matsen

#!/bin/sh

# Convert all arguments (assumed SVG) to a TIFF acceptable to PLOS
# Requires Inkscape and ImageMagick 6.8 (doesn't work with 6.6.9)

for i in $@; do
  BN=$(basename $i .svg)
  inkscape --without-gui --export-png="$BN.png" --export-dpi 300 $i
  convert -compress LZW -alpha remove $BN.png $BN.tiff
  mogrify -alpha off $BN.tiff

matsen

r () {
        if [[ -n $TMUX ]]
        then
                NEW_SSH_AUTH_SOCK=`tmux showenv|grep "^SSH_AUTH_SOCK"|cut -d = -f 2` 
                if [[ -n $NEW_SSH_AUTH_SOCK ]] && [[ -S $NEW_SSH_AUTH_SOCK ]]
                then
                        echo "New auth sock: $NEW_SSH_AUTH_SOCK"
                        SSH_AUTH_SOCK=$NEW_SSH_AUTH_SOCK 
                fi
                NEW_DISPLAY=`tmux showenv|grep "^DISPLAY"|cut -d = -f 2` 

matsen

For sane jupyter notebook diffs

• Install the nbconvert package, though you probably already have it if you are using jupyter.
• Put the nb2md script below in your path and make executable
• Add the following to your .gitattributes file, which can be in your home directory (use nb2md for all projects) or in the root of your project:

*.ipynb diff=nb2md

• Run

matsen

#!/bin/sh

set -e
set -o

sudo apt-get update
sudo apt-get upgrade -y

sudo apt-get install -y \
    autojump \

matsen

# A modification of `gallifrey` to show virtualenv information.
# I also found the return code information to be annoying, so it's commented out.
#local return_code="%(?..%{$fg[red]%}%? ↵%{$reset_color%})"

PROMPT='%{$fg[green]%}%m%{$reset_color%} $(virtualenv_prompt_info)%2~ $(git_prompt_info)%{$reset_color%}%B»%b '
#RPS1="${return_code}"

ZSH_THEME_GIT_PROMPT_PREFIX="%{$fg[yellow]%}‹"
ZSH_THEME_GIT_PROMPT_SUFFIX="› %{$reset_color%}"

matsen

\documentclass{amsart}

\usepackage[round]{natbib}
\usepackage{graphicx}
\usepackage[notref,notcite]{showkeys}
\usepackage{url}

% in case of supplementary material
% \usepackage{xr}
% \externaldocument{lcfit_supp}

matsen

#!/bin/sh

# sudo visudo
# matsen ALL = (root) NOPASSWD: /usr/local/bin/xiwi,/usr/bin/evince,/usr/bin/inkscape


set -e
set -o

sudo hostnamectl set-hostname flyx

matsen

#!/usr/bin/env python

"""
Turn a sequence file into a PNG, with a specified number of pixels per symbol.
Gaps are shown in light gray.
Unknown symbols, including N and X, are shown in pink.

Requires matplotlib, seqmagick, and their dependencies.
"""

matsen

matsen

%%For arXiv, uncomment this block and comment the next block.
%\documentclass{amsart}
%\usepackage{amsmath,amsfonts,amssymb,amsthm}
%\usepackage[english]{babel}
%\usepackage{graphicx}
%\usepackage{url}
%\usepackage[round]{natbib}
%\newcommand{\forarxiv}[1]{#1}
%\newcommand{\notforarxiv}[1]{}