IPYTHON INTERACTIVE COMPUTING AND VISUALIZATION COOKBOOK

A comprehensive tutorial covering the state-of-the-art methods you can utilize in IPython, including various real-world examples to help you learn in a practical and effective manner. The book illustrates topics in applied mathematics, scientific modeling, and statistical learning., This book is intIPython Interactive Computing andVisualization cookbookCopyright c 2014 Packt PublishingAll rights reserved. No part of this book may be reproduced, stored in a retrieval system, ortransmitted in any form or by any means, without the prior written permission of the publisher,except in the case of brief quotations embedded in critical articles or reviewsEvery effort has been made in the preparation of this book to ensure the accuracy of theinformation presented. However, the information contained in this book is sold withoutwarranty, either express or implied. Neither the author, nor Packt Publishing, and its dealersand distributors will be held liable for any damages caused or alleged to be caused directlyor indirectly by this bookPackt Publishing has endeavored to provide trademark information about all of the companiesand products mentioned in this book by the appropriate use of capitals. However, PacktPublishing cannot guarantee the accuracy of this information.First published: September 2014Production reference: 1190914Published by Packt Publishing LtdLivery place35 Livery Streetgham B3 2PB, UKSBN9781783284818www.packtpub.comCoverimagebyaniketSawant(aniketsawantphotography@hotmail.com)CreditsAuPrCyrille rossantSimran BhogalMartin diveReviewersMaria gouldChetan giridhaAmeesha greeRobert johanssonPaul hindleMaurice HT Linge AnpingCommissioning EditorTejal SonGraphicsAcqulsition EditSheetal AuteGreg wildRonak dhruvDisha haContent development ditorSriram NeelakantanProduction CoordinatorsD'saAdonia jonesMadhuri dasManu jeTaabish khanSaiprasad KadaiPratik moreNilesh r mohiKomal RamchandaniCopy EditorsJanbal dharmaAlwin roDeepa nambiaNitesh thakurKaruna narayanarWorkProject coordinateAlwin RoyJudie」oseAbout the AuthorCyrille Rossant is a researcher in neuroinformatics, and is a graduate of Ecole NormaleSuperieure, Paris, where he studied mathematics and computer science. He has worked atPrinceton University, University College London, and college de franceAs part of his data science and software engineering projects, he gained experiencein machine learning, high-performance computing, parallel computing, and big datavisualization. He is one of the developers of vispy, a high-performance visualizationpackage in Python He is the author of learning iPython for Interactive computing and dataVisualization, Packt Publishing, a beginner-level introduction to data analysis in Python, andthe prequel of this book.I would like to thank the IPython development team for their supportI am also deeply grateful to Nick Fiorentini and his partner Darbie Whitmanfor their invaluable help during the later stages of editingFinally, I would like to thank my relatives and notably my wife claireAbout the reviewersChetan Giridhar is an open source evangelist and Python enthusiast he has been invitedto talk at international Python conferences on topics such as filesystems, search engines, andreal-time communication He is a lso working as an associate editor at python editorial, thePython Papers AnthologyChetan works as a lead engineer and evangelist at BlueJeans Network(http://bluejeans.com/),aleadingvideoconferencingsiteonCloudCompanyHe has co-authored an e-book, Design Patterns in Python, Testing Perspective, and hasreviewed books on Python programming at Packt PublishingId like to thank my parents Jayant and Jyotsana Giridhar), my wife Deeptiand my friends/colleagues for supporting and inspiring meRobert Johansson has a phd in Theoretical Physics from Chalmers University ofTechnology, Sweden He is currently working as a researcher at the InterdisciplinaryTheoretical Science Research Group at RIKEN, Japan, focusing on computationalcondensed-matter physics and quantum mechanicsMaurice HT Ling completed his PhD in Bioinformatics and BSc(Hons)in Molecular andCell Biology from The University of Melbourne, Australia. He is currently a research fellowin Nanyang Technological University, Singapore, and an honorary fellow in the University ofMelbourne, Australia. Maurice coedits The Python Papers and cofounded the Python UserGroup( singapore), where he has served as an executive committee member since 2010His research interests lies in life-biological and artificial life, and artificial intelligence-usingcomputer science and statistics as tools to understand life and its numerous aspects. Hispersonalwebsiteishttp://maurice.vodien.comJose Unpingco is the author of the Python for Signal Processing blog and thecorresponding book. a graduate from University of California, San Diego, he has spent almost20 years in the industry as an analyst, instructor, engineer, consultant, and technical directorin the area of signal processing. His interests include time-series analysis, statistical signalprocessing, random processes, and large-scale interactive computingUnpingco has been an active member of the scientific Python community for over a decadeand developed some of the first video tutorials on IPython and scientific Python. He has alsohelped fund a number of scientific Python efforts in a wide variety of disciplineswww.packtpub.comSupport files, eBooks, discount offers, and moreYoumightwanttovisitwww.Packtpub.comforsupportfilesanddownloadsrelatedtoyour bookDid you know that Packt offers eBook versions of every book published, with PDF and ePubfilesavailableYoucanupgradetotheeBookversionatwww.Packtpub.comandasaprintbook customer, you are entitled to a discount on the e book copy. get in touch with us atservice@packtpub com for more detailsAtwww.Packtpub.comyoucanalsoreadacollectionoffreetechnicalarticlessignupfor a range of free newsletters and receive exclusive discounts and offers on Packt booksand ebooks6PACKTLIBhttp://packtlib.paCktpub.comDo you need instant solutions to your it questions? PacktLib is Packt's online digital booklibrary. Here, you can access, read and search across Packt's entire library of booksWhy Subscribe?Fully searchable across every book published by packtCopy and paste, print and bookmark contentOn demand and accessible via web browserFree Access for packt account holdersIfyouhaveanaccountwithpacktatwww.packtpub.comyoucanusethistoaccessPacktLib today and view nine entirely free books. Simply use your login credentials forimmediate accessTable of contentsPrefaceChapter 1: A Tour of Interactive Computing with IPythonIntroductionIntroducing the IPython notebook13Getting started with exploratory data analysis in IPython22Introducing the multidimensional array in Num Py for fast array computations 28Creating an IPython extension with custom magic commands32Mastering IPython's configuration system36Creating a simple kernel for IPython39Chapter 2: Best Practices in Interactive Computing45Introduction45Choosing or not between Python 2 and Python 346Efficient interactive computing workflows with IPython50Learning the basics of the distributed version control system Git53A typical workflow with Git branching6Ten tips for conducting reproducible interactive computing experiments59Writing high-quality Python code63Writing unit tests with nose67Debugging your code with IPython74Chapter 3: Mastering the Notebook79Introduction79Teaching programming in the notebook with IPython blocks84Converting an IPython notebook to other formats with nbconvert89Adding custom controls in the notebook toolbar94Customizing the css style in the notebook96Using interactive widgets- a piano in the notebook99