[fredRos]

@pluegh First of thanks a lot for starting this pull request. I hope I will find some time over the weekend to have a more detailed look but I support the idea of replacing prints with logging.

Out of curiosity: how would this help with eos?

[dvandyk]

Out of curiosity: how would this help with eos?

@fredRos EOS now pipes all log messages into a logging.logger when used from within IPython or a Jupyter notebook.
We can easily turn off the most intrusive log messages, but switching pypmc's (very useful) diagnostic messages, e.g. in the PMC update steps, cannot be handled in the same way yet. I've asked @pluegh to fix that, and he delivered!

[dvandyk]

This creates sub loggers, with a name of pypmc.mix_adapt.hierarchical, correct?
Is there an easy way to get to all loggers that belong to the pypmc root logger?

[pluegh]

Correct.
Checking the logging documentation, I don't think it's designed such that you can get a list of all child loggers. Instead, you are supposed to configure the parent logger (pypmc or pypmc.mix_adapt). This has the advantage that child loggers, which are instantiated later also adhere to the parent.

[dvandyk]

Weird, but apparently the recommended approach.

[dvandyk]

I approve, but I would like to have also @fredRos to approve, if possible.

[dvandyk]

@fredRos merging now. Please holler if you find something untoward a-posterior 😄

[fredRos]

@dvandyk Sorry, I was overwhelmed with work and family. I know git revert but I'm pretty sure we won't need that.