General update to logging.

[ketch]

Make all loggers inherit from pyclaw logger.
Add convenience function for setting console logging level in controller (h/t @ahmadia).

I see two main use cases where one wants to adjust the logging:

1. Turn off logging to stdout (IPython notebooks)
2. Turn off all logging (or set all to CRITICAL) (Shaheen)

For 1, we want to selectively modify the level of the console handler for the controller logger. This can now be done via

claw.verbosity = 0

Meanwhile, the controller will still write to the log file.

For case 2, one can do

import logging
logger = logging.getLogger('pyclaw')
logger.setLevel(logging.CRITICAL)

which propagates to the other loggers.

For completeness, the logger name changes are:

io -> pyclaw.io
solution -> pyclaw.solution
evolve -> pyclaw.solver

and there is a new logger pyclaw.controller.

[ahmadia]

This is currently failing in Travis:

..........................S..E
======================================================================
ERROR: Failure: ValueError (Attempted relative import beyond toplevel package)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/travis/virtualenv/python2.7/local/lib/python2.7/site-packages/nose/loader.py", line 413, in loadTestsFromName
    addr.filename, addr.module)
  File "/home/travis/virtualenv/python2.7/local/lib/python2.7/site-packages/nose/importer.py", line 47, in importFromPath
    return self.importFromDir(dir_path, fqname)
  File "/home/travis/virtualenv/python2.7/local/lib/python2.7/site-packages/nose/importer.py", line 94, in importFromDir
    mod = load_module(part_fqname, fh, filename, desc)
  File "/home/travis/build/clawpack/pyclaw/src/pyclaw/__init__.py", line 23, in <module>
    from .controller import Controller
  File "/home/travis/build/clawpack/pyclaw/src/pyclaw/controller.py", line 20, in <module>
    from ..pyclaw import LOGGING_LEVELS
ValueError: Attempted relative import beyond toplevel package
----------------------------------------------------------------------
Ran 30 tests in 167.205s

[ketch]

@ahmadia thanks for the heads up. I've fixed it now.

[mandli]

Is there a way to merge the functionality of replace_stream_handlers in runclaw.py, it would be nice to have a consistent method of interacting with the loggers.

[ketch]

Can you explain why you use replace_stream_handlers? It seems like the same thing can be accomplished more easily and cleanly with this PR, but I may have missed something.

[mandli]

Actually, I was just hoping that you could outline how we would replace that function with this PR. If there's anything missing than perhaps we could include it.

[ketch]

I don't think this PR should change replace_stream_handlers. It does change a couple of logger names, so we'll need to make the corresponding changes in the places where replace_stream_handlers is called.

Honestly, after a couple of hours of reading, Python's logging module doesn't make much sense. It's extremely unpythonic -- there are 100 ways to do anything, and none is clearly the best.

[ahmadia]

@ketch - I think it's designed to support a very different use case than the one most scientists are interested in.

[ahmadia]

This looks like it's passing tests, are you ready to have this merged in?

[mandli]

I am fine merging it in now, I did not want to duplicate functionality but it sounds like it won't be that much of an issue.