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1. Select Markdown from the list. Then run the markdown code. Alternatively, you can press the key M on your keyboard to switch the selected cell to markdown. Hit the key Y to switch back to Code mode. However, to get a better hold of the markdown property, you can check out the Jupyter Notebook Markdown Cells docs.
2. This is a common feature and is supported by RStudio within R Markdown for example. Surprisingly, Jupyter Notebooks do not support the inclusion of variables in Markdown Cells out of the box. If you still use Jupyter Notebooks there is a readily solution: the Python Markdown extension.
3. Jupyter Notebook is a great tool for data analysis. And one of its greatest features is that you can easily combine runnable code with rich-text annotations. Markdown cells that contain such annotations support both HTML and Markdown syntax.

Learning Objectives

• Explain what the Markdown format is.
• Describe the role of Markdown for documentation of earth data science workflows.
• Use Markdown syntax in Jupyter Notebook to:
  • Create headers and lists
  • Bold and italicize bold text
  • Render images and create hyperlinks to web pages

What is Markdown?

Now lets briefly discuss the markdown syntaxes which is supported by Jupyter Notebook. Convert cell type from Code to Markdown Heading: There are six types of headings each start with hash symbols (#) followed by a space where the largest heading uses a single hash and the smallest use six hash sign. I am able to convert part of the text in span to latex and jupyter renders the latex in red. – Shishir Pandey Aug 11 '15 at 15:59 @ShishirPandey: What I was referring to with 'conversion of the notebook to latex' is that you can normally convert a notebook to LaTex (a typesetting language) using ipython nbconvert -to latex mynotebook.ipynb.

Markdown is a human readable syntax (also referred to as a markup language) for formatting text documents. Markdown can be used to produce nicely formatted documents including PDFs and web pages.

When you format text using Markdown in a document, it is similar to using the format tools (e.g. bold, heading 1, heading 2) in a word processing tool like Microsoft Word or Google Docs. However, instead of using buttons to apply formatting, you use syntax such as **this syntax bolds text in markdown** or # Here is a heading.

Markdown syntax allows you to format text in many ways, such as making headings, bolding and italicizing words, creating bulleted lists, adding links, formatting mathematical symbols and making tables. These options allow you to format text in visually appealing and organized ways to present your ideas.

You can use Markdown to format text in many different tools including GitHub.com, R using RMarkdown, and Jupyter Notebook, which you will learn more about this page.

Data Tip: Learn more about how you can use Markdown to format text and document workflows in a variety of tools.

Markdown in Jupyter Notebook

A great benefit of Jupyter Notebook is that it allows you to combine both code (e.g. Python) and Markdown in one document, so that you can easily document your workflows.

A Jupyter Notebook file uses cells to organize content, and it can contain both cells that render text written using the Markdown syntax as well as cells that contain and run Python code.

Thus, you can use a combination of Markdown and Python code cells to organize and document your Jupyter Notebook for others to easily read and follow your workflow.

Data Tip: Learn more about Markdown for Jupyter Notebook.

If you render your Jupyter Notebook file to HTML or PDF, this Markdown will appear as formatted text in the output document.

Data Tip: In fact, this web page that you are reading right now is generated from a Markdown document! On this page, you will learn the basic syntax of Markdown.

Benefits of Markdown for Earth Data Science

Being able to include both Markdown and code (e.g. Python) cells in a Jupyter Notebook file supports reproducible science by allowing you to:

• Document your workflow: You can add text to the document that describes the steps of your processing workflow (e.g. how data is being processed and what results are produced).
• Describe your data: You can describe the data that you are using (e.g. source, pre-processing, metadata).
• Interpret code outputs: You can add some text that interprets or discusses the outputs.

all in one document!

When used effectively, Markdown documentation can help anyone who opens your Jupyter Notebook to follow, understand and even reproduce your workflow.

Format Text in Jupyter Notebook with Markdown

Markdown Cells in Jupyter Notebook

In the previous chapter on Jupyter Notebook, you learned how to add new Markdown cells to your Jupyter Notebook files using Menu tools and Keyboard Shortcuts to create new cells.

You also learned how to change the default type of the cell by clicking in the cell and selecting a new cell type (e.g. Markdown) in the cell type menu in the toolbar. Furthermore, you learned that in a Jupyter Notebook file, you can double-click in any Markdown cell to see the syntax, and then run the cell again to see the Markdown formatting.

Note: if you type text in a Markdown cell with no additional syntax, the text will appear as regular paragraph text. You can add additional syntax to that text to format it in different ways.

On this page, you will learn basic Markdown syntax that you can use to format text in Jupyter Notebook files.

Section Headers

You can create a heading using the pound (#) sign. For the headers to render properly, there must be a space between the # and the header text.

Heading one is denoted using one # sign, heading two is denoted using two ## signs, etc, as follows:

Here is a sample of the rendered Markdown:

Heading Three

Heading Four

Note: the titles on this page are actually formatted using Markdown (e.g. the words Section Headers above are formatted as a heading two).

