Commands as language objects by default

[wlandau]

Summary

Until now, drake has used text to represent commands. It worked, but it was naive.

plan <- drake_plan(
  raw_data = readxl::read_excel(file_in("raw_data.xlsx")),
  data = raw_data %>%
    mutate(Species = forcats::fct_inorder(Species)),
  hist = create_plot(data),
  fit = lm(Sepal.Width ~ Petal.Width + Species, data),
  report = rmarkdown::render(
    knitr_in("report.Rmd"),
    output_file = file_out("report.html"),
    quiet = TRUE
  )
)

plan
#> # A tibble: 5 x 2
#>   target   command                                                         
#>   <chr>    <chr>                                                           
#> 1 raw_data "readxl::read_excel(file_in(\"raw_data.xlsx\"))"                
#> 2 data     raw_data %>% mutate(Species = forcats::fct_inorder(Species))    
#> 3 hist     create_plot(data)                                               
#> 4 fit      lm(Sepal.Width ~ Petal.Width + Species, data)                   
#> 5 report   "rmarkdown::render(knitr_in(\"report.Rmd\"), output_file = file…

In this PR, the command column is now a list of language objects by default. drake still understands character columns, and wildcard functions still work.

library(drake)
plan <- drake_plan(
  raw_data = readxl::read_excel(file_in("raw_data.xlsx")),
  data = raw_data %>%
    mutate(Species = forcats::fct_inorder(Species)),
  hist = create_plot(data),
  fit = lm(Sepal.Width ~ Petal.Width + Species, data),
  report = rmarkdown::render(
    knitr_in("report.Rmd"),
    output_file = file_out("report.html"),
    quiet = TRUE
  )
)

plan
#> # A tibble: 5 x 2
#>   target   command                                                         
#>   <chr>    <S3: langs>                                                     
#> 1 raw_data readxl::read_excel(file_in("raw_data.xlsx"))                   …
#> 2 data     raw_data %>% mutate(Species = forcats::fct_inorder(Species))   …
#> 3 hist     create_plot(data)                                              …
#> 4 fit      lm(Sepal.Width ~ Petal.Width + Species, data)                  …
#> 5 report   rmarkdown::render(knitr_in("report.Rmd"), output_file = file_ou…

str(plan$command)
#> List of 5
#>  $ raw_data: language readxl::read_excel(file_in("raw_data.xlsx"))
#>  $ data    : language raw_data %>% mutate(Species = forcats::fct_inorder(Species))
#>  $ hist    : language create_plot(data)
#>  $ fit     : language lm(Sepal.Width ~ Petal.Width + Species, data)
#>  $ report  : language rmarkdown::render(knitr_in("report.Rmd"), output_file = file_out("report.html"),      quiet = TRUE)

^{Created on 2019-02-02 by the reprex package (v0.2.1)}

Note <S3: langs> in the above tibble. Until r-lib/pillar#34 is solved, we have a custom print() method that deparses the commands before displaying them. This could be slow for large plans, but I think it is still worth being able to see the commands.

Related GitHub issues and pull requests

• Ref: Use language objects for commands #700

Checklist

• I have read drake's code of conduct, and I agree to follow its rules.
• I have listed any substantial changes in the development news.
• I have added testthat unit tests to tests/testthat to confirm that any new features or functionality work correctly.
• I have tested this pull request locally with devtools::check()
• This pull request is ready for review.
• I think this pull request is ready to merge.

[codecov-io]

Codecov Report

Merging #708 into master will not change coverage.
The diff coverage is 100%.

@@          Coverage Diff          @@
##           master   #708   +/-   ##
=====================================
  Coverage     100%   100%           
=====================================
  Files          72     72           
  Lines        5809   5841   +32     
=====================================
+ Hits         5809   5841   +32

Impacted Files	Coverage Δ
R/utils-deprecate.R	100% <ø> (ø)	⬆️
R/api-mapreduce.R	100% <100%> (ø)	⬆️
R/test-testthat.R	100% <100%> (ø)	⬆️
R/api-plan.R	100% <100%> (ø)	⬆️
R/api-wildcards.R	100% <100%> (ø)	⬆️
R/utils-utils.R	100% <100%> (ø)	⬆️
R/vis-graphinfo.R	100% <100%> (ø)	⬆️
R/preprocess-sanitize.R	100% <100%> (ø)	⬆️
R/preprocess-codeanalysis.R	100% <100%> (ø)	⬆️
R/exec-standardize.R	100% <100%> (ø)	⬆️
... and 3 more

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[wlandau]

FYI: I updated the type summary. <S3: langs> was too obtuse, so I changed it to <expr>.

plan <- drake_plan(
  raw_data = readxl::read_excel(file_in("raw_data.xlsx")),
  data = raw_data %>%
    mutate(Species = forcats::fct_inorder(Species)),
  hist = create_plot(data),
  fit = lm(Sepal.Width ~ Petal.Width + Species, data),
  report = rmarkdown::render(
    knitr_in("report.Rmd"),
    output_file = file_out("report.html"),
    quiet = TRUE
  )
)
plan
#> # A tibble: 5 x 2
#>   target   command                                                         
#>   <chr>    <expr>                                                          
#> 1 raw_data readxl::read_excel(file_in("raw_data.xlsx"))                   …
#> 2 data     raw_data %>% mutate(Species = forcats::fct_inorder(Species))   …
#> 3 hist     create_plot(data)                                              …
#> 4 fit      lm(Sepal.Width ~ Petal.Width + Species, data)                  …
#> 5 report   rmarkdown::render(knitr_in("report.Rmd"), output_file = file_ou…