Submitting a journal article as a single tex file

Question

Although many academic journals readily accept submissions in some format of TeX, indeed some enlightened ones insist on it, it is rare that one can simply send exactly the same document that one has been working on as a submission. Most journals insist on authors using their "house class file", and some have specific style files that define "common macros". Some journals further make one or both of the following demands:

1. That the submission be a single file,
2. That all unnecessary macros be removed.

For example in BioMed Central TeX template files (the linked page seems to be an unofficial copy, but I could not find an official one online), Sections 2.2 and 2.3 say:

2.2: In order to submit a manuscript as a .tex file to BioMed Central, you must

• use the BioMed Central template
• format your references with BibTeX using the bmc_article.bst style file
• not rely on any non-standard macros, classes or files

2.3: Make sure that you only a single .tex document for the entire manuscript, as you will need to upload it as a single file (together with its associated formatted bibliography file). Do not use the \input command to include other .tex files.

Obviously, some journals adhere to these more strictly than others and the first thing to do is to determine whether these requests are enforced or not (and what, exactly, is considered "non-standard"). So let us suppose that this has been done and the answer is: yes, these are enforced. Then the question is: how does one do this?

In all likelihood, there is not a simple answer, in which case it will be extremely valuable to know what strategies and workflows others have employed. (But please do not name-and-shame journals who make these requests. It may not be the journal but the publisher, and I'm sure that the journals could provide equally horrific stories of the TeX-mangling that they've received.)

One thing to take note of is that the additional files may not just be style files or bibliography files but images as well. For example, in the BioMed instructions given above, the reason given for this request is that the upload is to be a single file (and let us, for the sake of argument, assume that archived files are not allowed).

Thus we can divide this into various scenarios:

1. The journal asks that the submission contain only one TeX file. So image files and bibliography files are fine as extras. We assume also that it is possible to identify which extra files should be included, but they may be a combination of user-written style files and packages downloaded from CTAN. The task is to fold all of these in to a single file. How do we make these in to a single file, and what pitfalls are there to be aware of?

2. The journal asks that the submission contain only one file in total. Now we wish to embed non-standard type files into our TeX file. Is this possible? and if so, how, and what pitfalls are there to be wary of?

3. The journal asks that unnecessary macros/commands be removed. Are there any strategies for going through a document and identifying those commands which have been defined but never used?

Answer 1

I'll start the ball rolling on this one. Two simple things:

1. If copying some style files in to ones preamble when using LaTeX, put \makeatletter beforehand and \makeatother afterwards (see What do \makeatletter and \makeatother do? for more details on these).

2. The cmdtrack package can be useful in figuring out which commands that have been defined have actually been used. It has some limitations (It can only check commands that have been defined using \newcommand, \newenvironment, and a few others, but not \def and its friends).

Answer 2

Regarding

2. The journal asks that the submission contain[s] only one file in total.

the bundledoc package comes to mind:

The bundledoc package is a post-processor for the snapshot package that bundles together all the classes, packages and files needed to build a given LaTeX document.

Answer 3

An alternative is arlatex. You have to specify the dependencies explicitly, I think, but it bundles them all up in one plain latex file which you can then upload and running latex on the resulting file will automatically extract the dependencies locally.

(See Martin Scharrer's answer to my question here.)

Answer 4

For scenarios 1 & 2 I have gathered from bits and pieces and added some stuff in a python script TexPublish, that automates many things with regards to the publication process:

• creates a new directory for publishable files
• copies files matching user defined regular expressions to the new directory
• copies all desired files that are used by the main tex document (like figures and tables)
• creates a parsed bibliography that includes only entries used by the main tex file
• flattens the tex file (inserts \input and \include commands and custom preambles in the main tex file)
• pastes the parsed bibliography to the flattened tex file if desired
• removes all comments from main tex file if desired
• BONUS: possibility to include/exclude desired versions (unrobust and requires customizing in the tex-file)

It is a bit hacky and might require some customization (but is also relatively simple to customize), but nonetheless does everything you need in one go and without any installations if you already use python.

Any suggestions for improvements are welcomed.

Usage:

A. In preamble of your tex file:

\RequirePackage{snapshot} 
% ..before documentclass[<options>]{<document class>}
% it will create a .dep file of the dependencies

%For equations (optional)
# \usepackage[active,generate=equations,extract-env={equation,align}]{extract}
%"generate" parameter is the name of the output .tex-file

B. Customize the file. At least:

include_bibliography_in_main_tex_file=True # False
EXTENSIONS = ['pdf', 'pdf_tex', 'png','tex'] # Which files used by main tex file to copy ?
# Regexes in the copy_non_floats() function calls (at least main tex file and bibliography)

C. Run with:

cd <YOUR DIRECTORY>
python TexPublish.py
# or directly from the file

BONUS Refer to the TexPublish code, under "Latex depencies" to include or exclude different versions of the file in the flattened file.