NEWS

tiledbsoma 1.14.5

Changes

Fixes a Python-only bug #3225

tiledbsoma 1.14.4

Changes

Add new Arrow-to-R type mapper #3161
Expose block/random writer for sparse arrays #3204

tiledbsoma 1.14.3

Changes

Handle numeric coords properly when reading arrays 3145

tiledbsoma 1.14.2

Changes

Fixes a Python-only bug #3074

tiledbsoma 1.14.1

Changes

Fixes a Python-only bug #3013

tiledbsoma 1.14.0

Changes

New resize and tiledbsoma_upgrade_shape accessors as part of the new-shape project
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

Includes a fix for appended enumerations #2903

tiledbsoma 1.13.0

Changes

Updates the TileDB Core dependency to 2.25.0
The used_shape function is deprecated; shape mods are upcoming scheduled for TileDB-SOMA 1.15
Change $reopen(mode = ) default to not flip modes; require explicit mode parameter to be passed
Add drop_levels to SOMAExperimentAxisQuery -> ecosystem outgestors to drop unused factor levels

tiledbsoma 1.12.3

Changes

Updates the TileDB Core dependency to 2.24.2

tiledbsoma 1.12.2

Changes

No R changes; only an update for Python

tiledbsoma 1.12.1

Changes

Updates to TileDB Core 2.24.1

tiledbsoma 1.12.0

Changes

Updates to TileDB Core 2.24 and TileDB-R 0.28
Connect re-indexer to blockwise iterator to return re-indexed tables and matrices

tiledbsoma 1.11.4

Changes

Fixes a couple bugs observed in Python

tiledbsoma 1.11.3

Changes

Fixes an intermittent segfault observed in Python

tiledbsoma 1.11.2

Changes

New reopen method available from R

tiledbsoma 1.11.1

Changes

No R changes; only an update for Python

tiledbsoma 1.11.0

Changes

Add support for ingestion of SeuratCommand logs
Add support for outgestion of SeuratCommand logs
Add support for reading *m and *p layers from SOMAExperimentAxisQuery
Add support for blockwise iteration
Make reopen() a public method for all TileDBObjects
Add support for resume-mode in write_soma()
Push default-setting for TileDBCreateOptions to $initialize() instead of in the accessors
Muffle warnings for missing command logs when outgesting SOMA to Seurat
Have SOMADataFrame$shape() throw a not-yet-implemented error
Disable running SeuratObject::.CalcN() when outgesting from SOMA to Seurat
Clear timestamp when using $reopen() to reopen at the current time
Add support for the re-indexer

tiledbsoma 1.10.2

Port resume-ingest mode from Python to R

tiledbsoma 1.10.1

This release contains a single Python-only bug fix

tiledbsoma 1.10.0

Changes

Add support for ingestion of SeuratCommand logs
Add support for outgestion of SeuratCommand logs
Add support for reading *m and *p layers from SOMAExperimentAxisQuery
Add support for blockwise iteration
Make reopen() a public method for all TileDBObjects
Add support for resume-mode in write_soma()

tiledbsoma 1.9.5

This release contains a single Python-only bug fix

tiledbsoma 1.9.4

This release contains an in-progress blockwise iterator, work on which will be completed in a subsequent release.
Reverted nanoarrow use to vendored versions and refactored the use throughout R and adjusted the build steps accordingly.

tiledbsoma 1.9.3

This release contains a single Python-only performance improvement

tiledbsoma 1.9.2

This release contains a single Python-only modification for an API backward-compatibility update

tiledbsoma 1.9.1

This release contains a single Python-only modification for its build process

tiledbsoma 1.9.0

Changes

Add support for ingestion of SeuratCommand logs
Add support for outgestion of SeuratCommand logs
Add support for reading *m and *p layers from SOMAExperimentAxisQuery

tiledbsoma 1.8.1

Changes

This is a release with Python changes only

tiledbsoma 1.8.0

Changes

Add support for ingestion of SeuratCommand logs
Add support for outgestion of SeuratCommand logs

tiledbsoma 1.7.0

Changes

Add support for registering arrays with their parent collection in write_soma()
Add write_soma.character() to encode character vectors as SOMA arrays

tiledbsoma 1.6.0

Fixes

SOMADataFrame, SOMASparseNDArray, and SOMADenseNDArray's write() method now correctly leaves the array open in write mode

tiledbsoma 1.5.0

Changes

Add support for I/O of R factors as enumerated types in SOMADataFrame
Add support for writing SummarizedExperiment and SingleCellExperiment object to SOMAs
Add support for bounding boxes for sparse arrays
Add support for creating SOMADataFrames with ordered() columns
Add support for I/O between SOMA and SingleCellExperiment
Add support for updating obs and var
Write string attrs as UTF-8 (Python compatibility)
Optimize export of obsm/varm arrays to Seurat
Add axis_query() method to SOMAExperiment
Add to_sparse_matrix() method to SOMAExperimentAxisQuery
Force exporting v3 assays with SeuratObject v5 installed

tiledbsoma 1.4.0

This is the initial release of the tiledbsoma R package.

Changes

Added a NEWS.md file to track changes to the package
TileDBGroup gains a names method to retrieve the names of group members
Added SOMAMeasurement and SOMAExperiment classes
spdl is now used for logging
TileDB performance statistics can now be collected for analysis
Added support for performing axis-based queries against a SOMAExperiment via the SOMAExperimentAxisQuery class
TileDBArray class gained a colnames() method that returns the names of both dimensions and attributes
Added internal helpers to centrally validate coords and value_filter arguments
All R6 classes' create() method now return self rather than nothing
Fixed calculating of relative paths when 1 of the URIs contains the file:// prefix
Added PlatformConfig and SOMATileDBContext classes to handle SOMA and TileDB configuration
Add Seurat outgestors for SOMAExperimentAxisQuery objects
Numeric coordinates passed to SOMADataFrame$read() are now automatically upcast to int64 when necessary
Add ingestors to read data from Seurat objects
Add methods for listing and accessing bundled datasets, which now includes a SOMAExperiment containing the pbmc_small dataset from the SeuratObject package
New vignettes describing SOMA objects, reading data from them, and querying SOMA experiments
Objects added to SOMACollection-based classes using the add_new_*() methods now pass through their parent context and platform config
SOMAExperimentAxisQuery gained a to_sparse_matrix() method for retrieving data as a named sparse matrix
SOMAExperiment gained axis_query() to construct a SOMAExperimentAxisQuery object
Add SingleCellExperiment outgestor for SOMAExperimentAxisQuery objects