From 4b3db37e5991362513148ed25fbdce23f76d4532 Mon Sep 17 00:00:00 2001
From: Mark Keller <7525285+keller-mark@users.noreply.github.com>
Date: Thu, 20 Jun 2024 10:43:49 -0400
Subject: [PATCH] importFrom for %dopar%; update docs

---
 NAMESPACE                      |  9 ++-------
 R/numcodecs.R                  | 10 ++++------
 R/options.R                    |  4 +---
 R/stores.R                     |  1 -
 R/zarr-array.R                 |  2 +-
 man/ZarrArray.Rd               |  8 +++++++-
 man/as_scalar.Rd               |  4 +++-
 man/ensure_integer_vec.Rd      | 14 ++++++++++++++
 man/ensure_list.Rd             | 14 ++++++++++++++
 man/is_integer.Rd              | 12 ++++++++++++
 man/is_integer_list.Rd         | 12 ++++++++++++
 man/is_integer_scalar.Rd       | 12 ++++++++++++
 man/is_integer_vec.Rd          | 14 ++++++++++++++
 man/is_scalar.Rd               |  4 ++--
 man/pizzarr_option_defaults.Rd | 16 ++++++++++++++++
 man/zb_slice.Rd                |  4 ++--
 16 files changed, 116 insertions(+), 24 deletions(-)
 create mode 100644 man/ensure_integer_vec.Rd
 create mode 100644 man/ensure_list.Rd
 create mode 100644 man/is_integer.Rd
 create mode 100644 man/is_integer_list.Rd
 create mode 100644 man/is_integer_scalar.Rd
 create mode 100644 man/is_integer_vec.Rd
 create mode 100644 man/pizzarr_option_defaults.Rd

diff --git a/NAMESPACE b/NAMESPACE
index b2ba27d..96c7983 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -27,6 +27,7 @@ export(is_key_error)
 export(is_scalar)
 export(is_slice)
 export(obj_list)
+export(pizzarr_option_defaults)
 export(pizzarr_sample)
 export(slice)
 export(zarr_create)
@@ -39,10 +40,4 @@ 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)
+importFrom(foreach,"%dopar%")
diff --git a/R/numcodecs.R b/R/numcodecs.R
index d39e6b6..99e1845 100644
--- a/R/numcodecs.R
+++ b/R/numcodecs.R
@@ -36,7 +36,6 @@ Codec <- R6::R6Class("Codec",
 #' ZSTD compressor for Zarr
 #' @title ZstdCodec Class
 #' @docType class
-#' @importFrom qs zstd_compress_raw zstd_decompress_raw
 #' @description
 #' Class representing a ZSTD compressor
 
@@ -62,7 +61,7 @@ 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 <- zstd_compress_raw(buf, self$level)
+      result <- qs::zstd_compress_raw(buf, self$level)
       return(result)
     },
     #' @description
@@ -71,7 +70,7 @@ ZstdCodec <- R6::R6Class("ZstdCodec",
     #' @param zarr_arr The ZarrArray instance.
     #' @return Un-compressed data.
     decode = function(buf, zarr_arr) {
-      result <- zstd_decompress_raw(buf)
+      result <- qs::zstd_decompress_raw(buf)
       return(result)
     },
     #' @description
@@ -89,7 +88,6 @@ ZstdCodec <- R6::R6Class("ZstdCodec",
 #' LZ4 compressor for Zarr
 #' @title Lz4Codec Class
 #' @docType class
-#' @importFrom qs lz4_compress_raw lz4_decompress_raw
 #' @description
 #' Class representing a LZ4 compressor
 #'
@@ -115,7 +113,7 @@ 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 <- lz4_compress_raw(buf, self$acceleration)
+       body <- qs::lz4_compress_raw(buf, self$acceleration)
 
        # The compressed output includes a 4-byte header storing the original size
        # of the decompressed data as a little-endian 32-bit integer.
@@ -135,7 +133,7 @@ Lz4Codec <- R6::R6Class("Lz4Codec",
      decode = function(buf, zarr_arr) {
       body <- buf[5:length(buf)]
 
-      result <- lz4_decompress_raw(body)
+      result <- qs::lz4_decompress_raw(body)
       return(result)
      },
      #' @description
diff --git a/R/options.R b/R/options.R
index 3e648a4..9612521 100644
--- a/R/options.R
+++ b/R/options.R
@@ -1,9 +1,6 @@
 # Adapted from https://github.com/IRkernel/IRkernel/blob/master/R/options.r
 
