NEWS

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tiledbsoma 0.0.0

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