What is the best approach to merging latex generated from nbconvert with other latex? In my case I have several company specified forms (which I have latex for) that I want to merge with the notebook/nbconvert generated latex. And, I want to follow the company template for headers/footers/page numbering/table of contents, etc. (these are already available in a latex project).
So with my very basic understanding, I see two possible approaches. Are either viable or is there something else that I am missing?
1) ipython notebook centric - is there a way to modify the preamble to include all the packages and other stuff that my forms need? Company header/footer? etc
or
2) including ipython nbconvert output as part of an external latex project with an include. Is there a way to break out the preamble stuff that nbconvert generates?
I don't have a good handle on how nbconvert pulls together the pieces. So, any adivce or information on how nbconvert deals with latex would be much appreciated.
Both 1) and 2) are possible. You can generate the most basic latex with nbconvert using the base template --template=base and insert that into your own company latex. You can even override existing blocks (cf Jinja Documentation) to extend and/or replace existing blocks. Cf this Old and not up to date explanation
Related
I'm trying to use lua filters to capture images in my manuscript and list their caption in a special \section at the end of it.
I am working on a rmarkdown document that itself uses a .tex template.
I wasn't able to get anywhere, so I run a very simple filter:
function Header (head) print(pandoc.utils.stringify(head)) end
and noticed that just the headers in the markdown were recognized, not the ones in the ones in the template.
The only way I found to have lua filters recognize the elements in the template was to rerun the produced .tex file with pandoc:
pandoc -f latex -t latex -o test2.tex --lua-filter=my_filters.lua test.tex
but that removed all latex formatting and structure content outside the body, e.g., \documentclass, \usepackage and other custom commands. So it's a no go.
So the question is, is there a way to force lua filter to be applied after the integration of a latex template when knitting a rmarkdown document?
There might be a way, but it most likely won't do what you need.
When pandoc reads a document, it parses it and converts it into it's internal data structure. That internal structure can then be modified with a filter. LaTeX is a very expressive and complex document format, and any conversion from LaTeX into pandoc's internal format will result in a loss of (layout) information. That's good enough in most cases, but would be a problem in your case.
There are two possible ways to do this: one is to post-process the output, which is probably tedious and error-prone. The other is to find a way to generate the desired output, e.g. via a pandoc filter, without adding it to the template first.
I believe your other question is the right way to go.
What is the best way to take care of citations in Ipython Notebook? Ideally, I would like to have a bibtex file, and then, as in latex, have a list of shorthands in Ipython markdown cells, with the full references at the end of the notebook.
The relevant material I found is this: http://nbviewer.ipython.org/github/ipython/nbconvert-examples/blob/master/citations/Tutorial.ipynb
But I couldn't follow the documentation very well. Can anyone explain it? Thanks so much!!
Summary
This solution is largely based on Sylvain Deville's excellent blog post. It allows you to simply write [#citation_key] in markdown cells. The references will be formatted after document conversion. The only requirements are LaTeX and pandoc, which are both widely supported. While there is never a guarantee, this approach should therefore still work in many years time.
Step-by-Step Guide
In addition to a working installation of jupyter you need:
LaTeX (installation guide).
Pandoc (installation guide).
A citation style language. Download a citation style, e.g., APA. Save the .csl file (e.g., apa.csl) into the same folder as your jupyter notebook (or specify the path to the .csl file later).
A .bib file with your references. I am using a sample bib file list.bib. Save to the same folder as your jupyter notebook (or specify the path to the .bib file later).
Once you completed these steps, the rest is easy:
Use markdown syntax for references in markdown cells in your jupyter notebook. E.g., [#Sh:1] where the syntax works like this: ([#citationkey_in_bib_file]). I much prefer this syntax over other solutions because it is so fast to type [#something].
At the end of your ipython notebook, create a code cell with the following syntax to automatically convert your document (note that this is R code, use an equivalent command to system() for python):
#automatic document conversion to markdown and then to word
#first convert the ipython notebook paper.ipynb to markdown
system("jupyter nbconvert --to markdown paper.ipynb")
#next convert markdown to ms word
conversion <- paste0("pandoc -s paper.md -t docx -o paper.docx",
" --filter pandoc-citeproc",
" --bibliography="listb.bib",
" --csl="apa.csl")
system(conversion)
Run this cell (or simply run all cells). Note that the 2nd system call is simply pandoc -s paper.md -t docx -o paper.docx --filter pandoc-citeproc --bibliography=listb.bib --csl=apa.csl. I merely used paste0() to be able to spread this over multiple lines and make it nicer to read.
The output is a word document. If you prefer another document, check out this guide for alternative syntax.
#Extras
If you do not like that your converted document includes the syntax for the document conversion, insert a markdown cell above and below the code cell with the syntax for the conversion. In the cell above, enter <!-- and in the cell below enter -->. This is a regular HTML command for a comment, so the syntax will in between these two cells will be evaluated but not printed.
