ENH: Reworking old dotfiles to use dotbot

.gitmodules

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+[submodule "dotbot"]
+	path = dotbot
+	url = https://github.com/anishathalye/dotbot

README.md

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+# Dotfiles
+
+```bash
+$ git clone https://github.com/thermokarst/dotfiles.git ~/.dotfiles
+$ cd ~/.dotfiles
+$ ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)"
+$ ./homebrew-install
+$ git clone https://github.com/chriskempson/base16-shell.git ~/.config/base16-shell
+$ echo "/usr/local/bin/zsh" | sudo tee -a /etc/shells
+$ chsh -s /usr/local/bin/zsh
+$ git clone --recursive https://github.com/sorin-ionescu/prezto.git "${ZDOTDIR:-$HOME}/.zprezto"
+$ ./install
+$ curl -fLo ~/.vim/autoload/plug.vim --create-dirs https://raw.githubusercontent.com/junegunn/vim-plug/master/plug.vim
+$ vim +PlugInstall
+```

aspell.en.pws

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+personal_ws-1.1 en 5 
+informatics
+microbiome
+Microbiome
+QIIME
+metadata

dotbot

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+Subproject commit ef558f85d917c7d2fb52c17db10f0996ef92cb3f

git/gitconfig

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+[user]
+    name = Matthew Dillon
+    email = matthewrdillon@gmail.com
+[core]
+    editor = vim
+    excludesfile = /Users/matthew/.gitignore_global
+    pager = diff-so-fancy | less --tabs=4 -RFX
+[color]
+    diff = auto
+    status = auto
+    branch = auto
+    interactive = auto
+    ui = auto
+[gc]
+    auto = 1
+[merge]
+    summary=true
+    tool = vimdiff
+    conflictstyle = diff3
+    prompt = false
+[alias]
+    unstage = reset HEAD
+    uncommit = reset --soft HEAD^
+    # http://stackoverflow.com/a/9074343
+    lg1 = log \
+        --graph \
+        --abbrev-commit \
+        --decorate \
+        --format=format:'%C(bold blue)%h%C(reset) - %C(bold green)(%ar)%C(reset) %C(white)%s%C(reset) %C(dim white)- %an%C(reset)%C(bold yellow)%d%C(reset)' \
+        --all
+    lg2 = log \
+        --graph \
+        --abbrev-commit \
+        --decorate \
+        --format=format:'%C(bold blue)%h%C(reset) - %C(bold cyan)%aD%C(reset) %C(bold green)(%ar)%C(reset)%C(bold yellow)%d%C(reset)%n''          %C(white)%s%C(reset) %C(dim white)- %an%C(reset)' \
+        --all
+    lg = !"git lg1"
+    # https://gist.github.com/mwhite/6887990
+    a = add
+    ap = add -p
+    c = commit --verbose
+    ca = commit -a --verbose
+    cm = commit -m
+    cam = commit -a -m
+    m = commit --amend --verbose
+    d = diff
+    ds = diff --stat
+    dc = diff --cached
+    s = status -s
+    co = checkout
+    cob = checkout -b
+    # list branches sorted by last modified
+    b = "!git for-each-ref --sort='-authordate' --format='%(authordate)%09%(objectname:short)%09%(refname)' refs/heads | sed -e 's-refs/heads/--'"
+    # list aliases
+    la = "!git config -l | grep alias | cut -c 7-"
+[push]
+    default = upstream
+[credential]
+    helper = osxkeychain
+[pull]
+    rebase = true