Lists

You can also use Markdown to create lists using the following syntax:

It will render as follows:

• This is a bullet list
• This is a bullet list
• This is a bullet list

1. And you can also create ordered lists
2. by using numbers
3. and listing new items in the lists
4. on their own lines

Notice that you have space between the * or 1. and the text. The space triggers the action to create the list using Markdown.

Bold and Italicize

You can also use ** to bold or * to italicize words. To bold and italicize words, the symbols have to be touching the word and have to be repeated before and after the word using the following syntax:

It will render as follows:

These are italicized words, not a bullet listThese are bold words, not a bullet list

• This is a bullet item with bold words
• This is a bullet item with italicized words

Highlight Code

If you want to highlight a function or some code within a plain text paragraph, you can use one backtick on each side of the text like this:

which renders like this:

Here is some code!

The symbol used is the backtick, or grave; not an apostrophe (on most US keyboards, it is on the same key as the tilde (~)).

Horizontal Lines (Rules)

You can also create a horizontal line or rule to highlight a block of Markdown syntax (similar to the highlighting a block of code using the backticks):

which renders like this:

Here is some important text!

Hyperlinks

You can also use HTML in Markdown cells to create hyperlinks to websites using the following syntax:

<a href='url' target='_blank'>hyperlinked words</a>

You can identify the words that will be hyperlinked (i.e. prompt a web page to open when clicked) by replacing hyperlinked words in the example above.

For example, the following syntax:

Our program website can be found at <a href='http://earthdatascience.org' target='_blank'>this link</a>.

will render as follows with this link as the hyperlinked words:

Our program website can be found at this link.

Render Images

You can also use Markdown to link to images on the web using the following syntax:

![alt text here](url-to-image-here)

The alt text is the alternative text that appears if an image fails to load on webpage; it is also used by screen-reading tools to identify the image to users of the screen-reading tools.

For example, the following syntax:

![Markdown Logo is here.](https://www.fullstackpython.com/img/logos/markdown.png)

will render as follows with an alt text of Markdown Logo is here.:

Local Images Using Relative Computer Paths

You can also add images to a Markdown cell using relative paths to files in your directory structure using:

![alt text here](path-to-image-here)

For relative paths (images stored on your computer) to work in Jupyter Notebook, you need to place the image in a location on your computer that is RELATIVE to your .ipynb file. This is where good file management becomes extremely important.

For a simple example of using relative paths, imagine that you have a subdirectory named images in your earth-analytics directory (i.e. earth-analytics/images/).

If your Jupyter Notebook file (.ipynb) is located in root of this directory (i.e. earth-analytics/notebook.ipynb), and all images that you want to include in your report are located in the images subdirectory (i.e. earth-analytics/images/), then the path that you would use for each image is:

images/image-name.png

If all of your images are in the images subdirectory, then you will be able to easily find them. This also follows good file management practices because all of the images that you use in your report are contained within your project directory.

Data tip: There are many free Markdown editors out there! The atom.io editor is a powerful text editor package by GitHub, that also has a Markdown renderer that allows you to preview the rendered Markdown as you write.

Additional Resources

Practice Your Markdown Skills

1. Open or create a new Jupyter Notebook file.

2. Add a new Markdown cell and include:
   • A title for the notebook (e.g. Intro to Earth Analytics - Chapter Four)
   • A bullet list with:
     • A bold word for Author: and then add text for your name.
     • A bold word for Date: and then add text for today’s date.
3. Add another Markdown cell and include:
   • A list of your top three favorite foods (e.g. blueberries, chocolate bars, avocados).
     • Italicize the first item in your list.
     • Add a hyperlink (i.e. webpages) for the second item in your list (include the name of the food in the title of the hyperlink).
     • Add an image for the last item in your list (include the name in the alt text of the image).

• Jupyter Tutorial

• IPython

• Jupyter

• QtConsole

• JupyterLab

• Jupyter Resources

• Selected Reading

Project Jupyter is a suite of software products used in interactive computing. IPython was originally developed by Fernando Perez in 2001 as an enhanced Python interpreter. A web based interface to IPython terminal in the form of IPython notebook was introduced in 2011. In 2014, Project Jupyter started as a spin-off project from IPython.

Packages under Jupyter project include −

• Jupyter notebook − A web based interface to programming environments of Python, Julia, R and many others

• QtConsole − Qt based terminal for Jupyter kernels similar to IPython

• nbviewer − Facility to share Jupyter notebooks

• JupyterLab − Modern web based integrated interface for all products.

Standard distribution of Python comes with a REPL (Read-Evaluate-Print Loop) environment in the form of Python shell with >>> prompt. IPython (stands for Interactive Python) is an enhanced interactive environment for Python with many functionalities compared to the standard Python shell.

Features of IPython

IPython offers more features compared to the standard Python. They are as follows −

• Offers a powerful interactive Python shell.

• Acts as a main kernel for Jupyter notebook and other front end tools of Project Jupyter.

• Possesses object introspection ability. Introspection is the ability to check properties of an object during runtime.

• Syntax highlighting.

