Jupyter Notebook Introduction

Acknowledgements

The material in this tutorial is specific to Pynq. Wherever possible, however, it re-uses generic documentation describing Jupyter notebooks. In particular, we have re-used content from the following example notebooks:

  1. What is the Jupyter Notebook?
  2. Notebook Basics
  3. Running Code
  4. Markdown Cells

The original notebooks and further example notebooks are available at Jupyter documentation

Introduction

If you are reading this documentation from the webpage, you should note that the webpage is a static html version of the notebook from which it was generated. If the Pynq platform is available, you can open this notebook from the Getting_Started folder in the Pynq portal.

The Jupyter Notebook is an interactive computing environment that enables users to author notebook documents that include: - Live code - Interactive widgets - Plots - Narrative text - Equations - Images - Video

These documents provide a complete and self-contained record of a computation that can be converted to various formats and shared with others using email, Dropbox, version control systems (like git/GitHub) or nbviewer.jupyter.org.

Components

The Jupyter Notebook combines three components:

  • The notebook web application: An interactive web application for writing and running code interactively and authoring notebook documents.
  • Kernels: Separate processes started by the notebook web application that runs users’ code in a given language and returns output back to the notebook web application. The kernel also handles things like computations for interactive widgets, tab completion and introspection.
  • Notebook documents: Self-contained documents that contain a representation of all content in the notebook web application, including inputs and outputs of the computations, narrative text, equations, images, and rich media representations of objects. Each notebook document has its own kernel.

Notebook web application

The notebook web application enables users to:

  • Edit code in the browser, with automatic syntax highlighting, indentation, and tab completion/introspection.
  • Run code from the browser, with the results of computations attached to the code which generated them.
  • See the results of computations with rich media representations, such as HTML, LaTeX, PNG, SVG, PDF, etc.
  • Create and use interactive JavaScript widgets, which bind interactive user interface controls and visualizations to reactive kernel side computations.
  • Author narrative text using the Markdown markup language.
  • Build hierarchical documents that are organized into sections with different levels of headings.
  • Include mathematical equations using LaTeX syntax in Markdown, which are rendered in-browser by MathJax.

Kernels

The Notebook supports a range of different programming languages. For each notebook that a user opens, the web application starts a kernel that runs the code for that notebook. Each kernel is capable of running code in a single programming language. There are kernels available in the following languages:

The default kernel runs Python code which is the language Pynq is based on.

Kernels communicate with the notebook web application and web browser using a JSON over ZeroMQ/WebSockets message protocol that is described here. Most users don’t need to know about these details, but it helps to understand that “kernels run code.”

Notebook documents

Notebook documents contain the inputs and outputs of an interactive session as well as narrative text that accompanies the code but is not meant for execution. Rich output generated by running code, including HTML, images, video, and plots, is embedded in the notebook, which makes it a complete and self-contained record of a computation.

When you run the notebook web application on your computer, notebook documents are just files on your local filesystem with a ``.ipynb`` extension. This allows you to use familiar workflows for organizing your notebooks into folders and sharing them with others.

Notebooks consist of a linear sequence of cells. There are four basic cell types:

  • Code cells: Input and output of live code that is run in the kernel
  • Markdown cells: Narrative text with embedded LaTeX equations
  • Heading cells: Deprecated. Headings are supported in Markdown cells
  • Raw cells: Unformatted text that is included, without modification, when notebooks are converted to different formats using nbconvert

Internally, notebook documents are JSON data with binary values base64 encoded. This allows them to be read and manipulated programmatically by any programming language. Because JSON is a text format, notebook documents are version control friendly.

Notebooks can be exported to different static formats including HTML, reStructeredText, LaTeX, PDF, and slide shows (reveal.js) using Jupyter’s nbconvert utility. Some of documentation for Pynq, including this page, was written in a Notebook and converted to html for hosting on the project’s documentation website.

Furthermore, any notebook document available from a public URL or on GitHub can be shared via nbviewer. This service loads the notebook document from the URL and renders it as a static web page. The resulting web page may thus be shared with others without their needing to install the Jupyter Notebook.

GitHub also renders notebooks, so any Notebook added to GitHub can be viewed as intended.

Notebook Basics

The Notebook dashboard

The Notebook server runs on the ARM® processor of the PYNQ-Z1. You can open the notebook dashboard by navigating to pynq:9090 when your board is connected to the network. The dashboard serves as a home page for notebooks. Its main purpose is to display the notebooks and files in the current directory. For example, here is a screenshot of the dashboard page for the Examples directory in the Jupyter repository:

The top of the notebook list displays clickable breadcrumbs of the current directory. By clicking on these breadcrumbs or on sub-directories in the notebook list, you can navigate your filesystem.

