Fix namespace

keller-mark · Sep 18, 2023 · 79ff801 · 79ff801
1 parent 1a8e187
commit 79ff801
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Showing 16 changed files with 72 additions and 38 deletions.
diff --git a/NAMESPACE b/NAMESPACE
@@ -1 +1,33 @@
-exportPattern("^[[:alpha:]]+")
+# Generated by roxygen2: do not edit by hand
+
+export(Attributes)
+export(BloscCodec)
+export(Bz2Codec)
+export(Codec)
+export(DirectoryStore)
+export(Dtype)
+export(GzipCodec)
+export(HttpStore)
+export(Lz4Codec)
+export(LzmaCodec)
+export(MemoryStore)
+export(NestedArray)
+export(Store)
+export(VLenUtf8Codec)
+export(ZarrArray)
+export(ZarrGroup)
+export(ZlibCodec)
+export(ZstdCodec)
+export(as_scalar)
+export(is_key_error)
+export(is_scalar)
+export(is_slice)
+export(obj_list)
+export(slice)
+export(zarr_create)
+export(zarr_create_array)
+export(zarr_create_empty)
+export(zarr_create_group)
+export(zarr_create_zeros)
+export(zarr_open_group)
+export(zb_slice)
diff --git a/R/atomic.R b/R/atomic.R
@@ -3,13 +3,15 @@
 #' Convert a value to a scalar to opt-out of R default vector casting behavior.
 #' @param obj The value to convert.
 #' @return The value wrapped as a scalar.
+#' @export
 as_scalar <- function(obj) {
   return(jsonlite::unbox(obj))
 }
 
 #' Check if a value is a scalar.
 #' @param s The value to check.
 #' @return TRUE if the value is a scalar, FALSE otherwise.
+#' @export
 is_scalar <- function(s) {
   if(class(s)[[1]] == "scalar") {
     return(TRUE)

diff --git a/R/creation.R b/R/creation.R
@@ -392,6 +392,7 @@ init_group <- function(
 #'     non-fill-value data are stored, at the expense of overhead associated
 #'     with checking the data of each chunk.
 #' @returns ZarrArray
+#' @export
 zarr_create <- function(
     shape,
     chunks=TRUE,
@@ -451,6 +452,7 @@ zarr_create <- function(
 #' @param shape : int or tuple of ints
 #' @param ... The params of zarr_create()
 #' @returns ZarrArray
+#' @export
 zarr_create_empty <- function(shape, ...) {
     return(zarr_create(shape=shape, fill_value=NA, ...))
 }
@@ -459,6 +461,7 @@ zarr_create_empty <- function(shape, ...) {
 #' @param data A base R array() or pizzarr NestedArray instance.
 #' @param ... The params of zarr_create()
 #' @returns ZarrArray
+#' @export
 zarr_create_array <- function(data, ...) {
     z <- zarr_create(...)
     z$set_item("...", data)
@@ -470,6 +473,7 @@ zarr_create_array <- function(data, ...) {
 #' @param shape : int or tuple of ints
 #' @param ... The params of zarr_create()
 #' @returns ZarrArray
+#' @export
 zarr_create_zeros <- function(shape, ...) {
     return(zarr_create(shape=shape, fill_value=0, ...))
 }
@@ -492,6 +496,7 @@ zarr_create_zeros <- function(shape, ...) {
 #' @param path : string, optional
 #'     Group path within store.
 #' @returns ZarrGroup
+#' @export
 zarr_create_group <- function(
     store = NA,
     overwrite = FALSE,
@@ -545,6 +550,7 @@ zarr_create_group <- function(
 #'     If using an fsspec URL to create the store, these will be passed to
 #'     the backend implementation. Ignored otherwise.
 #' @returns ZarrGroup
+#' @export
 zarr_open_group <- function(
     store = NA,
     mode = NA,

diff --git a/R/dtypes.R b/R/dtypes.R
@@ -140,7 +140,7 @@ get_dtype_asrtype <- function(dtype) {
 #' @description
 #' 
 #' @rdname Dtype
-#' @keywords internal
+#' @export
 Dtype <- R6::R6Class("Dtype",
   public = list(
     #' @field dtype The original dtype string, like "<f4".

diff --git a/R/indexing.R b/R/indexing.R
@@ -1,12 +1,12 @@
+# Reference: https://github.com/zarr-developers/zarr-python/blob/5dd4a0/zarr/indexing.py#L655
+
 #' The Zarr OIndex class.
 #' @title OIndex Class
 #' @docType class
 #' @description
-#' @keywords internal
-#' Reference: https://github.com/zarr-developers/zarr-python/blob/5dd4a0/zarr/indexing.py#L655
 #'
 #' @rdname OIndex
-#' @export
+#' @keywords internal
 OIndex <- R6::R6Class("OIndex",
   public = list(
     #' @field array
@@ -21,15 +21,15 @@ OIndex <- R6::R6Class("OIndex",
   )
 )
 
