Rewrite only the references that cannot work as written

Every script runs in the repository as the authors organised it, with every file at its own path, from the folder .repro_run_folders() chooses. A reference is then:

• left as written when it names a file's path from the top ("raw_data/scan1/log.csv"), also when other files share the name (20 scan folders each with a log.csv), and when it is a relative path that names no file and no file with its name was found, or the file found has a path that ends in the path as written: the code probably joins it with a folder of its own (os.path.join(base, "fig7/x.csv")), and rewriting it to the full path gave processed_data/fig7/processed_data/fig7/x.csv;

• rewritten to the one file with its name elsewhere in the repository when it names no file as written ("./data/x.csv" with the file in exploratory/): the authors moved or left out a folder when they deposited;

• rewritten to the file's path from the top when it names a file relative to the script's own folder (source("helpers.R"), "../raw_data/scores.csv"), since the script does not run from there;

• rewritten as repro_rewrite_paths() found, by the file's name, when it is an absolute path (Z:/Strontium/... on the author's computer) or goes up out of the package.

Usage

.repro_keep_working_refs(
  rw,
  plan,
  script_path = NA_character_,
  run_dir = ".",
  here_dir = "."
)

Arguments

rw

a repro_rewrite_paths() result for one script

plan

the package layout's plan (.repro_package_plan())

script_path

the script's own path in the package

run_dir

the folder the script runs from, from the top of the package (see .repro_run_folders()); a reference works as written when it names a file counted from there, and a rewritten path is counted from there too

here_dir

the folder here() starts in, from the top of the package (see .repro_here_start()): a path that is the one argument of here() (in_here) counts from there, not from run_dir

Value

rw with a logical as_written column

Details

A reference left as written is marked as_written; it is not counted as rewritten, and not as a missing input, unless it names no file and no file with its name is in the repository. Another exception is a file the package has only inside an archive, read at the path unpacking it would give: as the package is, that path does not exist, so the reference is not found, and the file becomes a missing input (in_archive in repro_missing_inputs()).