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erik_petigura_s_paper_writing_workflow [2013/02/02 05:00] – jwschwaberik_petigura_s_paper_writing_workflow [2013/02/04 07:37] – [Josiah's Paper Writing Workflow] nroth
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 =====Paper writing workflow===== =====Paper writing workflow=====
  
-==== Josiah's Paper Writing Workflow ====+==== Erik's Paper Writing Workflow ====
  
-=== Preamble ===+=== Philosophy === 
 +When I write a paper, it begins as a largely creative processes where I'm trying to effectively convey my scientific contribution. By submission time, I feel like a typesetter tracking down TeX errors, fixing broken references, and changing my figures to f1.eps, f2.eps, etc. I find the typesetting aspect distracting and I put it off as long as possible.
  
-Workflows are personal.  The two factors that most strongly shape my +=== Drafting === 
-own workflow is that my editor of choice is emacs and that I do not +I like to quickly hammer out a rough draft of a paper in a no-frills text editor. I like EverNote because it's easy to throw figures into the document, and since your note is on the cloud, you can work on your paper from any computer.
-work in large collaborations.  (It doesn't hurt that I like to +
-tinker.)  +
-The emacs learning curve can be quite steep, but because I do so many +
-different things in it, small increases in proficieny have a magnified +
-impact.  Also, I tend to be easily distracted, so the fewer times I +
-switch between apps, the better. +
-Instead of desribing things in gory detail, I just tried to give a +
-general overview.  If you have specific questions, or want to see +
-something in action, swing by my cube, D-343.  I'm usually happy to +
-talk about such things.+
  
-=== Write an Outline ===+=== Move into TeX === 
 +Once the paper is nearly done, I'll move it into a TeX document. I like to use TeXShop for Mac because it updates the PDF view of the paper with every compile. I use pdfTeX since I've found it's easier to throw in different sorts of files (.jpg, .png, .pdf). I also like to have these packages in the preamble.
  
-The first thing I do is write an outline using [org-mode].  This is a a +<code> 
-plain text draft of the paper, though I do write the equations using +\usepackage{\ensuremath}   % user-defined commands will be typeset in math-mode in text- and math-mode. 
-TeX.  Once things are reasonably converged, I export my org-mode file +\usepackage{\xspace}       % intelligently puts spaces after mathmode. 
-to TeX, using built-in exporter.  This converts my outline headings +\usepackage[T1]{fontenc}   % greater-than and less-than symbols don't turn into upside-down question marks
-into LaTeX sections, among other nifty things.+
  
-[org-mode]: http://orgmode.org/+% For example: 
 +\newcommand{\Rsun}{\ensuremath{R_{\odot}}\xspace}             
 +%\Rsun Gives the right symbol in text and math-mode.               
  
 +</code>
  
-=== Use Version Control ===+=== Version control === 
 +I track the TeX source documents (.tex & .bib) and all figures with. The <code>git diff --color-words</code> command shows the specific words (not just the lines that were changed).
  
-I start a git repository with the rough draft TeX file from the +=== References === 
-previous step.  When I send a draft to a co-author, I make a branch +I use BibDesk to manage my references. It's pretty easy to import the bibTeX citation directly from ADS into BibDesk.
-for him/her, incoportate the comments when I get them back, and then +
-merge this back into my master branch.  +
  
-=== TeX Editing in emacs ===+http://bibdesk.sourceforge.net/
  
-I use [AUCTeX] which the default emacs TeX editing mode.  It has all +=== Collaboration === 
-sorts of goodies: easy math-mode editing, cross reference support, +This obviously depends on how savvy your collaborators are. I'll email a .zip file of my TeX source to my collaborators and instruct them to edit the TeX source directly, reminding them that I've got version control running so I'll see all their changes. I'm keeping an eye on the ShareLaTeX product. It promisses to make working collaboratively on a TeX doc like a working on a Google doc. I'm not quite ready to use it yet, but I think it has promise.
-commands for creating environments, etc.+
  
-[AUCTeX]: http://www.gnu.org/software/auctex/+https://www.sharelatex.com/
  
- 
-=== BibTeX === 
- 
-I do not have a solution I'm completely happy with here.  I tend to 
-make an ADS private library for each paper and then export to BibTeX 
-occasionally.  I've played with both BibDesk and Papers and not been 
-all that happy with either (though I do like Papers for 
-reading/emailing). 
  

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