+# Reference: https://github.com/zarr-developers/zarr-python/blob/5dd4a0/zarr/indexing.py#L811
+
 #' The Zarr VIndex class.
 #' @title VIndex Class
 #' @docType class
 #' @description
-#' @keywords internal
-#' Reference: https://github.com/zarr-developers/zarr-python/blob/5dd4a0/zarr/indexing.py#L811
 #'
 #' @rdname VIndex
-#' @export
+#' @keywords internal
 VIndex <- R6::R6Class("VIndex",
   public = list(
     #' @field array
@@ -44,16 +44,15 @@ VIndex <- R6::R6Class("VIndex",
   )
 )
 
+# Reference: https://github.com/zarr-developers/zarr-python/blob/5dd4a0/zarr/indexing.py#L138
 
 #' The Zarr IntDimIndexer class.
 #' @title IntDimIndexer Class
 #' @docType class
 #' @description
-#' @keywords internal
-#' Reference: https://github.com/zarr-developers/zarr-python/blob/5dd4a0/zarr/indexing.py#L138
 #'
 #' @rdname IntDimIndexer
-#' @export
+#' @keywords internal
 IntDimIndexer <- R6::R6Class("IntDimIndexer",
   inherit = DimIndexer,
   public = list(
@@ -95,15 +94,15 @@ IntDimIndexer <- R6::R6Class("IntDimIndexer",
   )
 )
 
+# Reference: https://github.com/zarr-developers/zarr-python/blob/5dd4a0/zarr/indexing.py#L163
+
 #' The Zarr SliceDimIndexer class.
 #' @title SliceDimIndexer Class
 #' @docType class
 #' @description
-#' @keywords internal
-#' Reference: https://github.com/zarr-developers/zarr-python/blob/5dd4a0/zarr/indexing.py#L163
 #'
 #' @rdname SliceDimIndexer
-#' @export
+#' @keywords internal
 SliceDimIndexer <- R6::R6Class("SliceDimIndexer",
   inherit = DimIndexer,
   public = list(
@@ -196,15 +195,15 @@ SliceDimIndexer <- R6::R6Class("SliceDimIndexer",
   )
 )
 
+# Reference: https://github.com/zarr-developers/zarr-python/blob/5dd4a0/zarr/indexing.py#L326
+
 #' The Zarr BasicIndexer class.
 #' @title BasicIndexer Class
 #' @docType class
 #' @description
-#' @keywords internal
-#' Reference: https://github.com/zarr-developers/zarr-python/blob/5dd4a0/zarr/indexing.py#L326
 #'
 #' @rdname BasicIndexer
-#' @export
+#' @keywords internal
 BasicIndexer <- R6::R6Class("BasicIndexer",
   inherit = Indexer,
   public = list(

diff --git a/R/meta.R b/R/meta.R
@@ -1,6 +1,7 @@
 
 
 # Reference: https://github.com/zarr-developers/zarr-python/blob/5dd4a0e6cdc04c6413e14f57f61d389972ea937c/zarr/meta.py#L14
+#' @keywords internal
 Metadata2 <- R6::R6Class("Metadata2",
     private = list(
         ZARR_FORMAT = 2

diff --git a/R/slicing.R b/R/slicing.R
@@ -86,6 +86,7 @@ Slice <- R6::R6Class("Slice",
 #' @param step The step size.
 #' @param zero_based The index of the dimension. By default, FALSE for R-like behavior.
 #' @return A Slice instance with the specified parameters.
+#' @export
 slice <- function(start, stop = NA, step = NA, zero_based = FALSE) {
   start_offset <- ifelse(zero_based, 0, -1)
   stop_offset <- ifelse(zero_based, 0, 0)
@@ -108,14 +109,15 @@ slice <- function(start, stop = NA, step = NA, zero_based = FALSE) {
 #' @param start The start index.
 #' @param stop The stop index.
 #' @param step The step size.
-#' @keywords internal
+#' @export
 zb_slice <- function(start, stop = NA, step = NA) {
   return(slice(start, stop, step, zero_based = TRUE))
 }
 
 #' Check if a value is a Slice instance.
 #' @param s The value to check.
 #' @return TRUE if the value is a Slice instance, FALSE otherwise.
+#' @export
 is_slice <- function(s) {
   if(class(s)[[1]] == "Slice") {
     return(TRUE)

diff --git a/R/string-utils.R b/R/string-utils.R
@@ -39,6 +39,7 @@ char_vec_to_raw <- function(char_vec, basic_type, num_chars, byte_order) {
   return(buf)
 }
 
