This lesson is being piloted (Beta version)

U-M Carpentries Curriculum: Setup

Pre-workshop setup steps

  1. Install the following software (all instructions are below).
    • For online workshop only: Zoom (make sure you have the latest version)
    • A Unix shell (e.g. zsh, bash)
    • git
    • Anaconda which is a Python distribution bundled with common scientific packages and other popular tools.
  2. Create a GitHub account if you do not already have one. You’ll need to know the email associated with your account during the git lesson of the workshop.
  3. After you have installed everything above, download un-report.zip. You’ll need the files included during the workshop.
    1. Move un-report.zip to your Desktop and unzip it (usually double-clicking it will work).
    2. Launch JupyterLab (see the Python instruction below.)
    3. Once JupyterLab is opened in your web browser, in the left file browser, go to your Desktop/, un-report/ folder and double-click the file check_setup.ipynb to open it in JupyterLab.
    4. In the toolbar at the top of the notebook, click the run button (▶). This will print out the versions of your Python and a few libraries that we will be using in this workshop.
    5. Take a screenshot of your JupyterLab window and send the screenshot to the lead instructor. If everything worked, they’ll give you the workshop location (or Zoom meeting ID). Otherwise, they’ll help you get everything setup correctly before giving you the information. Please note since you are taking a screenshot of your browser window, make sure the screenshot do not contain any sensitive information that you do not wish to share.

If at any point you get stuck or run into problems, please don’t hesitate to ask us for help!

Software Installation Instructions

For online workshop

Install the videoconferencing client

If you haven't used Zoom before, go to the official website to download and install the Zoom client for your computer.

Set up your workspace

Like other Carpentries workshops, you will be learning by "coding along" with the Instructors. To do this, you will need to have both the window for the tool you will be learning about (a terminal, JupyterLab, your web browser, etc..) and the window for the Zoom video conference client open. In order to see both at once, we recommend using one of the following set up options:

This blog post includes detailed information on how to set up your screen to follow along during the online workshop.

The Unix Shell

The Unix shell is a command-line interface that gives you the power to do tasks more quickly and reproducibly.

  1. Download the Git for Windows installer.
  2. Run the installer and follow the steps below:
    1. Click on "Next" four times (two times if you've previously installed Git). You don't need to change anything in the Information, location, components, and start menu screens.
    2. From the dropdown menu, "Choosing the default editor used by Git", select "Use the Nano editor by default" (NOTE: you will need to scroll up to find it) and click on "Next".
    3. On the page that says "Adjusting the name of the initial branch in new repositories", ensure that "Let Git decide" is selected. This will ensure the highest level of compatibility for our lessons.
    4. Ensure that "Git from the command line and also from 3rd-party software" is selected and click on "Next". (If you don't do this Git Bash will not work properly, requiring you to remove the Git Bash installation, re-run the installer and to select the "Git from the command line and also from 3rd-party software" option.)
    5. Select "Use bundled OpenSSH".
    6. Ensure that "Use the native Windows Secure Channel Library" is selected and click on "Next".
    7. Ensure that "Checkout Windows-style, commit Unix-style line endings" is selected and click on "Next".
    8. Ensure that "Use Windows' default console window" is selected and click on "Next".
    9. Ensure that "Default (fast-forward or merge) is selected and click "Next"
    10. Ensure that "Git Credential Manager" is selected and click on "Next".
    11. Ensure that "Enable file system caching" is selected and click on "Next".
    12. Click on "Install".
    13. Click on "Finish" or "Next".
  3. If your "HOME" environment variable is not set (or you don't know what this is):
    1. Open command prompt (Open Start Menu then type cmd and press Enter)
    2. Type the following line into the command prompt window exactly as shown:

      setx HOME "%USERPROFILE%"

    3. Press Enter, you should see SUCCESS: Specified value was saved.
    4. Quit command prompt by typing exit then pressing Enter

This will provide you with both Git and Bash in the Git Bash program.

Video Tutorial

The default shell in newer versions of macOS is Z shell, also known as zsh, and it comes pre-installed with your MacOS. You access shell from the Terminal, which can be launched with a Spotlight Search by typing "terminal" or in /Applications/Utilities. See the Git installation video tutorial for an example on how to launch the Terminal. You may want to keep Terminal in your dock for this workshop.

If you use an earlier version of MacOS with a different shell, see this Apple Support article and follow the instructions on how to make zsh the default shell.

Video Tutorial

The default shell is usually Bash and there is usually no need to install anything.

To see if your default shell is Bash type echo $SHELL in a terminal and press the Enter key. If the message printed does not end with '/bash' then your default is something else and you can run Bash by typing bash.

Git

Git is a version control system that lets you track who made changes to what when and has options for easily updating a shared or public version of your code on github.com. You will need a supported web browser.

You will need an account at github.com for parts of the Git lesson. Basic GitHub accounts are free. We encourage you to create a GitHub account if you don't have one already. Before signing up, you may want to review this short list of GitHub username advice. Please also consider what personal information you'd like to reveal. For example, you may want to review these instructions for keeping your email address private provided at GitHub.