• Stores the history of interactions.

• Tab completion of keywords, variables and function names.

• Magic command system useful for controlling Python environment and performing OS tasks.

• Ability to be embedded in other Python programs.

• Provides access to Python debugger.

History and Development

IPython was originally developed by Fernando Perez in 2001. Its current version is IPython7.0.1 which requires Python 3.4 version or higher. IPython 6.0 was the first version to support Python 3. Users having Python 2.7 should work with IPython’s version 2.0 to 5.7

The concept of computational notebooks started in 80s decade when MATLAB and Mathematica were released. These GUI frontends to the interactive shell had features like text formatting, adding graphics, table and adding mathematical symbols. Sage notebook is also a web based notebook.

Creaters of IPython started working on notebook interface for IPython shell in 2005. IPython notebook soon added support of other languages like R and Julia. It was in 2014, that Perez started Jupyter project as a spin-off project from IPython, since IPython project was becoming big with products like notebook server and Qt console added to it.

Since IPython 4.0, all additional components were shifted to Project Jupyter and adding support of other languages to IPython notebook. IPython continues to focus on improvement of its enhanced interpreter feature. It also provides primary kernel to Jupyter notebook frontend.

IPython is included by default in Anaconda distribution of Python. It can be downloaded from Anaconda’s download page www.anaconda.com/download/ Binaries for all major OS (Windows, MacOS and Linux) and architecture (32 bit and 64 bit) are available on this link.

To install IPython separately in standard Python installation, you can use pip command as shown below −

IPython internally uses following packages −

In general, all dependencies get installed automatically. Else, you can install them individually using pip.

This chapter will explain how to get started with working on IPython.

Starting IPython from Command Prompt.

Before proceeding to understand about IPython in depth, note that instead of the regular >>>, you will notice two major Python prompts as explained below −

• In[1] appears before any input expression.

• Out[1] appears before the Output appears.

Besides, the numbers in the square brackets are incremented automatically. Observe the following screenshot for a better understanding −

Now, if you have installed Anaconda distribution of Python, open Anaconda prompt from start menu.

Start IPython from conda prompt

When compared to regular Python console, we can notice a difference. The IPython shell shows syntax highlighting by using different colour scheme for different elements like expression, function, variable etc.

Another useful enhancement is tab completion. We know that each object has one or more methods available as defined in its class. IPython pops up appropriate list of methods as you press tab key after dot in front of object.

In the following example, a string is defined. As a response, the methods of string class are shown.

IPython provides information of any object by putting ‘?’ in front of it. It includes docstring, function definitions and constructor details of class. For example to explore the string object var defined above, in the input prompt enter var?. The result will show all information about it. Observe the screenshot given below for a better understanding −

Magic Functions

IPython’s in-built magic functions are extremely powerful. There are two types of magic functions.

• Line magics, which work very much like DOS commands.
• Cell magics, which work on multiple lines of code.

We shall learn about line magic functions and cell magic functions in detail in subsequent chapters.

In this chapter, let us understand how to run and edit a Python script.

Run Command

You can use run command in the input prompt to run a Python script. The run command is actually line magic command and should actually be written as %run. However, the %automagic mode is always on by default, so you can omit this.

Edit Command

IPython also provides edit magic command. It invokes default editor of the operating system. You can open it through Windows Notepad editor and the script can be edited. Once you close it after saving its input, the output of modified script will be displayed.

Note that hello.py initially contained only one statement and after editing one more statement was added. If no file name is given to edit command, a temporary file is created. Observe the following code that shows the same.

IPython preserves both the commands and their results of the current session. We can scroll through the previous commands by pressing the up and down keys.

Besides, last three objects of output are stored in special variables _, __ and ___. The history magic command shows previous commands in current session as shown in the screenshot given below −

If the statement in the input cell starts with the exclamation symbol (!), it is treated as a system command for underlying operating system. For example, !ls (for linux) and !dir (for windows) displays the contents of current directory

The output of system command can also be assigned to a Python variable as shown below −

The variable stores output without colors and splits at newline characters.

It is also possible to combine Python variables or expressions with system command calls. Variable in curly brackets {} can be embedded in command text. Observe the following example −

Here is another example to understand that prefixing Python variable with $ also achieves the same result.

In this chapter, let us understand how to work with various command line options in IPython.

Invoking IPython Program

You can invoke an IPython program using the following options −

The file option is a Python script with .py extension. If no other option is given, the script is executed and command prompt reappears.

Subcommands and Parameters

An IPython command accepts the following subcommand options −

• Profile − Create and manage IPython profiles.

• Kernel − Start a kernel without an attached frontend.

• Locate − Print the path to the IPython dir.

• History − Manage the IPython history database.

An IPython profile subcommand accepts the following parameters −

• ipython profile create myprofile − Creates a new profile.

• ipython profile list − Lists all available profiles.

• ipython locate profile myprofile − Locates required profile.

To install new IPython kernel, use the following command −

To print the path to the IPython dir, use the following command −

Besides, we know that −

• The history subcommand manages IPython history database.