You can also include a yaml header in your first cell. E.g.,
---
title: This is a great title.
author: Author Name
abstract: This is a great abstract
---
You can use the Document Tools of the Calico suite, which can be installed separately with:
sudo ipython install-nbextension https://bitbucket.org/ipre/calico/downloads/calico-document-tools-1.0.zip
Read the tutorial and watch the YouTube video for more details.
Warning: only the cited references are processed. Therefore, if you fail to cite an article, it won't appear in the References section. As a little working example, copy the following in a Markdown cell and press the "book" icon.
<!--bibtex
#Article{PER-GRA:2007,
Author = {P\'erez, Fernando and Granger, Brian E.},
Title = {{IP}ython: a System for Interactive Scientific Computing},
Journal = {Computing in Science and Engineering},
Volume = {9},
Number = {3},
Pages = {21--29},
month = may,
year = 2007,
url = "http://ipython.org",
ISSN = "1521-9615",
doi = {10.1109/MCSE.2007.53},
publisher = {IEEE Computer Society},
}
#article{Papa2007,
author = {Papa, David A. and Markov, Igor L.},
journal = {Approximation algorithms and metaheuristics},
pages = {1--38},
title = {{Hypergraph partitioning and clustering}},
url = {http://www.podload.org/pubs/book/part\_survey.pdf},
year = {2007}
}
-->
Examples of citations: [CITE](#cite-PER-GRA:2007) or [CITE](#cite-Papa2007).
This should result in the following added Markdown cell:
References
^ Pérez, Fernando and Granger, Brian E.. 2007. IPython: a System for Interactive Scientific Computing. URL
^ Papa, David A. and Markov, Igor L.. 2007. Hypergraph partitioning and clustering. URL
I was able to run it with the following approach:
Insert the html citation as in the tutorial you mentioned.
Create ipython.bib in the "standard" bibtex format. It goes into the same file as your *.ipynb notebook file.
Create the template file as in the tutorial, also in the same directory or else in the (distribution dependent) directory with the other templates. On my system, that's /usr/local/lib/python2.7/dist-packages/IPython/nbconvert/templates/latex.
The tutorial has the template extend latex_article.tplx. On my distribution, it's article.tplx (without latex_).
Run nbconvert with --to latex; that generates an .aux file among other things. Latex will complain about missing references.
Run bibtex yournotebook.aux; this generates yournotebook.bbl. You only need to re-run this if you change references.
Re-run nbconvert either with --to latex or with --to pdf. This generates a .tex file, or else runs all the way to a .pdf.
If you want html output, you can use pandoc to assemble the references into a tidy citation page. This may require some hand-editing to make an html page you can reference from your main document.
If you know that you will be converting your notebook to latex anyway, consider simply adding a "Raw" cell (Ctrl+M R) to the end of the document, containing the bibliography just as you would put it in pure LaTeX.
For example, when I need to reference a couple of external links, I would not even care to do a proper BibTeX thing and simply have a "Raw" cell at the end of the notebook like that:
\begin{thebibliography}{1}
\bibitem{post1}
Holography in Simple Terms. K.Tretyakov (blog post), 2015.\\
\url{http://fouryears.eu/2015/07/24/holography-in-simple-terms/}
\bibtem{book1}
The Importance of Citations. J. Smith. 2010.
\end{thebibliography}
The items can be cited in other Markdown cells using the usual <cite data-cite="post1">(KT, 2015)</cite>
Of course, you can also use proper BibTeX as well. Just add the corresponding Raw cell, e.g:
\bibliographystyle{unsrt}
\bibliography{papers}
This way you do not have to bother editing a separate template file (at the price of cluttering the notebook's HTML export with raw Latex, though).
You should have a look at the latex_envs extension in https://github.com/ipython-contrib/IPython-notebook-extensions (install from this repo, it is the most recent version). This extension contains a way to integrate bibliography using bibtex files and standard latex notation, and generates a bibliography section at the end of the notebook. Style of citations can be (to some extent) customized. Some documentation here https://rawgit.com/jfbercher/latex_envs/master/doc/latex_env_doc.html
I have a "project book" which uses LaTeX's \documentclass{report} ("report" is like a more compact version of \documentclass{book}). I would like to include into this book an appendix with the Doxygen-generated API documentation for the software in the project.
I have achieved this by setting Doxygen's config options LATEX_HEADER and LATEX_FOOTER to an empty file. This makes the resulting latex/refman.tex have top level commands like: \section{\-Namespace \-Index}, at which point I can wrap this with a top level document like:
\documentclass{report}
\usepackage{doxygen.sty}
% the "import" package helps to find Doxygen files in the latex/ subdirectory
\usepackage{import}
% [...] title page and the rest of the book
\appendix
\chapter{API reference (generated by Doxygen)
subimport{latex/}{refman.tex}
% [...] final stuff
\end{document}
This works reasonably well and I get doxygen.sty with this special doxygen invocation:
doxygen -w latex /dev/null /dev/null doxygen.sty
One problem is that this puts an "autogenerated" header on the entire document (not just on the doxygen appendix). I can get rid of this by editing doxygen.sty (I also rename it for my inclusion, actually) and commenting out the block that starts with % Setup fancy headings.
