proglog 0.1.8

Proglog
=========

.. image:: https://raw.githubusercontent.com/Edinburgh-Genome-Foundry/Proglog/master/logo.png
:align: center

Proglog is a progress logging system for Python. It allows to build complex
libraries while giving the user control on the management of logs, callbacks and progress bars.

**What problems does it solve ?** Libraries like `tqdm <https://github.com/noamraph/tqdm>`_ or `progress <https://github.com/verigak/progress/>`_ are great for quickly adding progress bars to your scripts, but become difficult to manage when building larger projects.

For instance, you will need to write different code depending on whether you are displaying the progress in a console, a Jupyter notebook, or a website.

Sometimes you need to channel the progress logs of different components into a same logger, at which case you may also let the final user choose which progress bars they want to display or to mute, even when these are handled deep down in your programs.

.. image:: https://raw.githubusercontent.com/Edinburgh-Genome-Foundry/Proglog/master/docs/run_and_get_progress.png
:align: center

You may also want to log more than just progress bars, have specific callback fonctions, print the logs in human-readable format... Proglog provides all these features.


Usage
-------

Assume that you are writing a library called ``my_library`` in which you define a routine as follows:

.. code:: python

import time # for simulating computing time
from proglog import TqdmProgressBarLogger

def my_routine(iterations=10, logger='bars'):
"""Run several loops to showcase Proglog."""
if logger == 'bars':
logger = TqdmProgressBarLogger()
for i in logger.iter_bar(iteration=range(iterations)):
for j in logger.iter_bar(animal=['dog', 'cat', 'rat', 'duck']):
time.sleep(0.1) # Simulate some computing time

Now when the library users run a program in the console, they will get a console progress bar:

.. code:: python

from my_library import my_routine
my_routine()

.. image:: https://raw.githubusercontent.com/Edinburgh-Genome-Foundry/Proglog/master/docs/console_bar.png
:align: center

If the users run the routine inside a Jupyter/IPython notebook, they only need to write ``proglog.notebook()`` at the beginning of the notebook to obtain HTML progress bars:

.. code:: python

import proglog
proglog.notebook()

from my_library import my_routine
my_routine()

.. image:: https://raw.githubusercontent.com/Edinburgh-Genome-Foundry/Proglog/master/docs/notebook_bar.png
:align: center

If the user wishes to turn off all progress bars:

.. code:: python

from my_library import my_routine
from proglog import MuteProgressBarLogger
my_routine(logger=MuteProgressBarLogger())

If the user is running the routine on a web server and would want to attach the
data to an asynchronous Python-RQ job, all they need is yet a different logger:

.. code:: python
from proglog import RqWorkerBarLogger
from my_library import my_routine

logger = RqWorkerBarLogger(job=some_python_rq_job)
my_routine(logger=logger)

This allows to then display progress bars on the website such as these (see the `EGF CUBA <https://github.com/Edinburgh-Genome-Foundry/CUBA>`_ project for an example of website using Proglog):

.. image:: https://raw.githubusercontent.com/Edinburgh-Genome-Foundry/Proglog/master/docs/website_bar.png
:align: center

The user may also want a custom progress logger which selectively ignores the ``animals`` progress bar, and only updates its bars every second (to save computing time):

.. code:: python

from proglog import TqdmProgressBarLogger
from my_library import my_routine

logger = TqdmProgressBarLogger(ignored_bars=('animal',),
min_time_interval=1.0)
my_routine(logger=logger)

Proglog loggers can be used for much more than just progress bars. They can in fact store any kind of data with a simple API:

.. code:: python
logger(message='Now running the main program, be patient...')
logger(current_animal='cat')
logger(last_number_tried=1235)

For more complex customization, such as adding callback functions which will be executed every time the logger's state is updated, simply create a new logger class:

.. code:: python

from proglog import ProgressBarLogger
from my_library import my_routine

class MyBarLogger(ProgressBarLogger):

def callback(self, **changes):
# Every time the logger is updated, this function is called with
# the `changes` dictionnary of the form `parameter: new value`.

for (parameter, new_value) in changes.items():
print ('Parameter %s is now %s' % (parameter, value))

logger = MyBarLogger()
my_routine(logger=logger)

When writing libraries which all log progress and may depend on each other, simply pass the Proglog logger from one program to its dependencies, to obtain one logger keeping track of all progress across libraries at once: (this implies that not two librairies use the same variables or loop names, which can be avoided by attributing prefixes to these names):

.. image:: https://raw.githubusercontent.com/Edinburgh-Genome-Foundry/Proglog/master/docs/loggers_schema.png
:align: center

Installation
-------------

You can install Proglog through PIP

.. code:: shell

sudo pip install proglog

Alternatively, you can unzip the sources in a folder and type

.. code:: shell

sudo python setup.py install

To use the ``tqdm`` notebook-style progress bars you need to install and enable
iwidgets:

.. code:: shell

sudo pip install ipywidgets
sudo jupyter nbextension enable --py --sys-prefix widgetsnbextension


Contribute !
-------------

Proglog is an open-source software originally written at the `Edinburgh Genome Foundry
<http://www.genomefoundry.io>`_ by `Zulko <https://github.com/Zulko>`_
and `released on Github <https://github.com/Edinburgh-Genome-Foundry/DnaCauldron>`_ under
the MIT licence (copyright Edinburgh Genome Foundry).

Proglog was not written by loggology experts, it *just works* with our projects and we use it a lot. Everyone is welcome to contribute if you find bugs or limitations !