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.