• The trim option reduces the IPython history database to the last 1000 entries.

• The clear option deletes all entries.

Some of the other important command line options of IPython are listed below −

The sample usage of some of the IPython command line options are shown in following table −

IPython has different ways of obtaining information about Python objects dynamically. In this chapter, let us learn the ways of dynamic object introspection in IPython.

Use of ? and ?? provides specific and more detailed information about the object. In the first example discussed below, a simple integer object a is created. Its information can be procured by typing a ? in the input cell.

In the second example, let us define a function and introspect this function object with ? and ??.

Note that the magic function %psearch is equivalent to the use of ? or ?? for fetching object information.

The input and output cells on IPython console are numbered incrementally. In this chapter, let us look into IO caching in Python in detail.

In IPython, inputs are retrieved using up arrow key. Besides, all previous inputs are saved and can be retrieved. The variables _i, __i, and ___i always store the previous three input entries. In addition, In and _in variables provides lists of all inputs. Obviously _in[n] retrieves input from nth input cell. The following IPython session helps you to understand this phenomenon −

Similarly, single, double and triple underscores act as variables to store previous three outputs. Also Out and _oh form a dictionary object of cell number and output of cells performing action (not including assignment statements). To retrieve contents of specific output cell, use Out[n] or _oh[n]. You can also use slicing to get output cells within a range.

Different environment variables influence Python’s behaviour. PYTHONSTARTUP environment variable is assigned to a Python script. As an effect, this script gets executed before Python prompt appears. This is useful if certain modules are to be loaded by default every time a new Python session starts.

The following script (start.py) imports IPython module and executes start_ipython() function to replace default Python shell with prompt (>>>) by IPython shell when Python executable is invoked.

Assuming that this file is stored in Python’s installation directory (c:python36), set PYTHONSTARTUP environment variable and start Python from command line. Then IPython shell appears as shown below −

Note that the environment variable can be permanently set using System Properties dialog in Windows and using export command on Linux.

IPython can read from standard Python console with default >>> prompt and another IPython session. The following screenshot shows a for loop written in standard Python shell −

Copy the code (along with Python prompt) and paste the same in IPython input cell. IPython intelligently filters out the input prompts (>>> and ..) or IPython ones (In [N]: and ..:)

Similarly, code from one IPython session can be pasted in another. The first screenshot given below shows definition of SayHello() function in one IPython window −

Now, let us select the code and paste in another IPython shell and call SayHello() function.

The embed() function of IPython module makes it possible to embed IPython in your Python codes’ namespace. Thereby you can leverage IPython features like object introspection and tab completion, in default Python environment.

Python objects present in the global namespace before embedding, will be available to IPython.

If new objects are formed while in IPython or previous objects are modified, they will be automatically available to default environment after exiting IPython. Embedded IPython shell doesn’t change the state of earlier code or objects.

However, if IPython is embedded in local namespace like inside a function, the objects inside it will not be available once it is closed. Here, we have defined a function add(). Inside add() we invoke IPython and declared a variable. If we try to access variable in IPython after it is closed, NameError exception will be raised.

Magic commands or magic functions are one of the important enhancements that IPython offers compared to the standard Python shell. These magic commands are intended to solve common problems in data analysis using Python. In fact, they control the behaviour of IPython itself.

Magic commands act as convenient functions where Python syntax is not the most natural one. They are useful to embed invalid python syntax in their work flow.

Types of Magic Commands

There are two types of magic commands −

• Line magics
• Cell magics

Line Magics

They are similar to command line calls. They start with % character. Rest of the line is its argument passed without parentheses or quotes. Line magics can be used as expression and their return value can be assigned to variable.

Cell Magics

They have %% character prefix. Unlike line magic functions, they can operate on multiple lines below their call. They can in fact make arbitrary modifications to the input they receive, which need not even be a valid Python code at all. They receive the whole block as a single string.

To know more about magic functions, the built-in magics and their docstrings, use the magic command. Information of a specific magic function is obtained by %magicfunction? Command. Let us now describe some of the built-in line and cell magic commands.

Built-in line magics

This magic function makes a function automatically callable without having to use parentheses. It takes three possible mode parameters: 0 (off), 1 (smart) is default or 2 (always on).

%automagic

Magic functions are callable without having to type the initial % if set to 1. Without arguments it toggles on/off. To deactivate, set to 0.

The following example shows a magic function %pwd (displays present working directory) being called without leading % when %automagic set to 1

%cd

This line magic changes the current directory. This command automatically maintains an internal list of directories you visit during your IPython session, in the variable _dh. You can also do ‘cd -<tab>’ to see directory history conveniently.

Usage

The %cd command can be used in the following ways −

• %cd <dir> − Changes current working directory to <dir>

• %cd. − Changes current directory to parent directory

• %cd − changes to last visited directory.

%dhist

This magic command prints all directories you have visited in current session. Every time %cd command is used, this list is updated in _dh variable.

%edit

This magic command calls upon the default text editor of current operating system (Notepad for Windows) for editing a Python script. The script is executed as the editor is closed.

