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anndataR 0.99.0

  • Bump required R version to 4.5 in preparation for Bioconductor submission (PR #309)
  • Remove deprecated functions and arguments (PR #311, PR #313)
  • Minor cleanups and improvements (PR #313).
  • Add more tests to increase coverage (PR #315)

anndataR 0.2.0

Breaking changes

  • Switch the HDF5 back end to use the {rhdf5} package instead of {hdf5r} (PR #283, Fixes #272, #175, #299)
    • This addresses various issues related to H5AD files and allows better integration with Bioconductor. Most of the previous known issues have now been resolved.
    • It also greatly improves compatibility with H5AD files written by Python anndata
    • NOTE: Make sure to install {rhdf5} instead of {hdf5r} to be able to read and write H5AD files!

Major changes

  • Updates for compatibility with Python anndata >= 0.12.0 (PR #305, Fixes #304)
    • Add helpers for reading/writing NULL values to/from H5AD files
    • Writing of NULL values can be disabled by setting option(anndataR.write_null = FALSE) to allow the files to be read by Python anndata < 0.12.0
  • A counts or data layer is no longer required during Seurat conversion (PR #284)
    • There will still be a warning if neither of this is present as it may affect compatibility with {Seurat} functions

Minor changes

  • Use accessor functions/methods instead of direct slot access where possible (PR #291)
  • Refactor superfluous for loops (PR #298)
  • Change uses of sapply() to vapply() (PR #294)
  • Ignore development_status.Rmd vignette when building package (PR #296)
  • Remove anndataR.Rproj file from repository (PR #292)

Bug fixes

  • Fix a bug where string arrays were not transposed correctly when writing to H5AD files (PR #305)
  • Fix a bug where the dimensions of dense arrays were not properly conserved when reading from H5AD (PR #305)

Documentation

  • Simplify and update vignettes (PR #282)
  • Add Bioconductor installation instructions in preparation for submission (PR #297)

Testing

  • Improvements to round trip testing (PR #283, PR #293, PR #305)
    • Most round trip tests are now enabled and pass successfully
    • Conversion helpers have been added to assist with {reticulate} tests

anndataR 0.1.0 (inital release candidate)

Initial release candidate of {anndataR} including:

  • Native reading and writing of H5AD files
  • R implementations of InMemoryAnnData and HDF5AnnData objects
  • Conversion between AnnData and SingleCellExperiment or Seurat objects
  • Extensive function documentation and vignettes demonstrating usage
  • Comprehensive unit testing and identification of known issues