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[r] Run styler::style_pkg() #3239

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[r] Run styler::style_pkg() #3239

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d288c8e
[r] Run `styler::style_pkg`
johnkerl Oct 25, 2024
05c076e
run devtools::document
johnkerl Oct 25, 2024
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62 changes: 32 additions & 30 deletions apis/r/R/BlockwiseIter.R
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Original file line number Diff line number Diff line change
Expand Up @@ -16,14 +16,12 @@ BlockwiseReadIterBase <- R6::R6Class(
#' @template param-coords-iter
#' @template param-dots-ignored
#'
initialize = function(
sr,
array,
coords,
axis,
...,
reindex_disable_on_axis = NA
) {
initialize = function(sr,
array,
coords,
axis,
...,
reindex_disable_on_axis = NA) {
super$initialize(sr)
stopifnot(
"'array' must be a 'SOMASparseNDArray'" = inherits(array, "SOMASparseNDArray")
Expand Down Expand Up @@ -99,8 +97,10 @@ BlockwiseReadIterBase <- R6::R6Class(
#'
#' @return \code{TRUE} if read is complete, otherwise \code{FALSE}
#'
read_complete = function() !self$coords_axis$has_next() ||
is.null(private$soma_reader_pointer),
read_complete = function() {
!self$coords_axis$has_next() ||
is.null(private$soma_reader_pointer)
},
#' @description Read the next chunk of the iterated read. If read
#' is complete, throws an \code{iterationCompleteWarning} warning and
#' returns \code{NULL}
Expand All @@ -109,7 +109,7 @@ BlockwiseReadIterBase <- R6::R6Class(
#'
read_next = function() {
if (is.null(private$soma_reader_pointer)) {
return(NULL)
return(NULL)
}
if (self$read_complete()) {
return(private$.readComplete())
Expand Down Expand Up @@ -156,8 +156,10 @@ BlockwiseReadIterBase <- R6::R6Class(
#' @field reindexable Shorthand to see if this iterator is poised to be
#' re-indexed or not
#'
reindexable = function() length(self$axes_to_reindex) ||
!bit64::as.integer64(self$axis) %in% self$reindex_disable_on_axis
reindexable = function() {
length(self$axes_to_reindex) ||
!bit64::as.integer64(self$axis) %in% self$reindex_disable_on_axis
}
),
private = list(
.array = NULL,
Expand All @@ -168,10 +170,12 @@ BlockwiseReadIterBase <- R6::R6Class(
.reindexers = list(),
# @description Throw an error saying that re-indexed
# iterators are not concatenatable
.notConcatenatable = function() stop(errorCondition(
message = "Re-indexed blockwise iterators are not concatenatable",
class = "notConcatenatableError"
)),
.notConcatenatable = function() {
stop(errorCondition(
message = "Re-indexed blockwise iterators are not concatenatable",
class = "notConcatenatableError"
))
},
# @description Reset internal state of SOMA Reader while keeping array open
reset = function() {
if (is.null(private$soma_reader_pointer)) {
Expand All @@ -183,7 +187,7 @@ BlockwiseReadIterBase <- R6::R6Class(
# @description Re-index an Arrow table
reindex_arrow_table = function(tbl) {
stopifnot(
"'tbl' must be an Arrow table" = R6::is.R6(tbl) && inherits(tbl, 'Table')
"'tbl' must be an Arrow table" = R6::is.R6(tbl) && inherits(tbl, "Table")
)
dname <- self$array$dimnames()[self$axis + 1L]
if (!dname %in% names(tbl)) {
Expand Down Expand Up @@ -289,15 +293,13 @@ BlockwiseSparseReadIter <- R6::R6Class(
#' @template param-dots-ignored
#' @template param-repr-read
#'
initialize = function(
sr,
array,
coords,
axis,
...,
repr = "T",
reindex_disable_on_axis = NA
) {
initialize = function(sr,
array,
coords,
axis,
...,
repr = "T",
reindex_disable_on_axis = NA) {
super$initialize(
sr,
array,
Expand All @@ -310,9 +312,9 @@ BlockwiseSparseReadIter <- R6::R6Class(
