NEWS

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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