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Writing a Ph.D. thesis with Org Mode

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Re: Writing a Ph.D. thesis with Org Mode

#21

Post by limist »

Back in the late 2000's I looked around for the right tool for my Ph.D. dissertation and quickly ruled out Word, Libre (or Open Office) Writer, or any wysiwyg tool, because they 1) lacked fast, easy ways to work at the structural (tree) level of the document, which is important when you have many sections and subsections to organize thoughts and arguments; 2) couldn't do mathematical notation well; 3) didn't integrate well with the reference management tool I was using then, Mendeley.

As an Emacs lover, I soon found Org, and it was (and remains) the perfect tool, for working in plain text — which will never be obsolete, and works easily with git or version control. Then and now, nothing could match Org speed and flexibility: structural editing (creating nodes, moving nodes, promote/out-dent a node, demote/in-dent a node) was and is fundamental to Org (unlike Markdown etc), and it's ridiculously easy to reorganize thinking and writing as you go. You can export to LaTeX (or HTML) and customize formatting as needed, while also including code blocks from multiple languages. Integration with BibTeX was tight, and made handling hundreds of references easy.

Where other writing tools for complex documents previously made me cringe and cuss, Org makes writing a pure joy, freeing the mind to work entirely on content and its structure.

Re: Writing a Ph.D. thesis with Org Mode

#22

Post by fredguth »

lol768 wrote: post #13
makerofspoons wrote: post #10

Earlier quoted context omitted.

When I was doing my thesis I was a big fan of Mathematica's right click -> copy as LaTeX feature. It saved a lot of time entering formulas and copying tables from the notebooks I was using for analysis.

+1 for this, it really helped me. Also, Mathpix is neat - especially if you're citing results and need to include some equations from those papers.

With arxiv papers, I usually download the Tex file and copy the formulas from there. Besides, sometimes you find interesting ideas that were commented due to space.

Re: Writing a Ph.D. thesis with Org Mode

#23

Post by kmundnic »

tgbugs wrote: post #14

I have been writing my thesis as an org-mode file in git that is automatically published [0] as a pdf every time I commit using a bash script tangled as a commit hook. Figures are (or can be) computed from live data, and org-ref can automatically manage and format all my references as I go without the insanity inducing workflows that one usually has to resort to. Another amazing thing about org-mode is that I can wri…

How do you deal with different sections from google docs? As in, how do you format these into markdown or latex sections?

I've been working with psychologists and I've taught them the basics of a latex document, but I see how extracting the sections they have written from a google doc could be useful.

Re: Writing a Ph.D. thesis with Org Mode

#24

Post by philsnow »

tgbugs wrote: post #14

I have been writing my thesis as an org-mode file in git that is automatically published [0] as a pdf every time I commit using a bash script tangled as a commit hook. Figures are (or can be) computed from live data, and org-ref can automatically manage and format all my references as I go without the insanity inducing workflows that one usually has to resort to. Another amazing thing about org-mode is that I can wri…

A while back when I still worked on academic papers, I had a great workflow where I had a Makefile that knew how to build everything (deriving .eps files from xfig diagrams, deriving a main pdf file from all the .tex files etc), and I used inotifytools to notice when any of the build dependencies changed, and that triggered a run of `make`.

xpdf has (... had?? apparently it got removed in the 4.0 series to get a release out the door) a "remote" option where you can send commands to a running xpdf instance, so I would have the above makefile notify the running xpdf to re-read the file.

Put $EDITOR on one side and xpdf on the other, and you've got a near-realtime-updated view of what you're working on, just save the file and see the rebuilt pdf. It usually took around a second or two depending on the complexity of what I was working on.

I didn't use emacs at the time, but if I had, I would try to integrate all of the above with flymake-mode to automatically build without me needing to save the file. (there are probably problems with this because if it builds while you're in the middle of typing a latex command, the latex process will fail to build)

Re: Writing a Ph.D. thesis with Org Mode

#25

Post by wolfram74 »

kleiba wrote: post #16
m000 wrote: post #6

I'm not sure about other fields, but most theses in computer science these days are usually a stitch-up of your papers + some glue text/backstory. I.e. 80% of your thesis is already in LaTeX format. Org Mode only adds complexity to your workflow.

I doubt that anyone can be familiar with "most theses in computer science these days".

Depends on your threshold for "familiarity". Anyone currently working on theirs will likely have a number of friends/colleagues working on ones of their own, include second and third hand knowledge accumulated from conferences and likely any modestly sociable CS doctoral candidate would know at least the loose structure, if not 30 second blurb of quite a large number of theses in progress.

