Submitting a journal article as a single tex file

Background: I think that Submitting a journal article as a single tex file is potentially a great question (it already has 10 upvotes), but I think it could do with a little polishing. I don't want to send it to CW inadvertently, and I want to check my edits with the original author, so I'm using this place as a "sandbox" to test my edits. Others are welcome to edit as well - I'm making this copy CW! If we can come up with a version that captures the original spirit and focusses the question, and the original author is happy with, then someone can copy it across to the original.

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 in to 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?

• Blast! I forgot that I can't make this CW by myself... have to wait for a moderator. – Loop Space Mar 4 '11 at 8:52
• @Andrew: You can, but it takes about an hour: Just edit it 10 (or 11?) times :-) – Hendrik Vogt Mar 4 '11 at 10:20
• @Hendrik: ha, ha. Fortunately a helpful moderator saved me the effort. – Loop Space Mar 4 '11 at 10:21
• Andrew, @Hendrik: It's funny that it can't be made CW by the original author afterwards. I CWed if for you Andrew. – Martin Scharrer Mar 4 '11 at 10:47
• @Martin: That's status-by-design, I'm afraid (see meta.SO for details). Only mods can make posts CW now (and thanks for doing so). On the main site, it makes a bit of sense, but here it's not so useful. It does mean that there's no place to do what I'm trying to do here. On MathOverflow's meta (which is a proper forum) we have a category "Is this question acceptable?" and sometimes people ask a question there first to get some feedback before posting it on the main site. – Loop Space Mar 4 '11 at 11:10
• @Andrew: I knew it is {status-by-design}, but I still think it is funny :-) – Martin Scharrer Mar 4 '11 at 11:41
• @Andrew: A stupid comment, but does one really have to keep those space-consuming breaks after "2.2" and "2.3" (that are also in the referred source)? I saw that they were gone at some stage and Faheem reintroduced them, but I think that when citing one doesn't have to adhere to strange layout decisions. – Hendrik Vogt Mar 4 '11 at 13:17
• @Hendrik: Is that better? – Loop Space Mar 4 '11 at 13:37
• CWify such questions: The bit that wants collaborative editing could be posted as an answer, no moderator intervention needed. – Charles Stewart Mar 4 '11 at 18:45
• @Andrew:(and others) Does "That all unnecessary macros be removed." cover all possibilities? Biomed uses the terminology "not rely on any non-standard macros, classes or files". I'm not sure how general the term "macro" is in a TeX context. – Faheem Mitha Mar 5 '11 at 5:05
• "That the submission be a single file," may not be accurate. It may be more correct to say that the submission is typically required to have only one TeX/LaTeX file (if this is indeed the case). So additional style or macro files are not allowed if nonstandard. However, for example PDF figure files are allowed (are there journal that don't allow these)? Also some form of bibliography file is typically allowed? – Faheem Mitha Mar 5 '11 at 5:47
• My field tends not to submit to journals, so I've never had to deal with this myself. I wonder what would happen if your single file consisted of a bunch of filecontents environments followed by the \documentclass. There's nothing quite like following the letter of the rule but not the spirit. =) – TH. Mar 19 '11 at 11:22
• @TH. You should post that as an answer to the real question on the main site. – Loop Space Mar 19 '11 at 16:48
• I just wrote another answer to "Submitting a journal article as a single tex file", which might be interesting also for this question here: tex.stackexchange.com/questions/12554/… – Stephen Sep 12 '11 at 16:58