Documentation updates.

NAMESPACE

@@ -40,3 +40,10 @@ export(zarr_open_array)
 export(zarr_open_group)
 export(zarr_save_array)
 export(zb_slice)
+importFrom(R6,R6Class)
+importFrom(memoise,memoise)
+importFrom(memoise,timeout)
+importFrom(qs,lz4_compress_raw)
+importFrom(qs,lz4_decompress_raw)
+importFrom(qs,zstd_compress_raw)
+importFrom(qs,zstd_decompress_raw)

R/array-nested.R

@@ -48,6 +48,7 @@ zero_based_to_one_based <- function(selection, shape) {
 #' Represents a multi-dimensional array that can be
 #' accessed and subsetted via list of Slice instances.
 #' @rdname NestedArray
+#' @importFrom R6 R6Class
 #' @export
 NestedArray <- R6::R6Class("NestedArray",
   private = list(

R/creation.R

@@ -243,7 +243,7 @@ require_parent_group <- function(
 #'     Primary compressor.
 #' @param fill_value : object
 #'     Default value to use for uninitialized portions of the array.
-#' @param order : {'C', 'F'}, optional
+#' @param order : \code{'C', 'F'}, optional
 #'     Memory layout to be used within each chunk.
 #' @param overwrite : bool, optional
 #'     If True, erase all data in `store` prior to initialisation.
@@ -256,7 +256,7 @@ require_parent_group <- function(
 #'     Sequence of filters to use to encode chunk data prior to compression.
 #' @param object_codec : Codec, optional
 #'     A codec to encode object arrays, only needed if dtype=object.
-#' @param dimension_separator : {'.', '/'}, optional
+#' @param dimension_separator : \code{'.', '/'}, optional
 #'     Separator placed between the dimensions of a chunk.
 #' @keywords internal
 init_array <- function(
@@ -307,15 +307,7 @@ init_array <- function(
 
 #' Initialize a group store. Note that this is a low-level function and there should be no
 #' need to call this directly from user code.
-#' @param store : Store
-#'     A mapping that supports string keys and byte sequence values.
-#' @param overwrite : bool, optional
-#'     If True, erase all data in `store` prior to initialisation.
-#' @param path : string, optional
-#'     Path under which array is stored.
-#' @param chunk_store : Store, optional
-#'     Separate storage for chunks. If not provided, `store` will be used
-#'     for storage of both chunks and metadata.
+#' @inheritParams init_array
 #' @keywords internal
 init_group <- function(
     store,
@@ -339,35 +331,14 @@ init_group <- function(
 
 
 #' Create an empty array
-#' @param shape : int or tuple of ints
-#'     Array shape.
+#' @inheritParams init_array
 #' @param chunks : int or tuple of ints, optional
 #'     Chunk shape. If True, will be guessed from `shape` and `dtype`. If
 #'     False, will be set to `shape`, i.e., single chunk for the whole array.
 #'     If an int, the chunk size in each dimension will be given by the value
 #'     of `chunks`. Default is True.
-#' @param dtype : string or dtype, optional
-#'     NumPy dtype.
-#' @param compressor : Codec, optional
-#'     Primary compressor.
-#' @param fill_value : object
-#'     Default value to use for uninitialized portions of the array.
-#' @param order : {'C', 'F'}, optional
-#'     Memory layout to be used within each chunk.
-#' @param store : MutableMapping or string
-#'     Store or path to directory in file system or name of zip file.
 #' @param synchronizer : object, optional
 #'     Array synchronizer.
-#' @param overwrite : bool, optional
-#'     If True, delete all pre-existing data in `store` at `path` before
-#'     creating the array.
-#' @param path : string, optional
-#'     Path under which array is stored.
-#' @param chunk_store : MutableMapping, optional
-#'     Separate storage for chunks. If not provided, `store` will be used
-#'     for storage of both chunks and metadata.
-#' @param filters : sequence of Codecs, optional
-#     Sequence of filters to use to encode chunk data prior to compression.
 #' @param cache_metadata : bool, optional
 #'     If True, array configuration metadata will be cached for the
 #'     lifetime of the object. If False, array metadata will be reloaded
@@ -379,10 +350,6 @@ init_group <- function(
 #'     to all attribute read operations.
 #' @param read_only : bool, optional
 #'     True if array should be protected against modification.
-#' @param object_codec : Codec, optional
-#'     A codec to encode object arrays, only needed if dtype=object.
-#' @param dimension_separator : {'.', '/'}, optional
-#'     Separator placed between the dimensions of a chunk.
 #' @param write_empty_chunks : bool, optional
 #'     If True (default), all chunks will be stored regardless of their
 #'     contents. If False, each chunk is compared to the array's fill value
@@ -449,7 +416,7 @@ zarr_create <- function(
 }
 
