Week 1 Tutorial: Introduction to Jupyter, CLI, Git

POP77001 Computer Programming for Social Scientists

Integrated Development Enviroments (IDEs)

  • There is a number of integrated development environments (IDEs) available for:
    • R (RStudio) and
    • Python (Spyder, PyCharm)
  • As well as text editors with R/Python-specific extensions (Visual Studio Code, Sublime Text, Vim)
  • Try different ones and choose what works best for you!

Jupyter Notebook

  • Jupyter Notebook is a language-agnostic web-based interactive computational environment.
  • It is available with backends (kernels) for different programming languages (Julia, Python, R = Jupyter)
  • Can be used both locally and remotely.
  • Combine both code (with comments) and code output.
  • Good for ad-hoc data analysis and visualization.

Jupyter Notebook vs Scripts

  • Written code is often distributed as scripts:
    • .R files - R scripts
    • .py files - Python scripts
  • Scripts are easier to work with in text editor.
  • But do not include output.

Jupyter Notebook Cells

  • Notebooks allow writing, executing and viewing the output of Python code within the same environment
  • All notebook files have .ipynb extension for interactive python notebook
  • The main unit of notebook is cell, a text input field (Python, Markdown, HTML)
  • Output of a cell can include text, table or figure

Jupyter Notebook Installation

  • To work with Jupyter Notebooks we recommend installing JupyterLab Desktop, a cross-platform desktop application for Jupyter Notebooks.
  • Alternatively, you can try using Kaggle Code, an online platform for hosting Jupyter Notebooks.
  • Its interface is slightly different and you need to register on Kaggle or have a Google account, but it does not require any local installations.
  • However, for this module and course more broadly we recommend installing toolchain for working with Jupyter Notebooks locally.

Starting Jupyter

  • To start Jupyter, open CLI/Terminal and type jupyter notebook
  • This will open a browser window with Jupyter Notebook displaying the directory, in which you executed the command above.
  • To create a new notebook press New and select Python from the drop-down menu

Using Jupyter

  • In order to run a Python command, create a new cell:
    • Press ➕ in the toolbar or click Insert, Insert Cell Below
    • Make sure that in the drop-down menu on the toolbar you select Code
    • Press CTRL+ENTER to run a command
  • Rather than running a Python command, you can also write Markdown in the cell (e.g. to create slides)
    • Select Markdown in the drop-down menu on the toolbar
    • Write Markdown (check Markdown Cheatsheet)
    • Press CTRL+ENTER to render Markdown cell

Jupyter Notebook Demonstration

Jupyter Notebook Demonstration

Stopping Jupyter Notebook

  • First, make sure you saved your work (!) by pressing Command+S / CTRL+S
  • You can close the running notebook by clicking File and then Close and Halt
  • Jupyter Notebook runs as a server
  • Which means that closing its tabs/web browser does not stop it
  • You need to press Quit in the upper right corner of your main Jupyter tab (located at http://localhost:8888/)
  • Alternatively, you can press CTRL+C in the terminal window

CLI Examples

Microsoft PowerShell (Windows)

Z shell, zsh (macOS)

bash (Linux/UNIX)

Some Useful CLI Commands

Command (Windows) Command (macOS/Linux) Description
exit exit close the window
cd cd change directory
cd pwd show current directory
dir ls list directories/files
copy cp copy file
move mv move/rename file
mkdir mkdir create a new directory
del rm delete a file

Extra

Introduction to CLI

Git/GitHub Workflow

Some Useful Git Commands

Command Description
git init <project name> Create a new local repository
git clone <project url> Download a project from remote repository
git status Check project status
git diff <file> Show changes between working directory and staging area
git add <file> Add a file to the staging area
git commit -m “<commit message>” Create a new commit from changes added to the staging area
git pull <remote> <branch> Fetch changes from remote and merge into merge
git push <remote> <branch> Push local branch to remote repository

Extra

Git Cheatsheet

Creating local Git repository

  • Let’s create a test project and track changes in it
  • Create a test directory by typing mkdir test in your CLI/Terminal
  • Go into the newly created directory with cd test command
  • To make Git track changes run git init command in this directory
  • Congratulations! You now have a local repository for your test project

Making a Commit

  • Open your text editor of choice (Notepad, Sublime Text, Visual Studio Code, Vim, Emacs, …)
  • Create a file called test.txt in your local test repository
  • Type whatever you like in this file
  • Add this file to your staging area (make Git aware of its existence) by running git add test.txt command
  • Commit this file to your local repository by running git commit -m "Added first file"
  • Note that all files that were added at the previous stage with git add <file> would be commited
  • Check the status of your repository by running git status (it should say ‘nothing to commit, working tree clean’)
  • Check the history of your repository by running git log and make sure that you see your commit

Remote Git repository: GitHub

  • Hosting platform for projects that rely on Git fo version control
  • Bought by Microsoft in 2018
  • Provides extensive tools for collaborative development and search functionality
  • Helpful for troubleshooting more narrow problems (check GitHub Issues of the package/library that you have a problem with)
  • GitHub is far from the only platform for hosting Git projects
  • Popular alternatives to GitHub include GitLab (🇺🇦), SourceForge, …

Creating remote repository on GitHub

  • Register and login into your account on GitHub
  • Create a new GitHub repository (choose private repository)
  • You should see a similar page with the project URL of the form:
https://github.com/<username>/<repository_name>.git

Synchronising local Git repository with GitHub

  • Go to your local Git repository (the one created in the previous step)
  • Add link from your local Git repository to remote repository on GitHub by running:
git remote add origin <project_url>
- where:
    - `git remote add` is the command,
    - `origin` is the name given to this link (`<remote>`), and
    - `<project_url>` is the URL of the repository on GitHub
  • Check the status of links between your local Git repository and remotes by running git remote -v
    • where:
      • git remote is the command, and
      • -v is the argument ‘verbose’

Pushing local Git changes to GitHub

  • Your local Git repository is now linked to the remote repository hosted on GitHub.
  • Let’s bring the changes made locally to the remote repository.
  • We will use the git push command for that.
  • One last thing to check before doing so is which branch we are currently on.
  • Run git branch to see the name of the branch you are on (it would be ‘main’ or ‘master’)
  • Finally, run git push <remote> <branch> (e.g. git push origin main)
    • where:
      • git push is the command,
      • <remote> is the name of the remote link, and
      • <branch> is the name of the branch.
  • Visit your GitHub repository to check that your commit is reflected there.

Week 1 Exercise (Unassessed)

  • Create a Jupyter notebook in your local repository
  • Commit it to your local repository in the same way as test.txt file