Difference between revisions of "Category:Python"

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The Python programming language is a powerful language which has gained popularity over the past several years. It is widely used in the scientific community, and there are numerous tools readily available for common data analysis tasks. At UiO there is a repository for Modules developed internally. The pages herein provide important information on working with Python on the UiO servers and also with your own PC.

Key Topics / Tips for Python at UiO

Python on the Servers

By Anne Fouilloux Published May 22, 2014 09:59 AM - Last modified May 22, 2014 10:17 AM

Python is an interpreted, interactive, object-oriented programming language. It incorporates modules, exceptions, dynamic typing, very high level dynamic data types, and classes. Python combines remarkable power with very clear syntax. It has interfaces to many system calls and libraries, as well as to various window systems, and is extensible in C or C++.

UiO Geosciences IT provides users with two different python distributions to work with:

• Enthought Python Distribution
• Anaconda - Continuum Analytics

Both are available on: Red Hat 6 linux servers and desktops, use e.g sverdrup.uio.no

How to start:

If you wish to use Enthought Python Distribution:

 module load python/canopy

or for Anaconda Python Distribution:

Before using Anaconda Python Distribution, you would need to get your own academic license. Academic licenses are free and can be generated for/by each user from:

• Anaconda

Once you receive the license file just place it in the $HOME/.continuum folder. Don't forget "." in front of the folder name (this folder is hidden); if it does not exist, you can create it:

 mkdir $HOME/.continuum

The email accompanying the license will have more detailed instructions. You may also reference the online anaconda documentation for further detail.

Then to set-up your environment:

 module load python/anaconda

If you have problems with the module command please follow this link.

Then for any of these two distributions:

 python

At the command line.

This link: [PYTHON] is the source guide from the Geoscience IT for the above documentation.

***IMPORTANT***

Once you have connected to the servers, in order to use Python it is important to know where the modules are, and how to set up your environment. Many of the commonly used modules are available already, and installed in a directory that has been added to your PYTHONPATH .

For more information see:

• /SettingPaths

Resources

/Resources

Best Practices

Let's start with some 'best practices' for programming with Python.

Code Style

First and foremost, one should become familiar with the PEP8. This is a 'Python Enhancement Proposal' (PEP). In Python this is the equivalent of a detailed featured request. PEP8 lays the foundation for how you should format your code.

One important feature of python to highlight are Documentation Strings:

    Conventions for writing good documentation strings (a.k.a. "docstrings")
    are immortalized in PEP 257 [3].
 
    - Write docstrings for all public modules, functions, classes, and
      methods.  Docstrings are not necessary for non-public methods, but you
      should have a comment that describes what the method does.  This comment
      should appear after the "def" line.
 
    - PEP 257 describes good docstring conventions.  Note that most
      importantly, the """ that ends a multiline docstring should be on a line
      by itself, and preferably preceded by a blank line, e.g.:
 
      """Return a foobang
 
      Optional plotz says to frobnicate the bizbaz first.
 
      """
 
    - For one liner docstrings, it's okay to keep the closing """ on the same
      line.

Import Statements & Namespaces

In python, almost all code will be preceded with some statements such as: import this (try that, by the way). These are 'import statements' which pull in other modules to use within your own code.

You may find some examples, particularly when learning matplotlib and working with 'pylab', where the tutorial uses:

from pylab import *

This is NOT recommended. This will contaminate your local namespace, meaning that the module from which you import everything indicated by the '*', may overwrite some of your own functions or even python builtins.

The RECOMMENDED way to import modules is to:

import pylab as plb

Then you can still use the example, but you may simply need to prefix some of the function calls with 'plb.', which refers to the 'pylab' namespace.

Specific for Matplotlib

There will be some pages dedicated to Matplotlib, but in the meantime, the 'best practice' for working with Matplotlib is to use the 'object oriented' approach:

import matplotlib.pyplot as plt
import numpy as np
 
x = np.arange(100)
y = np.sin(x)
 
fig = plt.figure()
ax = fig.add_subplot(111)
ax.plot(x, y)
 
plt.show()

Here we have shown an example of both the import of matplotlib.pyplot into the 'plt.' namespace, and numpy into the 'np.' namespace.

Useful Software / Modules

• /Sphinx
• /Numpy
• /Scipy
• /Matplotlib
• /Ipython
• /netcdf4-python
• /pygrib
• /pflexpart
• /netrc
• Plone -- Old notes for reference