Hi Jake,

Jacob Gerlach <jacobgerl...@gmail.com> writes:

> I'm starting writing my thesis, for which I hope to remain in org-mode
> rather than regular LaTeX.

Others have already given you good advice, but since I am also writing
my thesis in Org, I thought I would chime in.  Like you, I felt a bit of
trepidation when I was deciding whether to write in Org or LaTeX; I
ultimately went with Org because (1) I find it much more pleasant to use
98% of the time; (2) I felt pretty confident I could plug the gaps in
the other 2% with help from Org's awesome community; and (3) I wanted
the option to export to other formats like HTML (though I haven't used
this much so far).

> I am working on adapting a thesis LaTeX template into org-mode. The
> template is set up with a main.tex having several individual files
> (chapters, appendices, etc) \include'd.
> I believe that I could parallel this using org's publishing mechanism. An
> alternate approach would be to use one single file, since I can simply fold
> chapters to focus my workflow.

Like others, I would recommend the one-file approach.  One advantage is
that it makes it easier to compile parts of your document by themselves,
since exporting a subtree from Org will inherit any #+LATEX_HEADER:
declarations that apply to the whole document (unless you override them
by setting the EXPORT_LATEX_HEADER property on the subtree).

> My first concern is losing the ability to use internal links if I use
> separate files. Another thought is compilation time if I use one file and
> must always run pdflatex over the entire document. I'm sure there are
> pitfalls either way that I'm not yet aware of.

If you decide you need to go the multiple-files route, you can probably
find a way to convert internal links into external ones.  I half-recall
someone posting code on this list to do this at some point...

Here are a couple of other things to think about.  When I decided to go
with Org, I took a few steps to ensure that if I ever need to switch to
pure LaTeX, I will be able to do so with minimal pain, just by exporting
my Org document to .tex and going from there.  (The big sticking point
here for me was making sure I could produce human-readable, stable
labels and refs for things like sections.  See the variable
org-latex-custom-id-as-label, which was introduced by a patch I wrote.)

If you're worried about ever having to make the switch, I would
recommend thinking ahead about each of the Org features you rely on and
seeing how they get exported to LaTeX.  If the default output is not
something you'd want to edit by hand, consider either limiting your use
of that feature, or customizing it so that it produces better output for
you.  Org provides a lot of ways to do the latter, from tweaking
variables to export filters to custom export backends.

Another thing to think ahead about is how you want to deal with your
bibliography.  People on this list use different approaches.  I
personally keep my reading tasks and notes in Org, then generate a .bib
file from this as needed during compilation of my thesis.  Others keep
bibliographic information directly in .bib.  I think you'll find there
are good tools for either approach, but one or the other will probably
fit better into your workflow, and may affect how easily you can export
to other formats.

Hope that's helpful!


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