git/gitignore_global

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+*~
+.DS_Store
+.idea

homebrew-install

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+#!/usr/bin/env zsh
+
+taps=(
+    homebrew/binary
+    caskroom/cask
+    caskroom/fonts
+)
+
+packages=(
+    ag
+    aspell
+    blackbox
+    brew-cask
+    cmake
+    cmus
+    diff-so-fancy
+    git
+    gnupg
+    go
+    gpg-agent
+    graphviz
+    heroku
+    htop-osx
+    httpie
+    hugo
+    imagemagick
+    node
+    openssl
+    pass
+    postgresql
+    python
+    python3
+    reattach-to-user-namespace
+    tmux
+    tree
+    vim
+    wget
+    xz
+    zsh
+)
+
+cask_packages=(
+    arq
+    dropbox
+    font-inconsolata
+    font-anonymous-pro
+    gitify
+    google-chrome
+    google-drive
+    java
+    macdown
+    pandoc
+    slack
+    spectacle
+    the-unarchiver
+    vagrant
+    virtualbox
+    xquartz
+)
+
+function log() {
+    echo $* > /dev/stderr
+}
+
+log "brew update"
+brew update
+
+log "brew upgrade"
+brew upgrade
+
+log "tapping"
+for name in $taps
+do
+    log "brew tap ${name}"
+    brew tap $name
+done
+
+log "installing"
+for name_and_args in $packages
+do
+    log "brew install ${=name_and_args}"
+    brew install "${=name_and_args}"
+done
+
+for name_and_args in $cask_packages
+do
+    log "brew cask install ${=name_and_args}"
+    brew cask install "${=name_and_args}"
+done
+
+log "brew cleanup"
+brew cleanup
+
+log "brew linkapps"
+brew linkapps

install

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+#!/usr/bin/env bash
+
+set -e
+
+CONFIG="install.conf.yaml"
+DOTBOT_DIR="dotbot"
+
+DOTBOT_BIN="bin/dotbot"
+BASEDIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
+
+cd "${BASEDIR}"
+git submodule update --init --recursive "${DOTBOT_DIR}"
+
+"${BASEDIR}/${DOTBOT_DIR}/${DOTBOT_BIN}" -d "${BASEDIR}" -c "${CONFIG}" "${@}"

install.conf.yaml

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+- clean: ['~']
+
+- link:
+    ~/.tmux.conf:        tmux.conf
+    ~/.gitconfig:        git/gitconfig
+    ~/.gitignore_global: git/gitignore_global
+    ~/.psqlrc:           psqlrc
+    ~/.zpreztorc:        zsh/zpreztorc
+    ~/.zlogin:           zsh/zlogin
+    ~/.zlogout:          zsh/zlogout
+    ~/.zprofile:         zsh/zprofile
+    ~/.zshenv:           zsh/zshenv
+    ~/.zshrc:            zsh/zshrc
+    ~/.aspell.en.pws:    aspell.en.pws
+    ~/.vimrc:            vimrc

psqlrc

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+\echo `date  +"%Y-%m-%d %H:%M:%S"`
+\set PROMPT1 '%M:%[%033[1;31m%]%>%[%033[0m%] %n@%/%R%#%x '
+\pset null '[NULL]'
+\pset border 2

tmux.conf

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+# Automatic window title
+setw -g automatic-rename
+
+# Fix LSOpenURLsWithRole() error on OS X. Requires reattach-to-user-namespace
+set -g default-command "reattach-to-user-namespace -l /usr/local/bin/zsh"
+
+# remap prefix to Control + a
+set -g prefix C-a
+unbind C-b
+bind C-a last-window
+
+set -g default-terminal "screen-256color"
+
+# http://www.unwiredcouch.com/2013/11/15/my-tmux-setup.html
+# Force a reload of the config file
+unbind r
+bind r source-file ~/.tmux.conf
+
+# Start window numbering at 1 for easier switching
+set -g base-index 1
+
+# Open new panes & splits in the same directory
+bind c new-window -c "#{pane_current_path}"
+bind % split-window -h -c "#{pane_current_path}"
+bind '"' split-window -c "#{pane_current_path}"
+
+# hjkl pane traversal
+bind h select-pane -L
+bind j select-pane -D
+bind k select-pane -U
+bind l select-pane -R
+
+set-option -g status-bg colour18
+set-option -g status-fg colour136
+set -g status-interval 0 # Changed for El Capitan issues
+set -g status-justify centre
+set -g status-left-length 50
+set -g status-right-length 140
+set -g status-left '#[fg=green]#H#[default] session:#S'
+set -g status-right '#[fg=white,bg=default]%a %l:%M:%S %p#[default] #[fg=blue]%m-%d-%Y'
+
+set-option -g renumber-windows on
+set -sg escape-time 0
+set-option -g destroy-unattached 'off'
+
+# Enable mouse control (clickable windows, panes, resizable panes)
+set -g mouse on
+
+bind-key -t vi-copy MouseDragEnd1Pane copy-pipe "pbcopy"
+bind-key -t vi-copy v begin-selection
+bind-key -t vi-copy y copy-pipe "reattach-to-user-namespace pbcopy"
+unbind -t vi-copy Enter
+bind-key -t vi-copy Enter copy-pipe "reattach-to-user-namespace pbcopy"

