Mac Guide

mac.md

Programs to install on your MacBook

Essentials

Homebrew

• Application manager for OS X
• some homebrew downloads you might need:

brew tap caskroom/cask
brew tap homebrew/science
brew install wget

• other useful Homebrew packages

# some GNU-like utilities that don't ship with macOS bash by default
brew install coreutils

# quick & easy batch image conversion in the Terminal
brew install imagemagick

# manipulation of PDFs
brew install ghostscript

# if you ran into .7z archives or other weird archives you need to extract
brew install p7zip

Anaconda, miniconda

• Pre-compiled binary package manager for Python and other system apps (including R and R libraries)
• conda: package manager, Anaconda: conda + Python + lots of Python libraries, Miniconda: conda + Python only
• you should use this preferentially for managing your Python installations and libraries
• some Python pacakges are not available in here, use pip instead, but pip can (and should) be used in conjunction with conda

Python Pip

• Package manager for Python
• the 'vanilla' Python package manager, required for some package installations

R

• For statistical and scientific programming and analysis
• also consider installations using conda

brew cask install r-app

RStudio

• interactive IDE for R

brew cask install rstudio

iTerm2

• Better terminal for OS X

MacTeX

• LaTeX PDF typesetting program installation for OS X

Atom Text Editor

• Text editor optimized for writing code. Has lots of add-on packages which are easier to manage & install than Sublime
• essential add-on Packages: minimap, highlight-selected, minimap-highlight-selected

Sublime Text editor [v3], [v2]

• Text editor optimized for writing code
• not quite as robust as Atom but a little more lightweight

The Unarchiver

• File unarchiver for .zip, .tar.gz, etc., files

Paintbrush, Skitch

• MS Paint alternatives for Mac. Quick & easy image editing. Or just use Preview.

Extras

Rodeo

• Interactive IDE for Python, similar to RStudio, development has currently ceased
• IMO, just use Atom + iTerm2 instead

PyCharm

• IDE for Python. Tons of features, though it doesn't have inline interactive code execution like Rodeo.
• IMO, just use Atom + iTerm2 instead

BetterTouch Tools

• Customization of touchpad gestures, key combos, and other handy stuff for mac
• free trial but worth the purchase

Spectacle

• Key-combo window management for Mac

Scroll Reverser

• Reverse scrolling direction of touchpad and/or mouse on Mac

VirtualBox

• Runs virtual machines, e.g. Windows or Linux inside your Mac

Docker (download here)

• Run containers; lightweight versions of virtual machines, with scripted build process
• can also be installed from Homebrew

Vagrant

• scripted virtual machine building and management
• can also be installed from Homebrew

Remote Server Management

CyberDuck

• File manager for remote servers; easy access to files on phoenix

Fetch

• Alternative to CyberDuck for accessing files on remote server.

XQuartz

• Enables graphical windows for terminal programs on remote servers

brew cask install xquartz

• after installation, make sure you log into the server with the -Y argument: ssh username@server.com -Y