Replace .ipynb with .md everywhere

mwouts/jupytext#263

.gitignore

@@ -67,6 +67,7 @@ docs/_build/
 target/
 
 # IPython Notebook
+*.ipynb
 .ipynb_checkpoints
 
 # pyenv
@@ -92,6 +93,8 @@ ENV/
 # Emacs
 *~
 
+# PyCharm
+.idea
 
 # Temporary data files
 notebooks/recipeitems-latest.json

README.md

@@ -1,9 +1,11 @@
 # Python Data Science Handbook
 
-> This is a fork of Jake Vanderplas' Python Data Science Handbook, in which every Jupyter notebook was transformed to a plain Markdown file using [Jupytext](https://github.com/mwouts/jupytext). See https://github.com/mwouts/jupytext/issues/263. 
+> This is a fork of Jake Vanderplas' Python Data Science Handbook, in which every Jupyter notebook was transformed to a plain Markdown file using [Jupytext](https://github.com/mwouts/jupytext).
+> - Open this fork on  [![Binder](https://mybinder.org/badge.svg)](https://mybinder.org/v2/gh/mwouts/PythonDataScienceHandbook/jupytext_no_ipynb?filepath=notebooks%2FIndex.md)
+> - See https://github.com/mwouts/jupytext/issues/263.
 
-[![Binder](https://mybinder.org/badge.svg)](https://mybinder.org/v2/gh/jakevdp/PythonDataScienceHandbook/master?filepath=notebooks%2FIndex.ipynb)
-[![Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/jakevdp/PythonDataScienceHandbook/blob/master/notebooks/Index.ipynb)
+[![Binder](https://mybinder.org/badge.svg)](https://mybinder.org/v2/gh/jakevdp/PythonDataScienceHandbook/master?filepath=notebooks%2FIndex.md)
+[![Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/jakevdp/PythonDataScienceHandbook/blob/master/notebooks/Index.md)
 
 This repository contains the entire [Python Data Science Handbook](http://shop.oreilly.com/product/0636920034919.do), in the form of (free!) Jupyter notebooks.
 
@@ -15,9 +17,9 @@ This repository contains the entire [Python Data Science Handbook](http://shop.o
 
 - Run the code using the Jupyter notebooks available in this repository's [notebooks](notebooks) directory.
 
-- Launch executable versions of these notebooks using [Google Colab](http://colab.research.google.com): [![Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/jakevdp/PythonDataScienceHandbook/blob/master/notebooks/Index.ipynb)
+- Launch executable versions of these notebooks using [Google Colab](http://colab.research.google.com): [![Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/jakevdp/PythonDataScienceHandbook/blob/master/notebooks/Index.md)
 
-- Launch a live notebook server with these notebooks using [binder](https://beta.mybinder.org/): [![Binder](https://mybinder.org/badge.svg)](https://mybinder.org/v2/gh/jakevdp/PythonDataScienceHandbook/master?filepath=notebooks%2FIndex.ipynb)
+- Launch a live notebook server with these notebooks using [binder](https://beta.mybinder.org/): [![Binder](https://mybinder.org/badge.svg)](https://mybinder.org/v2/gh/jakevdp/PythonDataScienceHandbook/master?filepath=notebooks%2FIndex.md)
 
 - Buy the printed book through [O'Reilly Media](http://shop.oreilly.com/product/0636920034919.do)
 
@@ -29,7 +31,7 @@ The book introduces the core libraries essential for working with data in Python
 Familiarity with Python as a language is assumed; if you need a quick introduction to the language itself, see the free companion project,
 [A Whirlwind Tour of Python](https://github.com/jakevdp/WhirlwindTourOfPython): it's a fast-paced introduction to the Python language aimed at researchers and scientists.
 
-See [Index.ipynb](http://nbviewer.jupyter.org/github/jakevdp/PythonDataScienceHandbook/blob/master/notebooks/Index.ipynb) for an index of the notebooks available to accompany the text.
+See [Index.md](http://nbviewer.jupyter.org/github/jakevdp/PythonDataScienceHandbook/blob/master/notebooks/Index.md) for an index of the notebooks available to accompany the text.
 