-#' @usage
 #' pizzarr_option_defaults
-#' 
-#' @rdname pizzarr-package
 #' @export
 pizzarr_option_defaults <- list(
     pizzarr.http_store_cache_time_seconds = 3600,
@@ -11,6 +8,7 @@ pizzarr_option_defaults <- list(
     pizzarr.parallel_write_enabled = FALSE
 )
 
+#' @keywords internal
 from_env <- list(
     PIZZARR_HTTP_STORE_CACHE_TIME_SECONDS = as.integer,
     PIZZARR_PARALLEL_READ_ENABLED = as.logical,
diff --git a/R/stores.R b/R/stores.R
index 052628f..80523ba 100644
--- a/R/stores.R
+++ b/R/stores.R
@@ -346,7 +346,6 @@ MemoryStore <- R6::R6Class("MemoryStore",
 #' HttpStore for Zarr
 #' @title HttpStore Class
 #' @docType class
-#' @importFrom memoise memoise timeout
 #' @description
 #' Store class that uses HTTP requests.
 #' Read-only. Depends on the `crul` package.
diff --git a/R/zarr-array.R b/R/zarr-array.R
index 9533c07..f015e60 100644
--- a/R/zarr-array.R
+++ b/R/zarr-array.R
@@ -3,7 +3,7 @@
 #' The Zarr Array class.
 #' @title ZarrArray Class
 #' @docType class
-#' @importFrom R6 R6Class
+#' @importFrom foreach %dopar%
 #' @description
 #' Instantiate an array from an initialized store.
 #' @param selection Selections are lists containing either scalars, strings, or Slice objects. Two character
diff --git a/man/ZarrArray.Rd b/man/ZarrArray.Rd
index df4d60f..9b69386 100644
--- a/man/ZarrArray.Rd
+++ b/man/ZarrArray.Rd
@@ -221,7 +221,13 @@ TODO
 TODO
 