To create a new notebook, click on the “New” button at the top of the list and select a kernel from the dropdown (as seen below).

Notebooks and files can be uploaded to the current directory by dragging a notebook file onto the notebook list or by the “click here” text above the list.

The notebook list shows green “Running” text and a green notebook icon next to running notebooks (as seen below). Notebooks remain running until you explicitly shut them down; closing the notebook’s page is not sufficient.

To shutdown, delete, duplicate, or rename a notebook check the checkbox next to it and an array of controls will appear at the top of the notebook list (as seen below). You can also use the same operations on directories and files when applicable.

To see all of your running notebooks along with their directories, click on the “Running” tab:

This view provides a convenient way to track notebooks that you start as you navigate the filesystem in a long running notebook server.

Overview of the Notebook UI

If you create a new notebook or open an existing one, you will be taken to the notebook user interface (UI). This UI allows you to run code and author notebook documents interactively. The notebook UI has the following main areas:

  • Menu
  • Toolbar
  • Notebook area and cells

The notebook has an interactive tour of these elements that can be started in the “Help:User Interface Tour” menu item.

Edit mode

Edit mode is indicated by a green cell border and a prompt showing in the editor area:

When a cell is in edit mode, you can type into the cell, like a normal text editor.

Enter edit mode by pressing Enter or using the mouse to click on a cell’s editor area.

Command mode

Command mode is indicated by a grey cell border with a blue left margin:

When you are in command mode, you are able to edit the notebook as a whole, but not type into individual cells. Most importantly, in command mode, the keyboard is mapped to a set of shortcuts that let you perform notebook and cell actions efficiently. For example, if you are in command mode and you press c, you will copy the current cell - no modifier is needed.

Don’t try to type into a cell in command mode; unexpected things will happen!

Enter command mode by pressing Esc or using the mouse to click outside a cell’s editor area.

Mouse navigation

All navigation and actions in the Notebook are available using the mouse through the menubar and toolbar, both of which are above the main Notebook area:

Cells can be selected by clicking on them with the mouse. The currently selected cell gets a grey or green border depending on whether the notebook is in edit or command mode. If you click inside a cell’s editor area, you will enter edit mode. If you click on the prompt or output area of a cell you will enter command mode.

If you are running this notebook in a live session on the PYNQ-Z1, try selecting different cells and going between edit and command mode. Try typing into a cell.

If you want to run the code in a cell, you would select it and click the play button in the toolbar, the “Cell:Run” menu item, or type Ctrl + Enter. Similarly, to copy a cell you would select it and click the copy button in the toolbar or the “Edit:Copy” menu item. Ctrl + C, V are also supported.

Markdown and heading cells have one other state that can be modified with the mouse. These cells can either be rendered or unrendered. When they are rendered, you will see a nice formatted representation of the cell’s contents. When they are unrendered, you will see the raw text source of the cell. To render the selected cell with the mouse, and execute it. (Click the play button in the toolbar or the “Cell:Run” menu item, or type Ctrl + Enter. To unrender the selected cell, double click on the cell.

Keyboard Navigation

There are two different sets of keyboard shortcuts: one set that is active in edit mode and another in command mode.

The most important keyboard shortcuts are Enter, which enters edit mode, and Esc, which enters command mode.

In edit mode, most of the keyboard is dedicated to typing into the cell’s editor. Thus, in edit mode there are relatively few shortcuts. In command mode, the entire keyboard is available for shortcuts, so there are many more. The Help->``Keyboard Shortcuts`` dialog lists the available shortcuts.

Some of the most useful shortcuts are:

  1. Basic navigation: enter, shift-enter, up/k, down/j
  2. Saving the notebook: s
  3. Change Cell types: y, m, 1-6, t
  4. Cell creation: a, b
  5. Cell editing: x, c, v, d, z
  6. Kernel operations: i, 0 (press twice)

Running Code

First and foremost, the Jupyter Notebook is an interactive environment for writing and running code. The notebook is capable of running code in a wide range of languages. However, each notebook is associated with a single kernel. Pynq, and this notebook is associated with the IPython kernel, which runs Python code.

Code cells allow you to enter and run code

Run a code cell using Shift-Enter or pressing the play button in the toolbar above. The button displays run cell, select below when you hover over it.

In [1]:
a = 10
In [ ]:
print(a)
10

There are two other keyboard shortcuts for running code:

  • Alt-Enter runs the current cell and inserts a new one below.
  • Ctrl-Enter run the current cell and enters command mode.