 ## Software
 

notebooks/00.00-Preface.md

@@ -21,9 +21,9 @@ jupyter:
 
 
 <!--NAVIGATION-->
-| [Contents](Index.ipynb) | [IPython: Beyond Normal Python](01.00-IPython-Beyond-Normal-Python.ipynb) >
+| [Contents](Index.md) | [IPython: Beyond Normal Python](01.00-IPython-Beyond-Normal-Python.md) >
 
-<a href="https://colab.research.google.com/github/jakevdp/PythonDataScienceHandbook/blob/master/notebooks/00.00-Preface.ipynb"><img align="left" src="https://colab.research.google.com/assets/colab-badge.svg" alt="Open in Colab" title="Open and Execute in Google Colaboratory"></a>
+<a href="https://colab.research.google.com/github/jakevdp/PythonDataScienceHandbook/blob/master/notebooks/00.00-Preface.md"><img align="left" src="https://colab.research.google.com/assets/colab-badge.svg" alt="Open in Colab" title="Open and Execute in Google Colaboratory"></a>
 
 
 
@@ -133,7 +133,7 @@ For more information on conda, including information about creating and using co
 <!-- #endregion -->
 
 <!--NAVIGATION-->
-| [Contents](Index.ipynb) | [IPython: Beyond Normal Python](01.00-IPython-Beyond-Normal-Python.ipynb) >
+| [Contents](Index.md) | [IPython: Beyond Normal Python](01.00-IPython-Beyond-Normal-Python.md) >
 
-<a href="https://colab.research.google.com/github/jakevdp/PythonDataScienceHandbook/blob/master/notebooks/00.00-Preface.ipynb"><img align="left" src="https://colab.research.google.com/assets/colab-badge.svg" alt="Open in Colab" title="Open and Execute in Google Colaboratory"></a>
+<a href="https://colab.research.google.com/github/jakevdp/PythonDataScienceHandbook/blob/master/notebooks/00.00-Preface.md"><img align="left" src="https://colab.research.google.com/assets/colab-badge.svg" alt="Open in Colab" title="Open and Execute in Google Colaboratory"></a>
 

notebooks/01.00-IPython-Beyond-Normal-Python.md

@@ -21,9 +21,9 @@ jupyter:
 
 
 <!--NAVIGATION-->
-< [Preface](00.00-Preface.ipynb) | [Contents](Index.ipynb) | [Help and Documentation in IPython](01.01-Help-And-Documentation.ipynb) >
+< [Preface](00.00-Preface.md) | [Contents](Index.md) | [Help and Documentation in IPython](01.01-Help-And-Documentation.md) >
 
-<a href="https://colab.research.google.com/github/jakevdp/PythonDataScienceHandbook/blob/master/notebooks/01.00-IPython-Beyond-Normal-Python.ipynb"><img align="left" src="https://colab.research.google.com/assets/colab-badge.svg" alt="Open in Colab" title="Open and Execute in Google Colaboratory"></a>
+<a href="https://colab.research.google.com/github/jakevdp/PythonDataScienceHandbook/blob/master/notebooks/01.00-IPython-Beyond-Normal-Python.md"><img align="left" src="https://colab.research.google.com/assets/colab-badge.svg" alt="Open in Colab" title="Open and Execute in Google Colaboratory"></a>
 
 
 
@@ -58,7 +58,7 @@ Before we start, some words on how to launch the IPython shell and IPython noteb
 
 This chapter, like most of this book, is not designed to be absorbed passively.
 I recommend that as you read through it, you follow along and experiment with the tools and syntax we cover: the muscle-memory you build through doing this will be far more useful than the simple act of reading about it.
-Start by launching the IPython interpreter by typing **``ipython``** on the command-line; alternatively, if you've installed a distribution like Anaconda or EPD, there may be a launcher specific to your system (we'll discuss this more fully in [Help and Documentation in IPython](01.01-Help-And-Documentation.ipynb)).
+Start by launching the IPython interpreter by typing **``ipython``** on the command-line; alternatively, if you've installed a distribution like Anaconda or EPD, there may be a launcher specific to your system (we'll discuss this more fully in [Help and Documentation in IPython](01.01-Help-And-Documentation.md)).
 
