Changes in version 1.146.0
Major changes
o
Add environment for *anndata* v0.10.9. This is now the default
environment for the Python reader/writer.
Minor changes
o
Avoid deprecation warning due to setting dtype when creating
Python AnnData objects
o
Standardise code styling using *styler*
o
Add test using the more complete example H5AD file
Bug fixes
o
Correctly assign levels to factors in R reader with *anndata*
v0.7 files
o
Correctly set filepath in the R reader with reading adata.raw`
with use_hdf5 = TRUE (PR from @GabrielHoffman)
Changes in version 1.14.0
Major changes
o
Add environment for *anndata* v0.10.6. This is now the default
environment for the Python reader/writer.
Minor changes
o
Improve warnings when converting matrices fails
o
Minor change to writing DelayedArray matrices for compatibility
with *HDF5Array* >= v1.31.1
Bug fixes
o
Correctly handle use_backed = TRUE with newer *anndata*
versions
o
Correctly instantiate the *anndata* v0.10.2 environment
o
Minor fixes for typos etc.
Changes in version 1.12.0
Major changes
o
Add environments for *anndata* v0.9.2 and v0.10.2. Version
0.10.20 is now the default envrionment for the Python
reader/writer.
Minor changes
o
Changes for compatibility with *rhdf5* v2.45.1 including enum
types that simplifies reading of nullable types in the native R
reader
o
Dimensions are now passed correctly when converting the raw
slot
o
Backed sparse matrices are now converted in AnnData2SCE()
Changes in version 1.10.0
Major changes
o
Add compatibility with the *anndata* v0.8 H5AD format to the
the native R writer (By @jackkamm and @mtmorgan)
o
Add functions for converting *pandas* arrays used by *anndata*
when arrays have missing values
Minor changes
o
Add Robrecht Cannoodt and Jack Kamm as contributors!
o
Minor adjustments to tests to match reader changes
Changes in version 1.8.0
Major changes
o
Improve compatibility with the R *anndata* package. This
required modifying conversion functions so that Python objects
are explicitly converted rather than relying on automatic
conversion.
o
Added support for *numpy* recarrays. This solves a
long-standing issue and allows results from *scanpy*'s
rank_genes_groups() function to be read.
Minor changes
o
The Python version is now pinned in the *anndata* v0.7.6
environment for compatibility with changes in *basilisk*
o
Instatiate Python environments so they can be properly picked
up by basilisk::configureBasiliskEnv()
o
Allow missing obs/var names when use_hdf5 = TRUE
o
Minor changes to the UI functions for compatibility with *cli*
v3.4.0
o
Minor changes for compatibility with *Matrix* v1.4-2
o
Improvements to the UI for warnings
o
Updates and improvments to tests
Changes in version 1.6.0
Major changes
o
Added support for multiple *basilisk* environments with
different *anndata* versions. Users can now specify the
environment to use with options in readH5AD() and writeH5AD().
To faciliate this some exported objects where converted to
functions but this should only effect developers.
o
Updated the default environment to use *anndata* v0.8.0. This
is a major update and files written with v0.8.0 cannot be read
by previous *anndata* versions. This was the motivation for
supporting multiple environments and users can select the
previous environment with *anndata* v0.7.6 if compatibility is
required.
o
Standardise naming in AnnData2SCE(). Column names of data
frames and names of list items will now be modified to match R
conventions (according to make.names()). When this happens a
warning will be issued listing the modifications. This makes
sure than everything in the created SingleCellExperiment is
accessible.
Minor changes
o
Allow data.frame's stored in varm to be converted in
SCE2AnnData()
o
Minor updates to the vignette and other documentation.
o
Updates to tests to match the changes above.
Changes in version 1.4.0
o
Add arguments to control how slots are converted in
AnnData2SCE() and SCE2AnnData(). Each slot can now be fully
converted, skipped entirely or only selected items converted.
o
Add support for converting the raw slot to an altExp in
AnnData2SCE()
o
Add recursive conversion of lists in AnnData2SCE()
o
Add progress messages to various functions. These can be
controlled by function arguments or a global variable.
o
Add long tests for various public datasets. This should help to
make the package more robust
o
Fix bug in converting dgRMatrix sparse matrices
o
Correctly handle DataFrame objects stored in adata.obsm
Changes in version 1.2.0
o
Update *anndata* and other Python dependencies, now using
*anndata* v0.7.6
o
Improved conversion checks for all slots in AnnData2SCE()
o
Enable return conversion of the varm slot in AnnData2SCE()
o
Avoid converting obsp and varp to dense matrices in
AnnData2SCE()
o
AnnData2SCE() should now always return dgCMatrix matrices when
assays are sparse
o
More consistent conversion of metadata to uns in SCE2AnnData()
o
Handle conversion of list columns in colData and rowData in
SCE2AnnData()
o
Better support for converting *anndata* SparseDataset arrays
o
Improved support for conversion of HDF5 backed AnnData objects
o
Better support for writing DelayedArray assays in writeH5AD()
o
Store X_name in AnnData2SCE() for use by SCE2AnnData() and add
an X_name argument to AnnData2SCE() and readH5AD()
o
Add a compression argument to writeH5AD()
o
Add an experimental native R reader to readH5AD()
o
Export zellkonverterAnnDataEnv for use by other packages
Changes in version 1.0.0
o Accepted into Bioconductor for Release 3.12
o
zellkonverter provides methods to convert between Python
AnnData objects and SingleCellExperiment objects. These are
primarily intended for use by downstream Bioconductor packages
that wrap Python methods for single-cell data analysis. It also
includes functions to read and write H5AD files used for saving
AnnData objects to disk.