...the authors should submit the final version as source files, including a word processor file of the text, such as Word or LateX (If using LaTeX, please use the standard article.sty as a style file and also send a PDF version of the LaTeX file)...
Please what they mean by the standard article.sty, they mean llncs format or which format should I use to write the final version of my paper?
As in the first comment to your question, they mean that you should use the article documentclass if you write in LaTeX. In this case, the first line of your main .tex file would be:
\documentclass[]{article}
with the options (or optional arguments) that you choose, separated by commas, between [ and ].
Here is the user guide to check the options and other matters but no worries about installation: you'll most likely have it included in your LaTeX distribution.
I know that sounds vague. Basically I just want Sublime to highlight custom syntax (color the text), just like it does with native syntax.
I am using Sublime to write LaTeX code. For those that don't know, LaTeX equations are typically enclosed by \[ \], e.g.
\[ E = m c^2 \]
Sublime understands that syntax and colors the enclosing code appropriately.
However, I use my custom defined command, \eq{ ... }, which wraps the \[ \] functionality (so I can globally change some settings by just redefining the \eq definition). e.g.
\eq{ E = m c^2 }
I don't know anything about Sublime under the hood beyond basic key bindings. I want to expand Sublime's understanding of syntax to incorporate my custom command without wasting a ton of time digging through tutorials and such.
Since you are mainly interested in the result and not in the reasoning, I will try to be as straight forward as I can.
The LaTeX syntax of Sublime Text will change in release 3119 and I would recommend to use that, if you want to change something.
Just download it from https://github.com/sublimehq/Packages and put the LaTeX folder into the folder, which opens when you select Preferences >> Browse Packages... in the Sublime Text menu.
Afterwards open the file LaTeX.sublime-syntax and search for ensuremath (LaTeX.sublime-syntax#L498). Duplicate that part (everything with a higher indent) and change the command to the command you wish, e.g. in your example this would be - match: '((\\)eq)(\{)'.
Aside the new syntax removes the highlighting of math environments as strings, because this has lead to several problems.
I made a small entry in the LaTeXTools wiki to explain, how you restore the highlight.
I wrote a draft of a paper in LaTeX. Now my advisor wants the whole thing in Lyx. Equations and all that import just fine using "File -> Import -> LaTeX (plain)" but the natbib references (e.g. \citet{nash1950game}) show us as ERT (evil red text, or LaTeX code in red boxes). Do I have to add all these references manually? Or is there a workaround?
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
As I'm writing Latex more and more on Sublime Text (3), I decide to totally move on to ST from TexnicCenter. However there's one thing I miss from TexnicCenter, that's the ability to show the project in outline view (e.g chapter/subchapter name,...)
For example, writing a long file with one master main.tex file, and each chapter is written in a separate file, TXC gives me this view on the outline panel:
Can I achieve such thing in ST3? (I know about Ctrl + R but it does not help in this case where the chapters are written separately.)
LaTeXing also offers a SHIFT+ Ctrl + R ("Goto Symbol in Project").
LaTeXing actually seems to consider all structure markers such as \chapter{test), irrespective of whether they are \input{} somewhere, so it's not the real logical structure of the document ...
Here's a screen shot:
It's still not just in the command palette, and not a real sidebar of the logical structure and there are some confusing duplications ... but still.
Maybe the folks over at atom latex will get on it at some point; atom might be more suited for this kind of flexible UI.