Compile citations from LaTeX to Markdown Text - latex

I would like to use Pandoc (although any tool is fine) to compile a latex document into markdown text format. Right now I compile…
pandoc --bibliography=bibCourse.bib --wrap=preserve -o Syllabus.md Syllabus.tex
…with the command (any of the following)…
\cite{Label2020}
\fullcite{Label2020}
\textcite{Label2020}
…what comes out is…
#Label2020
I am pretty sure that's how the default compile is supposed to work, but not what I want. I want the output to be…
AuthorLast, AuthorFirst. Year. *Title* etc.
…in the text file. I have also tried adding various csl files which always yields the same result.

Related

knitr/rmarkdown/Latex: How to cross-reference figures and tables in 2 different pdf files?

I'm trying to write a scientific article and the associated supplementary materials entirely in RStudio with rmarkdown.
It seems clear that book down is the way to go to cross-reference between files (https://stackoverflow.com/a/38884378/576684), but I also would like to be able to reference figures produced in one pdf in the other pdf.
Although my latex has got quite rusty with time, I imagine it could be achieved as follows:
compile the article tex and SuppMat tex a first time using rmarkdown::render()
compile these tex files from the command line in order to keep the corresponding .aux file with their references (missing references won't be resolved at this time)
recompile the 2 tex files from the command line another time where all references should now be resolved
Is it a reasonable way to do it? am I overlooking something simpler?
In any case, it requires:
a different numbering of figures in each pdf file (covered by https://stackoverflow.com/a/51337664/576684)
to prevent rmarkdown from trashing the .aux files (it seems that pandoc doesn't allow this, hence the need to create the aux file using standalone latex)
to tell latex to use the additional .aux file if it is found (probably using header-includes: in the YAML header). how can I achieve that?
Thank you very much for your help!
It turns out that the xr package is one way to go: https://texblog.org/2016/08/23/adding-references-from-an-external-file/
so this works from R:
rmarkdown::render("myarticle_ms.Rmd",
bookdown::pdf_book(base_format=rticles::plos_article),
clean=FALSE)
rmarkdown::render("myarticle_SM.Rmd",
bookdown::pdf_book(base_format=rticles::plos_article),
clean=FALSE)
tinytex::pdflatex("myarticle_ms.tex", clean=FALSE)
tinytex::pdflatex("myarticle_SM.tex", clean=FALSE)
tinytex::pdflatex("myarticle_ms.tex")
tinytex::pdflatex("myarticle_SM.tex")
with the following in the YAML header of myarticle_ms.Rmd (and the corresponding one the SuppMat file header):
header-includes:
\usepackage{xr} \externaldocument{myarticle_SM}
Hope it makes life easier for a few others :)

How to add a (large) code appendix in LaTeX / LyX?

I'd like to add a code appendix to my LyX document. There are a few options I already considered, but they all have their problems.
I know a bit about listings, but one problem with those is that, if I copy & paste my code into them, I lose all enters/newlines. Since the code is too large to correct by hand, I was wondering if there is an alternative.
In LyX there is the possibility of inserting child documents, but that seems to be only for .tex files. Would have been ideal if I could just insert my .java file as a child document.
I could print the code to PDF, but it will include margins that mess up the final document, since the PDF is placed on the left margin of the final document and then there is the margin of the PDF. Also, this PDF always contains the entire code and white areas where not the entire page has been filled.
Does anyone have good alternative?
The listings package found here
http://www.ctan.org/tex-archive/macros/latex/contrib/listings/
allows the include of external source code files (look into the reference for \lstinputlisting).
EDIT: here you find some samples how to use it:
http://en.wikibooks.org/wiki/LaTeX/Packages/Listings
If you need to copy-paste code to LyX listing box then use Edit -> Paste Special -> Seletion or Ctrl+Alt+V.
For what it's worth, at least the 2.0 versions of LyX have the ability to include listings as child documents. Insert, File, Child Document, and choose from the dropdown box "Program Listing". This uses the listings package and lets you keep your source in its own file.
If listings doesn't support your language, you can always use something like highlight or source-highlight to generate a latex snippet of syntax-highlighted code that you can add as a child document of type "Input"
Yes, if you copy&paste code into the LyX listings box, you lose all newlines, but you can preprocess your code (insert an extra newline below each line):
$ cat foo.java | sed -e 's/$/\n/' > bar.java
Then you can copy&paste the new file bar.java and everything will be ok.

How to include LaTeX snippets directly in Doxygen comments?

