diff --git a/apis/r/DESCRIPTION b/apis/r/DESCRIPTION index 8d556fb61d..68f13ef250 100644 --- a/apis/r/DESCRIPTION +++ b/apis/r/DESCRIPTION @@ -6,7 +6,7 @@ Description: Interface for working with 'TileDB'-based Stack of Matrices, like those commonly used for single cell data analysis. It is documented at ; a formal specification available is at . -Version: 1.14.99 +Version: 1.14.99.1 Authors@R: c( person(given = "Aaron", family = "Wolen", role = c("cre", "aut"), email = "aaron@tiledb.com", diff --git a/apis/r/NEWS.md b/apis/r/NEWS.md index 3a4f286f88..a24e892df0 100644 --- a/apis/r/NEWS.md +++ b/apis/r/NEWS.md @@ -1,5 +1,28 @@ # Unreleased +## Changes + +* Remove unused `fragment_count` accessor [#3054](https://github.com/single-cell-data/TileDB-SOMA/pull/3054) + +# tiledbsoma 1.14.1 + +## Changes + +* Fixes a Python-only bug [#3013](https://github.com/single-cell-data/TileDB-SOMA/pull/3013) + +# tiledbsoma 1.14.0 + +## Changes + +* New `resize` and `tiledbsoma_upgrade_shape` accessors as part of the [new-shape project](https://github.com/single-cell-data/TileDB-SOMA/issues/2407) +* Make use of timestamp ranges in libtiledbsoma +* Simplify timestamp ranges; strengthen assumptions about `tiledb_timestamp` +* Use cached timestamps in `$write()` and `$create()` +* Fix bug in blockwise iteration +* Lay groundwork for cached SOMA contexts within objects rather than re-creating contexts +* SOMA context objects are used throughout SOMA object creation +* Add value-checking for `axis` parameter when initializing blockwise reads + # tiledbsoma 1.13.1 ## Changes diff --git a/apis/r/R/TileDBArray.R b/apis/r/R/TileDBArray.R index 64923c82b0..3f990dd093 100644 --- a/apis/r/R/TileDBArray.R +++ b/apis/r/R/TileDBArray.R @@ -291,13 +291,6 @@ TileDBArray <- R6::R6Class( #' @return A character vector with the array index (dimension) names index_column_names = function() { self$dimnames() - }, - - #' @description Get number of fragments in the array (lifecycle: maturing) - fragment_count = function() { - tiledb::tiledb_fragment_info_get_num( - tiledb::tiledb_fragment_info(self$uri) - ) } ), diff --git a/apis/r/man/SOMAArrayBase.Rd b/apis/r/man/SOMAArrayBase.Rd index 61ba26420e..246111ddac 100644 --- a/apis/r/man/SOMAArrayBase.Rd +++ b/apis/r/man/SOMAArrayBase.Rd @@ -39,7 +39,6 @@ experimental)
  • tiledbsoma::TileDBArray$colnames()
  • tiledbsoma::TileDBArray$dimensions()
  • tiledbsoma::TileDBArray$dimnames()
    • -
  • tiledbsoma::TileDBArray$fragment_count()
  • tiledbsoma::TileDBArray$get_metadata()
  • tiledbsoma::TileDBArray$index_column_names()
  • tiledbsoma::TileDBArray$maxshape()
    • diff --git a/apis/r/man/SOMADataFrame.Rd b/apis/r/man/SOMADataFrame.Rd index 89e7ed55e7..5f872002ef 100644 --- a/apis/r/man/SOMADataFrame.Rd +++ b/apis/r/man/SOMADataFrame.Rd @@ -40,7 +40,6 @@ row and is intended to act as a join key for other objects, such as
  • tiledbsoma::TileDBArray$colnames()
  • tiledbsoma::TileDBArray$dimensions()
  • tiledbsoma::TileDBArray$dimnames()
    • -
  • tiledbsoma::TileDBArray$fragment_count()
  • tiledbsoma::TileDBArray$get_metadata()
  • tiledbsoma::TileDBArray$index_column_names()
  • tiledbsoma::TileDBArray$ndim()
    • diff --git a/apis/r/man/SOMADataFrameCreate.Rd b/apis/r/man/SOMADataFrameCreate.Rd index 0eb3452361..36a6cfbdbd 100644 --- a/apis/r/man/SOMADataFrameCreate.Rd +++ b/apis/r/man/SOMADataFrameCreate.Rd @@ -11,7 +11,8 @@ SOMADataFrameCreate( ingest_mode = c("write", "resume"), platform_config = NULL, tiledbsoma_ctx = NULL, - tiledb_timestamp = NULL + tiledb_timestamp = NULL, + soma_context = NULL ) } \arguments{ diff --git a/apis/r/man/SOMADataFrameOpen.Rd b/apis/r/man/SOMADataFrameOpen.Rd index 30ecfbf105..7e39712c2b 100644 --- a/apis/r/man/SOMADataFrameOpen.Rd +++ b/apis/r/man/SOMADataFrameOpen.Rd @@ -9,7 +9,8 @@ SOMADataFrameOpen( mode = "READ", platform_config = NULL, tiledbsoma_ctx = NULL, - tiledb_timestamp = NULL + tiledb_timestamp = NULL, + soma_context = NULL ) } \arguments{ diff --git a/apis/r/man/SOMADenseNDArray.Rd b/apis/r/man/SOMADenseNDArray.Rd index e2156ec384..f508dffafd 100644 --- a/apis/r/man/SOMADenseNDArray.Rd +++ b/apis/r/man/SOMADenseNDArray.Rd @@ -51,7 +51,6 @@ The \code{write} method is currently limited to writing from 2-d matrices.