 #' Create an array filled with NAs.
-#' @param shape : int or tuple of ints
+#' @inheritParams zarr_create
 #' @param ... The params of zarr_create()
 #' @returns ZarrArray
 #' @export
@@ -470,7 +437,7 @@ zarr_create_array <- function(data, ...) {
 }
 
 #' Create an array filled with zeros.
-#' @param shape : int or tuple of ints
+#' @inheritParams zarr_create
 #' @param ... The params of zarr_create()
 #' @returns ZarrArray
 #' @export
@@ -479,22 +446,8 @@ zarr_create_zeros <- function(shape, ...) {
 }
 
 #' Create a group.
-#' @param store : MutableMapping or string, optional
-#'     Store or path to directory in file system.
-#' @param overwrite : bool, optional
-#'     If True, delete any pre-existing data in `store` at `path` before
-#'     creating the group.
-#' @param chunk_store : MutableMapping, optional
-#'     Separate storage for chunks. If not provided, `store` will be used
-#'     for storage of both chunks and metadata.
-#' @param cache_attrs : bool, optional
-#'     If True (default), user attributes will be cached for attribute read
-#'     operations. If False, user attributes are reloaded from the store prior
-#'     to all attribute read operations.
-#' @param synchronizer : object, optional
-#'     Array synchronizer.
-#' @param path : string, optional
-#'     Group path within store.
+#' @inheritParams init_array
+#' @inheritParams zarr_create
 #' @returns ZarrGroup
 #' @export
 zarr_create_group <- function(
@@ -529,23 +482,8 @@ zarr_create_group <- function(
 }
 
 #' Open a group using file-mode-like semantics.
-#' @param store : MutableMapping or string, optional
-#'     Store or path to directory in file system or name of zip file.
-#' @param mode : {'r', 'r+', 'a', 'w', 'w-'}, optional
-#'     Persistence mode: 'r' means read only (must exist); 'r+' means
-#'     read/write (must exist); 'a' means read/write (create if doesn't
-#'     exist); 'w' means create (overwrite if exists); 'w-' means create
-#'     (fail if exists).
-#' @param cache_attrs : bool, optional
-#'     If True (default), user attributes will be cached for attribute read
-#'     operations. If False, user attributes are reloaded from the store prior
-#'     to all attribute read operations.
-#' @param synchronizer : object, optional
-#'     Array synchronizer.
-#' @param path : string, optional
-#'     Group path within store.
-#' @param chunk_store : MutableMapping or string, optional
-#'     Store or path to directory in file system or name of zip file.
+#' @inheritParams zarr_open
+#' @inheritParams zarr_create
 #' @param storage_options : dict
 #'     If using an fsspec URL to create the store, these will be passed to
 #'     the backend implementation. Ignored otherwise.
@@ -617,66 +555,10 @@ zarr_open_group <- function(
 }
 
