#!/usr/bin/env python
# coding: utf-8

# # Scientific modules and IPython

# Nikolay Koldunov
# 
# 
# koldunovn@gmail.com

# This is part of [**Python for Geosciences**](https://github.com/koldunovn/python_for_geosciences) notes.

# In[1]:


get_ipython().run_line_magic('matplotlib', 'inline')
import matplotlib.pylab as plt


# ## Core scientific packages

# When people say that they do their scientific computations in Python it's only half true. Python is a construction set, similar to MITgcm or other models. Without packages it's only a core, that although very powerful, does not seems to be able to do much by itself.
# 
# There is a set of packages, that almost every scientist would need:
# 
# <img  height="200" src="files/core.png">

# We are going to talk about all exept Sympy

# ## Installation

# Installation instructions can be found in the README.md file of this repository. Better to use [rendered version from GitHub](https://github.com/koldunovn/python_for_geosciences/blob/master/README.md).
# 

# ## IPython

# In order to be productive you need comfortable environment, and this is what IPython provides. It was started as enhanced python interactive shell, but with time become architecture for interactive computing.

# ## Jupyter notebook 

# Since the 0.12 release, IPython provides a new rich text web interface - IPython notebook. Here you can combine:

# #### Code execution

# In[3]:


print('I love Python')


# #### Text (Markdown)

# IPython [website](http://ipython.org/).
# 
# List:
# 
# * [Python on Codeacademy](http://www.codecademy.com/tracks/python)
# * [Google's Python Class](https://developers.google.com/edu/python/)
# 
# Code:
# 
#     print('hello world')
# 

# #### $\LaTeX$ equations

# $$\int_0^\infty e^{-x^2} dx=\frac{\sqrt{\pi}}{2}$$
# $$
# F(x,y)=0 ~~\mbox{and}~~
# \left| \begin{array}{ccc}
#   F''_{xx} & F''_{xy} &  F'_x \\
#   F''_{yx} & F''_{yy} &  F'_y \\
#   F'_x     & F'_y     & 0 
#   \end{array}\right| = 0
# $$

# #### Plots

# In[4]:


x = [1,2,3,4,5]
plt.plot(x);


# #### Rich media

# In[5]:


from IPython.display import YouTubeVideo
YouTubeVideo('F4rFuIb1Ie4')


# * [IPython website](http://ipython.org/)
# * [Notebook gallery](https://github.com/ipython/ipython/wiki/A-gallery-of-interesting-IPython-Notebooks) 

# ## Run notebook

# In order to start Jupyter notebook you have to type:
# 
#     jupyter notebook
# 

# ### You can download and run this lectures:

# Web version can be accesed from the [github repository](https://github.com/koldunovn/python_for_geosciences).

# ## Main IPython features

# ### Getting help

# You can use question mark in order to get help. To execute cell you have to press *Shift+Enter*

# In[36]:


get_ipython().show_usage()


# Question mark after a function will open pager with documentation. Double question mark will show you source code of the function. 

# In[38]:


get_ipython().run_line_magic('pinfo2', 'plt.plot')


# Press SHIFT+TAB after opening bracket in order to get help for the function (list of arguments, doc string).

# In[ ]:


sum()


# ### Accessing the underlying operating system

# You can access system functions by typing exclamation mark.

# In[6]:


get_ipython().system('pwd')


# If you already have some netCDF file in the directory and *ncdump* is installed, you can for example look at its header.

# In[7]:


get_ipython().system('ncdump -h test_netcdf.nc')


# ## Magic functions

# The magic function system provides a series of functions which allow you to
# control the behavior of IPython itself, plus a lot of system-type
# features.

# Let's create some set of numbers using [range](http://docs.python.org/2/library/functions.html#range) command:

# In[9]:


list(range(10))


# And find out how long does it take to run it with *%timeit* magic function:

# In[10]:


get_ipython().run_line_magic('timeit', 'list(range(10))')


# Print all interactive variables (similar to Matlab function):

# In[11]:


get_ipython().run_line_magic('whos', '')


# ### Cell-oriented magic

# Receive as argument both the current line where they are declared and the whole body of the cell. 

# In[12]:


get_ipython().run_cell_magic('timeit', '', 'range(10)\nrange(100)\n')


# Thre are several cell-oriented magic functions that allow you to run code in other languages:

# In[13]:


get_ipython().run_cell_magic('bash', '', '\necho "My shell is:" $SHELL\n')


# In[14]:


get_ipython().run_cell_magic('perl', '', '\n$variable = 1;\nprint "The variable has the value of $variable\\n";\n')


# You can write content of the cell to a file with *%%writefile* (or *%%file* for ipython < 1.0):

# In[15]:


get_ipython().run_cell_magic('writefile', 'hello.py', "#if you use ipython < 1.0, use %%file comand\n#%%file \na = 'hello world!'\nprint(a)\n")


# And then run it:

# In[16]:


get_ipython().run_line_magic('run', 'hello.py')


# The *%run* magic will run your python script and load all variables into your interactive namespace for further use.

# In[17]:


get_ipython().run_line_magic('whos', '')


# In order to get information about all magic functions type:

# In[18]:


get_ipython().run_line_magic('magic', '')


# ### Links:

# [The cell magics in IPython](http://nbviewer.ipython.org/urls/raw.github.com/ipython/ipython/1.x/examples/notebooks/Cell%20Magics.ipynb)