  • tiledbsoma::TileDBArray$colnames()
  • tiledbsoma::TileDBArray$dimensions()
  • tiledbsoma::TileDBArray$dimnames()
    • -
  • tiledbsoma::TileDBArray$fragment_count()
  • tiledbsoma::TileDBArray$get_metadata()
  • tiledbsoma::TileDBArray$index_column_names()
  • tiledbsoma::TileDBArray$maxshape()
    • diff --git a/apis/r/man/SOMANDArrayBase.Rd b/apis/r/man/SOMANDArrayBase.Rd index 1f43ce1306..514cd0e48d 100644 --- a/apis/r/man/SOMANDArrayBase.Rd +++ b/apis/r/man/SOMANDArrayBase.Rd @@ -35,7 +35,6 @@ Adds NDArray-specific functionality to the \code{\link{SOMAArrayBase}} class.
  • tiledbsoma::TileDBArray$colnames()
  • tiledbsoma::TileDBArray$dimensions()
  • tiledbsoma::TileDBArray$dimnames()
    • -
  • tiledbsoma::TileDBArray$fragment_count()
  • tiledbsoma::TileDBArray$get_metadata()
  • tiledbsoma::TileDBArray$index_column_names()
  • tiledbsoma::TileDBArray$maxshape()
    • diff --git a/apis/r/man/SOMASparseNDArray.Rd b/apis/r/man/SOMASparseNDArray.Rd index 7a030c04f0..b69003a99c 100644 --- a/apis/r/man/SOMASparseNDArray.Rd +++ b/apis/r/man/SOMASparseNDArray.Rd @@ -51,7 +51,6 @@ the object are overwritten and new index values are added. (lifecycle: maturing)
  • tiledbsoma::TileDBArray$colnames()
  • tiledbsoma::TileDBArray$dimensions()
  • tiledbsoma::TileDBArray$dimnames()
    • -
  • tiledbsoma::TileDBArray$fragment_count()
  • tiledbsoma::TileDBArray$get_metadata()
  • tiledbsoma::TileDBArray$index_column_names()
  • tiledbsoma::TileDBArray$maxshape()
    • diff --git a/apis/r/man/TileDBArray.Rd b/apis/r/man/TileDBArray.Rd index eb3225c57e..3f07005e7d 100644 --- a/apis/r/man/TileDBArray.Rd +++ b/apis/r/man/TileDBArray.Rd @@ -41,7 +41,6 @@ Base class for representing an individual TileDB array. \item \href{#method-TileDBArray-attrnames}{\code{TileDBArray$attrnames()}} \item \href{#method-TileDBArray-colnames}{\code{TileDBArray$colnames()}} \item \href{#method-TileDBArray-index_column_names}{\code{TileDBArray$index_column_names()}} -\item \href{#method-TileDBArray-fragment_count}{\code{TileDBArray$fragment_count()}} \item \href{#method-TileDBArray-clone}{\code{TileDBArray$clone()}} } } @@ -359,16 +358,6 @@ Retrieve names of index (dimension) columns (lifecycle: maturing) \subsection{Returns}{ A character vector with the array index (dimension) names } -} -\if{html}{\out{
    }} -\if{html}{\out{}} -\if{latex}{\out{\hypertarget{method-TileDBArray-fragment_count}{}}} -\subsection{Method \code{fragment_count()}}{ -Get number of fragments in the array (lifecycle: maturing) -\subsection{Usage}{ -\if{html}{\out{
    }}\preformatted{TileDBArray$fragment_count()}\if{html}{\out{
    }} -} - } \if{html}{\out{
    }} \if{html}{\out{}} diff --git a/apis/r/man/TileDBObject.Rd b/apis/r/man/TileDBObject.Rd index ae17275794..3aa8406c8c 100644 --- a/apis/r/man/TileDBObject.Rd +++ b/apis/r/man/TileDBObject.Rd @@ -46,7 +46,8 @@ Create a new TileDB object. (lifecycle: maturing) platform_config = NULL, tiledbsoma_ctx = NULL, tiledb_timestamp = NULL, - internal_use_only = NULL + internal_use_only = NULL, + soma_context = NULL )}\if{html}{\out{}} } diff --git a/apis/r/man/soma_context.Rd b/apis/r/man/soma_context.Rd index e910fafcaa..e052e0dda5 100644 --- a/apis/r/man/soma_context.Rd +++ b/apis/r/man/soma_context.Rd @@ -16,3 +16,7 @@ An external pointer object containing a shared pointer instance of \code{SOMACon \description{ Create and cache a SOMA Context Object } +\examples{ +cfgvec <- as.vector(tiledb::tiledb_config()) # TileDB Config in vector form +sctx <- soma_context(cfgvec) +}