[Bug]: 'output_and_quantities' chunk in skeleton missing line to load in model results

[sbreitbart-NOAA]

Describe the bug

When create_template() is run with rerender_skeleton = TRUE and the model results are added, the 'output_and_quantities' chunk in the skeleton is missing the line to load in model results and the code below that doesn't work.

Describe how to reproduce the bug

Example from the NSAW workshop:

create_template(
    format = "pdf",
    type = "SAR",
    office = "NWFSC",
    region = "U.S. West Coast",
    species = "Petrale sole",
    spp_latin = "Eopsetta jordani",
    authors = c("Samantha Schiano" = "OST", "Jane Doe" = "SWFSC-LJCA"),
    file_dir = getwd()
)

petrale <- stockplotr::convert_output(
    file.path("example_output", "Report.sso"),
    save_dir = file.path(getwd(), "report", "petrale_conout.rda"))

asar::create_template(
    rerender_skeleton = TRUE,
    file_dir = file.path(getwd(), "report"),
    authors = c("John Doe"="NEFSC"),
    model_results = file.path(getwd(), "report", "petrale_conout.rda"),
    custom = TRUE,
    new_section = "Changes to the Model",
    section_location = "after-introduction"
)

Screenshots

The top of the 'output_and_quantities' chunk:

#| label: 'output_and_quantities'
#| warning: false 
#| eval: true 
#| include: false
# load converted output from stockplotr::convert_output() 

# Call reference points and quantities below 
output <-file.path(getwd(), "report", "petrale_conout.rda") |>
  dplyr::mutate(estimate = as.numeric(estimate), 
    uncertainty = as.numeric(uncertainty))
source("preamble.R") 
# Available quantities
start_year
...

Which OS are you seeing the problem on?

Windows

Which version of asar are you seeing the problem on?

2.0.1

Additional Context

No response

[Schiano-NOAA]

I tested this a little and realized that this functionality works properly when you select to replace the preamble. Imo, this makes sense because if there are results already presented and then we don't want to overwrite that. Also there is the assumption that results are present if there are customizations to the preamble and we want to replace the preamble when adding new results.

A future development to improve this would be to allow model_results to replace the current output file when rerendering, but I think this operates as expected.

[Schiano-NOAA]

@sbreitbart-NOAA can you retest this then lmk if it works as intended? I think this issue can be closed out.

[sbreitbart-NOAA]

Yes, now that you mention that the preamble should be replaced, this does work as expected. I think a small change that would clarify what's going on, behind the scenes, for users would be to alter the console message from "Do you want to keep the current preamble? (Y/N)" to "Update the preamble to match entered arguments? (Y/N)"

[Schiano-NOAA]

Good idea. I will leave this open and mark it for future development