Re: Writing a Ph.D. thesis with Org Mode

#26

Post by tgbugs »

kmundnic wrote: post #23
tgbugs wrote: post #14

I have been writing my thesis as an org-mode file in git that is automatically published [0] as a pdf every time I commit using a bash script tangled as a commit hook. Figures are (or can be) computed from live data, and org-ref can automatically manage and format all my references as I go without the insanity inducing workflows that one usually has to resort to. Another amazing thing about org-mode is that I can wri…

How do you deal with different sections from google docs? As in, how do you format these into markdown or latex sections? I've been working with psychologists and I've taught them the basics of a latex document, but I see how extracting the sections they have written from a google doc could be useful.

I wrote a docs api v1 -> org converter in python. I just pulled it into its own repo and it still has a bunch of dependencies related to how I handle auth for other projects, but if you want to take a look it is at [0]. There is an example of how I use the Docs class in an org source bock in the readme (note that I use evil mode, and that you need to view raw to see everything that is going on with the headers). It currently requires a little dance to get everything in the right place at the right indent level, but it could be fully automated. I'm in the process of writing a converter going the other direction in elisp, and I will probably rewrite the python into elisp at some point as well, but for now, following the keystrokes is faster for me than trying to reimplement it to integrate with the org-mode api.

As an overview I use the heading level in the google doc as the corresponding * level (e.g. h1 -> , h2 -> *, etc.). Nearly every construct in the google doc has a 1:1 mapping with some org mode convention (there are some things that I still write in org-syntax in the google doc, such as figure captions and stuff like that.

If I need to export to markdown from org I usually try pandoc (I very rarely do this though). Importing from markdown I use pandoc as well, newer versions do a pretty good job and only need a few tweaks from time to time. Latex export is straight forward using org-mode's built in exporter [1] via the export dispatcher. For full pdf export I use lualatex via texlive with all the pain that that entails.

0. https://github.com/tgbugs/gdocorgpy 1. https://orgmode.org/manual/LaTeX-export.html 2. https://orgmode.org/manual/The-Export-Dispatcher.html#The-Ex...

Re: Writing a Ph.D. thesis with Org Mode

#27

Post by _emacsomancer_ »

yur3i__ wrote: post #3
pvaldes wrote: post #2

Could be be done, but does not feel like the appropriate tool. Org mode translates to a basic latex only, that is a huge waste of TeX power. I did my thesis entirely in LaTeX, so I have some experience in the theme, and it was a rollercoaster. There is always some really special table, graph, arrangement, extra space needs, that you can do only programming with the real stuff. Doing the same with org mode would have…

You can insert any LaTeX markup in org mode as well as just using their syntax.

This is more fragile than you would expect. If most of what you're doing is going to be LaTeX, it's easier just to write in .tex and eliminate the .org middle man. (I say this with a great love of Org mode, which I use everywhere else.)

Re: Writing a Ph.D. thesis with Org Mode

#28

Post by pvaldes »

_emacsomancer_ wrote: post #27
yur3i__ wrote: post #3

Earlier quoted context omitted.

You can insert any LaTeX markup in org mode as well as just using their syntax.

This is more fragile than you would expect. If most of what you're doing is going to be LaTeX, it's easier just to write in .tex and eliminate the .org middle man. (I say this with a great love of Org mode, which I use everywhere else.)

Org mode would (probably) make a mess with R chunks included in the .tex file, for example. You can't compile from R to org to latex to pdf, so this can be a problem. Same problem with Python to Latex path if you put org in the middle of the way.

By the way, I use .org files a lot also. Is handy for small and simple documents.

Re: Writing a Ph.D. thesis with Org Mode

#29

Post by _emacsomancer_ »

pvaldes wrote: post #28
_emacsomancer_ wrote: post #27

Earlier quoted context omitted.

This is more fragile than you would expect. If most of what you're doing is going to be LaTeX, it's easier just to write in .tex and eliminate the .org middle man. (I say this with a great love of Org mode, which I use everywhere else.)

Org mode would (probably) make a mess with R chunks included in the .tex file, for example. You can't compile from R to org to latex to pdf, so this can be a problem. Same problem with Python to Latex path if you put org in the middle of the way. By the way, I use .org files a lot also. Is handy for small and simple documents.

Even with plain LaTeX I've had trouble with Org mode trying to decide when to 'smartly' switch into maths mode, and what should be literal, e.g. `\latexfunction{...}` is sometimes translated as `\\\latexfunction{...}` because Org decides it should escape the backslash.
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