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‎01-preface-with-jupyter-book.rst

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Preface
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===============================================================================
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.. contents:: **Contents**
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:local:
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About the author
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----------------
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`Nicolas P. Rougier`_ is a full-time research scientist at Inria_ which is the
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French national institute for research in computer science and control. This is
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a public scientific and technological establishment (EPST) under the double
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supervision of the Research & Education Ministry, and the Ministry of Economy
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Finance and Industry. Nicolas P. Rougier is working within the Mnemosyne_
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project which lies at the frontier between integrative and computational
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neuroscience in association with the `Institute of Neurodegenerative
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Diseases`_, the Bordeaux laboratory for research in computer science
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(LaBRI_), the `University of Bordeaux`_ and the national center for scientific
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research (CNRS_).
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He has been using Python for more than 15 years and NumPy for more than 10
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years for modeling in neuroscience, machine learning and for advanced
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visualization (OpenGL). Nicolas P. Rougier is the author of several online
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resources and tutorials (Matplotlib, NumPy, OpenGL) and he's teaching Python,
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NumPy and scientific visualization at the University of Bordeaux and in various
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conferences and schools worldwide (SciPy, EuroScipy, etc). He's also the author
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of the popular article `Ten Simple Rules for Better Figures`_ and a popular
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`matplotlib tutorial
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<http://www.labri.fr/perso/nrougier/teaching/matplotlib/matplotlib.html>`_.
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About this book
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---------------
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This book has been written in |ReST|_ format and generated using the
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`rst2html.py` command line available from the docutils_ python package.
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If you want to rebuild the html output, from the top directory, type:
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.. code-block::
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$ rst2html.py --link-stylesheet --cloak-email-addresses \
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--toc-top-backlinks --stylesheet=book.css \
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--stylesheet-dirs=. book.rst book.html
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The sources are available from https://github.com/rougier/from-python-to-numpy.
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.. |ReST| replace:: restructured text
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.. _ReST: http://docutils.sourceforge.net/rst.html
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.. _docutils: http://docutils.sourceforge.net/
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About the Jupyter Book
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++++++++++++++++++++++
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**html version**
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To generate the `Jupyter Book`_ from the top directory:
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1. Install the most up to date version of jupyter-book:
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.. code-block::
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$ pip install -U jupyter-book
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2. Go to the root directory of the repository and run:
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.. code-block::
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$ jupyter-book build . --path-output jupyter-book/.
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3. Copy the data folder into the html directory:
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.. code-block::
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$ cp -r data jupyter-book/_build/html/.
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4. Open Jupyter-book at: `jupyter-book/_build/html/index.html`
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**pdf version**
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To generate a pdf versio 67F4 n of the book, you will need pyppeteer_ installed,
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then in the top directory, run:
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.. code-block::
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$ jupyter-book build . --builder pdfhtml --path-output jupyter-book/.
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The pdf version of the book is available at `jupyter-book/_build/pdf/book.pdf`
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.. _Jupyter Book: https://jupyterbook.org
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.. _pyppeteer: https://pypi.org/project/pyppeteer/
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Prerequisites
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+++++++++++++
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This is not a Python beginner guide and you should have an intermediate level in
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Python and ideally a beginner level in NumPy. If this is not the case, have
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a look at the bibliography_ for a curated list of resources.
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Conventions
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+++++++++++
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We will use usual naming conventions. If not stated explicitly, each script
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should import NumPy, scipy and matplotlib as:
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.. code-block:: python
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import numpy as np
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import scipy as sp
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import matplotlib.pyplot as plt
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We'll use up-to-date versions (at the date of writing, i.e. January, 2017) of the
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different packages:
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=========== =========
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Packages Version
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=========== =========
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Python 3.6.0
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----------- ---------
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NumPy 1.12.0
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----------- ---------
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Scipy 0.18.1
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----------- ---------
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Matplotlib 2.0.0
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=========== =========
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How to contribute
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+++++++++++++++++
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If you want to contribute to this book, you can:
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* Review chapters (please contact me)
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* Report issues (https://github.com/rougier/from-python-to-numpy/issues)
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* Suggest improvements (https://github.com/rougier/from-python-to-numpy/pulls)
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* Correct English (https://github.com/rougier/from-python-to-numpy/issues)
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* Design a better and more responsive html template for the book.
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* Star the project (https://github.com/rougier/from-python-to-numpy)
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Publishing
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++++++++++
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If you're an editor interested in publishing this book, you can `contact me
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<mailto:Nicolas.Rougier@inria.fr>`_ if you agree to have this version and all
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subsequent versions open access (i.e. online at `this address
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<http://www.labri.fr/perso/nrougier/from-python-to-numpy>`_), you know how to
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deal with `restructured text <http://docutils.sourceforge.net/rst.html>`_ (Word
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is not an option), you provide a real added-value as well as supporting
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services, and more importantly, you have a truly amazing latex book template
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(and be warned that I'm a bit picky about typography & design: `Edward Tufte
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<https://www.edwardtufte.com/tufte/>`_ is my hero). Still here?
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License
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--------
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**Book**
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This work is licensed under a `Creative Commons Attribution-Non Commercial-Share
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Alike 4.0 International License <https://creativecommons.org/licenses/by-nc-sa/4.0/>`_. You are free to:
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* **Share** — copy and redistribute the material in any medium or format
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* **Adapt** — remix, transform, and build upon the material
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The licensor cannot revoke these freedoms as long as you follow the license terms.
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**Code**
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The code is licensed under the `OSI-approved BSD 2-Clause License
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<LICENSE-code.txt>`_.
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.. --- Links ------------------------------------------------------------------
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.. _Nicolas P. Rougier: http://www.labri.fr/perso/nrougier/
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.. _Inria: http://www.inria.fr/en
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.. _Mnemosyne: http://www.inria.fr/en/teams/mnemosyne
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.. _LaBRI: https://www.labri.fr/
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.. _CNRS: http://www.cnrs.fr/index.php
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.. _University of Bordeaux: http://www.u-bordeaux.com/
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.. _Institute of Neurodegenerative Diseases:
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http://www.imn-bordeaux.org/en/
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.. _Ten Simple Rules for Better Figures:
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http://dx.doi.org/10.1371/journal.pcbi.1003833
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.. ----------------------------------------------------------------------------
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‎_config.yml

