tests/testthat/test-check_beast2_options.R

In richelbilderbeek/beastier: Call 'BEAST2'

test_that("use", {
  expect_silent(check_beast2_options(create_beast2_options()))

  # 'rng_seed' can be both NA and a value
  expect_silent(
    check_beast2_options(
      create_beast2_options(
        rng_seed = NA
      )
    )
  )
    expect_silent(
      check_beast2_options(
        create_beast2_options(
          rng_seed = 1
      )
    )
  )

  # 'n_threads' can be both NA and a value
    expect_silent(
      check_beast2_options(
        create_beast2_options(
          n_threads = NA
      )
    )
  )
  expect_silent(
    check_beast2_options(
      create_beast2_options(
        n_threads = 1
      )
    )
  )

  # Must stop on nonsense
  expect_error(check_beast2_options(beast2_options = "nonsense"))
  expect_error(check_beast2_options(beast2_options = NULL))
  expect_error(check_beast2_options(beast2_options = NA))
})

test_that("in-depth use", {

  good_beast2_options <- create_beast2_options()
  expect_silent(check_beast2_options(good_beast2_options))

  # Wrong parameter names
  beast2_options <- good_beast2_options
  beast2_options$rng_seed <- NULL
  expect_error(
    check_beast2_options(beast2_options),
    "'rng_seed' must be an element of an 'beast2_options'"
  )

  beast2_options <- good_beast2_options
  beast2_options$n_threads <- NULL
  expect_error(
    check_beast2_options(beast2_options),
    "'n_threads' must be an element of an 'beast2_options'"
  )

  beast2_options <- good_beast2_options
  beast2_options$use_beagle <- NULL
  expect_error(
    check_beast2_options(beast2_options),
    "'use_beagle' must be an element of an 'beast2_options'"
  )

  beast2_options <- good_beast2_options
  beast2_options$overwrite <- NULL
  expect_error(
    check_beast2_options(beast2_options),
    "'overwrite' must be an element of an 'beast2_options'"
  )
  beast2_options <- good_beast2_options
  beast2_options$beast2_path <- NULL
  expect_error(
    check_beast2_options(beast2_options),
    "'beast2_path' must be an element of an 'beast2_options'"
  )
  beast2_options <- good_beast2_options
  beast2_options$verbose <- NULL
  expect_error(
    check_beast2_options(beast2_options),
    "'verbose' must be an element of an 'beast2_options'"
  )


  ##############################################################################
  # Wrong parameter values
  ##############################################################################
  # output_state_filename
  expect_error(
    check_beast2_options(
      create_beast2_options(input_filename = 314)
    ),
    "is_one_string"
  )

  # output_state_filename
  expect_error(
    check_beast2_options(
      create_beast2_options(output_state_filename = NULL)
    ),
    "is_one_string"
  )

  # rng_seed
  expect_error(
    check_beast2_options(
      create_beast2_options(rng_seed = "nonsense")
    ),
    "'rng_seed' should be one NA or one non-zero positive value"
  )

  # n_threads
  expect_error(
    check_beast2_options(
      create_beast2_options(n_threads = "nonsense")
    ),
    "'n_threads' should be one NA or one non-zero positive value"
  )

  # use_beagle
  expect_error(
    check_beast2_options(
      create_beast2_options(use_beagle = "nonsense")
    ),
    "'use_beagle' must be one boolean"
  )

  # overwrite
  expect_error(
    check_beast2_options(
      create_beast2_options(overwrite = "nonsense")
    ),
    "'overwrite' must be one boolean"
  )

  # beast2_path
  expect_error(
    check_beast2_options(
      create_beast2_options(beast2_path = NULL)
    ),
    "is_one_string"
  )
  # beast2_path
  #
  # Do not check if an error is given if the BEAST2 path
  # does not exist. It shouldn't be checked by 'check_beast2_options'.
  # instead, only when running BEAST2 should this be checked
  expect_silent(
    check_beast2_options(
      create_beast2_options(
        beast2_path = get_beastier_tempfilename(pattern = "absent")
      )
    )
  )


  # verbose
  expect_error(
    check_beast2_options(
      create_beast2_options(verbose = "nonsense")
    ),
    "'verbose' must be one boolean"
  )

  # Duplicate filenames
  beast2_options <- good_beast2_options
  beast2_options$input_filename <- beast2_options$output_state_filename
  expect_error(
    check_beast2_options(
      beast2_options
    ),
    "'input_filename' and 'output_state_filename' must differ"
  )
})