test_that("usage", {
input_filename <- get_beautier_path("anthus_aco.fas")
inference_model <- init_inference_model(
input_filename = input_filename,
inference_model = create_inference_model()
)
expect_silent(
create_beast2_input_run(
input_filename = input_filename,
inference_model = inference_model
)
)
})
test_that("v2.4", {
input_filename <- get_fasta_filename()
inference_model <- init_inference_model(
input_filename = input_filename,
inference_model = create_inference_model(
beauti_options = create_beauti_options_v2_4()
)
)
created <- create_beast2_input_run(
input_filename = input_filename,
inference_model = inference_model
)
expect_true(
created[1] == "<run id=\"mcmc\" spec=\"MCMC\" chainLength=\"10000000\">" ||
created[1] == "<run id=\"mcmc\" spec=\"MCMC\" chainLength=\"1e+07\">"
)
expect_equal(length(created), 76)
expect_equal(
created[76],
"</run>"
)
})
test_that("v2.6", {
input_filename <- get_fasta_filename()
inference_model <- init_inference_model(
input_filename = input_filename,
inference_model = create_inference_model(
beauti_options = create_beauti_options_v2_6()
)
)
created <- create_beast2_input_run(
input_filename = input_filename,
inference_model = inference_model
)
# New in v2.6
expect_length(stringr::str_subset(created, "spec=\"Logger\" "), 3)
expect_length(stringr::str_subset(created, "OperatorSchedule"), 1)
})
test_that("abuse", {
expect_error(
create_beast2_input_run(
input_filename = c("a", "b")
)
)
expect_error(
create_beast2_input_run(
input_filename = get_beautier_path("anthus_aco.fas"),
inference_model = "nonsense"
)
)
})
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