%env

This magic command will list all environment variables. It also reads value of particular variable or set the value of environment variable.

Usage

The %cd command can be used in the following ways −

• %env − Lists all environment variables

• %env var − Gets value for var

• %env var val − Sets value for var

%gui [GUINAME]

When used without argument this command enables or disables IPython GUI event loop integration. With GUINAME argument, this magic replaces the default GUI toolkits by the specified one.

%lsmagic

Displays all magic functions currently available

%matplotlib

This function activates matplotlib interactive support during an IPython session. However, it does not import matplotlib library. The matplotlib default GUI toolkit is TkAgg. But you can explicitly request a different GUI backend. You can see a list of the available backends as shown −

The IPython session shown here plots a sine wave using qt toolkit −

While using Jupyter notebook, %matplotlib inline directive displays plot output in the browser only.

%notebook

This function converts current IPython history into an IPython notebook file with ipynb extension. The input cells in previous example are saved as sine.ipynb

%pinfo

This function is similar to object introspection ? character. To obtain information about an object, use the following command −

This is synonymous to object? or ?object.

%precision

This magic function restricts a floating point result to specified digits after decimal.

%pwd

This magic function returns the present working directory.

%pylab

This function populates current IPython session with matplotlib, and numpy libraries.

%recall

When executed without any parameter, this function executes previous command.

Note that in %recall n, number in front of it is input cell number. Hence the command in the nth cell is recalled. You can recall commands in section of cells by using command such as %recall 1-4. Current input cell is populated with recalled cell and the cursor blinks till the enter key is pressed.

%run

This command runs a Python script from within IPython shell.

%time

This command displays time required by IPython environment to execute a Python expression.

%timeit

This function also displays time required by IPython environment to execute a Python expression. Time execution of a Python statement or expression uses the timeit module. This function can be used both as a line and cell magic as explained here −

• In line mode you can time a single-line.

• In cell mode, the statement in the first line is used as setup code and the body of the cell is timed. The cell body has access to any variables created in the setup code.

%who

This line magic prints all interactive variables, with some minimal formatting. If any arguments are given, only variables whose type matches one of these are printed.

IPython Custom Line Magic function

IPython’s core library contains register_line_magic decorator. A user defined function is converted into a line magic function using this decorator.

Project Jupyter started as a spin-off from IPython project in 2014. IPython’s language-agnostic features were moved under the name – Jupyter. The name is a reference to core programming languages supported by Jupyter which are Julia, Python and RProducts under Jupyter project are intended to support interactive data science and scientific computing.

The project Jupyter consists of various products described as under −

• IPykernel − This is a package that provides IPython kernel to Jupyter.

• Jupyter client − This package contains the reference implementation of the Jupyter protocol. It is also a client library for starting, managing and communicating with Jupyter kernels.

• Jupyter notebook − This was earlier known as IPython notebook. This is a web based interface to IPython kernel and kernels of many other programming languages.

• Jupyter kernels − Kernel is the execution environment of a programming language for Jupyter products.

Jupyter Markdown Italicize

The list of Jupyter kernels is given below −

• Qtconsole − A rich Qt-based console for working with Jupyter kernels

• nbconvert − Converts Jupyter notebook files in other formats

• JupyterLab − Web based integrated interface for notebooks, editors, consoles etc.

• nbviewer − HTML viewer for notebook files

IPython notebook was developed by Fernando Perez as a web based front end to IPython kernel. As an effort to make an integrated interactive computing environment for multiple language, Notebook project was shifted under Project Jupyter providing front end for programming environments Juila and R in addition to Python.

A notebook document consists of rich text elements with HTML formatted text, figures, mathematical equations etc. The notebook is also an executable document consisting of code blocks in Python or other supporting languages.

Jupyter notebook is a client-server application. The application starts the server on local machine and opens the notebook interface in web browser where it can be edited and run from. The notebook is saved as ipynb file and can be exported as html, pdf and LaTex files.

If you are new to Jupyter, you can try features of Jupyter notebook before installing on your local machine. For this purpose, visit https://jupyter.org in your browser and choose ‘Try Jupyter with Python’ option.

This will open home page of https://mybinder.org From the File menu, choose new notebook option to open a blank Jupyter in your browser. The input cell, as similar to that in IPython terminal, will be displayed. You can execute any Python expression in it.

You can easily install Jupyter notebook application using pip package manager.

To start the application, use the following command in the command prompt window.

The server application starts running at default port number 8888 and browser window opens to show notebook dashboard.

Observe that the dashboard shows a dropdown near the right border of browser with an arrow beside the New button. It contains the currently available notebook kernels. Now, choose Python 3, then a new notebook opens in a new tab. An input cell as similar to that of in IPython console is displayed.

You can execute any Python expression in it. The result will be displayed in the Out cell.

The dashboard of Jupyter Notebook contains three tabs as shown in the screenshot given below −

Files Tab

The 'Files' tab displays files and folders under current directory from which notebook app was invoked. The row corresponding to a notebook which is currently open and the running status is shown just beside the last modified column. It also displays Upload button using which a file can be uploaded to notebook server.

