improvements for interactive use

[jayhesselberth]

update testthat and tests

closes #392

[jayhesselberth]

still need to handle empty function calls, ideally these would use cli_abort(). :

library(valr)

# this error is partcularly uninformative
bed_intersect()
#> Error in y_tbl[[1]]: subscript out of bounds

bed_flank()
#> Error in check_interval(x): argument "x" is missing, with no default

bed_slop()
#> Error in check_interval(x): argument "x" is missing, with no default

^{Created on 2022-10-04 with reprex v2.0.2}

[jayhesselberth]

with new changes:

library(valr)

bed_intersect()
#> Error in `bed_intersect()`:
#> ! `x` is absent but must be supplied.

#> Backtrace:
#>     ▆
#>  1. └─valr::bed_intersect()
#>  2.   └─rlang::check_required(x) at valr/R/bed_intersect.r:90:2
#>  3.     └─rlang::abort(msg, call = call)

bed_flank()
#> Error in `bed_flank()`:
#> ! `x` is absent but must be supplied.

#> Backtrace:
#>     ▆
#>  1. └─valr::bed_flank()
#>  2.   └─rlang::check_required(x) at valr/R/bed_flank.r:58:2
#>  3.     └─rlang::abort(msg, call = call)

bed_slop()
#> Error in `bed_slop()`:
#> ! `x` is absent but must be supplied.

#> Backtrace:
#>     ▆
#>  1. └─valr::bed_slop()
#>  2.   └─rlang::check_required(x) at valr/R/bed_slop.r:50:2
#>  3.     └─rlang::abort(msg, call = call)

^{Created on 2022-10-04 with reprex v2.0.2}

[jayhesselberth]

behavior in pipes looks better now too:

library(valr)

x <- tibble::tribble(
  ~chrom, ~start, ~end,
  'chr1', 25,      50,
  'chr1', 100,     125
)

y <- tibble::tribble(
  ~chrom, ~start, ~end,
  'chr1', 30,     75
)

bed_intersect()
#> Error in `bed_intersect()`:
#> ! `x` is absent but must be supplied.

#> Backtrace:
#>     ▆
#>  1. └─valr::bed_intersect()
#>  2.   └─rlang::check_required(x) at valr/R/bed_intersect.r:90:2
#>  3.     └─rlang::abort(msg, call = call)

bed_intersect(x)
#> Error in `bed_intersect()`:
#> ! One or more tbls required in `...`

#> Backtrace:
#>     ▆
#>  1. └─valr::bed_intersect(x)
#>  2.   └─cli::cli_abort("One or more tbls required in {.var ...}") at valr/R/bed_intersect.r:93:4
#>  3.     └─rlang::abort(...)

bed_flank()
#> Error in `bed_flank()`:
#> ! `x` is absent but must be supplied.

#> Backtrace:
#>     ▆
#>  1. └─valr::bed_flank()
#>  2.   └─rlang::check_required(x) at valr/R/bed_flank.r:58:2
#>  3.     └─rlang::abort(msg, call = call)

bed_slop()
#> Error in `bed_slop()`:
#> ! `x` is absent but must be supplied.

#> Backtrace:
#>     ▆
#>  1. └─valr::bed_slop()
#>  2.   └─rlang::check_required(x) at valr/R/bed_slop.r:50:2
#>  3.     └─rlang::abort(msg, call = call)

# pipe behavior
bed_intersect(x, y) |>
  bed_flank()
#> Error in `bed_flank()`:
#> ! `genome` is absent but must be supplied.

#> Backtrace:
#>     ▆
#>  1. └─valr::bed_flank(bed_intersect(x, y))
#>  2.   └─rlang::check_required(genome) at valr/R/bed_flank.r:59:2
#>  3.     └─rlang::abort(msg, call = call)

^{Created on 2022-10-04 with reprex v2.0.2}

[kriemo]

LGTM, thanks for the updates.