create_format_terra_vect: temp fix for issue with replacing function body and {covr}

[brownag]

This is a workaround for replacement of a function body not working properly within the evaluation environment created by covr, targets tests, and testthat.

More commentary in new issue #38

[njtierney]

I wonder if we even actually need to modify the function body directly? I'm fairly sure those parts will be evaluated appropriately?

E.g.,

example_funfun <- function(sep_type){
  .write_fun <- function(object, file){
    # loudly declare the quote type when writing
    readr::write_lines(x = object,
                       file = file,
                       sep = sep_type)
    cat("Hi! The separation marker is: '", sep_type,"'", sep = "")
    cat("\n")
    cat("We wrote the file out to:\n", file, sep = "")
  }
  
  return(
    list(
      read = readr::read_csv,
      write = .write_fun
    )
  )
  
}

my_example <- example_funfun(",")

# sep_type isn't evaluated yet
my_example$write
#> function(object, file){
#>     # loudly declare the quote type when writing
#>     readr::write_lines(x = object,
#>                        file = file,
#>                        sep = sep_type)
#>     cat("Hi! The separation marker is: '", sep_type,"'", sep = "")
#>     cat("\n")
#>     cat("We wrote the file out to:\n", file, sep = "")
#>   }
#> <environment: 0x12a2669e0>

# but sep_type gets evaluated later when the function is used:
my_example$write(
  object = "1,2,3,4", 
  file = tempfile(fileext = ".csv")
  )
#> Hi! The separation marker is: ','
#> We wrote the file out to:
#> /var/folders/9c/k3wqmhhx4qsb3fd66n4prhlw0000gq/T//RtmpUdvv1a/file104a0120aafb7.csv

^{Created on 2024-03-16 with reprex v2.1.0}

Session info

sessioninfo::session_info()
#> ─ Session info ───────────────────────────────────────────────────────────────
#>  setting  value
#>  version  R version 4.3.3 (2024-02-29)
#>  os       macOS Sonoma 14.3.1
#>  system   aarch64, darwin20
#>  ui       X11
#>  language (EN)
#>  collate  en_US.UTF-8
#>  ctype    en_US.UTF-8
#>  tz       Australia/Hobart
#>  date     2024-03-16
#>  pandoc   3.1.1 @ /Applications/RStudio.app/Contents/Resources/app/quarto/bin/tools/ (via rmarkdown)
#> 
#> ─ Packages ───────────────────────────────────────────────────────────────────
#>  package     * version date (UTC) lib source
#>  bit           4.0.5   2022-11-15 [1] CRAN (R 4.3.0)
#>  bit64         4.0.5   2020-08-30 [1] CRAN (R 4.3.0)
#>  cli           3.6.2   2023-12-11 [1] CRAN (R 4.3.1)
#>  crayon        1.5.2   2022-09-29 [1] CRAN (R 4.3.0)
#>  digest        0.6.34  2024-01-11 [1] CRAN (R 4.3.1)
#>  evaluate      0.23    2023-11-01 [1] CRAN (R 4.3.1)
#>  fansi         1.0.6   2023-12-08 [1] CRAN (R 4.3.1)
#>  fastmap       1.1.1   2023-02-24 [1] CRAN (R 4.3.0)
#>  fs            1.6.3   2023-07-20 [1] CRAN (R 4.3.0)
#>  glue          1.7.0   2024-01-09 [1] CRAN (R 4.3.1)
#>  hms           1.1.3   2023-03-21 [1] CRAN (R 4.3.0)
#>  htmltools     0.5.7   2023-11-03 [1] CRAN (R 4.3.1)
#>  knitr         1.45    2023-10-30 [1] CRAN (R 4.3.1)
#>  lifecycle     1.0.4   2023-11-07 [1] CRAN (R 4.3.1)
#>  magrittr      2.0.3   2022-03-30 [1] CRAN (R 4.3.0)
#>  pillar        1.9.0   2023-03-22 [1] CRAN (R 4.3.0)
#>  pkgconfig     2.0.3   2019-09-22 [1] CRAN (R 4.3.0)
#>  purrr         1.0.2   2023-08-10 [1] CRAN (R 4.3.0)
#>  R.cache       0.16.0  2022-07-21 [2] CRAN (R 4.3.0)
#>  R.methodsS3   1.8.2   2022-06-13 [2] CRAN (R 4.3.0)
#>  R.oo          1.26.0  2024-01-24 [2] CRAN (R 4.3.1)
#>  R.utils       2.12.3  2023-11-18 [2] CRAN (R 4.3.1)
#>  R6            2.5.1   2021-08-19 [1] CRAN (R 4.3.0)
#>  readr         2.1.5   2024-01-10 [1] CRAN (R 4.3.1)
#>  reprex        2.1.0   2024-01-11 [2] CRAN (R 4.3.1)
#>  rlang         1.1.3   2024-01-10 [1] CRAN (R 4.3.1)
#>  rmarkdown     2.25    2023-09-18 [1] CRAN (R 4.3.1)
#>  rstudioapi    0.15.0  2023-07-07 [1] CRAN (R 4.3.0)
#>  sessioninfo   1.2.2   2021-12-06 [2] CRAN (R 4.3.0)
#>  styler        1.10.2  2023-08-29 [2] CRAN (R 4.3.0)
#>  tibble        3.2.1   2023-03-20 [1] CRAN (R 4.3.0)
#>  tidyselect    1.2.0   2022-10-10 [1] CRAN (R 4.3.0)
#>  tzdb          0.4.0   2023-05-12 [1] CRAN (R 4.3.0)
#>  utf8          1.2.4   2023-10-22 [1] CRAN (R 4.3.1)
#>  vctrs         0.6.5   2023-12-01 [1] CRAN (R 4.3.1)
#>  vroom         1.6.5   2023-12-05 [1] CRAN (R 4.3.1)
#>  withr         3.0.0   2024-01-16 [1] CRAN (R 4.3.1)
#>  xfun          0.42    2024-02-08 [1] CRAN (R 4.3.1)
#>  yaml          2.3.8   2023-12-11 [1] CRAN (R 4.3.1)
#> 
#>  [1] /Users/nick/Library/R/arm64/4.3/library
#>  [2] /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library
#> 
#> ──────────────────────────────────────────────────────────────────────────────

