Generate an SSH key pair

First, check to see if one already exists.

ls -l ~/.ssh/id_rsa*
# Remove existing keys
rm ~/.ssh/id_rsa*

Create a new keypair.

ssh-keygen -t rsa -b 4096 -f ~/.ssh/id_rsa -C <EMAIL>

On macOS Sierra, you have to enable keychain storage in ~/.ssh/config to save your passphrase.

Host *
    UseKeychain yes

Add the newly created private key to the macOS keychain.

ssh-add -K ~/.ssh/id_rsa

Copy the public key to the clipboard.

cat ~/.ssh/id_rsa.pub | pbcopy

Add your newly created public key to the ~/.ssh/authorized_keys file of the remote server. Be sure to ensure the correct permissions of both the remote ~/.ssh folder (700) and ~/.ssh/authorized_keys (600).

Use Homebrew to manage programs

Homebrew is an incredibly useful package and application manager for macOS.

Install Homebrew

Create sbin/ directory and set permissions.

sudo mkdir -p /usr/local/sbin/
sudo chown -R $(whoami) /usr/local/sbin/

Install Xcode command line tools (CLT).

xcode-select --install

Run the Homebrew install script.

/usr/bin/ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)"

For reference, here’s how to uninstall.

/usr/bin/ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/uninstall)"

Upgrades

Homebrew needs to be updated on a regular schedule.

brew update
brew upgrade
brew cask outdated | xargs brew cask reinstall

Status

echo "Homebrew leaves ===="
brew leaves

echo "Homebrew versions ===="
brew list --versions

echo "Homebrew dependencies ===="
brew deps --installed --tree
brew outdated
brew cask outdated
brew missing

echo "Homebrew doctor ===="
brew doctor

Clean up

Periodically, clean up should be performed. Otherwise, downloaded installers will take up a lot of local disk space, and can max out an SSD.

brew cleanup -s
brew cask cleanup
brew prune

Note that R should be installed using brew cask install r instead of brew install r. This command will install the latest official R.app binary, which has two main advantages: (1) support in the RStudio IDE, and (2) fast downloading of pre-compiled packages from CRAN.

Configure Python

Python is useful for scripting workflows. Homebrew can manage installations of both versions 2 and 3 and the launcher application automatically.

pip install --upgrade pip setuptools
pip3 install --upgrade pip setuptools wheel

Preferences and settings

Monospace fonts

Color palettes

Download the base16 templates:

Ocean is the preferred color scheme.

Download our Coda.app and Terminal.app profiles.

Atom

r-exec enables the user to run R code directly from Atom.

apm install r-exec

Microsoft Excel

Turn off “Display this number of decimal places”.
Default font should be set to Body Font.
Preserve display of dates entered with four-digit years should be on.
Turn off AutoComplete.

Change system defaults

Unhide the user library.

chflags nohidden ~/Library

Speed up user interface animations.

defaults write com.apple.dock autohide-delay -float 0
defaults write com.apple.dock autohide-time-modifier -int 0
defaults write com.apple.finder DisableAllAnimations -bool true
defaults write NSGlobalDomain NSWindowResizeTime .001
killall Dock
killall Finder

Don’t write .DS_Store files to network storage.

defaults write com.apple.desktopservices DSDontWriteNetworkStores true

Save screenshots into ~/Documents/, instead of ~/Desktop/.

screenshots_dir="${HOME}/Documents/Screenshots"
mkdir -p "$screenshots_dir"
defaults write com.apple.screencapture disable-shadow -bool true
defaults write com.apple.screencapture location "$screenshots_dir"
defaults write com.apple.screencapture name Screenshot
killall SystemUIServer

Disable podcasts in iTunes.

defaults write com.apple.itunes disablePodcasts -bool YES

Final steps

Add custom dictionary on iCloud to Microsoft Word.
Automount NFS shares on NAS.
Exclude ~/Desktop and ~/Downloads from Time Machine.

References

Rob Griffiths: Speed up your Mac via hidden prefs