dotfiles

Here are my dotfiles and general instructions on how I set up my Mac OS X laptops (this will not work for Linux).

Prerequisites

1. Install OS X Command Line Tools. Homebrew will also try to do this automatically.

2. Install homebrew, then install git (to clone this repo):

    brew install git
   

3. Install Anaconda. Download link (I use the Python 3 version) and installation instructions. Be sure to install for a single user on OS X only; the system-wide installs cause issues with permissions. This cannot be done via the command line.

Bootstrapping a new installation

For a new OS X development environment, clone this repository to the ~ directory and use the following to install:

git clone --recursive [email protected]:vsbuffalo/dotfiles.git
cd dotfiles
sh setup.sh

If you forget --recursive (as I often do), use:

git submodule update --init --recursive

This script does the following:

• Installs Git, NeoVim, Ag, zsh, lesspipe, and tmux (from Homebrew, since these are dependencies)
• Installs oh-my-zsh pretzo
• Installs Futurama quotes
• Links ~/.zshrc to dotfiles/zshrc
• Links ~/.gitconfig
• Links ~/.tmux.conf
• Links ~/.ipython/
• Creates ~/.global_ignore from Github's .gitignore files and sets up Git colors
• Links ~/.Rprofile and installs some R packages
• Stores and links NeoVim's files (see below).
• Installs joe, which is a nifty tool for getting gitignore files.

Things to do manually after a new bootstrap

1. Set up a conda profile (e.g. basesci), install ipython, etc.

Linux minimum environment

For Linux, a minimum environment is set up. Since yum or apt-get may be used, this boostraph script does not install anything itself. This expects neovim and zsh to be installed, and copies over the configuration files of both (and creates global git ignore files, etc). Run:

sh min_setup.sh

Installed R and Bioconductor Packages

See install_rpkgs.R:

• ggplot2
• plyr
• reshape
• BiocInstaller
• GenomicRanges
• ggbio
• Gviz
• GenomicRanges
• VariantAnnotation

NeoVim

Annoyed with Emacs running evil-mode (and clashing with packages like polyweb), I decided to try NeoVim. I'm happy to report that it's terrific, and is likely my permanent text editor. Using the vim-rsi plugin, I can use emacs mappings in insert mode (this is a big deal). There's also great support for Ag, Git through fugitive, really terrific Python, C/C++ completion through the unbeatable YouCompleteMe, and some hacky vimscript I wrote to send lines of code to the new, awesome NeoVim terminal. You can see all of my configurations in .nvim*. I will keep my old Vim configurations around too.

If YouCompleteMe install isn't working:

xcrun -find c++
xcrun -find cc
export CC=`which cc`;export CXX=/Library/Developer/CommandLineTools/usr/bin/c++;./install.py --clang-completer

Pretzo

Recently, I have migrated from oh-my-zsh to pretzo.

git submodule add https://github.com/sorin-ionescu/prezto.git
git submodule update --init --recursive

I then link my own dotfiles/.zshrc to ~, not the one included in dotfiles/prezto/runcoms/. See install_prezto.zsh for more info -- this is adopted from the pretzo readme.

If you need to update Pretzo:

cd $ZPREZTODIR
git pull
git submodule update --init --recursive

Sane Jupyter Notebook Diffs

From Erick Matsen: https://gist.github.com/matsen/37521f504a14aede644d

LaTeX

I use basic LaTeX, and then install

sudo tlmgr install collection-fontsrecommended
sudo tlmgr install preprint
sudo tlmgr install wasysym
sudo tlmgr install biblatex
sudo tlmgr install logreq
sudo tlmgr install xstring
sudo tlmgr install units  

git-latexdiff

[email protected]:git-latexd

JupyterLab stuff:

Some good extensions are listed here.

pip install jupyterlab_latex
jupyter labextension install jupyterlab_vim
jupyter labextension install @jupyter-widgets/jupyterlab-manager