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# Book settings
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title: From Python to Numpy
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author: Nicolas P. Rougier
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author: Nicolas P. Rougier; Loïc Houpert
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logo: data/cubes.png
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‎_toc.yml

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format: jb-article
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root: book
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root: book-jupyterbook
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title: From Python to Numpy
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sections:
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- file: 01-preface
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- file: 01-preface-with-jupyter-book
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- file: 02-introduction
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- file: 03-anatomy
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- file: 04-code-vectorization

‎book-jupyterbook.rst

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.. ----------------------------------------------------------------------------
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.. Title: From Python to Numpy
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.. Author: Nicolas P. Rougier
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.. Date: January 2017
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.. License: Creative Commons Share-Alike Non-Commercial International 4.0
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.. ----------------------------------------------------------------------------
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.. meta::
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:description: An open-source book about numpy vectorization techniques, based on experience, practice and descriptive examples
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:viewport: width=device-width, initial-scale=1, maximum-scale=1
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.. |date| date:: %B %Y
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===============================================================================
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From Python to Numpy
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===============================================================================
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Copyright (c) 2021 - Nicolas P. Rougier <Nicolas.Rougier@inria.fr> & Loïc Houpert <loic@lhoupert.fr>
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.. default-role:: code
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.. container:: title-logos
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.. image:: data/cc.large.png
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:width: 40px
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.. image:: data/by.large.png
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:width: 40px
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.. image:: data/sa.large.png
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:width: 40px
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.. image:: data/nc.large.png
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:width: 40px
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|
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| Latest version - |date|
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| DOI: `10.5281/zenodo.225783 <http://doi.org/10.5281/zenodo.225783>`_
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.. ----------------------------------------------------------------------------
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.. container:: title-logos
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.. image:: data/cubes.png
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:width: 100%
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.. ----------------------------------------------------------------------------
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There are already a fair number of books about Numpy (see Bibliography_) and a
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legitimate question is to wonder if another book is really necessary. As you
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may have guessed by reading these lines, my personal answer is yes, mostly
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because I think there is room for a different approach concentrating on the
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migration from Python to Numpy through vectorization. There are a lot of
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techniques that you don't find in books and such techniques are mostly learned
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through experience. The goal of this book is to explain some of these
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techniques and to provide an opportunity for making this experience in the
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process.
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**Website:** http://www.labri.fr/perso/nrougier/from-python-to-numpy
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.. ----------------------------------------------------------------------------
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.. contents:: **Table of Contents**
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:class: main-content
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:depth: 2
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|
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|
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**Disclaimer:** All external pictures should have associated credits. If there
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are missing credits, please tell me, I will correct it. Similarly, all excerpts
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should be sourced (wikipedia mostly). If not, this is an error and I will
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correct it as soon as you tell me.
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The book is open-access (you're reading it) but **if you insist on buying it**,
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my advice would be to read it first and then decide if you still want to buy it
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(!?). If this is the case, you can do it via `Paypal
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<https://www.paypal.me/NicolasPRougier/>`_, price is free (`5 euros
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<https://www.paypal.me/NicolasPRougier/5>`_, `10 euros
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<https://www.paypal.me/NicolasPRougier/10>`_, `25 euros
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<https://www.paypal.me/NicolasPRougier/25>`_). You won't get anything extra but
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it might help me with the writing of the upcoming **Python and OpenGL for
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Scientific Visualization** (May 2018).
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.. ----------------------------------------------------------------------------
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.. |WIP| image:: https://img.shields.io/badge/status-WIP-orange.svg?style=flat-square
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.. ----------------------------------------------------------------------------
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.. include< 7CBC /span>:: 01-preface-with-jupyter-book.rst
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.. include:: 02-introduction.rst
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.. include:: 03-anatomy.rst
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.. include:: 04-code-vectorization.rst
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.. include:: 05-problem-vectorization.rst
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.. include:: 06-custom-vectorization.rst
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.. include:: 07-beyond-numpy.rst
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.. include:: 08-conclusion.rst
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.. include:: 09-quick-reference.rst
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.. include:: 10-bibliography.rst
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.. --- Compilation ------------------------------------------------------------
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.. rst2html.py --link-stylesheet --stylesheet=markdown.css book.rst book.html

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