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Mac Setup
Instructions for setting up on Mac

Bash shell

You already have it! Depending on which version of Mac OS you’re running you may need to type bash inside the terminal to access it. To check whether this is necessary, follow these steps:

  1. Open a terminal and type echo $SHELL. If it reads /bin/bash then you are all set!

Note: If you are using Mac Catalina (10.15.X) then it is possible your default shell is NOT CORRECT. To set the default to bash, type chsh -s /bin/bash in the terminal, enter your password when prompted, and then close + re-open the terminal.

Git

You may already have it! Try opening a terminal and typing git --version. If you do not see something like “git version X.XX.X” printed out, then follow these steps:

  1. Follow this link to automatically download an installer.
  2. Double click the downloaded file (git-2.23.0-intel-universal-mavericks.dmg) and then double click the git-2.23.0-intel-universal-mavericks.pkg icon inside the dmg that is opened.
  3. Follow the on-screen instructions to install the package.

VSCode

  1. Go to this page and click the download button.
  2. Unzip the downloaded file (e.g., VSCode-darwin-stable.zip) and moving the resulting Visual Studio Code file to your Applications directory.

VSCode extensions

  1. Open the Visual Studio Code application
  2. Type Cmd+Shift+P and then enter "Shell command: Install 'code' command in PATH" into the search bar that appears at the top of the screen. Select the highlighted entry. A notification box should appear in the bottom-right corner indicating that the command was installed successfully.
  3. Type Cmd+Shift+P again and then enter "Extensions: Install extensions" into the search bar. Select the appropriate entry from the dropdown menu that appears (there should be four entries; simply select the one that reads "Extensions: Install extensions").
  4. A new panel should appear on the left-hand side of the screen with a search bar. Search for each of the following extensions and press Install for the first entry that appears. (The author listed for all of these extensions should be "Microsoft".)
    • Python (n.b., you will need to reload VSCode after installing this)
    • Live Share (n.b., you may need to press "Ctrl/Cmd+Shift+P" and type "install extensions" again after installing this)
    • Live Share Extension Pack
    • Docker

Python

  1. Open a new terminal and type the following lines (separately) into the terminal, pressing Enter after each one:

    curl -O https://repo.anaconda.com/miniconda/Miniconda3-latest-MacOSX-x86_64.sh
bash Miniconda3-latest-MacOSX-x86_64.sh

  2. A license agreement will be displayed and the bottom of the terminal will read --More--. Press Enter or the space bar until you are prompted with "Do you accept the license terms? [yes|no]." Type yes and then press Enter

  3. The installation script will inform you that it is going to install into a default directory (e.g., /home/$USER/miniconda3). Leave this default and press Enter.

  4. When you are asked "Do you wish the installer to initialize Miniconda3 by running conda init? [yes|no]," type yes and press Enter. Exit the terminal once the installation has finished.

  5. Re-open a terminal. Type which python into the terminal and it should return a path (e.g., /home/$USER/miniconda3/bin/python).

    • If you do not see a path like this then please try typing conda init, closing your terminal, and repeating this step. If your issue is still not resolved skip the following step and contact an instructor on the #help-installation channel of the BHS Slack.

  6. Type the following to remove the installation script that was downloaded:

    rm ./Miniconda3-latest-MacOSX-x86_64.sh

Python packages

Open a terminal and type the following commands:

conda config --append channels conda-forge
conda config --set channel_priority strict
conda create -n qlsc612 -y python=3.9 flake8 ipython jupyter jupyterlab matplotlib nibabel nilearn numpy pandas scipy seaborn bokeh
conda activate qlsc612

Docker

  1. Go to this page and press “Get Docker”.
  2. Open the “Docker.dmg” file that is downloaded and drag and drop the icon to the Applications folder
  3. Open the Docker application and enter your password. An icon will appear in the status bar in the top-left of the screen. Wait until it reads “Docker Desktop is now up and running!”
  4. Open a new terminal and type docker run hello-world. A brief introductory message should be printed to the screen.

(The above step-by-step Docker instructions are distilled from here. If you have questions during the installation procedure please check that link for potential answers!)

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