vimrc

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+call plug#begin()
+  Plug 'chriskempson/base16-vim'
+  Plug 'wakatime/vim-wakatime'
+  Plug 'nvie/vim-flake8'
+  Plug 'vim-airline/vim-airline'
+  Plug 'vim-airline/vim-airline-themes'
+  Plug 'airblade/vim-gitgutter'
+  Plug 'ntpeters/vim-better-whitespace'
+call plug#end()
+
+set t_Co=256
+
+if filereadable(expand("~/.vimrc_background"))
+  let base16colorspace=256
+  source ~/.vimrc_background
+endif
+set background=dark
+
+let g:airline_theme='base16'
+
+" default encoding
+set encoding=utf-8
+
+" Enable file type detection and do language-dependent indenting.
+filetype plugin indent on
+
+" turn on syntax highlighting
+syntax enable
+syntax on
+
+" turn on line numbering
+set number
+
+" make backspace behave as expected
+set backspace=indent,eol,start
+
+" set up whitespace substitutions
+set list
+set listchars=tab:▸\ ,extends:>,precedes:<,trail:~
+
+" highlight current line
+set cursorline
+
+" show matching ({[]})
+set showmatch
+
+" show a vertical bar on right side of editor
+set colorcolumn=80
+
+highlight LineNr ctermfg=DarkGrey
+
+" number of visual spaces per tab
+set tabstop=4
+
+" number of spaces in tab when editing
+set softtabstop=4
+
+" tabs are spaces
+set expandtab
+
+" self-explanatory
+set autoindent
+"
+" show airline all the time
+set laststatus=2
+
+" set up central backups
+set backup
+set backupdir=~/.vim-tmp,~/.tmp,~/tmp,/var/tmp,/tmp
+set backupskip=/tmp/*,/private/tmp/*
+set directory=~/.vim-tmp,~/.tmp,~/tmp,/var/tmp,/tmp
+set writebackup
+
+" change the mapleader from \ to ,
+let mapleader=" "
+
+" netrw config
+let g:netrw_liststyle=0         " thin (change to 3 for tree)
+let g:netrw_banner=0            " no banner
+let g:netrw_altv=1              " open files on right
+let g:netrw_preview=1           " open previews vertically
+let g:netrw_list_hide='\.git,\.idea,.*\.swp$,.*\.pyc$,__pycache__,\.DS_Store'
+
+" http://ivanbrennan.nyc/blog/2014/01/16/rigging-vims-netrw/
+fun! VexOpen(dir)
+    let g:netrw_browse_split=4
+    let vex_width=25
+    execute "Vexplore " . a:dir
+    let t:vex_buf_nr = bufnr("%")
+    wincmd H
+    call VexSize(vex_width)
+endf
+
+fun! VexClose()
+    let cur_win_nr = winnr()
+    let target_nr = ( cur_win_nr == 1 ? winnr("#") : cur_win_nr )
+    1wincmd w
+    close
+    unlet t:vex_buf_nr
+    execute (target_nr - 1) . "wincmd w"
+    call NormalizeWidths()
+endf
+
+fun! VexSize(vex_width)
+    execute "vertical resize" . a:vex_width
+    set winfixwidth
+    call NormalizeWidths()
+endf
+
+fun! NormalizeWidths()
+    let eadir_pref = &eadirection
+    set eadirection=hor
+    set equalalways! equalalways!
+    let &eadirection = eadir_pref
+endf
+
+fun! VexToggle(dir)
+    if exists("t:vex_buf_nr")
+        call VexClose()
+    else
+        call VexOpen(a:dir)
+    endif
+endf
+
+noremap <Leader><Tab> :call VexToggle(getcwd())<CR>
+noremap <Leader>` :call VexToggle("")<CR>
+
+augroup NetrwGroup
+    autocmd! BufEnter * call NormalizeWidths()
+augroup END
+
+" PEP8 formatting
+au BufNewFile,BufRead *.py
+    \ set tabstop=4 |
+    \ set softtabstop=4 |
+    \ set shiftwidth=4 |
+    \ set textwidth=79 |
+    \ set expandtab |
+    \ set autoindent |
+    \ set fileformat=unix |
+
+" Everybody else
+au BufNewFile,BufRead *.js, *.html, *.css
+    \ set tabstop=2 |
+    \ set softtabstop=2 |
+    \ set shiftwidth=2 |
+
+" Stop the YAML madness
+autocmd FileType yaml setl indentkeys-=<:>
+
+" show open buffers in airline
+let g:airline#extensions#tabline#enabled = 1
+
+" show just the filename
+let g:airline#extensions#tabline#fnamemod = ':t'
+
+" cycle to next buffer
+nmap <leader>l :bnext<CR>
+
+" cycle to previous buffer
+nmap <leader>h :bprevious<CR>

