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.
I am a relatively new IPython Notebook user and I am using IPython 3.2.1. So upfront, my apologies if I did not read some documentation carefully!
I am trying to typeset some LaTeX in my Notebook intended for a presentation. I tried to utilize MathJax capabilities better than what's (supposedly) available by default and so tried incorporating other extensions that come with MathJax explicitly. In particular, I tried getting my IPython Notebook to load AMScd.js, AMSsymbols.js and unicode.js through the following sequence of steps:
Obtain the .js files for these extensions from the latest MathJax (v2.5) source
Add them to my ~/.ipython/nbextensions
Modify custom.js in ~/.ipython/profile_<mine>/static/custom by appending IPython.load_extensions("AMScd"), etc.
Now, all these work fine, and I am able to typeset commutative diagrams nicely in my IPython notebook. So, while at all this, I decided to also include/load AMSmath.js that comes along with MathJax and this is problematic. (To me, this seems like a natural thing to do given that other extensions work well!) However, attempting to include AMSmath.js via IPython.load_extensions("AMSmath") causes LaTeX math in my Notebook to display [Math Processing Error] everywhere. Here's my minimal example and the output with and without including IPython.load_extensions("AMSmath").
Markup:
## A minimal working example
\\[
\Delta u = f \text{ on } \Omega
\\]
(I would totally like to include images here, alas, my not being an active participant in the community here leaves me with not even 10 reputation!)
So, what am I missing here? Why is this inclusion of AMSmath problematic? Any help would be appreciated! Thanks!
It should work without extra configuration. Have a look here.
Your example in a markdown cell should be
(If you want the equation inline you can use $...$)
Inline equation $\Delta u = f \text{ on } \Omega$
(Or if you want the equation centered in their own line you can use $$...$$)
$$\Delta u = f \text{ on } \Omega$$
The result of both snippets in the same markdown cell is rendered as:
How it is loaded?
IPython/Jupyter notebook preloads some MathJax extensions including the extension you want to load. This extension is not an IPYthon/Jupyter extension so it shouldn't work if you try to load this MathJax extension as an IPython/Jupyter extension. See here to know more about how to load other MathJax extensions.
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
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
When I write papers or documentation it makes think using LaTeX or OpenOffice is overkill as I usually only need some markup elements (bold, headlines, lists, ...) . I'd like to write my documents using a wiki style markup as this is very efficient.
For example:
= Introduction =
'''HTML''' is a markup language...
In the end I'd like to simply convert it to PDF. (Cross-platform was nice too.)
compiler.exe -pdf input.wiki output.pdf
Is there a tool (or simple tool chain) to do this job?
I'd personally like to not make use of LaTeX as a transformation step. There are tools doing this job transforming lightweight syntax to TeX and then to PDF/PS.
You might find that MarkDown gets pretty close to what you want.
MarkDown is a simple technique for marking up text files so that they can be post-processed into other forms. One of the nice things about MarkDown is their goal that a marked-up document should be simply readable as a straight text file:
The overriding design goal for
Markdown’s formatting syntax is to
make it as readable as possible. The
idea is that a Markdown-formatted
document should be publishable as-is,
as plain text, without looking like
it’s been marked up with tags or
formatting instructions.
PanDoc looks like it might be good companian tool to convert the MarkDown straight into PDF files. There may well be other choices - PanDoc is just the best tool I found with a quick Google search.
reStructuredText.
You can use Sphinx to generate HTML and LaTeX (and later PDF with pdflatex).
There is also rst2pdf, don't know if it's mature.
You could use Markdown (example) and then use Pandoc (which also works with reStructuredText and several other wiki-like syntaxes) to convert to PDF.