remove references to rhdf5

R/write_h5ad_helpers.R

@@ -252,46 +252,6 @@ write_h5ad_nullable_boolean <- function(value, file, name, compression, version
   write_h5ad_encoding(file, name, "nullable-boolean", version)
 }
 
-#' Write H5AD boolean array
-#'
-#' Write a boolean array to an H5AD file as a custom ENUM dataset
-#'
-#' @noRd
-#'
-#' @param value Value to write
-#' @param file Path to a H5AD file or an open H5AD handle
-#' @param name Name of the element within the H5AD file
-write_h5ad_boolean_array <- function(value, file, name) {
-  # Based on https://stackoverflow.com/a/74653515/4384120
-
-  h5file <- rhdf5::H5Fopen(file)
-  on.exit(rhdf5::H5Fclose(h5file))
-
-  value <- as.integer(value)
-  if (!is.null(dim(value))) {
-    dims <- dim(value)
-  } else {
-    dims <- length(value)
-  }
-
-  # Create the dataspace for the data to write
-  h5space <- rhdf5::H5Screate_simple(dims = dims, NULL, native = TRUE)
-  on.exit(rhdf5::H5Sclose(h5space), add = TRUE)
-
-  # Create the Boolean ENUM datatype (TRUE = 1 FALSE = 0)
-  tid <- rhdf5::H5Tenum_create(dtype_id = "H5T_NATIVE_UCHAR")
-  rhdf5::H5Tenum_insert(tid, name = "TRUE", value = 1L)
-  rhdf5::H5Tenum_insert(tid, name = "FALSE", value = 0L)
-
-  # Create the dataset with this new datatype
-  h5dataset <- rhdf5::H5Dcreate(h5file, name, tid, h5space)
-  on.exit(rhdf5::H5Dclose(h5dataset), add = TRUE)
-
-  # Write the data. We have to use as.raw() because our base type is 8-bit and
-  # R integers are 32-bit
-  rhdf5::H5Dwrite(h5dataset, as.raw(value), h5type = tid)
-}
-
 
 #' Write H5AD nullable integer
 #'
@@ -520,8 +480,8 @@ write_h5ad_data_frame <- function(value, file, name, compression, index = NULL,
 #' one of `"none"`, `"gzip"` or `"lzf"`. Defaults to `"none"`.
 #' @param version The H5AD version to write
 write_empty_h5ad <- function(file, obs, var, compression, version = "0.1.0") {
-  h5file <- rhdf5::H5Fcreate(file)
-  rhdf5::H5Fclose(h5file)
+  # h5file <- rhdf5::H5Fcreate(file)
+  # rhdf5::H5Fclose(h5file)
 
   write_h5ad_encoding(file, "/", "anndata", "0.1.0")