zsh/zlogin

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+#
+# Executes commands at login post-zshrc.
+#
+# Execute code that does not affect the current session in the background.
+{
+  # Compile the completion dump to increase startup speed.
+  zcompdump="${ZDOTDIR:-$HOME}/.zcompdump"
+  if [[ -s "$zcompdump" && (! -s "${zcompdump}.zwc" || "$zcompdump" -nt "${zcompdump}.zwc") ]]; then
+    zcompile "$zcompdump"
+  fi
+} &!

zsh/zlogout

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+#
+# Executes commands at logout.
+

zsh/zpreztorc

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+#
+# Sets Prezto options.
+#
+
+# General
+#
+
+# Set case-sensitivity for completion, history lookup, etc.
+# zstyle ':prezto:*:*' case-sensitive 'yes'
+
+# Color output (auto set to 'no' on dumb terminals).
+zstyle ':prezto:*:*' color 'yes'
+
+# Set the Zsh modules to load (man zshmodules).
+# zstyle ':prezto:load' zmodule 'attr' 'stat'
+
+# Set the Zsh functions to load (man zshcontrib).
+# zstyle ':prezto:load' zfunction 'zargs' 'zmv'
+
+# Set the Prezto modules to load (browse modules).
+# The order matters.
+zstyle ':prezto:load' pmodule \
+  'environment' \
+  'terminal' \
+  'editor' \
+  'history' \
+  'directory' \
+  'spectrum' \
+  'utility' \
+  'completion' \
+  'git' \
+  'prompt' \
+  'tmux' \
+  'gpg'
+
+#
+# Editor
+#
+
+# Set the key mapping style to 'emacs' or 'vi'.
+zstyle ':prezto:module:editor' key-bindings 'vi'
+
+# Auto convert .... to ../..
+# zstyle ':prezto:module:editor' dot-expansion 'yes'
+
+#
+# Git
+#
+
+# Ignore submodules when they are 'dirty', 'untracked', 'all', or 'none'.
+# zstyle ':prezto:module:git:status:ignore' submodules 'all'
+
+#
+# GNU Utility
+#
+
+# Set the command prefix on non-GNU systems.
+# zstyle ':prezto:module:gnu-utility' prefix 'g'
+
+#
+# History Substring Search
+#
+
+# Set the query found color.
+# zstyle ':prezto:module:history-substring-search:color' found ''
+
+# Set the query not found color.
+# zstyle ':prezto:module:history-substring-search:color' not-found ''
+
+# Set the search globbing flags.
+# zstyle ':prezto:module:history-substring-search' globbing-flags ''
+
+#
+# Pacman
+#
+
+# Set the Pacman frontend.
+# zstyle ':prezto:module:pacman' frontend 'yaourt'
+
+#
+# Prompt
+#
+
+# Set the prompt theme to load.
+# Setting it to 'random' loads a random theme.
+# Auto set to 'off' on dumb terminals.
+zstyle ':prezto:module:prompt' theme 'cloud'
+
+#
+# Screen
+#
+
+# Auto start a session when Zsh is launched in a local terminal.
+# zstyle ':prezto:module:screen:auto-start' local 'yes'
+
+# Auto start a session when Zsh is launched in a SSH connection.
+# zstyle ':prezto:module:screen:auto-start' remote 'yes'
+
+#
+# SSH
+#
+
+# Set the SSH identities to load into the agent.
+# zstyle ':prezto:module:ssh:load' identities 'id_rsa' 'id_rsa2' 'id_github'
+
+#
+# Syntax Highlighting
+#
+
+# Set syntax highlighters.
+# By default, only the main highlighter is enabled.
+# zstyle ':prezto:module:syntax-highlighting' highlighters \
+#   'main' \
+#   'brackets' \
+#   'pattern' \
+#   'cursor' \
+#   'root'
+#
+# Set syntax highlighting styles.
+# zstyle ':prezto:module:syntax-highlighting' styles \
+#   'builtin' 'bg=blue' \
+#   'command' 'bg=blue' \
+#   'function' 'bg=blue'
+#
+
+#
+# Terminal
+#
+
+# Auto set the tab and window titles.
+zstyle ':prezto:module:terminal' auto-title 'yes'
+
+#
+# Tmux
+#
+
+# Auto start a session when Zsh is launched in a local terminal.
+# zstyle ':prezto:module:tmux:auto-start' local 'yes'
+
+# Auto start a session when Zsh is launched in a SSH connection.
+# zstyle ':prezto:module:tmux:auto-start' remote 'yes'

