Add automatic dates at the end of QC report

[Sal4321]

This is a feature update request which is close to #181 . Can we modify visc_pdf_document function to add an automatic date at the output file so that we don't have to manually add dates everytime we generate a qc report ? Note that we add dates at the end of qc report when we are sending qc reports to the lab. The modification might look something like this:

visc_pdf_document <- function(latex_engine = "pdflatex",
                              keep_tex = TRUE,
                              ...) {
  template <- find_resource("visc_report", "template.tex")

  logo_path_scharp <- find_resource("visc_report", "SCHARP_logo.png")
  logo_path_fh <- find_resource("visc_report", "FredHutch_logo.png")
  logo_path_visc <- find_resource("visc_report", "VISC_logo.jpg")

  # If no project-level bib file creating report specific bib
  if (!file.exists(here::here('docs', 'bibliography.bib'))) {
    file.copy(from = system.file("templates", 'bibliography.bib',
                                 package = "VISCtemplates"),
            to = "bibliography.bib",
            overwrite = FALSE)
   }

  file.copy(from = find_resource("visc_report", "README_PT_Report.md"),
            to = "README.md",
            overwrite = FALSE)

  # Get the current date in the desired format (e.g., YYYY-MM-DD)
  current_date <- format(Sys.Date(), "%Y-%m-%d")

  # Append the date to the output file name
  rmarkdown::render(input = "inputfile", output_file = paste("outputFile",current_date))
  bookdown::pdf_document2(
    template = template,
    keep_tex = keep_tex,
    fig_caption = TRUE,
    latex_engine = latex_engine,
    pandoc_args = c(
      "-V", paste0("logo_path_scharp=", logo_path_scharp),
      "-V", paste0("logo_path_fh=", logo_path_fh),
      "-V", paste0("logo_path_visc=", logo_path_visc)
    )
    ...)
}

I can also suggest how to incorporate it properly here after some tests

[kelliemac]

@asatofh and @mayerbry what do you think about this? My main concerns are 1) whether this will inhibit tracking of changes to pdf documents using git/GitHub, and 2) cluttering people's working directories if they are frequently knitting reports. On the other hand, the only kind of pdf changes we can track with git are a binary did change / did not change, so that's not much different than deleting a file and adding a new one. And if re-knitting a report multiple times within one day, it would just be overwritten, so a new file would only be created on a new working day - which might actually help people see the before/after of their recent changes more easily.

[slager]

There was some discussion this week, and the consensus was that we will think about putting dated QC reports into a separate folder to help organize data-raw/, but probably not implement auto-adding dates to QC reports, since 1) having a date manually added denotes it was manually sent to the lab, and 2) we often re-knit QC reports repeatedly during development, and wouldn't really want to have intermediate reports under development being given automatic dates on each unique day we're working on them. Closing this as "unplanned" for now but this generated some very useful discussion, thanks @Sal4321.

[Sal4321]

Thanks @slager for putting the summary of the discussions !