Messages, logging, and exception

[drewejohnson]

Closes #16

Added a messages module that contains functions for various status updates.
A custom Logger is created, and all updates, warnings, and debug statements pass through this object.
This is hidden with double underscores, __logger__, as to be super private.

All the updates are passed to one of four functions: messages.debug, messages.info, messages.warnings, and messages.error.
If we decide to change the underlying error reporting, by adding some file logs, or something totally crazy, as long as every other program just uses these functions, nothing should break.

Usage Examples

In the project

From the depletion reader:

def read(self):
        """Read through the depletion file and store requested data."""
        messages.info('Preparing to read {}'.format(self.filePath))
        # reading
        messages.info('Done reading depletion file')
        messages.debug('  found {} materials'.format(len(self.materials)))

Currently, the depletion reader does not play well with materials that contain underscores, because of variables like ING_TOX.
A warning is printed to inform the user of this fact:

if any(['_' in pat for pat in patterns]):
        messages.warning('Materials with underscores are not supported.')`

Any time a setting is changed, a debug statement is printed
messages.debug('Updated setting {} to {}'.format(name, value))

The error function has an additional setting: fatal.
If this value is true, a critical message is created, but also a SerpentToolsException is raised with the same message.
This may be redundant, but the exception can be caught and suppressed, while the message should still be raised.
If fatal is false, then an error message is posted.

Outward facing

To the user, the notices look as follows:

[ajohnson400@core serpent-tools]$ python
Python 3.6.0 |Anaconda 4.3.1 (64-bit)| (default, Dec 23 2016, 12:22:00)
[GCC 4.4.7 20120313 (Red Hat 4.4.7-1)] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import serpentTools
INFO    : serpentTools   : Using version 1.0b0+3.gb8a02ab
>>> from serpentTools.settings import rc
>>> rc['verbosity'] = 'debug'
DEBUG   : serpentTools   : Updated setting verbosity to debug
>>> rc['depletion.processTotal'] = False
DEBUG   : serpentTools   : Updated setting depletion.processTotal to False

Exception

As mentioned above, a custom SerpentToolsException was created.
This is for any exception that is unique to this project and not covered by the base exceptions.
This can be subclassed for unique exceptions, e.g.

class ReaderSpecificException(SerpentToolsException):
    pass

[DanKotlyar]

Thank you Drew. This is great.
But, in the future we do need to fix the '_' issue in material definition.

[drewejohnson]

Reopened to squash and merge