One command to upgrade npm, Atom packages & Homebrew. Based on http://blog.thibmaekelbergh.be/2015/12/15/5-minute-guide-to-keeping-your-system-updated.html

.bash_profile

# Note: You won't have access to this command until you run `source ~/.bash_profile` or log back in!

# Call this from cron or run manually as needed.
function update() {
        echo "" ; echo "`date`: RUNNING: npm update"
        npm install npm -g # Update npm itself
        echo "`date`: FINISHED: npm update" ; echo "" ; echo "`date`: RUNNING: npm package updates"
        npm update -g # Update installed npm packages
        echo "`date`: FINISHED: npm package updates" ; echo "" ; echo "`date`: RUNNING: atom update"
        apm upgrade -c false # Update Atom packages & themes
        echo "`date`: FINISHED: atom update" ; echo "" ; echo "`date`: RUNNING: brew update"
        brew update # Update Homebrew
        echo "`date`: FINISHED: brew update" ; echo "" ; echo "`date`: RUNNING: brew upgrade"
        brew upgrade --all # Update Homebrew taps & bottles
        echo "`date`: FINISHED: brew upgrade" ; echo "" ; echo "`date`: RUNNING: brew cleanup"
        brew cleanup # Clear Homebrew cache
        echo "`date`: FINISHED: brew cleanup"
}

I use this but i've cleaned up a ton of it since
https://github.com/jasontucker/dotfiles

Mine looks like:
alias update='sudo softwareupdate -i -a; brew update; brew upgrade; brew cleanup; npm install npm -g; npm update -g; sudo gem update --system; sudo gem update'