When writing a new document, I begin from one of these templates. I have found these fundamental to my workflow.

Your preferences may vary.

Use latexmk. It's powerful. My day-to-day use is: 1. write text in Vim; 2. run latexmk -C and latexmk -pdf main in the terminal; 3. ??? profit.

In terms of packages:

• I use MacTeX.
• I use additional LaTeX packages listed here.
• I use mtpro2 as a default font. It is proprietary and requires manual installation.

I use the minted package for code snippets.

I'm a big fan of a custom \draftdisclaimer command when distributing paper drafts to colleagues. See papers/preamble/preamble.tex for its code.

Style nits:

• Don't write the extension to filenames. It's unnecessarily explicit and less readable: use \input{preamble} instead of \input{preamble.tex}, and \includegraphics{figures/edward_calibration} instead of \includegraphics{figures/edward_calibration.pdf}.

• Use PDF-rendered figures, not PNG, so that the text scales with the paper format. You can even go a step further with TiKZ to make plots in LaTeX.

• Use author names in your citation style, not numbers: (MacKay, 1992) instead of [12]. Numbers save space but make it impossible to know what the citation is without tediously crawling back-and-forth. With author names, the citation is part of the sentence, helping substantiate its statement:

  Weakly informative priors such as the Cauchy are often preferred for robustness as they concentrate less probability at the mean thanks to heavier tails (Gelman et al., 2006).

• For notation, take advantage of emphasis, not just Greek alphabet for extra symbols. For example, plain can represent a scalar and boldface (\mathbf) can represent a matrix or vector. I often leave capital letters to represent the event space such as a\in A or constants: number of datapoints N.

I made a rant on Twitter in May 2021. Other nits and style tips are noted there.