Overview

Teaching: 15 min
Exercises: 0 min

Questions

• How can I run Python programs?

Objectives

• Launch the Jupyter Notebook, create new notebooks, and exit the Notebook.

• Create Markdown cells in a notebook.

• Create and run Python cells in a notebook.

Python programs are plain text files.

• They have the “.py” extension to let everyone (including the operating system) know it is a Python program.
  • This is convention, not a requirement.
• It’s common to write them using a text editor but we are going to use the Jupyter Notebook.
• The bit of extra setup is well worth it because the Notebook provides code completion and other helpful features.
• Notebook files have the extension “.ipynb” to distinguish them from plain-text Python programs.

Use the Jupyter Notebook for editing and running Python.

• The Anaconda package manager is an automated way to install the Jupyter notebook.
  • See the setup instructions for Anaconda installation instructions.
• It also installs all the extra libraries it needs to run.

• Once you have installed Python and the Jupyter Notebook requirements, open a shell and type:

  $ jupyter notebook
  

• This will start a Jupyter Notebook server and open your default web browser.
• The server runs locally on your machine only and does not use an internet connection.
• The server sends messages to your browser.
• The server does the work and the web browser renders the notebook.
• You can type code into the browser and see the result when the web page talks to the server.
• This has several advantages:
  • You can easily type, edit, and copy and paste blocks of code.
  • Tab complete allows you to easily access the names of things you are using and learn more about them.
  • It allows you to annotate your code with links, different sized text, bullets, etc to make it more accessible to you and your collaborators.
  • It allows you to display figures next to the code that produces them to tell a complete story of the analysis.
• The notebook is stored as JSON but can be saved as a .py file if you would like to run it from the bash shell or a python interpreter.
• Just like a webpage, the saved notebook looks different to what you see when it gets rendered by your browser.

FIXME: diagram

How It’s Stored

• The notebook file is stored in a format called JSON.
• Just like a webpage, what’s saved looks different from what you see in your browser.
• But this format allows Jupyter to mix software (in several languages) with documentation and graphics, all in one file.

The Notebook has Control and Edit modes.

• Open a new notebook from the dropdown menu in the top right corner of the file browser page.
• Each notebook contains one or more cells of various types.

Code vs. Text

We often use the term “code” to mean “the source code of software written in a language such as Python”. A “code cell” in a Notebook is a cell that contains software; a “text cell” is one that contains ordinary prose written for human beings.

• If you press “esc” and “return” alternately, the outer border of your code cell will change from gray to green.
  • The difference in color is subtle.
• These are the control (gray) and edit (green) modes of your notebook.
• If you use the “esc” and “return” keys to make the surround gray and then press the “H” key, a list of all the shortcut keys will appear.
• When in control mode (esc/gray),
  • The “B” key will make a new cell below the currently selected cell.
  • The “A” key will make one above.
  • The “X” key will delete the current cell.
• There are lots of shortcuts you can try out and most actions can be done with the menus at the top of the page if you forget the shortcuts.
• If you remember the “esc” and “H” shortcut, you will be able to find out all the rest.

Use the keyboard and mouse to select and edit cells.

• Pressing the “return” key turns the surround green to signify edit mode and you can type into the cell.
• Because we want to be able to write many lines of code in a single cell, pressing the “return” key when the border is green moves the cursor to the next line in the cell just like in a text editor.
• We need some other way to tell the Notebook we want to run what’s in the cell.
• Pressing the “return” key and the “shift” key together will execute the contents of the cell.
• Notice that the “return” and “shift” keys on the right of the keyboard are right next to each other.

The Notebook will turn Markdown into pretty-printed documentation.

• Notebooks can also render Markdown.
  • A simple plain-text format for writing lists, links, and other things that might go into a web page.
  • Equivalently, a subset of HTML that looks like what you’d send in an old-fashioned email.
• Turn the current cell into a Markdown cell by entering the control mode (esc/gray) and press the “M” key.
• In [ ]: will disappear to show it is no longer a code cell and you will be able to write in Markdown.
• Turn the current cell into a Code cell by entering the control mode (esc/gray) and press the “Y” key.

Markdown does most of what HTML does.

*   Use asterisks
*   to create
*   bullet lists.

1.  Use numbers
1.  to create
1.  numbered lists.

# A Level-1 Heading

## A Level-2 Heading (etc.)

Line breaks
don't matter.

But blank lines
create new paragraphs.

[Create links](http://software-carpentry.org) with `[...](...)`.
Or use [named links][data_carpentry].

[links]: http://datacarpentry.org

Creating Lists in Markdown

Create a nested list in a Markdown cell in a notebook that looks like this:

1. Get funding.
2. Do work.
   • Design experiment.
   • Collect data.
   • Analyze.
3. Write up.
4. Publish.

More Math

What is displayed when a Python cell in a notebook that contains several calculations is executed? For example, what happens when this cell is executed?

7 * 3
2 + 1

Change an Existing Cell from Code to Markdown

What happens if you write some Python in a code cell and then you switch it to a Markdown cell? For example, put the following in a code cell:

x = 6 * 7 + 12
print(x)

And then run it with shift+return to be sure that it works as a code cell. Now go back to the cell and use escape+M to switch the cell to Markdown and “run” it with shift+return. What happened and how might this be useful?

Mathematics

Standard Markdown (such as we’re using for these notes) won’t render equations, but the Notebook will. Create a new Markdown cell and enter the following:

$\Sigma_{i=1}^{N} 2^{-i} \approx 1$

(It’s probably easier to copy and paste.) What does it display? What do you think the underscore _, circumflex ^, and dollar sign $ do?

Key Points

• Python programs are plain text files.

• Use the Jupyter Notebook for editing and running Python.

• The Notebook has Control and Edit modes.

• Use the keyboard and mouse to select and edit cells.

• The Notebook will turn Markdown into pretty-printed documentation.

• Markdown does most of what HTML does.