Running Tab

The 'Running' tab shows which of the notebooks are currently running.

Cluster Tab

The third tab, 'Clusters', is provided by IPython parallel. IPython's parallel computing framework, an extended version of the IPython kernel.

From the New dropdown choose Terminal to open a cmd window. You can now start an IPython terminal here.

In the user interface of Jupyter, just beside the logo in the header, the file name is displayed.

You can find the menu bar below the header. Each menu contains many options that will be discussed later.

Drivers powerteq. A row of icons forming toolbar helps user to perform often required operations

The notebook has two modes − Command mode and Edit mode. Notebook enters edit mode when a cell is clicked. Notice the pencil symbol just besides name of kernel.

Kernel indicator symbol is displayed just to the right of kernel name. Note that a hollow circle means kernel is idle and solid circle means it is busy.

File Menu

The following are the options available in the File menu −

The file formats that are available are shown below −

Edit Menu

Edit menu consists of buttons to perform cut, copy and paste cells, delete selected cell, split and merge cells, move cells up and down, find and replace within notebook, cut/copy attachments and insert image.

View Menu

Buttons in this menu help us to hide/display header, toolbar and cell numbers.

Insert Menu

This menu gives you options for inserting cell before or after the current cell.

Cell Menu

The options in this menu let user run all or specific cells in the notebook. You can also set the cell type to code type, markdown or raw nbconvert type.

Kernel Menu

From this menu you can start, interrupt, restart or shutdown the kernel. You can also start a new kernel.

Widgets Menu

From this menu you can save, clear, download or embed widget state.

Help menu

Various predefined keyboard shortcuts are displayed from this menu. You can also edit the shortcuts as per your convenience.

Cells in Jupyter notebook are of three types − Code, Markdown and Raw.

Code Cells

Contents in this cell are treated as statements in a programming language of current kernel. Default kernel is Python. So, we can write Python statements in a code cell. When such cell is run, its result is displayed in an output cell. The output may be text, image, matplotlib plots or HTML tables. Code cells have rich text capability.

Markdown Cells

These cells contain text formatted using markdown language. All kinds of formatting features are available like making text bold and italic, displaying ordered or unordered list, rendering tabular contents etc. Markdown cells are especially useful to provide documentation to the computational process of the notebook.

Raw Cells

Contents in raw cells are not evaluated by notebook kernel. When passed through nbconvert, they will be rendered as desired. If you type LatEx in a raw cell, rendering will happen after nbconvert is applied.

While the menu bar and toolbar lets you perform various operations on notebook, it is desirable to be able to use keyboard shortcuts to perform them quickly.

Jupyter Notebooks have two different keyboard input modes −

• Command Mode − Binds the keyboard to notebook level actions. Indicated by a grey cell border with a blue left margin.

• Edit Mode − When you are typing in a cell. Indicated by a green cell border.

Command Mode (press Esc to enable)

Edit Mode (press Enter to enable)

Markdown cell displays text which can be formatted using markdown language. In order to enter a text which should not be treated as code by Notebook server, it must be first converted as markdown cell either from cell menu or by using keyboard shortcut M while in command mode. The In[] prompt before cell disappears.

Header cell

A markdown cell can display header text of 6 sizes, similar to HTML headers. Start the text in markdown cell by # symbol. Use as many # symbols corresponding to level of header you want. It means single # will render biggest header line, and six # symbols renders header of smallest font size. The rendering will take place when you run the cell either from cell menu or run button of toolbar.

Following screenshot shows markdown cells in edit mode with headers of three different levels.

When cells are run, the output is as follows −

Note that Jupyter notebook markdown doesn’t support WYSWYG feature. The effect of formatting will be rendered only after the markdown cell is run.

Ordered Lists

To render a numbered list as is done by <ol> tag of HTML, the First item in the list should be numbered as 1. Subsequent items may be given any number. It will be rendered serially when the markdown cell is run. To show an indented list, press tab key and start first item in each sublist with 1.

If you give the following data for markdown −

It will display the following list −

Bullet lists

Each item in the list will display a solid circle if it starts with – symbol where as solid square symbol will be displayed if list starts with * symbol. The following example explains this feature −

The rendered markdown shows up as below −

Hyperlinks

Markdown text starting with http or https automatically renders hyperlink. To attach link to text, place text in square brackets [] and link in parentheses () optionally including hovering text. Following screenshot will explain this.

The rendered markdown appears as shown below −

Bold and Italics

To show a text in bold face, put it in between double underscores or two asterisks. To show in italics, put it between single underscores or single asterisks.

The result is as shown below −

Images

To display image in a markdown cell, choose ‘Insert image’ option from Edit menu and browse to desired image file. The markdown cell shows its syntax as follows −

Image will be rendered on the notebook as shown below −

Table

In a markdown cell, a table can be constructed using | (pipe symbol) and – (dash) to mark columns and rows. Note that the symbols need not be exactly aligned while typing. It should only take respective place of column borders and row border. Notebook will automatically resize according to content. A table is constructed as shown below −

The output table will be rendered as shown below −

In this chapter, let us understand cell magic functions and their functionalities.