 
-TODO
+For parallel usage
+
+
+For parallel usage
+
+
+For non-parallel usage
 
 
 TODO
diff --git a/man/as_scalar.Rd b/man/as_scalar.Rd
index 1708c1d..3f4a75d 100644
--- a/man/as_scalar.Rd
+++ b/man/as_scalar.Rd
@@ -2,7 +2,8 @@
 % Please edit documentation in R/atomic.R
 \name{as_scalar}
 \alias{as_scalar}
-\title{Convert a value to a scalar to opt-out of R default vector casting behavior.}
+\title{Convert a value to a scalar to opt-out of R default vector casting behavior.
+This uses the \code{jsonlite::unbox} function to "tag" the value as a scalar.}
 \usage{
 as_scalar(obj)
 }
@@ -14,4 +15,5 @@ The value wrapped as a scalar.
 }
 \description{
 Convert a value to a scalar to opt-out of R default vector casting behavior.
+This uses the \code{jsonlite::unbox} function to "tag" the value as a scalar.
 }
diff --git a/man/ensure_integer_vec.Rd b/man/ensure_integer_vec.Rd
new file mode 100644
index 0000000..752e1c8
--- /dev/null
+++ b/man/ensure_integer_vec.Rd
@@ -0,0 +1,14 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/atomic.R
+\name{ensure_integer_vec}
+\alias{ensure_integer_vec}
+\title{Ensure that scalars and lists of integers are converted to
+an R vector of integers.}
+\usage{
+ensure_integer_vec(selection)
+}
+\description{
+Ensure that scalars and lists of integers are converted to
+an R vector of integers.
+}
+\keyword{internal}
diff --git a/man/ensure_list.Rd b/man/ensure_list.Rd
new file mode 100644
index 0000000..ef1875d
--- /dev/null
+++ b/man/ensure_list.Rd
@@ -0,0 +1,14 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/atomic.R
+\name{ensure_list}
+\alias{ensure_list}
+\title{Ensure that scalars, single slices, and R integer vectors are converted
+to a list containing either R integer vectors or slice instances as values.}
+\usage{
+ensure_list(selection)
+}
+\description{
+Ensure that scalars, single slices, and R integer vectors are converted
+to a list containing either R integer vectors or slice instances as values.
+}
+\keyword{internal}
diff --git a/man/is_integer.Rd b/man/is_integer.Rd
new file mode 100644
index 0000000..94d726c
--- /dev/null
+++ b/man/is_integer.Rd
@@ -0,0 +1,12 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/atomic.R
+\name{is_integer}
+\alias{is_integer}
+\title{Check if a value is an integer R vector or scalar.}
+\usage{
+is_integer(s)
+}
+\description{
+Check if a value is an integer R vector or scalar.
+}
+\keyword{internal}
diff --git a/man/is_integer_list.Rd b/man/is_integer_list.Rd
new file mode 100644
index 0000000..54be216
--- /dev/null
+++ b/man/is_integer_list.Rd
@@ -0,0 +1,12 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/atomic.R
+\name{is_integer_list}
+\alias{is_integer_list}
+\title{Check that a value is a list of one or more integers.}
+\usage{
+is_integer_list(s)
+}
+\description{
+Check that a value is a list of one or more integers.
+}
+\keyword{internal}
diff --git a/man/is_integer_scalar.Rd b/man/is_integer_scalar.Rd
new file mode 100644
index 0000000..e3d5ef7
--- /dev/null
+++ b/man/is_integer_scalar.Rd
@@ -0,0 +1,12 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/atomic.R
+\name{is_integer_scalar}
+\alias{is_integer_scalar}
+\title{Check if a value is both a scalar (tagged by as_scalar) and an integer.}
+\usage{
+is_integer_scalar(s)
+}
+\description{
+Check if a value is both a scalar (tagged by as_scalar) and an integer.
+}
+\keyword{internal}
diff --git a/man/is_integer_vec.Rd b/man/is_integer_vec.Rd
new file mode 100644
index 0000000..65ae76c
--- /dev/null
+++ b/man/is_integer_vec.Rd
@@ -0,0 +1,14 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/atomic.R
+\name{is_integer_vec}
+\alias{is_integer_vec}
+\title{Check that a value is a vector of one or more integers and has not been
+explicitly tagged as a scalar.}
+\usage{
+is_integer_vec(s)
+}
+\description{
+Check that a value is a vector of one or more integers and has not been
+explicitly tagged as a scalar.
+}
+\keyword{internal}
diff --git a/man/is_scalar.Rd b/man/is_scalar.Rd
index 49d8dab..9e1ae67 100644
--- a/man/is_scalar.Rd
+++ b/man/is_scalar.Rd
@@ -2,7 +2,7 @@
 % Please edit documentation in R/atomic.R
 \name{is_scalar}
 \alias{is_scalar}
-\title{Check if a value is a scalar.}
+\title{Check if a value is a scalar (i.e., a one-element vector that was converted with as_scalar).}
 \usage{
 is_scalar(s)
 }
@@ -13,5 +13,5 @@ is_scalar(s)
 TRUE if the value is a scalar, FALSE otherwise.
 }
 \description{
-Check if a value is a scalar.
+Check if a value is a scalar (i.e., a one-element vector that was converted with as_scalar).
 }
diff --git a/man/pizzarr_option_defaults.Rd b/man/pizzarr_option_defaults.Rd
new file mode 100644
index 0000000..2bca041
--- /dev/null
+++ b/man/pizzarr_option_defaults.Rd
@@ -0,0 +1,16 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/options.R
+\docType{data}
+\name{pizzarr_option_defaults}
+\alias{pizzarr_option_defaults}
+\title{pizzarr_option_defaults}
+\format{
+An object of class \code{list} of length 3.
+}
+\usage{
+pizzarr_option_defaults
+}
+\description{
+pizzarr_option_defaults
+}
+\keyword{datasets}
diff --git a/man/zb_slice.Rd b/man/zb_slice.Rd
index f32517c..f4c0203 100644
--- a/man/zb_slice.Rd
+++ b/man/zb_slice.Rd
@@ -2,7 +2,7 @@
 % Please edit documentation in R/slicing.R
 \name{zb_slice}
 \alias{zb_slice}
-\title{Convenience function for the internal Sliceclass constructor
+\title{Convenience function for the internal Slice class constructor
 with zero-based indexing and exclusive stop index.}
 \usage{
 zb_slice(start, stop = NA, step = NA)
@@ -15,6 +15,6 @@ zb_slice(start, stop = NA, step = NA)
 \item{step}{The step size.}
 }
 \description{
-Convenience function for the internal Sliceclass constructor
+Convenience function for the internal Slice class constructor
 with zero-based indexing and exclusive stop index.
 }