 Once you do this, you should see a prompt like the following:
 ```
@@ -103,7 +103,7 @@ If the browser does not open automatically, you can open a window and manually o
 <!-- #endregion -->
 
 <!--NAVIGATION-->
-< [Preface](00.00-Preface.ipynb) | [Contents](Index.ipynb) | [Help and Documentation in IPython](01.01-Help-And-Documentation.ipynb) >
+< [Preface](00.00-Preface.md) | [Contents](Index.md) | [Help and Documentation in IPython](01.01-Help-And-Documentation.md) >
 
-<a href="https://colab.research.google.com/github/jakevdp/PythonDataScienceHandbook/blob/master/notebooks/01.00-IPython-Beyond-Normal-Python.ipynb"><img align="left" src="https://colab.research.google.com/assets/colab-badge.svg" alt="Open in Colab" title="Open and Execute in Google Colaboratory"></a>
+<a href="https://colab.research.google.com/github/jakevdp/PythonDataScienceHandbook/blob/master/notebooks/01.00-IPython-Beyond-Normal-Python.md"><img align="left" src="https://colab.research.google.com/assets/colab-badge.svg" alt="Open in Colab" title="Open and Execute in Google Colaboratory"></a>
 

notebooks/01.01-Help-And-Documentation.md

@@ -21,9 +21,9 @@ jupyter:
 
 
 <!--NAVIGATION-->
-< [IPython: Beyond Normal Python](01.00-IPython-Beyond-Normal-Python.ipynb) | [Contents](Index.ipynb) | [Keyboard Shortcuts in the IPython Shell](01.02-Shell-Keyboard-Shortcuts.ipynb) >
+< [IPython: Beyond Normal Python](01.00-IPython-Beyond-Normal-Python.md) | [Contents](Index.md) | [Keyboard Shortcuts in the IPython Shell](01.02-Shell-Keyboard-Shortcuts.md) >
 
-<a href="https://colab.research.google.com/github/jakevdp/PythonDataScienceHandbook/blob/master/notebooks/01.01-Help-And-Documentation.ipynb"><img align="left" src="https://colab.research.google.com/assets/colab-badge.svg" alt="Open in Colab" title="Open and Execute in Google Colaboratory"></a>
+<a href="https://colab.research.google.com/github/jakevdp/PythonDataScienceHandbook/blob/master/notebooks/01.01-Help-And-Documentation.md"><img align="left" src="https://colab.research.google.com/assets/colab-badge.svg" alt="Open in Colab" title="Open and Execute in Google Colaboratory"></a>
 
 
 
@@ -281,7 +281,7 @@ I find this type of flexible wildcard search can be very useful for finding a pa
 <!-- #endregion -->
 
 <!--NAVIGATION-->
-< [IPython: Beyond Normal Python](01.00-IPython-Beyond-Normal-Python.ipynb) | [Contents](Index.ipynb) | [Keyboard Shortcuts in the IPython Shell](01.02-Shell-Keyboard-Shortcuts.ipynb) >
+< [IPython: Beyond Normal Python](01.00-IPython-Beyond-Normal-Python.md) | [Contents](Index.md) | [Keyboard Shortcuts in the IPython Shell](01.02-Shell-Keyboard-Shortcuts.md) >
 
-<a href="https://colab.research.google.com/github/jakevdp/PythonDataScienceHandbook/blob/master/notebooks/01.01-Help-And-Documentation.ipynb"><img align="left" src="https://colab.research.google.com/assets/colab-badge.svg" alt="Open in Colab" title="Open and Execute in Google Colaboratory"></a>
+<a href="https://colab.research.google.com/github/jakevdp/PythonDataScienceHandbook/blob/master/notebooks/01.01-Help-And-Documentation.md"><img align="left" src="https://colab.research.google.com/assets/colab-badge.svg" alt="Open in Colab" title="Open and Execute in Google Colaboratory"></a>
 