%%html

This cell magic function renders contents of code cell as html script.

%%js or %%javascript

You can embed javascript code in Jupyter notebook cell with the help of this cell magic command.

%%writefile

Contents of code cell are written to a file using this command.

IPython kernel of Jupyter notebook is able to display plots of code in input cells. It works seamlessly with matplotlib library. The inline option with the %matplotlib magic function renders the plot out cell even if show() function of plot object is not called. The show() function causes the figure to be displayed below in[] cell without out[] with number.

Now, add plt.show() at the end and run the cell again to see the difference.

Note that the %matplotlib notebook magic renders interactive plot.

Jupyter Markdown

Just below the figure, you can find a tool bar to switch views, pan, zoom and download options.

Importantly, if you modify the data underneath the plot, the display changes dynamically without drawing another plot.

In the above example, change the data sets of x and y in the cell below and plot the figure again, the figure above will get dynamically refreshed.

Jupyter notebook files have .ipynb extension. Notebook is rendered in web browser by the notebook app. It can be exported to various file formats by using download as an option in the file menu. Jupyter also has a command line interface in the form of nbconvert option. By default, nbconvert exports the notebook to HTML format. You can use the following command for tis purpose −

This will convert mynotebook.ipynb to the mynotebook.html. Other export format is specified with `--to` clause.

Note that other options include ['asciidoc', 'custom', 'html', 'latex', 'markdown', 'notebook', 'pdf', 'python', 'rst', 'script', 'slides']

HTML includes 'basic' and 'full' templates. You can specify that in the command line as shown below −

LaTex is a document preparation format used specially in scientific typesetting. Jupyter includes 'base', 'article' and 'report' templates.

To generate PDF via latex, use the following command −

Notebook can be exported to HTML slideshow. The conversion uses Reveal.js in the background. To serve the slides by an HTTP server, add --postserve on the command-line. To make slides that does not require an internet connection, just place the Reveal.js library in the same directory where your_talk.slides.html is located.

The markdown option converts notebook to simple markdown output. Markdown cells are unaffected, and code cells indented 4 spaces.

You can use rst option to convert notebook to Basic reStructuredText output. It is useful as a starting point for embedding notebooks in Sphinx docs.

This is the simplest way to get a Python (or other language, depending on the kernel) script out of a notebook.

IPyWidgets is a Python library of HTML interactive widgets for Jupyter notebook. Each UI element in the library can respond to events and invokes specified event handler functions. They enhance the interactive feature of Jupyter notebook application.

In order to incorporate widgets in the notebook, we have to import the following module as shown below −

Some basic IPyWidgets are explained here −

Text input

The widgets.text() function renders widgets in the notebook. It is similar to text box form element in HTML. The object of this widget has on_submit() method which listens to activity of the text field and can invoke event handler given as an argument to it.

Button

This widget is similar to HTML button. When it is clicked, the event is registered by on_click() method which calls the click event handler.

IntSlider

A slider control which displays the incrementing integer values. There is also a FloatSlider and IntRangeSlider (changing integer between a range)

Label

This widget is useful to display non editable text in the notebook.

display()

This function from ipywidgets module renders the widget object in notebook’s input cell.

Interact

This function automatically renders a widget depending upon type of data argument given to it. First argument to this function is the event handler and second is a value passed to event handler itself.

Following example shows three label widgets, two text widgets and a button with ‘add’ caption. When the button is clicked, sum of numbers in two text input fields is displayed on the lowermost label.

In this chapter, let us understand how to get started with QtConsole. This chapter will give you an overview about this software and explains its installation steps.

Overview

The Qt console is a GUI application similar to IPython terminal. However, it provides a number of enhancements which are not available in text based IPython terminal. The enhance features are inline figures, multi-line editing with syntax highlighting, graphical calltips, etc. The Qt console can use any Jupyter kernel, default being IPython kernel.

Installation

Jupyter QtConsole is a part of Project Jupyter. Anaconda distribution is already having QTconsole application in it. In order to install it individually, use pip command as shown below −

You can also use the conda command for this purpose −

You can start Jupyter console from Anaconda navigator. To start it from the command line, you should use the following command, either from the Windows command prompt or Anaconda prompt −

You get a terminal similar to IPython terminal with first In[] prompt. You can now execute any Python expression exactly like we do in IPython terminal or Jupyter notebook

Multiline editing is one of the features which is not available in IPython terminal. In order to enter more than one statements in a single input cell, press ctrl+enter after the first line. Subsequently, just pressing enter will go on adding new line in the same cell. To stop entering new lines and running cell, press enter key one more time at the end. The cell will run and output will be displayed in next out[] cell.

Another important enhancement offered by QtConsole is the ability to display inline graphics, especially plots. The feature works well with Matplotlib as well as other plotting libraries.