zsh/zprofile

@@ -0,0 +1,4 @@
+#
+# Executes commands at login pre-zshrc.
+#
+

zsh/zshenv

@@ -0,0 +1,72 @@
+#
+# Defines environment variables.
+#
+
+#
+# Browser
+#
+
+if [[ "$OSTYPE" == darwin* ]]; then
+  export BROWSER='open'
+fi
+
+#
+# Editors
+#
+
+export EDITOR='vim'
+export VISUAL='vim'
+export PAGER='less'
+
+#
+# Language
+#
+
+if [[ -z "$LANG" ]]; then
+  export LANG='en_US.UTF-8'
+fi
+
+#
+# Paths
+#
+
+typeset -gU cdpath fpath mailpath path
+
+# Set the the list of directories that cd searches.
+# cdpath=(
+#   $cdpath
+# )
+
+# Set the list of directories that Zsh searches for programs.
+path=(
+  /usr/local/{bin,sbin}
+  $path
+)
+
+#
+# Less
+#
+
+# Set the default Less options.
+# Mouse-wheel scrolling has been disabled by -X (disable screen clearing).
+# Remove -X and -F (exit if the content fits on one screen) to enable it.
+export LESS='-F -g -i -M -R -S -w -X -z-4'
+
+# Set the Less input preprocessor.
+if (( $+commands[lesspipe.sh] )); then
+  export LESSOPEN='| /usr/bin/env lesspipe.sh %s 2>&-'
+fi
+
+#
+# Temporary Files
+#
+
+if [[ ! -d "$TMPDIR" ]]; then
+  export TMPDIR="/tmp/$USER"
+  mkdir -p -m 700 "$TMPDIR"
+fi
+
+TMPPREFIX="${TMPDIR%/}/zsh"
+if [[ ! -d "$TMPPREFIX" ]]; then
+  mkdir -p "$TMPPREFIX"
+fi

zsh/zshrc

@@ -0,0 +1,36 @@
+# Matthew Dillon
+# matthewrdillon@gmail.com
+#
+# source Prezto.
+if [[ -s "${ZDOTDIR:-$HOME}/.zprezto/init.zsh" ]]; then
+  source "${ZDOTDIR:-$HOME}/.zprezto/init.zsh"
+fi
+
+# set up local bin dirs
+export PATH="$PATH:$HOME/bin:$HOME/.bin"
+
+# shortcuts to projects
+export CDPATH="$CDPATH:$HOME/caporaso/qiime2"
+export CDPATH="$CDPATH:$HOME/projects"
+
+# shortcuts
+alias mailserver="sudo python -m smtpd -n -c DebuggingServer localhost:25"
+alias mongod="mongod --config /usr/local/etc/mongod.conf"
+alias postgres="postgres -D /usr/local/var/postgres"
+alias venv="source venv/bin/activate"
+alias devenv="deactivate"
+alias q="source activate q2dev"
+alias i="ipython3"
+
+# set up golang
+export GOPATH="/Users/matthew/go"
+export PATH="$PATH:$GOPATH/bin"
+export CDPATH="$CDPATH:$GOPATH/src/github.com:$GOPATH/src/code.google.com/p:$GOPATH/src/bitbucket.org"
+
+# set miniconda3 bin dir last
+export PATH="$PATH:$HOME/miniconda3/bin"
+
+BASE16_SHELL=$HOME/.config/base16-shell/
+[ -n "$PS1" ] && [ -s $BASE16_SHELL/profile_helper.sh ] && eval "$($BASE16_SHELL/profile_helper.sh)"
+
+alias tmux="TERM=xterm-256color tmux"