notebooks/01.02-Shell-Keyboard-Shortcuts.md

@@ -21,9 +21,9 @@ jupyter:
 
 
 <!--NAVIGATION-->
-< [Help and Documentation in IPython](01.01-Help-And-Documentation.ipynb) | [Contents](Index.ipynb) | [IPython Magic Commands](01.03-Magic-Commands.ipynb) >
+< [Help and Documentation in IPython](01.01-Help-And-Documentation.md) | [Contents](Index.md) | [IPython Magic Commands](01.03-Magic-Commands.md) >
 
-<a href="https://colab.research.google.com/github/jakevdp/PythonDataScienceHandbook/blob/master/notebooks/01.02-Shell-Keyboard-Shortcuts.ipynb"><img align="left" src="https://colab.research.google.com/assets/colab-badge.svg" alt="Open in Colab" title="Open and Execute in Google Colaboratory"></a>
+<a href="https://colab.research.google.com/github/jakevdp/PythonDataScienceHandbook/blob/master/notebooks/01.02-Shell-Keyboard-Shortcuts.md"><img align="left" src="https://colab.research.google.com/assets/colab-badge.svg" alt="Open in Colab" title="Open and Execute in Google Colaboratory"></a>
 
 
 
@@ -145,7 +145,7 @@ Once you develop that muscle memory, I suspect you will even find yourself wishi
 
 
 <!--NAVIGATION-->
-< [Help and Documentation in IPython](01.01-Help-And-Documentation.ipynb) | [Contents](Index.ipynb) | [IPython Magic Commands](01.03-Magic-Commands.ipynb) >
+< [Help and Documentation in IPython](01.01-Help-And-Documentation.md) | [Contents](Index.md) | [IPython Magic Commands](01.03-Magic-Commands.md) >
 
-<a href="https://colab.research.google.com/github/jakevdp/PythonDataScienceHandbook/blob/master/notebooks/01.02-Shell-Keyboard-Shortcuts.ipynb"><img align="left" src="https://colab.research.google.com/assets/colab-badge.svg" alt="Open in Colab" title="Open and Execute in Google Colaboratory"></a>
+<a href="https://colab.research.google.com/github/jakevdp/PythonDataScienceHandbook/blob/master/notebooks/01.02-Shell-Keyboard-Shortcuts.md"><img align="left" src="https://colab.research.google.com/assets/colab-badge.svg" alt="Open in Colab" title="Open and Execute in Google Colaboratory"></a>
 

notebooks/01.03-Magic-Commands.md

@@ -21,9 +21,9 @@ jupyter:
 
 
 <!--NAVIGATION-->
-< [Keyboard Shortcuts in the IPython Shell](01.02-Shell-Keyboard-Shortcuts.ipynb) | [Contents](Index.ipynb) | [Input and Output History](01.04-Input-Output-History.ipynb) >
+< [Keyboard Shortcuts in the IPython Shell](01.02-Shell-Keyboard-Shortcuts.md) | [Contents](Index.md) | [Input and Output History](01.04-Input-Output-History.md) >
 
-<a href="https://colab.research.google.com/github/jakevdp/PythonDataScienceHandbook/blob/master/notebooks/01.03-Magic-Commands.ipynb"><img align="left" src="https://colab.research.google.com/assets/colab-badge.svg" alt="Open in Colab" title="Open and Execute in Google Colaboratory"></a>
+<a href="https://colab.research.google.com/github/jakevdp/PythonDataScienceHandbook/blob/master/notebooks/01.03-Magic-Commands.md"><img align="left" src="https://colab.research.google.com/assets/colab-badge.svg" alt="Open in Colab" title="Open and Execute in Google Colaboratory"></a>
 
 
 
@@ -155,7 +155,7 @@ In [9]: %%timeit
 ```
 
