NEWS
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
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