Benjamin Morgan bjmorgan

## compile
#!/usr/bin/env bash

# Help text

description="A bash script for compiling JOSS and JOSE papers locally";

doc="compile [-j <journal>] [-d <doi>] [-v <volume>] [-i <issue>] [-p <page>]
        [-s <submitted>] [-u <published>] [-r <review>] [-g <repository>] [-a <archive>] FILE

Compile a markdown FILE to a JOSS or JOSE paper.

## environment.py
#! /usr/bin/env python3

import platform
import pip
import sys

def pip_freeze():
    try:
        from pip._internal.operations import freeze
    except ImportError:  # pip < 10.0

## VASP_5.4.4_VDATCAR_patch
*** vasp.5.4.4/src/main.F	Sat Nov 18 09:31:39 2017
--- vasp.5.4.4.vel/src/main.F	Sat Nov 18 13:18:45 2017
***************
*** 479,484 ****
--- 479,485 ----
        OPEN(UNIT=16,FILE=DIR_APP(1:DIR_LEN)//'DOSCAR',STATUS='UNKNOWN')
        OPEN(UNIT=17,FILE=DIR_APP(1:DIR_LEN)//'OSZICAR',STATUS='UNKNOWN')
        OPEN(UNIT=60,FILE=DIR_APP(1:DIR_LEN)//'PCDAT',STATUS='UNKNOWN')
+       OPEN(UNIT=62,FILE=DIR_APP(1:DIR_LEN)//'VDATCAR',STATUS='UNKNOWN')
        OPEN(UNIT=61,FILE=DIR_APP(1:DIR_LEN)//'XDATCAR',STATUS='UNKNOWN')

## Find in OmniFocus.scpt
on handle_string(the_string)
	if (length of the_string is 0) then
		display dialog "Search OmniFocus for:" default answer ""
	end if
	open location "x-launchbar:hide"
	my search_in_omnifocus(the_string)
end handle_string

on search_in_omnifocus(the_search_string)
	tell application "OmniFocus"

## activation_energies.rb
#!/usr/local/bin/ruby

# September 16, 2013

require 'optparse'

options = {}

executable_name = File.basename($PROGRAM_NAME)

## meansqerror.rb
#! /home/morgan/bin/ruby/bin/ruby

# Calculates the mean squared error between two data sets
# http://en.wikipedia.org/wiki/Mean_squared_error

# BJM 26/06/13

def check_files_exist( filenames )
  all_files_exist = true
  filenames.each do |filename|

## Default (OSX).sublime.keymap
[
  // Run LaTeX plugin to insert reference code
  {
  	"keys": ["super+l", "super+r"],
  	"command": "insert_latex_reference",
  	"context": [
              { "key": "selector", "operator": "equal", "operand": "text.tex.latex" }
             ]
  }
]

## Sections.tmPreferences
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE plist PUBLIC "-//Apple Computer//DTD PLIST 1.0//EN" "http://www.apple.com/DTDs/PropertyList-1.0.dtd">
<plist version="1.0">
<dict>
  <key>name</key>
	<string>Symbol List</string>
	<key>scope</key>
	<string>meta.function.section.latex</string>
	<key>settings</key>
	<dict>

## figure.latex.sublime-snippet
<snippet>
    <content><![CDATA[\begin{figure}[tb]
  \begin{center}
		\resizebox{${3:8.5}cm}{!}{\includegraphics*{${1:filename}.eps}} % $4
		\caption{\label{fig:${1:label}}${2:Caption}}
	\end{center}
\end{figure}

$0]]></content>
    <tabTrigger>figure</tabTrigger>

## table.latex.sublime-snippet
<snippet>
    <content><![CDATA[\begin{table}[htb]
  \begin{center}
		\begin{tabular}{$3}
			$0 \\\\
		\end{tabular}
	\caption{\label{tab:${1:label}}${2:CAPTION}}
	\end{center}
\end{table}