For macOS, install Git for Mac by downloading and running the most recent "mavericks" installer from this list. Because this installer is not signed by the developer, you may have to right click (control click) on the .pkg file, click Open, and click Open on the pop up window. After installing Git, there will not be anything in your /Applications folder, as Git is a command line program. For older versions of OS X (10.5-10.8) use the most recent available installer labelled "snow-leopard" available here.

Video Tutorial

If Git is not already available on your machine you can try to install it via your distro's package manager. For Debian/Ubuntu run sudo apt-get install git and for Fedora run sudo dnf install git.

Text Editor

When you're writing code, it's nice to have a text editor that is optimized for writing code, with features like automatic color-coding of key words. The default text editor on macOS and Linux is usually set to Vim, which is not famous for being intuitive. If you accidentally find yourself stuck in it, hit the Esc key, followed by :+Q+! (colon, lower-case 'q', exclamation mark), then hitting Return to return to the shell.

nano is a basic editor and the default that instructors use in the workshop. It is installed along with Git.

nano is a basic editor and the default that instructors use in the workshop. See the Git installation video tutorial for an example on how to open nano. It should be pre-installed.

Video Tutorial

nano is a basic editor and the default that instructors use in the workshop. It should be pre-installed.

Python

Python is a popular general-purpose programming language. Installing Python and its scientific packages individually can be a bit difficult, so we recommend Anaconda, a Python distribution bundled with common scientific packages and other popular tools.

We will teach Python using JupyterLab, a programming environment that runs in a web browser. For this to work you will need a reasonably up-to-date web browser. The latest versions of the Chrome, Safari and Firefox browsers are all supported. Note you do not need to install JupyterLab separately as it comes pre-installed with Anaconda.

Note if you have already installed Anaconda previously, you don't need to install it again for this workshop. However, you do need to make sure your Python libraries meet the version requirements for this workshop by running the provided check_setup.ipynb file. If a library does not meet a version requirement, you can run pip install library_name --upgrade in your command window (i.e., Anaconda Prompt for windows and Terminal for MacOS/Linux) to upgrade the library.

Install Anaconda
  1. Open https://www.anaconda.com/download with your web browser.
  2. Download the Anaconda for Windows installer.
  3. Run the Anaconda Installer, using all of the defaults for installation except make sure to check Add Anaconda to my PATH environment variable.
  4. Once Anaconda is installed, launch the Anaconda Prompt by going to the Windows search bar, type in anaconda prompt, and press Enter.
  5. In the Anaconda Prompt type jupyter lab and press Enter. This will open JupyterLab in your browser.
Launch JupyterLab
  1. Once Anaconda is installed, launch the Anaconda Prompt by going to the Windows search bar, type in anaconda prompt, and press Enter.
  2. In the Anaconda Prompt type jupyter lab and press Enter. This will launch JupyterLab in your browser.
  3. Note to keep the JupyterLab running, do not close the command line window (you can minimize it), as it works as JupterLab's "local host server".
Install Anaconda
  1. Open https://www.anaconda.com/download with your web browser.
  2. Download the Anaconda Installer for macOS. You may need to choose an installer between an Intel-chip Mac and Apple silicon (e.g., M1/M2) Mac.
  3. Run the Anaconda Installer, using all of the defaults for installation.
  4. Once Anaconda is installed, type jupyter lab in your Terminal and press Return. This will launch JupyterLab in your browser.
Launch JupyterLab
  1. Once Anaconda is installed, launch the Terminal window, type in jupyter lab, and press Return. This will launch JupyterLab in your browser.
  2. Note to keep the JupyterLab running, do not close the Terminal window (you can minimize it), as it works as JupterLab's "local host server".
Install Anaconda
  1. Open https://www.anaconda.com/download with your web browser.
  2. Download the Anaconda Installer for Linux.
    (The installation requires using the shell. If you aren't comfortable doing the installation yourself stop here and request help at the workshop.)
  3. Open a terminal window and navigate to the directory where the executable is downloaded (e.g., `cd ~/Downloads`).
  4. Type bash Anaconda3- and then press Tab to autocomplete the full file name. The name of file you just downloaded should appear.
  5. Press Enter (or Return depending on your keyboard). You will follow the text-only prompts. To move through the text, press Spacebar. Type yes and press enter to approve the license. Press Enter (or Return) to approve the default location for the files. Type yes and press Enter (or Return) to prepend Anaconda to your PATH (this makes the Anaconda distribution the default Python).
  6. Once Anaconda is installed, type jupyter lab in your Terminal and press Return. This will launch JupyterLab in your browser.
Launch JupyterLab
  1. Once Anaconda is installed, launch the Terminal window, type in jupyter lab, and press Return. This will launch JupyterLab in your browser.
  2. Note to keep the JupyterLab running, do not close the Terminal window (you can minimize it), as it works as JupterLab's "local host server".