# Example data for testing
example_counts <- matrix(1:20, nrow = 4, ncol = 5)
example_pg_ids <- data.frame(id = 1:4)
example_sample_metadata <- data.frame(id = 1:5, replicate = factor(c(1, 1, 2, 2, 3)), timepoint = factor(c("T0", "T0", "T1", "T1", "T2")))

# Test elements inside output list
test_that("setup_data() works correctly", {
  result <- setup_data(counts = example_counts,
                       pg_ids = example_pg_ids,
                       sample_metadata = example_sample_metadata)

  expect_s3_class(result, "gimap_dataset")
  expect_equal(result$raw_counts, example_counts)
  expect_equal(result$metadata$pg_ids, example_pg_ids)
  expect_equal(result$metadata$sample_metadata, example_sample_metadata)
  expect_equal(result$counts_per_sample, apply(example_counts, 2, sum))
})