I would like to be able to edit LaTeX parts of some Doxygen comments externally with some suitable editor. I would use that only for complex environments. To do that, I figured I can have LaTeX-only files and include them from Doxygen. I did create Doxygen aliases for \begin and \end to make the syntax compatible.
(For example, I know how to set-up Emacs/AUCTex for working with LaTeX snippets that have no preamble and document structure.)
Is there a way to include the contents of a .tex file inside a Doxygen comment? I look for something analogous to \htmlinclude, but for TeX files. Is there some way to emulate the functionality, given my requirements for having a TeX-only external source?
You may use something like
\latexonly
\input <file>
\endlatexonly
where <file> is the path to the file to include, either absolute or relative to the directory in which the latex documentation is generated.
Have you tried the \verbinclude command? This command includes any file verbatim in the documentation (in contrast to \include, which is used to include source files).
From the doxygen manual:
\verbinclude <file-name>
This command includes the file <file-name> verbatim in the documentation. The command is equivalent to pasting the file in the documentation and placing \verbatim and \endverbatim commands around it.
Files or directories that doxygen should look for can be specified using the EXAMPLE_PATH tag of doxygen's configuration file.
Edit: I just had a thought that you may wish to strip the preamble from your .tex file before including the rest of the file in the documentation. you could do this using the \dontinclude command which, together with the \line, \skip, \skipline, and \until commands allows you to include specific lines/blocks of a particular file. See the example in the \dontinclude documentation.

Compiling LaTex bib source

I am writing my thesis in Latex, and I have the references in an own thesis.bib
file which look as follows
#Article{xxx,
author = "D.A. Reinhard",
title = "Case Study",
year = "1985",
}
and I reference them in my main document as ~\cite{xxx}
When I compile then the main document with: pdflatex main.tex than
it shows me question marks instead of the proper references to the bibliography.
Do I also need to compile the bib source on its own? If yes, can somebody please
tell me the command for Linux
Many thanks!
You need to compile the bibtex file.
Suppose you have article.tex and article.bib. You need to run:
latex article.tex (this will generate a document with question marks in place of unknown references)
bibtex article (this will parse all the .bib files that were included in the article and generate metainformation regarding references)
latex article.tex (this will generate document with all the references in the correct places)
latex article.tex (just in case if adding references broke page numbering somewhere)
You have to run 'bibtex':
latex paper.tex
bibtex paper
latex paper.tex
latex paper.tex
dvipdf paper.dvi
I am using texmaker as the editor.
you have to compile it in terminal as following:
pdflatex filename (with or without extensions)
bibtex filename (without extensions)
pdflatex filename (with or without extensions)
pdflatex filename (with or without extensions)
but sometimes, when you use \citep{}, the names of the references don't show up. In this case, I had to open the references.bib file , so that texmaker could capture the references from the references.bib file. After every edition of the bib file, I had to close and reopen it!! So that texmaker could capture the content of new .bbl file each time. But remember, you have to also run your code in texmaker too.
Just in case it helps someone, since these questions (and answers) helped me really much; I decided to create an alias that runs these 4 commands in a row:
Just add the following line to your ~/.bashrc file (modify the main keyword accordingly to the name of your .tex and .bib files)
alias texbib = 'pdflatex main.tex && bibtex main && pdflatex main.tex && pdflatex main.tex'
And now, by just executing the texbib command (alias), all these commands will be executed sequentially.

Odd Bibtex behaviour in a Latex document

I added a line "\cite{test}" as a test to my working Latex document. When I compiled the bibtex "!bibtex name_of_my_file, I got the expected error:
Warning--I didn't find a database entry for "test"
Then, I removed the line and compiled the bibtex again, hoping to have a working Latex file again. However, the same error occurs, even with a fresh shell. I cannot understand the behaviour. What is the logic? How can I get my Latex document working again?
[Updated Info]
The problem dissapeared as unexpectedly as it emerged. I have no idea why but it works now. Do you know the reason for the odd behaviour?
I think you are tripping over the multi-pass nature of LaTex plus Bibtex. If you look at Step 3 in this discussion, you'll see the following:
The first run (through latex)
generates an auxiliary file,
paper.aux, containing information
about citations (and other types of
references), the bibliography style
used, and the name of the bibtex
database. The second run (through
bibtex) uses the information in the
auxiliary file, along with the data
contained in the bibtex database, to
create a file paper.bbl. This file
contains a thebibliography environment
with \bibitem entries formatted
according to the bibliography style
specified.
So, what I think is happening is that your name_of_my_file.aux file still contains your placeholder \cite{test}. If you remove the auxiliary file, you should be able to start over with:
latex name_of_my_file
bibtex name_of_my_file
latex name_of_my_file
latex name_of_my_file
[Update based on additional info]: The problem was that you had a .aux file with your \cite{} still embedded. The second time that you ran latex, you overrode the old file with the new. That's why the complete set of steps includes an initial latex call, a bibtex call and two follow-up latex calls. Think of it as a multi-pass compiler and it might be more intuitive.
You could have a look at latexmk, which will take care of the fix point compilation for you.
Anyway, you should be able to build the document (pdflatex blah.tex), even if you're missing a bibliography item. The corresponding references will just appear as question marks in the PDF.
Rerun latex to regenerate the aux file.
Have a look at this discussion for pointers to a bit more information. Basically, you may have taken your citation out of the .tex file, but it still exists in one of the derived files (aux, bbl, whatever...)
Check if your bib file has the extension .bib and not .tex.
If it is .tex, just change it to .bib and that should do it.
Once I changed it accidentally to tex, by adding some references, and saving it with the "save as" option, without specifying the bib extension. That's how it can happen all of a sudden.
delete all your .aux and temporal files, re run with latex and then bibtex and then latex twice.

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