test_that("cleanup_folders works with defaults", {
  folders <- get_folders()
  result <- create_folders(folders)
  cleanup_result <- cleanup_folders(folders)
  names(cleanup_result) <- basename(names(cleanup_result))
  cleanup_result_default <- c(
    code = 0,
    conf = 0,
    data = 0,
    doc = 0,
    figures = 0,
    results = 0
  )
  expect_equal(cleanup_result, cleanup_result_default)
})

test_that("cleanup_folders works with configuration file specified", {
  conf_file <- tempfile("folders.yml")
  folders <- get_folders(conf_file)
  expect_equal(file.exists(conf_file), TRUE)
  result <- create_folders(folders)
  cleanup_result <- cleanup_folders(folders, conf_file)
  names(cleanup_result) <- basename(names(cleanup_result))
  cleanup_result_default <- c(
    code = 0,
    conf = 0,
    data = 0,
    doc = 0,
    figures = 0,
    results = 0
  )
  expect_equal(cleanup_result, cleanup_result_default)
  expect_equal(file.exists(conf_file), TRUE)
  expect_equal(unlink(conf_file), 0)
})

test_that("cleanup_folders works with configuration file removal", {
  conf_file <- tempfile("folders.yml")
  folders <- get_folders(conf_file)
  folders <- lapply(folders, function(x) file.path(tempdir(), x))
  expect_equal(file.exists(conf_file), TRUE)
  result <- create_folders(folders)
  cleanup_result <- cleanup_folders(folders, conf_file, keep_conf = FALSE)
  names(cleanup_result) <- basename(names(cleanup_result))
  cleanup_result_default <- c(
    code = 0,
    conf = 0,
    data = 0,
    doc = 0,
    figures = 0,
    results = 0,
    conf_file = 0
  )
  expect_equal(cleanup_result, cleanup_result_default)
  expect_equal(file.exists(conf_file), FALSE)
})

test_that("cleanup_folders works with configuration file removal from 'conf'", {
  conf_file <- tempfile("folders.yml", file.path(tempdir(), "conf"))
  folders <- get_folders(conf_file)
  folders <- lapply(folders, function(x) file.path(tempdir(), x))
  expect_equal(file.exists(conf_file), TRUE)
  result <- create_folders(folders)
  cleanup_result <- cleanup_folders(folders, conf_file, keep_conf = FALSE)
  names(cleanup_result) <- basename(names(cleanup_result))
  cleanup_result_default <- c(
    code = 0,
    conf = 0,
    data = 0,
    doc = 0,
    figures = 0,
    results = 0,
    conf_file = 0
  )
  expect_equal(cleanup_result, cleanup_result_default)
  expect_equal(file.exists(conf_file), FALSE)
})

test_that("cleanup_folders works with non-empty folders", {
  conf_file <- tempfile("folders.yml")
  folders <- get_folders(conf_file)
  folders <- lapply(folders, function(x) file.path(tempdir(), x))
  result <- create_folders(folders)
  file_path <- file.path(folders$data, 'data.csv')
  write.csv(data.frame(x = 1:3), file_path)
  cleanup_result <- cleanup_folders(folders, conf_file)
  names(cleanup_result) <- basename(names(cleanup_result))
  cleanup_result_default <- list(
    code = 0,
    conf = 0,
    data = NULL,
    doc = 0,
    figures = 0,
    results = 0
  )
  expect_equal(cleanup_result, cleanup_result_default)
  expect_equal(file.exists(conf_file), TRUE)
  expect_equal(file.exists(file_path), TRUE)
  unlink(conf_file)
  unlink(file_path)
  unlink(file.path(folders$data), recursive = TRUE)
  expect_equal(file.exists(conf_file), FALSE)
  expect_equal(dir.exists(file.path(folders$data)), FALSE)
  expect_equal(file.exists(file_path), FALSE)
})

test_that("cleanup_folders works recursively with non-empty folders", {
  conf_file <- tempfile("folders.yml")
  folders <- get_folders(conf_file)
  folders <- lapply(folders, function(x) file.path(tempdir(), x))
  result <- create_folders(lapply(folders, file.path, 'test'))
  file_path <- file.path(folders$data, 'test', 'data.csv')
  write.csv(data.frame(x = 1:3), file_path)
  cleanup_result <- cleanup_folders(folders, conf_file, recursive = TRUE)
  names(cleanup_result) <- gsub(paste0(tempdir(), '/'), '', 
                                names(cleanup_result), fixed = TRUE)
  cleanup_result_default <-
    list(
      `results/test` = 0,
      results = 0,
      `figures/test` = 0,
      figures = 0,
      `doc/test` = 0,
      doc = 0,
      `data/test` = NULL,
      data = NULL,
      `conf/test` = 0,
      conf = 0,
      `code/test` = 0,
      code = 0
    )
  expect_equal(cleanup_result, cleanup_result_default)
  expect_equal(file.exists(conf_file), TRUE)
  expect_equal(file.exists(file_path), TRUE)
  unlink(conf_file)
  unlink(file_path)
  unlink(file.path(folders$data), recursive = TRUE)
  expect_equal(file.exists(conf_file), FALSE)
  expect_equal(dir.exists(file.path(folders$data)), FALSE)
  expect_equal(file.exists(file_path), FALSE)
})