How do I list target dependencies in quarto.yml? [help]

[daranzolin]

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Description

In the documentation I read:

tar_quarto() looks for target dependencies in all the source documents (e.g. listed in _quarto.yml)...

How do I specify the dependencies in _quarto.yml? What is the 'key' for the key-value pair? I currently have:

 project:
  post-render:
    - copy_report.R

[joelnitta]

I am honestly not quite sure what the reference to _quarto.yml is about (perhaps parameterized reports?) but generally what I do to load targets built during the workflow into a quarto report is include a chunk with calls to tar_load() and tar_read(), for example like this:

#| label: load
#| message: false
targets::tar_load(model_predictions)
targets::tar_load(model_summaries)

[daranzolin]

I see that's the default way of loading targets, but my qmds are not in the project root, but a Reports directory one level 'deeper.'

So I load my targets like this:

proj_read <- purrr::partial(targets::tar_read, store = path(here(), "_targets"))
model_predictions <- proj_read(model_predictions)
model_summaries <- proj_read(model_summaries)

And so in _targets.R I have:

tar_quarto(my_report, "Reports/my_report.qmd", execute_params = list(...))

But this is leading to some awkwardness and I've also ended up wrapping quarto::quarto_render in some other functions. I thought maybe if specifying the targets in _quarto.yml would be simpler and more elegant.

[joelnitta]

I'm not sure, but I suspect calling tar_read() like that within purrr::partial() could make it tough for targets to detect dependencies.

I've also had problems with quarto documents in nested folders, in particular when trying to get the output rendered to a subfolder.

I tried various things, but found that in the end it was easier to just stick the qmd in the project root and live with it.

[daranzolin]

I was just about to reach the same conclusion! This was my last attempt to preserve my original project structure. Thanks for responding!

[gorkang]

Not sure if this is what you need, but I have qmd reports in subfolders that are fed from other targets:

My _quarto.yml:

project:
  output-dir: outputs
  render:
    - Qmd/REPORT.qmd

_targets.R

  tarchetypes::tar_quarto(NAME_target,
                          path = getwd()
   )

And in a chunk in Qmd/REPORT.qmd

targets::tar_load(DF_raw, store = here::here("_targets/"))

[daranzolin]

Does tarchetypes::tar_knitr_deps("Qmd/REPORT.qmd") return the target dependencies?

[joelnitta]

Cool! This works for me, and I do get the dependency that I loaded with tar_load() in my qmd when I run tarchetypes::tar_knitr_deps().

[joelnitta]

(note that _quarto.yml goes in the project root, and that I don't think you actually need path = getwd() for tarchetypes::tar_quarto(), since it uses the project directory for path by default anyways).

[daranzolin]

This works for me too! I think this is the way to go, I was close with my purrr::partial, but this makes much more sense. Thanks @gorkang !

[Aariq]

I've had some success with putting tar_config_set(store = "../_targets/") at the top of a .qmd not in the root folder, and then just using tar_read() like "normal". Of course, filepaths from targets with format = "file" won't be relative to the .qmd document, so then I do things like include_graphics(tar_read(my_figure) |> fs::path_rel("docs")). I'm still not sure what the "correct" way to do all this is though ('all this' meaning rendering a quarto/rmd doc not in the project root with a targets pipeline while still having the report work well when interactively running code chunks)

[Aariq]

Oh, nope, nevermind. Just realized that doesn't work because it creates a second _targets store when you run the pipeline. 🤦‍♂️. I've also tried using _quarto.yml to set the execute dir to be "project", but I can't remember why that didn't work. Would be nice to have a vignette of how to do this the "right" way.

[daranzolin]

Cosign! Not a huge deal, but it seems reasonable to want your qmd reports in separate directory and write:

tar_quarto(my_report, "Reports/my_report.qmd")

in _targets.R.