Or is there some deeper stuff happening with targets here?

[brownag]

I don't think that will work, or at least I tried it before arriving at the body<- solution I proposed in #11 here. Tried doing it again now because I hoped I had missed something.

What you propose works fine interactively in your global environment, or in a reprex, etc. but the context where those tar_format() functions get evaluated you will not have the e.g. sep_type object defined.

Essentially the functions tar_format() uses need to be self-contained, not relying on the prior parent frame. You actually want sep_type to be evaluated sooner as it is when we modify the function body.

If you implement your suggestion for tar_terra_rast() you will get something like this:

Loading required namespace: terra
▶ dispatched target test_terra_rast
✖ errored target test_terra_rast
✖ errored pipeline [0.13 seconds]
Error:
! Error running targets::tar_make()
Error messages: targets::tar_meta(fields = error, complete_only = TRUE)
Debugging guide: https://books.ropensci.org/targets/debugging.html
How to ask for help: https://books.ropensci.org/targets/help.html
Last error message:
    _store_ object 'filetype' not found
Last error traceback:
    No traceback available.

# tar-terra-rast.R: create_format_terra_raster
#...
 .myfun <- function(filetype, gdal) {
        .write_terra_raster <- function(object, path) {
            terra::writeRaster(
                object,
                path,
                filetype = filetype,
                overwrite = TRUE,
                gdal = gdal, 
            )
        }
        return(list(write = .write_terra_raster))
    }

    targets::tar_format(
        read = function(path) terra::rast(path),
        write = .myfun(filetype, gdal)$write,
        marshal = function(object) terra::wrap(object),
        unmarshal = function(object) terra::unwrap(object)
    )
# ...

Some other ideas I tried were using purrr::partial() to compose functions with some arguments pre-specified and couldn't get that working. Also forcing evaluation and injecting values with {rlang} metaprogramming operators also did not appear to work, but that might be worth re-investigating now.

[njtierney]

Gotcha, thanks for explaining that! It looks like we lose all reference to the parent frames here, I guess it might be evaluated in a separate R process, so making changes directly to the body of the function makes sense. I'm surprised that metaprogramming things from {rlang} don't work out, it feels like this is the sort of thing where you want to change some aspect of the AST or something. But effectively, I think, that's what you're doing with the clever body()<- calls.

If it continues to be a problem we can re-evaluate some possible solutions with rlang - I might even tag in Will into the issues to see if he has had this problem?

[brownag]

We now have a better way to do this, that does not require body<- nor getting package options inside write function body