test_that("sample data paths exist", {
  expect_true(file.exists(agmate_sample_candidate()))
  expect_true(file.exists(agmate_sample_reference()))
})

test_that("run_agmate produces expected outputs", {
  outdir <- file.path(tempdir(), "agmate_test_outputs")
  unlink(outdir, recursive = TRUE)

  res <- run_agmate(
    candidate = agmate_sample_candidate(),
    reference = agmate_sample_reference(),
    n_crosses = 3,
    iterations = 1,
    output_dir = outdir,
    run_plots = TRUE
  )

  expect_true(file.exists(res$part1$pedigree_file))
  expect_true(file.exists(res$part1$a_matrix_file))
  expect_true(file.exists(res$part2$mating_list_file))
  expect_true(file.exists(res$part3$density_file))
  expect_true(file.exists(res$part3$index_file))
})