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Changelog

Source: NEWS.md

tiledbsoma 2.1.0

This release adds support for ingestion of BPCells-backed Seurat objects in write_soma(), adds warnings for new deprecations, and updates the TileDB core version to 2.29.1.

Added

Changed

Deprecated

  • Mark SOMANDArrayBase$set_data_type() for deprecation. (#4279)
  • Mark setting domain to NULL in SOMADataFrame$create() for deprecation. (#4274)

tiledbsoma 2.0.0

This release is the first TileDB-SOMA release that follows our new versioning policy (see the developer docs). It introduces the new DELETE mode and deprecates removing elements from a Collection in WRITE mode. It also updates the core TileDB version to 2.28.1.

Added

  • Add delete mode specified by mode="DELETE". (#4125)

Changed

Deprecated

  • Deprecate removing elements from a collection in write mode. In the future, all new removals will need to be done in delete mode. (#4125)

tiledbsoma 1.18.0

Added

  • New SOMAObject base class to serve as root for SOMAArrayBase and SOMACollectionBase (#3771)
  • New field SOMACollectionBase$members to get a list with the members of a collection (#3771)

Changed

  • Handshake internal_use_only = "allowed_use" for $new(), $open(), and $create() has been replaced with environment scoping; use of factory functions for opening and creation is now mandatory (#3771)
  • TileDBObject, TileDBArray, and TileDBGroup classes have been removed (#3771)
  • SOMACollection$to_list() and SOMACollection$to_data_frame() have been removed as they were unused public internal methods inherited from TileDBGroup (#3771)

Removed

  • SOMAArray$object has been removed (#3771)

tiledbsoma 1.17.0

Removed

  • TileDBURI class has been removed (#3644)
  • arrow <> TileDB-R helpers have been removed (#3644)
    • arrow_field_from_tiledb_dim()
    • arrow_field_from_tiledb_attr()
    • arrow_schema_from_tiledb_schema()

Added

Changed

  • Update TileDB core to 2.28.0 (#4057)
  • TileDBArray$attributes() has been promoted to SOMAArrayBase$attributes() and returns a named list instead of an external pointer (#3644)

Fixed

  • Fix C++20 flag to be a configuration option instead of hard-coded (#4051)

tiledbsoma 1.16.0

  • Encode string metadata as TILEDB_STRING_UTF8 instead of TILEDB_STRING_ASCII
  • Use S3 method dispatch on integer64 instead of directly calling the S3 methods
  • [c++] Replace SOMAArray read and write calls with ManagedQuery #3678
  • Remove used_shape, which was deprecated in 1.15 with scheduled removal in 1.16 #3723

tiledbsoma 1.15.7

  • This release contains Python-only bugfixes

tiledbsoma 1.15.6

  • This release contains Python-only bugfixes

tiledbsoma 1.15.5

  • This release contains a Python-only bugfix

tiledbsoma 1.15.4

  • This release contains Python-only updates for spatial transcriptomics

tiledbsoma 1.15.3

  • This release contains Python-only bugfixes

tiledbsoma 1.15.2

  • This release contains a Python-only bugfix

tiledbsoma 1.15.1

  • Encode string metadata as TILEDB_STRING_UTF8 instead of TILEDB_STRING_ASCII #3469

tiledbsoma 1.15.0

Changes

  • Remove unused fragment_count accessor #3054
  • Implement missing domain argument to SOMADataFrame create #3032
  • Use libtiledbsoma for R schema evolution #3100
  • Push attrnames down to C++ #3121
  • Push schema accessor down to libtiledbsoma #3079
  • Handle numeric coords properly when reading arrays
  • Remove two more tiledb::schema callsites #3160
  • Add new Arrow-to-R type mapper
  • Add transitional/non-exported parse_query_condition_new #3162
  • Apply new parse_query_condition #3174
  • Apply new non_empty_domain #3176
  • Support for dense current domain with core 2.27 #3180
  • Fix is_named_list bug for half-named lists #3183
  • Expose block/random writer for sparse arrays #3204
  • Min-sizing for dataframes/arrays with new shape feature #3208
  • Proper prefixing for shape-related methods #3237
  • Bindings for upgrade_domain #3238
  • Apply styler::style_pkg() #3239
  • Plumb old-style SOMATileDBContext into new-style soma_context() #3252
  • Fixes for dense arrays and yet-to-be-released core 2.27 #3270
  • More fixes for unit-test cases with dense + core 2.27 #3280
  • Add initial support for ragged array writing for Seurat v5 by @mojaveazure in #2523
  • Remove 2.27-related feature flag by @johnkerl in #3368
  • Revert #3300 by @johnkerl in #3358
  • Enforce dataframe domain lower bound == 0 by @johnkerl in #3300
  • Data refresh for new shapes by @johnkerl in #3303
  • Move beyond the new-shape feature flag by @johnkerl in #3301
  • Note on dev installs and spdlog failures by @johnkerl in #3324
  • Remove tiledb-r specific install by @mojaveazure in #3319
  • Try to unbreak r-valgrind CI by @johnkerl in #3318
  • Avoid log truncation with “Last 13 lines of output” by @johnkerl in #3313
  • Run tests in closer to internal-dependency order by @johnkerl in #3311
  • Use standard name zzz.R for init code by @johnkerl in #3332
  • Address two more compiler warnings by @johnkerl in #3320
  • Add support for writing Seurat v5 ragged arrays
  • Update docstrings for domain argument to create #3396
  • Vignette for new-shape feature #3302
  • Fix blockwise iterator + re-indexer to return re-indexed shape instead of full domain
  • Docstring audit for new shape #3399
  • Add check_only support for domain/shape updates #3400
  • Adjust blockwise + re-indexer to return condensed matrix, not full domain #3395
  • [c++] Use core 2.27.0.rc5 #3410
  • [c++] Use core 2.27.0 #3422

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

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 1.13.0

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 1.6.0

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