test_that("coglasso works", {
  expect_no_error(coglasso(multi_omics_sd_micro, p = 4, nlambda_w = 3, nlambda_b = 3, nc = 3, verbose = FALSE))
})

test_that("nlambda_w works", {
  n <- 3
  expect_length(coglasso(multi_omics_sd_micro, p = 4, nlambda_w = n, nlambda_b = n, nc = n, verbose = FALSE)$lambda_w, n)
})

test_that("nlambda_b works", {
  n <- 3
  expect_length(coglasso(multi_omics_sd_micro, p = 4, nlambda_w = n, nlambda_b = n, nc = n, verbose = FALSE)$lambda_b, n)
})

test_that("nc works", {
  n <- 3
  expect_length(coglasso(multi_omics_sd_micro, p = 4, nlambda_w = n, nlambda_b = n, nc = n, verbose = FALSE)$c, n)
})

test_that("lambda_w_max works", {
  n <- 3
  lambda_w_max <- 0.8
  expect_equal(max(coglasso(multi_omics_sd_micro, p = 4, nlambda_w = n, nlambda_b = n, nc = n, lambda_w_max = lambda_w_max, verbose = FALSE)$lambda_w), lambda_w_max)
})

test_that("lambda_b_max works", {
  n <- 3
  lambda_b_max <- 0.8
  expect_equal(max(coglasso(multi_omics_sd_micro, p = 4, nlambda_w = n, nlambda_b = n, nc = n, lambda_b_max = lambda_b_max, verbose = FALSE)$lambda_b), lambda_b_max)
})

test_that("c_max works", {
  n <- 3
  c_max <- 20
  expect_equal(max(coglasso(multi_omics_sd_micro, p = 4, nlambda_w = n, nlambda_b = n, nc = n, c_max = c_max, verbose = FALSE)$c), c_max)
})

test_that("lambda_w_min_ratio works", {
  n <- 3
  lambda_w_min_ratio <- 0.2
  actual_min_lambda_w <- min(coglasso(multi_omics_sd_micro, p = 4, nlambda_w = n, nlambda_b = n, nc = n, lambda_w_min_ratio = lambda_w_min_ratio, verbose = FALSE)$lambda_w)
  actual_max_lambda_w <- max(coglasso(multi_omics_sd_micro, p = 4, nlambda_w = n, nlambda_b = n, nc = n, lambda_w_min_ratio = lambda_w_min_ratio, verbose = FALSE)$lambda_w)
  expect_equal(actual_min_lambda_w/actual_max_lambda_w, lambda_w_min_ratio)
})

test_that("lambda_b_min_ratio works", {
  n <- 3
  lambda_b_min_ratio <- 0.2
  actual_min_lambda_b <- min(coglasso(multi_omics_sd_micro, p = 4, nlambda_w = n, nlambda_b = n, nc = n, lambda_b_min_ratio = lambda_b_min_ratio, verbose = FALSE)$lambda_b)
  actual_max_lambda_b <- max(coglasso(multi_omics_sd_micro, p = 4, nlambda_w = n, nlambda_b = n, nc = n, lambda_b_min_ratio = lambda_b_min_ratio, verbose = FALSE)$lambda_b)
  expect_equal(actual_min_lambda_b/actual_max_lambda_b, lambda_b_min_ratio)
})

test_that("c_min_ratio works", {
  n <- 3
  c_min <- 0.2
  actual_min_c <- min(coglasso(multi_omics_sd_micro, p = 4, nlambda_w = n, nlambda_b = n, nc = n, c_min = c_min, verbose = FALSE)$c)
  expect_equal(actual_min_c, c_min)
})

test_that("single lambda_w works and overrides nlambda_w", {
  n <- 3
  lambda_w <- 0.5
  actual_lambda_w <- coglasso(multi_omics_sd_micro, p = 4, lambda_w = lambda_w, nlambda_w = n, nlambda_b = n, nc = n, verbose = FALSE)$lambda_w
  expect_length(actual_lambda_w, 1)
})

test_that("single lambda_b works and overrides nlambda_b", {
  n <- 3
  lambda_b <- 0.5
  actual_lambda_b <- coglasso(multi_omics_sd_micro, p = 4, lambda_b = lambda_b, nlambda_w = n, nlambda_b = n, nc = n, verbose = FALSE)$lambda_b
  expect_length(actual_lambda_b, 1)
})

test_that("single c works and overrides nc", {
  n <- 3
  c <- 0.5
  actual_c <- coglasso(multi_omics_sd_micro, p = 4, c = c, nlambda_w = n, nlambda_b = n, nc = n, verbose = FALSE)$c
  expect_length(actual_c, 1)
})

test_that("Verbose mode works", {
  expect_output(coglasso(multi_omics_sd_micro, p = 4, nlambda_w = 3, nlambda_b = 3, nc = 3))
})

test_that("Covariance as input works", {
  S <- stats::cor(multi_omics_sd_micro)
  expect_no_error(coglasso(S, p = 4, nlambda_w = 3, nlambda_b = 3, nc = 3, verbose = FALSE))
  expect_output(coglasso(S, p = 4, nlambda_w = 3, nlambda_b = 3, nc = 3))
})

test_that("Default run works", {
  expect_no_error(coglasso(multi_omics_sd_micro, p = 4, verbose = FALSE))
})

test_that("Deprecation warning for pX works", {
  expect_warning(coglasso(multi_omics_sd_micro, pX = 4, nlambda_w = 3, nlambda_b = 3, nc = 2, verbose = FALSE))
})

test_that("print.coglasso works", {
  expect_snapshot({
    cg <- coglasso(multi_omics_sd_micro, p = 4, nlambda_w = 3, nlambda_b = 3, nc = 2, verbose = FALSE)
    print(cg)
  })
})

test_that("General |D| implementation works for c = 0", {
  expect_no_error(coglasso(multi_omics_sd_micro, p = c(2,2,2), nlambda_w = 3, nlambda_b = 3, c = 0, verbose = FALSE))
})

test_that("Mode lock_lambdas works", {
  cg <- coglasso(multi_omics_sd_micro, p = 4, nlambda_w = 3, nc = 1, lock_lambdas = TRUE, verbose = FALSE)
  expect_equal(dim(cg$hpars)[1], 3)
})