"Sparse reads only work with two-dimensional arrays" = self$array$ndim() == 2L
)
reprs <- c(
'T',
if (!bit64::as.integer64(0L) %in% self$reindex_disable_on_axis)'R',
if (!bit64::as.integer64(1L) %in% self$reindex_disable_on_axis) 'C'
"T",
if (!bit64::as.integer64(0L) %in% self$reindex_disable_on_axis) "R",
if (!bit64::as.integer64(1L) %in% self$reindex_disable_on_axis) "C"
)
private$.repr <- match.arg(repr, choices = reprs)
private$.shape <- sapply(coords, length)
Expand Down
4 changes: 2 additions & 2 deletions apis/r/R/ConfigList.R
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Original file line number Diff line number Diff line change
Expand Up @@ -10,7 +10,7 @@
#' @noMd
#'
ConfigList <- R6::R6Class(
classname = 'ConfigList',
classname = "ConfigList",
inherit = MappingBase,
public = list(
#' @param param Outer key or \dQuote{parameter} to fetch
Expand Down Expand Up @@ -54,7 +54,7 @@ ConfigList <- R6::R6Class(
"'param' must be a single character" = is_scalar_character(param)
)
parammap <- super$get(key = param, default = ScalarMap$new())
if (missing(key) && inherits(x = value, what = 'ScalarMap')) {
if (missing(key) && inherits(x = value, what = "ScalarMap")) {
parammap$update(map = value)
super$set(key = param, value = parammap)
return(invisible(x = self))
Expand Down
34 changes: 20 additions & 14 deletions apis/r/R/CoordsStrider.R
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Original file line number Diff line number Diff line change
Expand Up @@ -41,7 +41,7 @@ CoordsStrider <- R6::R6Class(
stopifnot(
"'start' must be a single integer value" = rlang::is_integerish(start, 1L, TRUE) ||
(inherits(start, "integer64") && length(start) == 1L && is.finite(start)),
"'end' must be a single integer value" = rlang::is_integerish(end, 1L, TRUE) ||
"'end' must be a single integer value" = rlang::is_integerish(end, 1L, TRUE) ||
(inherits(end, "integer64") && length(end) == 1L && is.finite(end)),
"'start' must be less than or equal to 'end'" = start <= end
)
Expand Down Expand Up @@ -140,18 +140,22 @@ CoordsStrider <- R6::R6Class(
#' @field start If set, the starting point of the iterated coordinates;
#' otherwise the minimum value of \code{self$coords}
#'
start = function() if (is.null(self$coords)) {
private$.start
} else {
bit64::min.integer64(self$coords)
start = function() {
if (is.null(self$coords)) {
private$.start
} else {
bit64::min.integer64(self$coords)
}
},
#' @field end If set, the end point of the iterated coordinates;
#' otherwise the maximum value of \code{self$coords}
#'
end = function() if (is.null(self$coords)) {
private$.end
} else {
bit64::max.integer64(self$coords)
end = function() {
if (is.null(self$coords)) {
private$.end
} else {
bit64::max.integer64(self$coords)
}
},
#' @field stride The stride, or how many coordinates to generate per
#' iteration; note: this field is settable, which will reset the iterator
Expand Down Expand Up @@ -184,10 +188,12 @@ CoordsStrider <- R6::R6Class(
.end = NULL,
.stride = NULL,
.index = NULL,
.stopIteration = function() stop(errorCondition(
"StopIteration",
class = "stopIteration"
))
.stopIteration = function() {
stop(errorCondition(
"StopIteration",
class = "stopIteration"
))
}
)
)

Expand Down Expand Up @@ -223,7 +229,7 @@ hasNext.CoordsStrider <- function(obj, ...) obj$has_next()
unlist64 <- function(x) {
stopifnot(
"'x' must be a list" = is.list(x),
"'x' must contain 'integer64' values" = all(vapply_lgl(x, inherits, what = 'integer64'))
"'x' must contain 'integer64' values" = all(vapply_lgl(x, inherits, what = "integer64"))
)
res <- bit64::integer64(sum(vapply_int(x, length)))
idx <- 1L
Expand Down
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