 We can immediately see that list comprehensions are about 10% faster than the equivalent ``for``-loop construction in this case.
-We'll explore ``%timeit`` and other approaches to timing and profiling code in [Profiling and Timing Code](01.07-Timing-and-Profiling.ipynb).
+We'll explore ``%timeit`` and other approaches to timing and profiling code in [Profiling and Timing Code](01.07-Timing-and-Profiling.md).
 <!-- #endregion -->
 
 <!-- #region -->
@@ -183,11 +183,11 @@ In [12]: %lsmagic
 ```
 
 Finally, I'll mention that it is quite straightforward to define your own magic functions if you wish.
-We won't discuss it here, but if you are interested, see the references listed in [More IPython Resources](01.08-More-IPython-Resources.ipynb).
+We won't discuss it here, but if you are interested, see the references listed in [More IPython Resources](01.08-More-IPython-Resources.md).
 <!-- #endregion -->
 
 <!--NAVIGATION-->
-< [Keyboard Shortcuts in the IPython Shell](01.02-Shell-Keyboard-Shortcuts.ipynb) | [Contents](Index.ipynb) | [Input and Output History](01.04-Input-Output-History.ipynb) >
+< [Keyboard Shortcuts in the IPython Shell](01.02-Shell-Keyboard-Shortcuts.md) | [Contents](Index.md) | [Input and Output History](01.04-Input-Output-History.md) >
 
-<a href="https://colab.research.google.com/github/jakevdp/PythonDataScienceHandbook/blob/master/notebooks/01.03-Magic-Commands.ipynb"><img align="left" src="https://colab.research.google.com/assets/colab-badge.svg" alt="Open in Colab" title="Open and Execute in Google Colaboratory"></a>
+<a href="https://colab.research.google.com/github/jakevdp/PythonDataScienceHandbook/blob/master/notebooks/01.03-Magic-Commands.md"><img align="left" src="https://colab.research.google.com/assets/colab-badge.svg" alt="Open in Colab" title="Open and Execute in Google Colaboratory"></a>
 

notebooks/01.04-Input-Output-History.md

@@ -21,9 +21,9 @@ jupyter:
 
 
 <!--NAVIGATION-->
-< [IPython Magic Commands](01.03-Magic-Commands.ipynb) | [Contents](Index.ipynb) | [IPython and Shell Commands](01.05-IPython-And-Shell-Commands.ipynb) >
+< [IPython Magic Commands](01.03-Magic-Commands.md) | [Contents](Index.md) | [IPython and Shell Commands](01.05-IPython-And-Shell-Commands.md) >
 
-<a href="https://colab.research.google.com/github/jakevdp/PythonDataScienceHandbook/blob/master/notebooks/01.04-Input-Output-History.ipynb"><img align="left" src="https://colab.research.google.com/assets/colab-badge.svg" alt="Open in Colab" title="Open and Execute in Google Colaboratory"></a>
+<a href="https://colab.research.google.com/github/jakevdp/PythonDataScienceHandbook/blob/master/notebooks/01.04-Input-Output-History.md"><img align="left" src="https://colab.research.google.com/assets/colab-badge.svg" alt="Open in Colab" title="Open and Execute in Google Colaboratory"></a>
 
 
 
@@ -130,7 +130,7 @@ Out[13]: 0.9092974268256817
 
 <!-- #region -->
 ## Suppressing Output
-Sometimes you might wish to suppress the output of a statement (this is perhaps most common with the plotting commands that we'll explore in [Introduction to Matplotlib](04.00-Introduction-To-Matplotlib.ipynb)).
+Sometimes you might wish to suppress the output of a statement (this is perhaps most common with the plotting commands that we'll explore in [Introduction to Matplotlib](04.00-Introduction-To-Matplotlib.md)).
 Or maybe the command you're executing produces a result that you'd prefer not like to store in your output history, perhaps so that it can be deallocated when other references are removed.
 The easiest way to suppress the output of a command is to add a semicolon to the end of the line:
 
@@ -161,11 +161,11 @@ In [16]: %history -n 1-4
 
 As usual, you can type ``%history?`` for more information and a description of options available.
 Other similar magic commands are ``%rerun`` (which will re-execute some portion of the command history) and ``%save`` (which saves some set of the command history to a file).
-For more information, I suggest exploring these using the ``?`` help functionality discussed in [Help and Documentation in IPython](01.01-Help-And-Documentation.ipynb).
+For more information, I suggest exploring these using the ``?`` help functionality discussed in [Help and Documentation in IPython](01.01-Help-And-Documentation.md).
 <!-- #endregion -->
 
 <!--NAVIGATION-->
-< [IPython Magic Commands](01.03-Magic-Commands.ipynb) | [Contents](Index.ipynb) | [IPython and Shell Commands](01.05-IPython-And-Shell-Commands.ipynb) >
+< [IPython Magic Commands](01.03-Magic-Commands.md) | [Contents](Index.md) | [IPython and Shell Commands](01.05-IPython-And-Shell-Commands.md) >
 
-<a href="https://colab.research.google.com/github/jakevdp/PythonDataScienceHandbook/blob/master/notebooks/01.04-Input-Output-History.ipynb"><img align="left" src="https://colab.research.google.com/assets/colab-badge.svg" alt="Open in Colab" title="Open and Execute in Google Colaboratory"></a>
+<a href="https://colab.research.google.com/github/jakevdp/PythonDataScienceHandbook/blob/master/notebooks/01.04-Input-Output-History.md"><img align="left" src="https://colab.research.google.com/assets/colab-badge.svg" alt="Open in Colab" title="Open and Execute in Google Colaboratory"></a>