Please Note: Everything on this page started out as my personal notes on installing various packages on my OS-X machines. Please feel free to use any of the information here. However, I can't be responsible for any problems that arise as a result of following these instructions. Use at your own risk.

Computing:

Homebrew

• Homebrew is an essential tool for installing public domain packages on the mac.
• Installation instructions are here
• FAQ
• You will first need to install XCode (from the App Store), and the activate the command line tools. To do the latter, type the following in Terminal:
  xcode-select --install
• To update homebrew and the pacakages type:
  brew update
  brew upgrade
• Key commands:
  brew update
  brew doctor
  brew install package
  brew outdated
  brew upgrade package
  brew cleanup package

MySQL

• Useful Medium articles:
  • Installing MySQL 5.7 using Homebrew.
  • Working With MySQL.
  • MySQL on Mac — Getting Started
  • Working efficiently with Large Data in pandas and MySQL (or any other RDBMS)
• Steps to install/start/run:
1. Use homebrew to install latest version of mysql, to start service, and to set up security:
   brew info mysql
brew install mysql
mysqladmin -u root -password 'pswd' (new pswd in single quotes)
brew tap homebrew/services
brew services list
brew services start mysql
mysql_secure_installation

2. Get MySQL Workbench
3. To connect to mysql in terminal:
   mysql -u root -p
   which will prompt for root password.

git/GitHub/bitbucket

installing git:

• install/update using Homebrew:
  brew install git
• Set up SSH/keygen for git on bitbucket.
• using ssh-copy-id; article from ssh-com

git learning resources:

• GitHub/git cheat sheet (pdf)
• Resources for learning git

Other git resources

• Installing git-latexdiff: brew install git-latexdiff

Python:

installation:

• The easiest way to install python on a Mac is using Homebrew (see below)
• To install python3 using homebrew run:
  brew install python
• Note: if you have previously installed python using homebrew, you might wish to uniinstall/clean the older versions before the new install:
  brew uninstall --force python
brew uninstall --force python@2
cd /usr/local/lib; rm -iv python*.*
cd /usr/local/bin; rm -iv *python*

updating python with pip:

• First upgrade pip:
  pip3 install --upgrade pip setuptools wheel
• For the packages I use, the installation command is:
  pip3 install numpy matplotlib pandas linearmodels datetime ipython jupyter wrds tables tabulate pandas_datareader seaborn yfinance fitbit cherrypy openpyxl pymysql mysql-connector-python sqlalchemy pint dateutil
• A number of other necessary packages will be installed as dependencies
• To list outdated packages:
  pip3 list --outdated
• To update outdated packages:
  pip list --outdated --format=freeze | grep -v '^\-e' | cut -d = -f 1 | xargs -n1 pip install -U
• As of 2018:09, there is an incompatability in pandas-datareader version 3.7, so I am using the development version of this, which you can get with:
  pip3 install git+https://github.com/pydata/pandas-datareader.git

python learning resources:

• Think Python (book by Allen B. Downey)
• Pandas (book -- resources)
• Medium Articles:
  • The Essential Python Libraries for Data Science
• Quantitative Economics -- Tom Sargent and John Stachurski -- python for quantitative economic modeling
• Python for Econometrics (Kevin Shepard)
• Remote iPython Notebook using an ssh tunnel

LaTeX/Emacs/AucTeX/etc. for Mac:

Two very good sets of instructions for installing an Emacs-based computing infrastructure are:

• Kieran Healy's An Emacs Starter Kit for the Social Sciences. He also has a couple of really good papers on how to use software to effectively organize and manage your work:
  • Choosing Your Workflow Applications
  • The Plain Person's Guide to Plain Text Social Science
• Setting up OSX for Data Analysis (Zachary Jones)
• Richard Stanton's page on writing finance papers using LaTeX.

LaTeX: installing and updating:

• Install the LaTeX distribution from MacTeX
• After installing, to fix permissions and update all packages, in Terminal type:
  • sudo chown -R $(whoami):admin /usr/local
  • tlmgr update --self
  • tlmgr update --all
• Shell commands for updating Latex using TeXLive (see TeXLive site):
  • tlmgr update --list (to list all updates)
  • tlmgr update --all (to perform all updates)
  • tlmgr install pkgname (to install pkgname)
• After making any changes (including those above), be sure to run:
  • texhash
  so that the changes will be found by the system.

emacs:

• Installing using homebrew:
brew cask install emacs
brew install aspell

• See Emacs for MacOS-X
• You may need to use package manger (command list-packages in emacs) to install "obsolete" packages.
• In the package-manager window, to upgrade all packages, in the package manger type U to mark all upgradable packages to be upgraded, and then x to actually perform the new updates.
• To configure, I use Kieran Healy's emacs-starter kit, almost without modification:
  • To install:
    cd ~
git clone https://github.com/kjhealy/emacs-starter-kit.git .emacs.d/
  • The replace the kjhealy.org file with an appropriately named .org file, modified for your environment.

