test_that("harris_from_contexts returns n x n matrix", {
  x <- archaeo_sim(n = 40, k = 2, seed = 1)
  H <- harris_from_contexts(x, z_col = "z", context_col = "context")
  expect_true(is.matrix(H))
  expect_equal(nrow(H), 40)
  expect_equal(ncol(H), 40)
  expect_true(isSymmetric(H))
})

test_that("read_harris reads CSV edge list", {
  tmp <- tempfile(fileext = ".csv")
  writeLines(c("from,to,weight", "SU_1,SU_2,1", "SU_2,SU_3,1"), tmp)
  contexts <- c("SU_1", "SU_2", "SU_3", "SU_1", "SU_2", "SU_3")
  H <- read_harris(tmp, contexts = contexts)
  expect_true(is.matrix(H))
  expect_equal(nrow(H), 6)
  unlink(tmp)
})

test_that("validate_phases_harris detects inconsistencies", {
  x <- archaeo_sim(n = 40, k = 2, seed = 1)
  fit <- fit_sef(x, k = 2, context = "context")
  result <- validate_phases_harris(fit)
  expect_true(is.data.frame(result))
  expect_true("consistent" %in% names(result))
})