Question: I want to start writing on an article that is probably going to be published in one of the IOP journals. There is a template for their publications, but it lacks some (for me) essential packages. Since I've never submitted an article myself, I want to be sure the editing process goes as smooth as possible by eliminating problems early. So here's the question:

Can I add all the packages I like to the template without pissing off the editor? I talk about things like `inputenc`, `fontenc`, `biblatex`, `microtype`, etc. Nothing fancy, but very basic LaTeX stuff. I also prefer to have a separate `.bib` file for my bibliography, since I have them already organized that way and do not want to manually copy the info into the bibliography as suggested in the template.

I already read the guidelines for authors and there was no mention of modifying the template, only that its use is highly appreciated. 

If anyone could provide any (preferrably inside info) on how editors work with submitted LaTeX files, that would help a lot! Thanks.

Answer: 
I usually publish in IOP journals and I can confirm [O. R. Mapper's](https://academia.stackexchange.com/a/73074/20058) remarks.

As an example, these are the packages included in a recent paper of mine:

```
\documentclass[10pt,a4paper]{iopart}
\usepackage[utf8]{inputenc}
\usepackage[T1]{fontenc}
\usepackage{iopams}
\usepackage{amsopn}
\usepackage{graphicx}
\usepackage{cite}
\usepackage{siunitx}
\usepackage{tikz}
\usepackage{array}
\usepackage{subfigure}
\usepackage{longtable}
\usepackage{listings}

```

Notice that for what concerns mathematics, there are a few idiosyncrasies related to the `iopart` class: e.g., this class is incompatible with the `amsmath` package, and it is suggested to use the `eqnarray` environment, which is otherwise deprecated. I thus suggest a careful reading of the IOP LaTeX guidelines, which can be found [here](ftp://ftp.iop.org/pub/journals/latex2e/IOPLaTeXGuidelines.pdf).

A few notes on the example above:

* The package `iopams` is an extension for `amssymb` to provide
predefined names for bold greek letters (thanks to Barbara Beeton for
pointing out this and Canageek for reporting it here).
* The package `subfigure` is obsolete but the the newer `subfig` package seems to be incompatible with `iopart` because it includes the `caption` package.
If these packages do not interfere with the paper layout than it is completely OK. However you should follow the instructions for authors style guidelines. For instance, if the template uses a specific package for generating tables, then you shouldn't change it. 
Regarding the bibliography I think that it is allowed to use bibtex and derivatives as long as the paper references style is preserved.