I just submitted a paper where I tried to follow my own advice to cite the code you use. This project was done with R, which makes it really easy to automatically generate citations for packages. With just a bit of glue code you can automatically generate in-text citations, too.

If you’re using papaja to prepare your manuscript in APA format, you can use the cite_r command to automatically generate citations for R and loaded packges (or any list of packages you want). I’m not using papaja because I’m a control freak and find it a thrill to wrestle with RMarkdown, pandoc, and various latex dialects all on my own, but it’s actually quite easy to implement this feature yourself:

library(glue)
library(knitr)

packages = c(
  'base',
  'knitr',
  'rmarkdown',
  # ... etc.
)

knitr::write_bib(packages, file="packages.bib", prefix="R-")

# generate in-text citations (skip base which is cited manually)
citation_strings <- glue("`{pkg}` [@R-{pkg}]", pkg=packages[-1])
# join with ", " and ", and " for last
citation_string <-
  str_c(
    lift(str_c)(
      head(citation_strings, -1), sep=", "
    ),
    ", and ",
    tail(citation_strings, 1)
  )

Then in the RMarkdown source you can do something like:

I am also indebted to the developers and maintainers of the R
language [@R-base], as well as the following R packages:
`r citation_string`.

This isn’t as fancy as the papaja version which also generates the loaded versions as well, but it gets the job done. You can omit the list of packages and knitr::write_bib will do all the packages you have loaded.