Export basic LaTeX manuscript

[dhimmel]

refs #249

[AppVeyorBot]

AppVeyor build 1.0.186 for commit 0394ec0 is now complete.

Found 52 potential spelling error(s). Preview:

content/02.delete-me.md:44:adipiscing
content/02.delete-me.md:44:aliqua
content/02.delete-me.md:44:amet
content/02.delete-me.md:44:consectetur
content/02.delete-me.md:44:dolore
content/02.delete-me.md:44:eiusmod
content/02.delete-me.md:44:elit
content/02.delete-me.md:44:incididunt
content/02.delete-me.md:44:ipsum
content/02.delete-me.md:44:labore
content/02.delete-me.md:44:Lorem
content/02.delete-me.md:44:magna
content/02...

The rendered manuscript from this build is temporarily available for download at:

• manuscript-1.0.186-0394ec0.html
• manuscript-1.0.186-0394ec0.pdf
• spelling-errors-1.0.186-0394ec0.txt
• spelling-error-locations-1.0.186-0394ec0.txt

[dhimmel]

manuscript.tex snippets

Here are parts of the output manuscript.tex separated by ...:

\begin{figure}
\hypertarget{fig:wide-image}{%
\centering
\includegraphics{https://github.com/manubot/resources/raw/15493970f8882fce22bef829619d3fb37a613ba5/test/wide.png}
\caption{\textbf{An image too wide to fit within page at full size.}
Loaded from a specific (hashed) version of the image on GitHub.}\label{fig:wide-image}
}
\end{figure}
...
Citation by DOI {[}\protect\hyperlink{ref-IhliSZDo}{1}{]}.
...
A LaTeX equation:

\begin{equation}\int_0^\infty e^{-x^2} dx=\frac{\sqrt{\pi}}{2}\label{eq:regular-equation}\end{equation}
...
\leavevmode\hypertarget{ref-6acIRW4q}{}%
6. \textbf{Open collaborative writing with Manubot} \\
Daniel S. Himmelstein, Vincent Rubinetti, David R. Slochower, Dongbo Hu, Venkat S. Malladi, Casey S. Greene, Anthony Gitter\\
\emph{Manubot} (2020-05-25) \url{https://greenelab.github.io/meta-review/}

So looks like citations have been rendered, but figures are still references and not yet numbered.

Adding standalone: true to defaults/latex.yaml adds a preamble and \begin{document}.

[habi]

So looks like citations have been rendered [...]

The main issue I always saw with submitting a final manuscript file as .tex is copying over the citations (from a Word or Markdown file) without introducing an error.
If the file does contain them that greatly minimizes any human errors!
I knew that I'd 'just' be able to pandoc the stuff together myself, but it's very convenient if the build pipeline does it automatically.

[...] but figures are still references and not yet numbered.

That should be easy to take care of with a little bit of 'search-and-replace'.
I think it's much less error-prone than manually copy-pasting 40+ citations :)

[dhimmel]

@agitter do you see value in merging this and keeping BUILD_LATEX off by default?

[agitter]

do you see value in merging this and keeping BUILD_LATEX off by default?

Yes, I think it's a small addition that won't clutter anything and can be a helpful starting point for LaTeX export.

I intend to comment on #249 based on our LaTeX experience in greenelab/covid19-review#943. I now have a better understanding of the gaps between this basic export and what LaTeX authors may want.