Doco (#81)

keller-mark · May 21, 2024 · 572ff32 · 572ff32
1 parent c74a9c3
commit 572ff32
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Showing 37 changed files with 1,601 additions and 179 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -29,7 +29,7 @@ Imports:
 Encoding: UTF-8
 LazyData: true
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.1
 Suggests: 
     testthat,
     knitr,

diff --git a/R/attributes.R b/R/attributes.R
@@ -10,7 +10,7 @@
 #' @export
 Attributes <- R6::R6Class("Attributes",
   private = list(
-    #' @field cached_aslist The attributes cached as a list.
+
     cached_aslist = NULL,
 
     get_nosync = function() {
@@ -55,6 +55,10 @@ Attributes <- R6::R6Class("Attributes",
     #' @description
     #' Create a new Attributes instance.
     #' @param store Attributes store, already initialized.
+    #' @param key description key to use for attributes (.attrs is default)
+    #' @param read_only logical
+    #' @param cache logical
+    #' @param synchronizer object
     #' @return An `Attributes` instance.
     initialize = function(store, key = NA, read_only = FALSE, cache = TRUE, synchronizer = NA) {
       if(is_na(key)) {
@@ -67,6 +71,9 @@ Attributes <- R6::R6Class("Attributes",
       private$cached_aslist <- NA
       self$synchronizer <- synchronizer
     },
+    #' @description
+    #' convert attributes to list
+    #' @return list
     to_list = function() {
       if(self$cache && !is_na(private$cached_aslist)) {
         return(private$cached_aslist)
@@ -77,21 +84,43 @@ Attributes <- R6::R6Class("Attributes",
       }
       return(d)
     },
+    #' @description
+    #' refresh attributes
+    #' @return None
     refresh = function() {
       if(self$cache) {
-        private$cached_aslist <- private$get_nosync()
+        new_val <- private$get_nosync()
+
+        private$cached_aslist <- new_val
       }
     },
+    #' @description
+    #' check if object contains item
+    #' @param x object
+    #' @return logical
     contains = function(x) {
       return(x %in% names(self$to_list()))
     },
+    #' @description
+    #' get attribute
+    #' @param item character
+    #' @return item as list
     get_item = function(item) {
       return(self$to_list()[[item]])
     },
+    #' @description
+    #' set attribute
+    #' @param item character
+    #' @param value value to add or update
+    #' @return none
     set_item = function(item, value) {
       # TODO: support synchronizer
       private$set_item_nosync(item, value)
     },
+    #' @description
+    #' delete attribute
+    #' @param item character
+    #' @return none
     del_item = function(item) {
       # TODO: support synchronizer
       private$del_item_nosync(item)

diff --git a/R/dtypes.R b/R/dtypes.R
@@ -138,7 +138,7 @@ get_dtype_asrtype <- function(dtype) {
 #' @title Dtype Class
 #' @docType class
 #' @description
-#' 
+#'  TODO
 #' @rdname Dtype
 #' @export
 Dtype <- R6::R6Class("Dtype",
@@ -182,12 +182,18 @@ Dtype <- R6::R6Class("Dtype",
 
       self$object_codec <- object_codec
     },
+    #' @description
+    #' Get as R type
     get_asrtype = function() {
       return(get_dtype_asrtype(self$dtype))
     },
+    #' @description
+    #' basic type R type
     get_rtype = function() {
       return(get_dtype_rtype(self$basic_type))
     },
+    #' @description
+    #' get typed array
     get_typed_array_ctr = function() {
       rtype <- self$get_rtype()
       return(function(dim) array(data = rtype, dim = dim))

