LogIt Documentation
===================

Use the LogIt class to make logging very simple. This short and sweet
class wraps around `logzero <https://github.com/metachris/logzero>`__
which allows color coded logging. We created our own default logger with
a default dateformat, logformat, and logging level (default is debug).

Note that LogIt automaticall capitalizes the logname.

1. Import the LogIt class and create a variable. ex: ``logit = LogIt()``
2. Create your logger. ex:
   ``blastn = logit.default('blastn', 'blastn.log')``
3. Start logging. ex:
   ``blastn.error('Your refseq accession was not found')``

Multiple loggers can exist for the same logfile and multiple loggers can
be set up for one script which is shown in the example below.

Example
-------

Simple logging
~~~~~~~~~~~~~~

.. code:: python

    from OrthoEvol.Tools import LogIt
    genbank_log = LogIt().default(logname="genbank", logfile=None)

Use logging with ETE3PAML
~~~~~~~~~~~~~~~~~~~~~~~~~

.. code:: python

    from OrthoEvol.Tools import LogIt
    from OrthoEvol.Orthologs.Phylogenetics import ETE3PAML

    # Set up your loggers
    logit = LogIt()

    # Log to one file
    logfile = 'align2paml.log'

    align, paml = logit.default('alignlog', logfile), logit.default('pamllog', logfile)

    # Start logging
    align.info('hi')
    paml.info('muah')

    # Shutdown the loggers and delete the logfile
    logit.deletelog(logfile=logfile)

    # Shutdown logging without deleting the logfile
    logit.shutdown()