Skim (a great PDF-viewer for use with Emacs/LaTeX):

• With the proper setup, use C-c C-v in emacs to highlight the line you are editing in Skim. In Skim, use Cmd+Shift+click to take you to that point in the tex file being edited in emacs. To setup:
  • In Skim -> Preferences -> Sync:
    • Check the box "Check for file changes."
    • Preset: -> Custom
    • Command: -> /usr/local/bin/emacsclient
    • Arguments -> -n +%line "%file"
  • In Skim -> PDF:
    • PDF Display -> Single Page
    • Check Automatically Resize
    • Size and position the View window, then click "Use Current View Settings as Default"
  • To force Skim to auto-reload the pdf file when it is changed, in a terminal window type:
    defaults write -app Skim SKAutoReloadFileUpdate -boolean true
    
• If you use Beamer for presentations, Skim can display presentation notes on a second monitor while your slides are presented on the main monitor. See:
  • Displaying Synchronized Presentation Notes.
  • Alternatively, you can convert the pdf output from latex presentation to keynote with PDF to Keynote

BibTeX:

• BibDesk
• BibTool
  • brew install bib-tool

latexdiff and git-latexdiff:

• If you use git, there is a command git-latexdiff that will compare various commits.
• To install use homebrew
  • brew install git-latexdiff
  which will install both, as latexdiff is a dependency.
• NOTE: The current version of latexdiff seems to put DOS CRLF's in the diff file, which means that it won't always compile. To fix this, run:
  • latexdiff old-file.tex new-file.tex | tr -d '\r' > diff.tex
  and then compile diff.tex using pdflatex (and bibtex, if necessary).
• To fix git-latexdiff, you can pull the extra carriage returns out of diff file by going to /usr/local/bin and running:
  • cat git-latexdiff | sed "s/> diff.tex/| tr -d '\\\r' > diff.tex/g" > git-latexdiff-mac
  • chmod a+x git-latexdiff-mac
  then use git-latexdiff-mac in place of git-latexdiff.

SoftwareUpdate

• lists and installs opertaing system and other updates
  • run softwareupdate -h for a list of commands
• Usage
  • To list available updates:
    softwareupdate -l
  • To install updates:
    softwareupdate -i package
    or
    softwareupdate -i -a
    to update all available packages
    

MacAppleStore (mas)

• install mac apps from the command line
• To install with homebrew:
  brew install mas
• key mas commands are:
  mas help
  mas list
  mas search app-name
  mas install app-number
  mas outdated
  mas upgrade package
  

Other Useful Mac Stuff:

pass
• a unix/command-line based password manager
• Quicksilver
• Inkscape
• To install with homebrew:
  brew tap homebrew/cask
  brew cask install inkscape
• After installing with homebrew, you can invoke inkscape from terminal with the command:
  inkscape &
• Also, see the TeXText add-in description below
• GeekTool
• icalBuddy
  • brew install ical-buddy
• Dragon Dictate
• QuickCal
• XQuartz
• iTerm + Oh My Zsh on Mac
• amazingly good replacement for Terminal
• System Monitoring and Control:
  • pmset
  • smcfanControl
    brew cask install smcfancontrol
• Get Apache, MySQL, PHP, and phpMyAdmin running on OSX 10.11

TeXText add-in for Inkscape:

• Inkscape (see the link above) is amazing for creating figures/illustrations. The TeXText extension allow you the label the figures using LaTeX.
• To install the textext extension, do the following:
  1. Install Inkscape
     • Important: You need to follow the instructions for configuring XQuartz appropriately on the Inkscape web site (here).
  2. Get the latest release of EggBot for OS-X from https://github.com/evil-mad/EggBot/releases/ and install.
  3. Get TeXtext from http://pav.iki.fi/software/textext/. Open the latest textext tar.gz file (as of 4/2015 this is textext-0.4.4.tar.gz). Open this archive and extract the python file textext.py and place it in the folder /usr/local/Cellar/inkscape/0.91_3/share/inkscape/extensions. Notes: (1) verion number may be different; (2) you may have to change the mode of textext.py ("chmod a+x textext.py")
  4. In a terminal window type:
     brew install pdf2svg.
     This will install a pdf->svg converter that texttext needs.
  5. You may also need to install imagemagick.
  6. Now, to run textext, go to Extensions->Tex Text in the Inkscape menu. A window will pop up in which you can place your latex equations (with $s). Hit OK and you will get the processed equation tex-code in your figure.
• Helpful sites for this were/are https://nicolasamiot.wordpress.com/2013/07/25/inkscape-textext-on-mac-os-x-mountain-lion/ and http://pav.iki.fi/software/textext/macports-inkscape-textext-howto.html.

Misc ssh-fixes:

• Once ssh is setup, and once key-authentication is setup, it is more secure to turn off password login.
• To do this, edit the file /private/etc/ssh/sshd_config, and make sure the following lines are set to no:
  PermitRootLogin no
PasswordAuthentication no
PermitEmptyPasswords no
ChallengeResponseAuthentication no

• To stop and restart SSHD:
  sudo launchctl stop com.openssh.sshd
sudo launchctl start com.openssh.sshd