diff --git a/R/indexing.R b/R/indexing.R
@@ -4,16 +4,17 @@
 #' @title OIndex Class
 #' @docType class
 #' @description
-#'
+#'  TODO
 #' @rdname OIndex
 #' @keywords internal
 OIndex <- R6::R6Class("OIndex",
   public = list(
-    #' @field array
+    #' @field array array
     #' @keywords internal
     array = NULL,
     #' @description
     #' Create a new OIndex instance.
+    #' @param array array
     #' @return An `OIndex` instance.
     initialize = function(array) {
       self$array <- array
@@ -27,16 +28,17 @@ OIndex <- R6::R6Class("OIndex",
 #' @title VIndex Class
 #' @docType class
 #' @description
-#'
+#'  TODO
 #' @rdname VIndex
 #' @keywords internal
 VIndex <- R6::R6Class("VIndex",
   public = list(
-    #' @field array
+    #' @field array array
     #' @keywords internal
     array = NULL,
     #' @description
     #' Create a new VIndex instance.
+    #' @param array array
     #' @return A `VIndex` instance.
     initialize = function(array) {
       self$array <- array
@@ -50,23 +52,26 @@ VIndex <- R6::R6Class("VIndex",
 #' @title IntDimIndexer Class
 #' @docType class
 #' @description
-#'
+#'  TODO
 #' @rdname IntDimIndexer
 #' @keywords internal
 IntDimIndexer <- R6::R6Class("IntDimIndexer",
   inherit = DimIndexer,
   public = list(
-    #' @field dim_sel
+    #' @field dim_sel TODO
     #' @keywords internal
     dim_sel = NULL,
-    #' @field dim_len
+    #' @field dim_len TODO
     #' @keywords internal
     dim_len = NULL,
-    #' @field dim_chunk_len
+    #' @field dim_chunk_len TODO
     #' @keywords internal
     dim_chunk_len = NULL,
     #' @description
     #' Create a new IntDimIndexer instance.
+    #' @param dim_sel integer dimention selection
+    #' @param dim_len integer dimension length
+    #' @param dim_chunk_len integer dimension chunk length
     #' @return A `IntDimIndexer` instance.
     initialize = function(dim_sel, dim_len, dim_chunk_len) {
       # Normalize
@@ -77,6 +82,9 @@ IntDimIndexer <- R6::R6Class("IntDimIndexer",
       self$dim_chunk_len <- dim_chunk_len
       self$num_items <- 1
     },
+    #' @description 
+    #' TODO
+    #' @return a `ChunkDimProjection` instance
     iter = function() {
       # TODO: use generator/yield features from async package
       dim_chunk_index <- floor(self$dim_sel / self$dim_chunk_len)
@@ -100,21 +108,35 @@ IntDimIndexer <- R6::R6Class("IntDimIndexer",
 #' @title SliceDimIndexer Class
 #' @docType class
 #' @description
-#'
+#'  TODO
 #' @rdname SliceDimIndexer
 #' @keywords internal
 SliceDimIndexer <- R6::R6Class("SliceDimIndexer",
   inherit = DimIndexer,
   public = list(
+    #' @field dim_len dimension length
+    #' @keywords internal
     dim_len = NULL,
+    #' @field dim_chunk_len dimension chunk length
+    #' @keywords internal
     dim_chunk_len = NULL,
+    #' @field num_chunks number of chunks
+    #' @keywords internal
     num_chunks = NULL,
+    #' @field start start
+    #' @keywords internal
     start = NULL,
+    #' @field stop stop
+    #' @keywords internal
     stop = NULL,
+    #' @field step step
+    #' @keywords internal
     step = NULL,
-
     #' @description
     #' Create a new SliceDimIndexer instance.
+    #' @param dim_sel integer dimention selection
+    #' @param dim_len integer dimension length
+    #' @param dim_chunk_len integer dimension chunk length
     #' @return A `SliceDimIndexer` instance.
     initialize = function(dim_sel, dim_len, dim_chunk_len) {
       # Reference: https://github.com/gzuidhof/zarr.js/blob/292804/src/core/indexing.ts#L311
@@ -130,6 +152,9 @@ SliceDimIndexer <- R6::R6Class("SliceDimIndexer",
       self$num_items <- max(0, ceiling((self$stop - self$start) / self$step))
       self$num_chunks <- ceiling(self$dim_len / self$dim_chunk_len)
     },
+    #' @description 
+    #' TODO
+    #' @return TODO
     iter = function() {
       # TODO: use generator/yield features from async package
       dim_chunk_index_from <- floor(self$start / self$dim_chunk_len)
@@ -201,17 +226,19 @@ SliceDimIndexer <- R6::R6Class("SliceDimIndexer",
 #' @title BasicIndexer Class
 #' @docType class
 #' @description
-#'
+#'  TODO
 #' @rdname BasicIndexer
 #' @keywords internal
 BasicIndexer <- R6::R6Class("BasicIndexer",
   inherit = Indexer,
   public = list(
-    #' @field dim_indexers
+    #' @field dim_indexers TODO
     #' @keywords internal
     dim_indexers = NULL,
     #' @description
     #' Create a new VIndex instance.
+    #' @param selection selection TODO
+    #' @param array array TODO
     #' @return A `VIndex` instance.
     initialize = function(selection, array) {
       shape <- array$get_shape()
@@ -249,6 +276,9 @@ BasicIndexer <- R6::R6Class("BasicIndexer",
 
       self$dim_indexers <- dim_indexers
     },
+    #' @description 
+    #' TODO
+    #' @return TODO
     iter = function() {
       # TODO: use generator/yield features from async package
       result <- list()