 #' Open an array using file-mode-like semantics.
-#' @param store : MutableMapping or string, optional
-#'     Store or path to directory in file system or name of zip file.
-#' @param storage_options : dict
-#'     If using an fsspec URL to create the store, these will be passed to
-#'     the backend implementation. Ignored otherwise.
-#' @param mode : {'r', 'r+', 'a', 'w', 'w-'}, optional
-#'     Persistence mode: 'r' means read only (must exist); 'r+' means
-#'     read/write (must exist); 'a' means read/write (create if doesn't
-#'     exist); 'w' means create (overwrite if exists); 'w-' means create
-#'     (fail if exists).
-#' @param shape : int or tuple of ints
-#'     Array shape.
-#' @param chunks : int or tuple of ints, optional
-#'     Chunk shape. If True, will be guessed from `shape` and `dtype`. If
-#'     False, will be set to `shape`, i.e., single chunk for the whole array.
-#'     If an int, the chunk size in each dimension will be given by the value
-#'     of `chunks`. Default is True.
-#' @param dtype : string or dtype, optional
-#'     NumPy dtype.
-#' @param compressor : Codec, optional
-#'     Primary compressor.
-#' @param fill_value : object
-#'     Default value to use for uninitialized portions of the array.
-#' @param order : {'C', 'F'}, optional
-#'     Memory layout to be used within each chunk.
-#' @param store : MutableMapping or string
-#'     Store or path to directory in file system or name of zip file.
-#' @param synchronizer : object, optional
-#'     Array synchronizer.
-#' @param overwrite : bool, optional
-#'     If True, delete all pre-existing data in `store` at `path` before
-#'     creating the array.
-#' @param path : string, optional
-#'     Path under which array is stored.
-#' @param chunk_store : MutableMapping, optional
-#'     Separate storage for chunks. If not provided, `store` will be used
-#'     for storage of both chunks and metadata.
-#' @param filters : sequence of Codecs, optional
-#     Sequence of filters to use to encode chunk data prior to compression.
-#' @param cache_metadata : bool, optional
-#'     If True, array configuration metadata will be cached for the
-#'     lifetime of the object. If False, array metadata will be reloaded
-#'     prior to all data access and modification operations (may incur
-#'     overhead depending on storage and data access pattern).
-#' @param cache_attrs : bool, optional
-#'     If True (default), user attributes will be cached for attribute read
-#'     operations. If False, user attributes are reloaded from the store prior
-#'     to all attribute read operations.
-#' @param object_codec : Codec, optional
-#'     A codec to encode object arrays, only needed if dtype=object.
-#' @param dimension_separator : {'.', '/'}, optional
-#'     Separator placed between the dimensions of a chunk.
-#' @param write_empty_chunks : bool, optional
-#'     If True (default), all chunks will be stored regardless of their
-#'     contents. If False, each chunk is compared to the array's fill value
-#'     prior to storing. If a chunk is uniformly equal to the fill value, then
-#'     that chunk is not be stored, and the store entry for that chunk's key
-#'     is deleted. This setting enables sparser storage, as only chunks with
-#'     non-fill-value data are stored, at the expense of overhead associated
-#'     with checking the data of each chunk.
+#' @inheritParams init_array
+#' @inheritParams zarr_create
+#' @inheritParams zarr_open
+#' @inheritParams zarr_open_group
 #' @returns ZarrArray
 #' @export
 zarr_open_array <- function(
@@ -784,8 +666,7 @@ zarr_open_array <- function(
 }
 
 #' Convenience function to save a ZarrArray to the local file system.
-#' @param store : MutableMapping or string
-#'     Store or path to directory in file system or name of zip file.
+#' @inheritParams init_array
 #' @param arr : ZarrArray
 #'     The array with data to save.
 #' @param ... Additional arguments to pass to zarr_create_array().
@@ -797,15 +678,12 @@ zarr_save_array <- function(store, arr, ...) {
 }
 
 #' Convenience function to open a group or array using file-mode-like semantics.
-#' @param store : MutableMapping or string, optional
-#'     Store or path to directory in file system or name of zip file.
-#' @param mode : {'r', 'r+', 'a', 'w', 'w-'}, optional
+#' @inheritParams init_array
+#' @param mode : \code{'r', 'r+', 'a', 'w', 'w-'}, optional
 #'     Persistence mode: 'r' means read only (must exist); 'r+' means
 #'     read/write (must exist); 'a' means read/write (create if doesn't
 #'     exist); 'w' means create (overwrite if exists); 'w-' means create
 #'     (fail if exists).
-#' @param path : str or NA, optional
-#'     The path within the store to open.
 #' @param ... Additional arguments to pass to zarr_open_array or zarr_open_group.
 #' @returns ZarrArray or ZarrGroup
 #' @export

R/numcodecs.R

@@ -40,6 +40,7 @@ Codec <- R6::R6Class("Codec",
 #' Class representing a ZSTD compressor
 
