This is a list of useful software we may need.
If brew is not already on your computer, see Install Homebrew at http://brew.sh and follow the prompts. Brew is the *nix package manager for OS X, and it largely has what we want.
git is the version control system we use. Some of our stuff is kept on github, which is a public repository of our code. See http://jklymak.github.com.
brew install git
You probably want to set up a github account.
sudo gem install jekyll
jekyll is the site generator for these webpages, and how we will serve the documentation for each project. Github runs it automatically if you follow the directions at http://jklymak.github.io/projtemplate. However, if you want to preview the webpage locally before committing and pushing it, then you can run
jekyll serve --baseurl ''
and you will be able to see it at http://localhost:4000/.
For general editing, I use Sublime Text or Emacs.
For formal document preparation, I keep a Latex files. For OS X use MacTeX and it will install TexShop and BibDesk
For LaTeX I use TexShop, or TexPad.
For my bibliographies, I use bibtex and Bibdesk.
For data analysis I almost exclusive use python now. All the libraries I use can be installed from Anaconda.
Most libraries not included with Anaconda can be included by running
conda update
conda install newlib
You may have to append sudo.
My libraries are at https://github.com/jklymak/pythonlib, and I’ll try to keep them up to date. The way to clone these using git is to go to the directory above where you want to install the library and:
cd ~/python
git clone git://github.com/jklymak/pythonlib.git
This will install a directory ~/python/pythonlib
To make sure python sees this, modify the PYTHONPATH by adding the following two lines to ~/.profile:
PYTHONPATH="/Users/yourlogin/python/pythonlib/:${PYTHONPATH}"
export PYTHONPATH
I run jupyter notebook for most of my analysis. To get this running I type:
% jupyter-notebook
Then, you need to open Firefox, to http://localhost:9999/ and your notebook will appear. You can start entering python code and running it. The result will be saved in Notebookname.ipynb in the directory you are working in (where you choose the Notebookname).