Allow passing a vector of paths in `where`

[Bisaloo]

library(lightr)

spec <- lr_get_spec(
  c(
    system.file("testdata", package = "lightr"), 
    system.file("testdata", "non_english", package = "lightr")
  ),
  ext = c(
    "TRM", "ttt", "jdx", "jaz", "JazIrrad", "csv", "txt",
    "Transmission", "spc"
  ),
  sep = ","
)
#> 20 files found; importing spectra:
#> Warning in file(file, "r"): cannot open file
#> '/home/hugo/.local/share/R/x86_64-pc-linux-gnu-library/4.3/lightr/testdata/non_english/FMNH6834.00000001.Master.Transmission':
#> No such file or directory
#> Warning in value[[3L]](cond): cannot open the connection
#> Warning in file(file, "r"): cannot open file
#> '/home/hugo/.local/share/R/x86_64-pc-linux-gnu-library/4.3/lightr/testdata/OO_comma.txt':
#> No such file or directory
#> Warning in value[[3L]](cond): cannot open the connection
#> Warning in file(file, "r"): cannot open file
#> '/home/hugo/.local/share/R/x86_64-pc-linux-gnu-library/4.3/lightr/testdata/non_english/OOusb4000.txt':
#> No such file or directory
#> Warning in value[[3L]](cond): cannot open the connection
#> Warning in file(file, "r"): cannot open file
#> '/home/hugo/.local/share/R/x86_64-pc-linux-gnu-library/4.3/lightr/testdata/non_english/OceanView.txt':
#> No such file or directory
#> Warning in value[[3L]](cond): cannot open the connection
#> Warning in file(file, "r"): cannot open file
#> '/home/hugo/.local/share/R/x86_64-pc-linux-gnu-library/4.3/lightr/testdata/OceanView_nonEN.txt':
#> No such file or directory
#> Warning in value[[3L]](cond): cannot open the connection
#> Warning in file(file, "r"): cannot open file
#> '/home/hugo/.local/share/R/x86_64-pc-linux-gnu-library/4.3/lightr/testdata/non_english/UK5.txt':
#> No such file or directory
#> Warning in value[[3L]](cond): cannot open the connection
#> Warning in file(con, "r"): cannot open file
#> '/home/hugo/.local/share/R/x86_64-pc-linux-gnu-library/4.3/lightr/testdata/non_english/avantes_export.ttt':
#> No such file or directory
#> Warning in value[[3L]](cond): cannot open the connection
#> Warning in file(filename, "rb"): cannot open file
#> '/home/hugo/.local/share/R/x86_64-pc-linux-gnu-library/4.3/lightr/testdata/non_english/avantes_trans.TRM':
#> No such file or directory
#> Warning in value[[3L]](cond): cannot open the connection
#> Warning in file(con, "r"): cannot open file
#> '/home/hugo/.local/share/R/x86_64-pc-linux-gnu-library/4.3/lightr/testdata/non_english/irrad.JazIrrad':
#> No such file or directory
#> Warning in value[[3L]](cond): cannot open the connection
#> Warning in file(file, "r"): cannot open file
#> '/home/hugo/.local/share/R/x86_64-pc-linux-gnu-library/4.3/lightr/testdata/non_english/spec.csv':
#> No such file or directory
#> Warning in value[[3L]](cond): cannot open the connection
#> Warning: Could not import one or more files:
#> /home/hugo/.local/share/R/x86_64-pc-linux-gnu-library/4.3/lightr/testdata/non_english/FMNH6834.00000001.Master.Transmission
#> /home/hugo/.local/share/R/x86_64-pc-linux-gnu-library/4.3/lightr/testdata/OO_comma.txt
#> /home/hugo/.local/share/R/x86_64-pc-linux-gnu-library/4.3/lightr/testdata/non_english/OOusb4000.txt
#> /home/hugo/.local/share/R/x86_64-pc-linux-gnu-library/4.3/lightr/testdata/non_english/OceanView.txt
#> /home/hugo/.local/share/R/x86_64-pc-linux-gnu-library/4.3/lightr/testdata/OceanView_nonEN.txt
#> /home/hugo/.local/share/R/x86_64-pc-linux-gnu-library/4.3/lightr/testdata/non_english/UK5.txt
#> /home/hugo/.local/share/R/x86_64-pc-linux-gnu-library/4.3/lightr/testdata/non_english/avantes_export.ttt
#> /home/hugo/.local/share/R/x86_64-pc-linux-gnu-library/4.3/lightr/testdata/non_english/avantes_trans.TRM
#> /home/hugo/.local/share/R/x86_64-pc-linux-gnu-library/4.3/lightr/testdata/non_english/irrad.JazIrrad
#> /home/hugo/.local/share/R/x86_64-pc-linux-gnu-library/4.3/lightr/testdata/non_english/spec.csv

head(spec)
#>    wl CRAIC_export FMNH6834.00000002.Master J_MUR_MARS_17_0001 OceanOptics
#> 1 300     5.710900                 3.178905           2.328048    125.9485
#> 2 301     5.794053                 2.940429           2.238900    125.0620
#> 3 302     4.326612                 2.697714           2.313921    127.3013
#> 4 303     4.178850                 2.544286           2.565386    127.9036
#> 5 304     3.671765                 2.756619           2.720976    127.9396
#> 6 305     2.784688                 2.816048           2.583169    128.0920
#>   OceanOptics_comma OceanOptics_period  avantes2 avantes_export_long  avasoft8
#> 1          126.3405           154.3030 12.964709           13.624678 252.16336
#> 2          127.2560           129.2981  8.262921            5.276307   0.00000
#> 3          126.8862           115.9120 11.605302           11.023560  74.36793
#> 4          126.2224           122.5818 13.189732           10.307208  34.58589
#> 5          127.8413           125.9307 15.073677            8.980705 101.20355
#> 6          127.9555           152.3136 14.371996            8.278200   0.00000
#>    jazspec
#> 1 13.78756
#> 2 13.10873
#> 3 12.70862
#> 4 12.93509
#> 5 13.02466
#> 6 13.64287

warnings()

^{Created on 2023-06-09 with reprex v2.0.2}

[Bisaloo]

@thomased @bittonp, could I get your opinion on this please?

I'm planning breaking changes in the coming weeks (likely to result in lightr 2.0.0) so it may be a good time to pull the plug here as well.

The idea is to allow users to more easily process only some files in a given folder or subfolder.

I went through the same question in https://hugogruson.fr/xlcutter/articles/design.html#why-do-i-need-to-pass-a-list-of-files-to-parse-rather-than-an-entire-folder.

I would probably keep pavo::getspec() unchanged by adding list.files() before calling lr_get_spec().