test-integer.r
In h5lite: Simplified 'HDF5' Interface

local({
  #test_that("Integer scalars and vectors work", {
  file <- tempfile(fileext = ".h5")
  on.exit(unlink(file))
  
  # 1. Simple Integer Vector
  vec <- 1:10
  h5_write(vec, file, "vec")
  expect_equal(h5_read(file, "vec"), vec)
  expect_equal(h5_class(file, "vec"), "numeric")
  expect_equal(h5_read(file, "vec", as = "integer"), vec)

  # 2. Integer Scalar (1D array of length 1)
  h5_write(42L, file, "scalar")
  expect_equal(h5_read(file, "scalar"), 42L)
  
  # 3. Explicit Scalar (I(x))
  h5_write(I(42L), file, "scalar_I")
  expect_equal(h5_dim(file, "scalar_I"), numeric(0)) # Rank 0
  expect_equal(h5_read(file, "scalar_I"), 42L)

  # 4. Integers with NA (Auto-promoted to float to store NA)
  vec_na <- c(1L, NA_integer_, 3L)
  h5_write(vec_na, file, "vec_na")
  expect_equal(h5_typeof(file, "vec_na"), "float64")
  read_back <- h5_read(file, "vec_na")
  expect_true(is.double(read_back))
  expect_true(is.na(read_back[2]))
  
  # 5. Named vector
  vec_named <- structure(c(1:5), names = letters[1:5])
  h5_write(vec_named, file, "vec_named")
  expect_equal(h5_read(file, "vec_named"), vec_named)
  expect_equal(h5_names(file, "vec_named"), letters[1:5])
  
  # Force read back as integer (NaN becomes NA_integer_)
  expect_equal(h5_read(file, "vec_na", as = "integer"), vec_na)
})

local({
  #test_that("Integer matrices and arrays work", {
  file <- tempfile(fileext = ".h5")
  on.exit(unlink(file))
  
  mat <- matrix(1:9, nrow = 3)
  h5_write(mat, file, "mat")
  expect_equal(h5_read(file, "mat"), mat)
  expect_equal(h5_dim(file, "mat"), c(3, 3))
  expect_equal(h5_names(file, "mat"), character(0))
  expect_equal(h5_length(file, "mat"), 9L)
  
  mat_named <- matrix(1:9, nrow = 3, dimnames = list(letters[1:3], LETTERS[1:3]))
  h5_write(mat_named, file, "mat_named")
  expect_equal(h5_read(file, "mat_named"), mat_named)
  expect_equal(h5_names(file, "mat_named"), LETTERS[1:3])
  
  mat_rownm <- matrix(1:9, nrow = 3, dimnames = list(letters[1:3], NULL))
  h5_write(mat_rownm, file, "mat_rownm")
  expect_equal(h5_read(file, "mat_rownm"), mat_rownm)
  expect_equal(h5_names(file, "mat_rownm"), character(0))
  
  mat_colnm <- matrix(1:9, nrow = 3, dimnames = list(NULL, LETTERS[1:3]))
  h5_write(mat_colnm, file, "mat_colnm")
  expect_equal(h5_read(file, "mat_colnm"), mat_colnm)
  expect_equal(h5_names(file, "mat_colnm"), LETTERS[1:3])
  
  arr3d <- array(
    data = 1:24, 
    dim = c(2,3,4), 
    dimnames = list(LETTERS[1:2], LETTERS[3:5], LETTERS[7:10]) )
  
  h5_write(arr3d, file, "arr3d")
  expect_equal(h5_read(file, "arr3d"), arr3d)
  expect_equal(h5_dim(file, "arr3d"), c(2,3,4) )
  expect_equal(h5_names(file, "arr3d"), LETTERS[3:5])
  expect_equal(h5_length(file, "arr3d"), prod(c(2,3,4)))
})

local({
  #test_that("Integer attributes work", {
  file <- tempfile(fileext = ".h5")
  on.exit(unlink(file))
  
  h5_write(1:5, file, "data")
  h5_write(100L, file, "data", attr = "meta")
  
  expect_equal(h5_read(file, "data", attr = "meta", as = "integer"), 100L)
  
  expect_null(h5_delete(file, "data", attr = "meta"))
  expect_null(h5_delete(file, "data"))
  expect_error(h5_write(1:5, file, "data", attr = "meta"))
})

local({
  #test_that("Specific integer types (int8-int64) can be forced", {
  file <- tempfile(fileext = ".h5")
  on.exit(unlink(file))
  
  val <- c(-100L, 100L)
  
  h5_write(val, file, "i8", as = "int8")
  expect_equal(h5_typeof(file, "i8"), "int8")
  expect_equal(h5_read(file, "i8", as = "integer"), val)

  # Can't write -100 to a uint
  expect_error(h5_write(val, file, "u8", as = "uint8"))
})

local({
  #test_that("Compression", {
  
  file_compressed   <- tempfile(fileext = ".h5")
  file_uncompressed <- tempfile(fileext = ".h5")
  on.exit(unlink(c(file_compressed, file_uncompressed)))
  
  
  vec <- 1:13
  
  h5_write(vec, file_compressed, "vec", compress = "none")
  expect_equal(h5_read(file_compressed, "vec"), vec)
  
  h5_write(vec, file_compressed, "vec", compress = "gzip-5")
  expect_equal(h5_read(file_compressed, "vec"), vec)
  
  h5_write(vec, file_compressed, "vec", compress = "szip-nn")
  expect_equal(h5_read(file_compressed, "vec"), vec)
  
  h5_write(vec, file_compressed, "vec", compress = "szip-ec")
  expect_equal(h5_read(file_compressed, "vec"), vec)
  
  
  vec <- rep(1L, 10000000)
  h5_write(vec, file_compressed,   "vec", compress = "gzip-5")
  h5_write(vec, file_uncompressed, "vec", compress = "none")
  expect_true(file.size(file_compressed) < file.size(file_uncompressed))
  
  
  # fallback to gzip for strings
  h5_write(letters, file_uncompressed, "letters", compress = "szip-nn")
  
  
  exit_if_not(at_home())
  #skip_on_cran()
  
  mtx <- matrix(vec, nrow = 100)
  h5_write(mtx, file_compressed, "mtx", compress = "gzip-5")
  expect_equal(h5_read(file_compressed, "mtx"), mtx)
  
  h5_write(mtx, file_compressed, "mtx", compress = "szip-nn")
  expect_equal(h5_read(file_compressed, "mtx"), mtx)
  
  h5_write(mtx, file_compressed, "mtx", compress = "szip-ec")
  expect_equal(h5_read(file_compressed, "mtx"), mtx)
  
  
  for (i in c(1, 2, 3, 7, 11, 19, 61, 1000)) {
    vec <- 1:i
    
    h5_write(vec, file_compressed, "vec", compress = "szip-nn")
    expect_equal(h5_read(file_compressed, "vec"), vec)
    
    h5_write(vec, file_compressed, "vec", compress = "szip-ec")
    expect_equal(h5_read(file_compressed, "vec"), vec)
  }
  
  
  # deprecated `compress` args
  vec <- 1:100
  h5_write(vec, file_compressed, "vec", compress = TRUE)
  h5_write(vec, file_compressed, "vec", compress = FALSE)
  h5_write(vec, file_compressed, "vec", compress = 5)
  
  
})