Reticulate backend

NAMESPACE

@@ -1,5 +1,7 @@
 # Generated by roxygen2: do not edit by hand
 
+S3method(py_to_r,collections.abc.Mapping)
+S3method(py_to_r,pandas.core.indexes.base.Index)
 export(AnnData)
 export(InMemoryAnnData)
 export(from_Seurat)
@@ -8,6 +10,7 @@ export(generate_dataset)
 export(read_h5ad)
 export(to_HDF5AnnData)
 export(to_InMemoryAnnData)
+export(to_ReticulateAnnData)
 export(to_Seurat)
 export(to_SingleCellExperiment)
 export(write_h5ad)

R/AbstractAnnData.R

@@ -162,10 +162,14 @@ AbstractAnnData <- R6::R6Class("AbstractAnnData", # nolint
     to_Seurat = function() {
       to_Seurat(self)
     },
-    #' @description Convert to an InMemory AnnData
+    #' @description Convert to an InMemoryAnnData
     to_InMemoryAnnData = function() {
       to_InMemoryAnnData(self)
     },
+    #' @description Convert to a ReticulateAnnData
+    to_ReticulateAnnData = function() {
+      to_ReticulateAnnData(self)
+    },
     #' @description Convert to an HDF5 Backed AnnData
     #' @param path The path to the HDF5 file
     to_HDF5AnnData = function(path) {
@@ -178,6 +182,7 @@ AbstractAnnData <- R6::R6Class("AbstractAnnData", # nolint
     # @param mat A matrix to validate
     # @param label Must be `"X"` or `"layer[[...]]"` where `...` is
     #   the name of a layer.
+
     # @param shape Expected dimensions of matrix
     # @param expected_rownames
     # @param excepted_colnames

R/Reticulate-Read.R

@@ -0,0 +1,52 @@
+
+# copied from https://github.com/dynverse/anndata/blob/main/R/reticulate_conversions.R#L1/
+py_to_r_ifneedbe <- function(x) {
+  requireNamespace("reticulate")
+  if (inherits(x, "python.builtin.object")) {
+    reticulate::py_to_r(x)
+  } else {
+    x
+  }
+}
+
+#' Convert between Python and R objects
+#'
+#' @param x A Python object.
+#' @param name A name
+#' @param value A value
+#'
+#' @return An \R object, as converted from the Python object.
+#'
+#' @name r-py-conversion
+#' @export
+# copied from https://github.com/dynverse/anndata/blob/main/R/reticulate_conversions.R#L61
+py_to_r.pandas.core.indexes.base.Index <- function(x) { # nolint
+  requireNamespace("reticulate")
+  python_builtins <- reticulate::import_builtins()
+  out <- python_builtins$list(x)
+  attr(out, "name") <- py_to_r_ifneedbe(x$name)
+  out
+}
+
+#' @name r-py-conversion
+#' @export
+# copied from https://github.com/dynverse/anndata/blob/main/R/reticulate_conversions.R#LL77C38-L90C2
+py_to_r.collections.abc.Mapping <- function(x) { # nolint
+  requireNamespace("reticulate")
+  python_builtins <- reticulate::import_builtins()
+
+  x_list <- python_builtins$dict(x)
+
+  # convert members of x_list if need be
+  for (i in seq_along(x_list)) {
+    if (inherits(x_list[[i]], "python.builtin.object")) {
+      x_list[[i]] <- py_to_r_ifneedbe(x_list[[i]])
+    }
+  }
+
+  x_list
+}
+
+# `py_to_r.collections.abc.Set` ?
+# `py_to_r.collections.abc.KeysView` ?
+# `py_to_r.scipy.sparse.csc.csc_matrix` ?