Managing the Kernel

Code is run in a separate process called the Kernel. The Kernel can be interrupted or restarted. Try running the following cell and then hit the stop button in the toolbar above. The button displays interrupt kernel when you hover over it.

In [ ]:
import time
time.sleep(10)

Cell menu

The “Cell” menu has a number of menu items for running code in different ways. These includes:

  • Run and Select Below
  • Run and Insert Below
  • Run All
  • Run All Above
  • Run All Below

Restarting the kernels

The kernel maintains the state of a notebook’s computations. You can reset this state by restarting the kernel. This is done from the menu bar, or by clicking on the corresponding button in the toolbar.

sys.stdout

The stdout and stderr streams are displayed as text in the output area.

In [ ]:
print("Hello from Pynq!")

Output is asynchronous

All output is displayed asynchronously as it is generated in the Kernel. If you execute the next cell, you will see the output one piece at a time, not all at the end.

In [ ]:
import time, sys
for i in range(8):
    print(i)
    time.sleep(0.5)

Large outputs

To better handle large outputs, the output area can be collapsed. Run the following cell and then single- or double- click on the active area to the left of the output:

In [ ]:
for i in range(50):
    print(i)

Markdown

Text can be added to Jupyter Notebooks using Markdown cells. Markdown is a popular markup language that is a superset of HTML. Its specification can be found here:

http://daringfireball.net/projects/markdown/

Markdown basics

You can make text italic or bold.

You can build nested itemized or enumerated lists:

  • One
    • Sublist
      • This
  • Sublist - That - The other thing
  • Two
  • Sublist
  • Three
  • Sublist

Now another list:

  1. Here we go
    1. Sublist
    2. Sublist
  2. There we go
  3. Now this

You can add horizontal rules:


Here is a blockquote:

Beautiful is better than ugly. Explicit is better than implicit. Simple is better than complex. Complex is better than complicated. Flat is better than nested. Sparse is better than dense. Readability counts. Special cases aren’t special enough to break the rules. Although practicality beats purity. Errors should never pass silently. Unless explicitly silenced. In the face of ambiguity, refuse the temptation to guess. There should be one– and preferably only one –obvious way to do it. Although that way may not be obvious at first unless you’re Dutch. Now is better than never. Although never is often better than right now. If the implementation is hard to explain, it’s a bad idea. If the implementation is easy to explain, it may be a good idea. Namespaces are one honking great idea – let’s do more of those!

And shorthand for links:

Jupyter’s website

Headings

You can add headings by starting a line with one (or multiple) # followed by a space, as in the following example:

# Heading 1
# Heading 2
## Heading 2.1
## Heading 2.2

Embedded code

You can embed code meant for illustration instead of execution in Python:

def f(x):
    """a docstring"""
    return x**2

or other languages:

if (i=0; i<n; i++) {
  printf("hello %d\n", i);
  x += 4;
}

LaTeX equations

Courtesy of MathJax, you can include mathematical expressions both inline: \(e^{i\pi} + 1 = 0\) and displayed:

\[e^x=\sum_{i=0}^\infty \frac{1}{i!}x^i\]\[Inline expressions can be added by surrounding the latex code with\]

$:

$e^{i\pi} + 1 = 0$

Expressions on their own line are surrounded by $$:

$$e^x=\sum_{i=0}^\infty \frac{1}{i!}x^i$$

GitHub flavored markdown

The Notebook webapp supports Github flavored markdown meaning that you can use triple backticks for code blocks:

<pre>
```python
print "Hello World"
```
</pre>

<pre>
```javascript
console.log("Hello World")
```
</pre>

Gives:

print "Hello World"
console.log("Hello World")

And a table like this:

<pre>
```

| This | is   |
|------|------|
|   a  | table|

```
</pre>

A nice HTML Table:

This is
a table

General HTML

Because Markdown is a superset of HTML you can even add things like HTML tables:

Header 1

Header 2

row 1, cell 1

row 1, cell 2

row 2, cell 1

row 2, cell 2

Local files

If you have local files in your Notebook directory, you can refer to these files in Markdown cells directly:

[subdirectory/]<filename>

Security of local files

Note that this means that the Jupyter notebook server also acts as a generic file server for files inside the same tree as your notebooks. Access is not granted outside the notebook folder so you have strict control over what files are visible, but for this reason it is highly recommended that you do not run the notebook server with a notebook directory at a high level in your filesystem (e.g. your home directory).

When you run the notebook in a password-protected manner, local file access is restricted to authenticated users unless read-only views are active.