This option to save the QtConsole output as HTML file is available in File menu. You can choose to create file with inline image or the plotted figure as external png file in an adjacent folder (named as qt_files).

You can open more than one tabs in Jupyter console application. Three options in File menu are provided for this purpose.

• New Tab with New kernel − You can load a new kernel with this file menu.

• New Tab with Existing kernel − Using this option, you can choose from additional kernels apart from IPython kernel.

• New Tab with Same Kernel − This creates a slave of kernel loaded on a particular tab. As a result, object initialized on master tab will be accessible in slave and vice versa.

There is a %qtconsole magic command available for use with Jupyter notebook. This invokes the QtConsole as a slave terminal to notebook frontend. As a result, data between notebook and Qtconsole terminal can be shared.

You can see that the variable in notebook is accessible within qtconsole window. Also, a new variable in Qtconsole is used back in notebook.

Observe that the input and output cells are numbered incrementally between the two.

Sharing Jupyter notebook – Using github and nbviewer

Jupyter Notebook files with .ipynb extension in a GitHub repository will be rendered as static HTML files when they are opened. The interactive features of the notebook, such as custom JavaScript plots, will not work in your repository on GitHub.

To share notebook file using github, login to https://github.comand create a public repository. Then upload your files using upload file button as shown below −

This will give you an option to commit the changes made to the repository. Then, the repository will show uploaded file as below −

Click on the uploaded file to view inside github viewer. You can share the highlighted URL to others.

Another way to view the notebook file online is by using nbviewer utility of Project Jupyter. Open https://nbviewer.jupyter.org/ and put URL of file in your repository in the textfield as shown. Press Go button to view the notebook.

Both these methods display notebook file as static html. To be able to execute code in the notebook, open it using Binder application of Jupyter project.

In the nbviewer window you will see ‘Execute on Binder’ button. Click on it and you will see the notebook file opened exactly like you open it from local dashboard of notebook server on your local machine. You can perform all actions like add/edit cells, run the cells etc.

Project Jupyter describes JupyterLab as a next generation web based user interfaces for all products under the Jupyter ecosystem. It enables you to work seamlessly with notebook, editors and terminals in an extensible manner.

Some of the important features of JupyterLab are discussed below −

• Code Console acts as scratchpad for running code interactively. It has full support for rich output and can be linked to a notebook kernel to log notebook activity.

• Any text file (Markdown, Python, R, LaTeX, etc.) can be run interactively in any Jupyter kernel.

• Notebook cell output can be shown into its own tab, or along with the notebook, enabling simple dashboards with interactive controls backed by a kernel.

• Live editing of document reflects in other viewers such as editors or consoles. It is possible to have live preview of Markdown, Delimiter-separated Values, or Vega/Vega-Lite documents.

JupyterLab can handle many file formats (images, CSV, JSON, Markdown, PDF etc.). It also displays rich output in these formats. JupyterLab provides customizable keyboard shortcuts uses key maps from many well-known text editors.

You can try online the features of JupyterLab before installing. Visit https://jupyter.org/try and choose ‘try JupyterLab’ option.

The launcher tab shows currently available kernels and consoles. You can start a new notebook based/terminal based on any of them. The left column is also having tabs for file browser, running kernels and tabs and settings view.

JupyterLab is normally installed automatically with Anaconda distribution. However, it can also be installed separately by using following conda command −

You can also use the pip command for this purpose −

To start JupyterLab application, most convenient way is from Anaconda Navigator if it is installed.

Alternately start it from command line from Windows/Linux command terminal or Anaconda prompt using this command −

Either way, the JupyterLab application’s launch screen looks like this −

To start a new notebook, click the desired kernel. In above screenshot, one kernel is seen that is Python3 kernel. Click it to start a Python notebook. Observe that its functionality is similar to the one we have studied in this tutorial.

Menu Bar

The menu bar is at the top of window. The default menus you can find in this are −

• File − Actions related to files and directories.

• Edit − Actions related to editing documents and other activities.

• View − Actions that alter the appearance of JupyterLab.

• Run − Actions for running code in different activities such as notebooks and code consoles.

• Kernel − Actions for managing kernels, which are separate processes for running code.

• Tabs − A list of the open documents and activities in the dock panel.

• Settings − Common settings and an advanced settings editor.

• Help − A list of JupyterLab and kernel help links.

The left sidebar shows buttons for starting a new launcher, adding a folder, uploading file and refresh file list. The right pane is the main working area where notebook, console and terminals are shown in tabbed view.

To start a new console, click + symbol in the left side bar to open a new launcher and then click the console option. The console will open in new tab on the right pane.

Note that the input cell is at the bottom, but when it is run, the cell and its corresponding output cell appears in upper part of console tab.

The launcher also allows you open a text editor and a terminal in which IPython shell can be invoked.

Project Jupyter now supports kernels of programming environments. We shall now see how to install R kernel in anaconda distribution.

In Anaconda prompt window enter following command −

Now, from the launcher tab, choose R kernel to start a new notebook.

The following is a screenshot of Jupyter notebook having R kernel −