 #' @rdname ZstdCodec
+#' @importFrom qs zstd_compress_raw zstd_decompress_raw
 #' @export
 ZstdCodec <- R6::R6Class("ZstdCodec",
   inherit = Codec,
@@ -61,7 +62,7 @@ ZstdCodec <- R6::R6Class("ZstdCodec",
     #' @return Compressed data.
     encode = function(buf, zarr_arr) {
       # Reference: https://github.com/traversc/qs/blob/84e30f4/R/RcppExports.R#L16
-      result <- qs::zstd_compress_raw(buf, self$level)
+      result <- zstd_compress_raw(buf, self$level)
       return(result)
     },
     #' @description
@@ -70,7 +71,7 @@ ZstdCodec <- R6::R6Class("ZstdCodec",
     #' @param zarr_arr The ZarrArray instance.
     #' @return Un-compressed data.
     decode = function(buf, zarr_arr) {
-      result <- qs::zstd_decompress_raw(buf)
+      result <- zstd_decompress_raw(buf)
       return(result)
     },
     #' @description
@@ -92,6 +93,7 @@ ZstdCodec <- R6::R6Class("ZstdCodec",
 #' Class representing a LZ4 compressor
 #'
 #' @rdname Lz4Codec
+#' @importFrom qs lz4_compress_raw lz4_decompress_raw
 #' @export
 Lz4Codec <- R6::R6Class("Lz4Codec",
    inherit = Codec,
@@ -113,7 +115,7 @@ Lz4Codec <- R6::R6Class("Lz4Codec",
      #' @return Compressed data.
      encode = function(buf, zarr_arr) {
        # Reference: https://github.com/traversc/qs/blob/84e30f4/R/RcppExports.R#L24
-       body <- qs::lz4_compress_raw(buf, self$acceleration)
+       body <- lz4_compress_raw(buf, self$acceleration)
 
        # The compressed output includes a 4-byte header storing the original size
        # of the decompressed data as a little-endian 32-bit integer.
@@ -133,7 +135,7 @@ Lz4Codec <- R6::R6Class("Lz4Codec",
      decode = function(buf, zarr_arr) {
       body <- buf[5:length(buf)]
 
-      result <- qs::lz4_decompress_raw(body)
+      result <- lz4_decompress_raw(body)
       return(result)
      },
      #' @description

R/slicing.R

@@ -94,7 +94,7 @@ Slice <- R6::R6Class("Slice",
   )
 )
 
-#' Convenience function for the internal Slice class constructor.
+#' Convenience function for the internal Slice R6 class constructor.
 #' @param start The start index.
 #' @param stop The stop index.
 #' @param step The step size.
@@ -119,11 +119,10 @@ slice <- function(start, stop = NA, step = NA, zero_based = FALSE) {
   ))
 }
 
-#' Convenience function for the internal Slice class constructor 
+#' Convenience function for the internal Slice R6 class constructor 
 #' with zero-based indexing and exclusive stop index.
-#' @param start The start index.
-#' @param stop The stop index.
-#' @param step The step size.
+#' @inheritParams slice
+#' @inherit slice return
 #' @export
 zb_slice <- function(start, stop = NA, step = NA) {
   return(slice(start, stop, step, zero_based = TRUE))

R/stores.R

@@ -351,6 +351,7 @@ MemoryStore <- R6::R6Class("MemoryStore",
 #' Read-only. Depends on the `crul` package.
 #'
 #' @rdname HttpStore
+#' @importFrom memoise memoise timeout
 #' @export
 HttpStore <- R6::R6Class("HttpStore",
   inherit = Store,
@@ -393,9 +394,9 @@ HttpStore <- R6::R6Class("HttpStore",
     },
     memoize_make_request = function() {
       if(private$cache_enabled) {
-        private$make_request_memoized <-  memoise::memoise(
+        private$make_request_memoized <-  memoise(
           function(key) private$make_request(key), 
-          ~memoise::timeout(private$cache_time_seconds)
+          ~timeout(private$cache_time_seconds)
         )
       } else {
         private$make_request_memoized <- private$make_request

R/zarr-array.R

@@ -1295,7 +1295,7 @@ ZarrArray <- R6::R6Class("ZarrArray",
 
 #' S3 method for as.array
 #'
-#' @param obj object 
+#' @param x object 
 #' @param ... not used
 #' @keywords internal
 #' @export