NEWS

---

tiledbsoma 2.3.0

Added

• A new SOMAContext method was added that replaces SOMATileDBContext. (#4355)
• New methods set_default_context and get_default_context for setting and getting the SOMAContext. (#4364)
• Added SOMAContext$is_tiledbv2() and SOMAContext$is_tiledbv3() methods to check the data protocol for a given URI.
• Added Carrara (TileDB v3) support for collection classes. Child objects created at nested Carrara URIs are automatically registered with their parent collection.

Changed

• SOMACollectionBase$set() now throws an unsupportedOperationError for Carrara URIs since the Carrara data model does not support adding external objects to collections. Use add_new_* methods instead.
• Reduced some internal diagnostic logging from INFO to DEBUG level.

Deprecated

• The function soma_context is deprecated. Use class SOMAContext instead. (#4355)
• The parameter tiledbsoma_ctx is deprecated in all functions/methods that use it. Use the parameter context instead. (#4355)
• SOMATileDBContext is deprecated. Use class SOMAContext instead. (#4355)

Fixed

• Fixed SOMACollectionBase$set() allowing replacement of existing members after reopening the collection. The method now consistently rejects duplicate keys both within the same session and across sessions. (#4378)
• SOMATileDBContext no longer replaces sm.mem.reader.sparse_global_order.ratio_array_data when set in the input config. (#4355)
• Fixed SOMACollectionBase$remove() incorrectly accessing self$mode instead of calling self$mode().
• Fixed collection member cache not properly handling DELETE mode.

tiledbsoma 2.2.0

Changed

• Update TileDB core version to 2.30.0. (#4324)

tiledbsoma 2.1.2

Action required: Users who ingested BPCells data with version 2.1.0 or 2.1.1 must re-ingest with this version to ensure data correctness.

Fixed

• Addressed bug in BPCells ingestion, where data ingested in an iterated manner would only be written at the top of the array. Ingestion now proceeds down the array for each iteration. (#4317)

tiledbsoma 2.1.1

Changed

• Update TileDB core version to 2.29.2. (#4309)

Deprecated

Removed

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

• Add support for ingestion of BPCells-backed Seurat objects in write_soma() (#4273)

Changed

• Update TileDB core version to 2.29.1. (#4284)

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

• Update TileDB core to 2.28.1. (#4077)
• Remove RcppSpdlog and spld as dependencies. Logs are no longer forwarded through R output.

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

• New function get_tiledb_object_type() to replace tiledb::tiledb_object_type() (#3644)
• New function get_tiledb_version() to replace tiledb::tiledb_version() (#3644)
• New method SOMAArrayBase$is_sparse() to replace tiledb::is.sparse() (#3644)
• New method SOMAArrayBase$allows_duplicates() to replace tiledb::allows_dups() (#3644)
• New method SOMADataFrame$levels() to replace tiledb-r enum accessors (#3644)

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 1.10.2

• 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