At this point I have something I can live with, but I would like to go one step further: the "doxygen" style modifies a lot of other aspects of the LaTeX document style, and I like it less.
So my question is (in two levels of excellence):
What would be a minimal set of LaTeX commands to put in a doxygen.sty file that would nicely render the doxygen appendix but not interfere with the rest of the LaTeX document?
Even better, has someone come up with a way of doing
\usepackage{doxygen_standalone}
% [... until you need doxygen]
\begin{doxygen}
% the stuff you need to insert your auto-generated doxygen API docs,
% for example the \subimport{latex/}{refman.tex} that I showed above
\end{doxygen}
This last approach is one I would consider very clean.
I'm hoping there is a really simple answer, such as "this already exists in doxygen.sty as an option, and you missed it!"
rename doxygen.sty to mydoxygen.sty, then modify it by inserting
\newenvironment{doxygen}{... most of doxygen.sty goes here ...}{}
I have fairly large Latex document with a lot of TikZ figures inside. I have a habit of frequent recompilation and it takes forever to compile it using pdflatex. Figures in TikZ take most of the time.
My question is what is the best way to split the document into separate tex files (figures/chapters) to achieve separate compilation of figures and chapters, separate chapter pdfs, and a whole document pdf file ?
Have you tried compiling each picture on its own and then including them in your tex file as pdf rather than the tikz code? You can use the package standalone so that the picture will be the exact size you need. So :
\documentclass{standalone}
\usepackage{tikz,pgf} %and any other packages or tikzlibraries your picture needs
\begin{document}
\begin{tikzpicture}
%your tikz code here
\end{tikzpicture}
\end{document}
The good thing about this is that you can either include the compile this document directly to get a pdf figure to include in your document, or you can use the command \input to include it in your main document as a tikz code by adding
\usepackage{standalone}
in your main document (together with the tikz packages and libraries), and then
\begin{figure}
\input{tikzfile.tex}
\end{figure}
There is a possibly better way (imho) to cache tikz-pictures. Add the following lines in your
preamble:
\usetikzlibrary{external}
\tikzexternalize[prefix=i/]
After a pdflatex-run you'll see all pictures in the subdirectory ./i .
If you update the code of a tikz-picture simply throw away its corresponding pdf-file and it will be regenerated. For more info see the manual of PFG/TikZ section 32.4 Externalizing Graphics
and possibly 32.5 Using External Graphics Without pgf Installed.
How about putting each chapter in a separate file and then using \include to put them into some master file? Then you can use \includeonly to only compile the chapter you're currently working on. That should save some time at least.
I expect some sort of makefile based solution would be even better than this, but I don't know anything about makefiles...
The way I generally do this is to apply Latex to just part of the file: Emacs and several other Latex editors allow you to compiler regions: with Auctex, you can run TeX-pin-region to specify the current chapter, and then TeX-command-region to run Latex on the selected region.
The traditional way to do this is cut parts of the big file into smaller parts that are \included, and then either comment out parts you don't want to work on, or put some macrology at the beginning and end of each file that allows them to be compiled separately.
I'm using the MLA authoring style. I would like to print out a bibliography subdivided into different sections. I also want annotations on each source. Is this possible with BibLaTeX? Should I just do it manually?
Yes, I think you can do that with Biblatex, but I think you should still just do it manually.
Note, though, that you are probably wanting to craft your notes differently for each citation from one paper to the next, which leads to the question: why use Bibtex at all? You can generate a Bibtex file the usual way, until all the references are there, then cut&paste the .bbl file into place in your Latex file, and annotate and reformat away to your heart's content.
So I think that Bibtex makes sense as a standard repository of the basic facts about citations you might make again and again: in particular you can get it error-free; my experience as a scientific editor is that most authors are sure that their bibliographies are error-free, most have between 10% and 60% of entries having errors in them. Latex users tend to be better that Word users in this respect, and I think that it is because of Bibtex.
Caveat: you will need to mess about with the thebibliography environment to do this. But that is another question... Also, if there are errors in your Bibtex file, you will need to correct them in two places.
Why I don't like Biblatex: the Bibtex prepresentation is a standard, and is accepted by all kinds of other document processors. You shouldn't put special Latex formatting into your bibliographic database: that will reduce the utility of that database. For m in particular, I use both Latex and Context: both use Bibtex, but only Latex uses Biblatex.
I managed to write a quite nice MLA-style bibliography with bibtex and the style provided by the Reed College (which is based on Natbib), and BibUnits to subdivide the entries in sections (as discussed here)
(let me know if you have any tips with MLA styles, my paper is not finished yet)
EDIT: my answer was for standard bibtex, not biblatex, sorry
yes, you can do it easily with biblatexwith the headings:
For instance:
\defbibheading{general}{\section*{General Architecture}}
\defbibheading{european}{\section*{European Architecture}}
\printbibliography[heading=general,keyword=general]
\printbibliography[heading=european,keyword=european]
and add the relevant keywords={architecture} keywords={general} in your *.bib files
Here is a biblatex MLA-style, if you need biblatex-mla (and a related question, you may also face this problem)