Unreleased

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)

Removed

Fixed

Security

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

1.10.2

Port resume-ingest mode from Python to R

1.10.1

This release contains a single Python-only bug fix

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()

1.9.5

This release contains a single Python-only bug fix

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.

1.9.3

This release contains a single Python-only performance improvement

1.9.2

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

1.9.1

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

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

1.8.1

Changes

This is a release with Python changes only

1.8.0

Changes

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

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

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

Uh oh!