+#' @keywords internal
 raw_to_char_vec <- function(raw_vec, basic_type, num_chars, byte_order) {
   # Reference: https://stat.ethz.ch/R-manual/R-devel/library/base/html/iconv.html
   if(basic_type == "S") {
@@ -101,4 +102,4 @@ raw_to_char_vec <- function(raw_vec, basic_type, num_chars, byte_order) {
   }
   char_vec <- iconv(list_of_raw, from = iconv_from, to = "UTF-8", toRaw = FALSE)
   return(char_vec)
-}
+}
diff --git a/R/utils.R b/R/utils.R
@@ -1,15 +1,14 @@
 #' Convert a string into a character vector.
 #' 
-#' @keywords internal
 #' @param s The string.
 #' @return A vector where each element is an individual character.
+#' @keywords internal
 str_to_vec <- function(s) {
   return(stringr::str_split(s, pattern = "")[[1]])
 }
 
 #' Create a list of zarray metadata.
 #' 
-#' @keywords internal
 #' @param shape
 #' @param chunks
 #' @param dtype
@@ -19,6 +18,7 @@ str_to_vec <- function(s) {
 #' @param filters
 #' @param dimension_separator
 #' @return A list.
+#' @keywords internal
 create_zarray_meta <- function(shape = NA, chunks = NA, dtype = NA, compressor = NA, fill_value = NA, order = NA, filters = NA, dimension_separator = NA) {
   # Reference: https://zarr.readthedocs.io/en/stable/spec/v2.html#metadata
   if(is.na(dimension_separator)) {
@@ -101,7 +101,7 @@ obj_list <- function(...) {
   retval
 }
 
-
+#' @keywords internal
 zip_numeric <- function(a, b) {
   result <- list()
   for(i in seq_len(length(a))) {
@@ -110,6 +110,7 @@ zip_numeric <- function(a, b) {
   return(result)
 }
 
+#' @keywords internal
 check_selection_length <- function(selection, shape) {
   if(length(selection) > length(shape)) {
     stop('TooManyIndicesError')
@@ -118,6 +119,7 @@ check_selection_length <- function(selection, shape) {
 
 # Returns both the sliceIndices per dimension and the output shape after slicing.
 # Reference: https://github.com/gzuidhof/zarr.js/blob/master/src/core/indexing.ts#L22
+#' @keywords internal
 selection_to_slice_indices <- function(selection, shape) {
   slice_indices_result <- list()
   out_shape <- c()
@@ -152,10 +154,10 @@ filter_list <- function(l, pred) {
 
 #' Convert user selections, potentially containing "...", to a list of slices
 #' that can be used internally.
-#' @keywords internal
 #' @param selection The user-provided selection list.
 #' @param shape The shape of the array, to be used to fill in ellipsis values.
 #' @returns A list of selections with ellipsis values converted to NA.
+#' @keywords internal
 replace_ellipsis <- function(selection, shape) {
   # Reference: https://github.com/gzuidhof/zarr.js/blob/master/src/core/indexing.ts#L67
 
@@ -215,9 +217,9 @@ replace_ellipsis <- function(selection, shape) {
   return(selection)
 }
 
-#' @keywords internal
 #' @param shape A shape vector
 #' @returns The product of shape elements.
+#' @keywords internal
 compute_size <- function(shape) {
   result <- 1
   for(val in shape) {
@@ -228,9 +230,9 @@ compute_size <- function(shape) {
 
 #' Check if a value, potentially a vector, is NA
 #'
-#' @keywords internal
 #' @param val The value to check
 #' @return Whether the value is NA
+#' @keywords internal
 is_na <- function(val) {
   if(length(val) != 1) {
     # Including when val is integer(0), character(0), etc.
@@ -255,6 +257,7 @@ chunk_fill <- function(chunk, value) {
 #' Check if an error is a KeyError.
 #' @param e The error to check.
 #' @return TRUE if the error is a KeyError, FALSE otherwise.
+#' @export
 is_key_error <- function(e) {
   return(grepl("KeyError", e$message))
 }
@@ -277,8 +280,8 @@ get_list_product_aux <- function(dim_indexer_iterables, i, partial_results) {
 
 #' Generate a product of lists.
 #' @param dim_indexer_iterables A list of lists.
-#' @keywords internal
 #' @return A list of lists.
+#' @keywords internal
 get_list_product <- function(dim_indexer_iterables) {
   # Reference: https://docs.python.org/3/library/itertools.html#itertools.product
   partial_results <- list()

diff --git a/man/BasicIndexer.Rd b/man/BasicIndexer.Rd
diff --git a/man/Dtype.Rd b/man/Dtype.Rd
diff --git a/man/IntDimIndexer.Rd b/man/IntDimIndexer.Rd
diff --git a/man/OIndex.Rd b/man/OIndex.Rd
diff --git a/man/SliceDimIndexer.Rd b/man/SliceDimIndexer.Rd