Version 1.1.1 (Bioconductor 3.23 - Development)

• Fix CI (PR #418).
• Add continuous benchmarking using bencher (PR #423, PR #425).
• Handle unnamed SingleCellExperiment assays in as_AnnData() by automatically assigning names with a warning (PR #420).
• Optimise sparse matrix reading performance by avoiding Matrix::sparseMatrix and constructing objects manually (PR #417).
• Allow manually setting chunk size for HDF5 writes (PR #424).
• Add auto-chunking for HDF5 writes to improve performance (PR #424).

Version 1.0.1 (Bioconductor 3.22)

Patch update to fix a few issues.

• Update author email address (PR #410).
• Fix linting issues (PR #412).
• Fix roundtrip test; ensure that X is always 2-dimensional (PR #413).
• Fix HDF5 write test; make sure to only pass CsparseMatrix to Seurat (PR #413).

Version 1.1.0 (Bioconductor 3.23 - Development)

First release for Bioconductor 3.23 (devel)

Version 1.0.0 (Bioconductor 3.22)

{anndataR} brings the AnnData object to R. It enables native reading and writing of H5AD files and conversion to/from SingleCellExperiment and Seurat objects.

Features

• An {R6} class to work with AnnData objects in R (either in-memory or on-disk)
• Natively read/write H5AD files without needing a Python environment
• Convert to/from SingleCellExperiment objects
• Convert to/from Seurat objects

Changes from v0.99.0

New features

• Implemented an AnnDataView class, which provides a lazy view of an AnnData object without copying data (PR #324)
• Implemented S3 methods for AbstractAnnData objects: dim, nrow, ncol, dimnames, rownames, colnames, and [ (PR #324)
• Add a ReticulateAnnData class for seamless Python integration via {reticulate} (PR #322, PR #372)
• Add a get_generator_types() function that returns allowed/example types for generate_dataset() (PR #354)

Major changes

• Refactor obs_names/var_names handling for improved data consistency (PR #328)
  • InMemoryAnnData now stores obs_names and var_names as separate private fields instead of relying on rownames of obs/var `data frames
  • HDF5AnnData maintains separate obs/var names management to ensure consistency between obs/var data frames and dim names
  • All matrix data (X, layers, obsm, varm, obsp, varp) is now stored internally without dim names for consistency
  • Dim names are added on-the-fly when users access data, ensuring proper obs/var` name display

Minor changes

• Handle slots that may have incomplete dimensions when converting from Seurat. These are now skipped with a warning instead of indirectly raising an error. (PR #369)
• Add a compression parameter to additional write operations in HDF5AnnData for consistency (PR #328)
• Refactor setter methods in HDF5AnnData and InMemoryAnnData to use pipe operators for cleaner code (PR #328)
• Generalise the layers created by generate_dataset() when format = "Seurat" (PR #354)
• Add checks for type arguments to generate_dataset() (PR #354)

Bug fixes

• Avoid writing character datasets to H5AD files with LZF compression as it causes R to crash (PR #356)
• Fix Seurat conversion for PCA loadings with variable feature subsets (PR #328)
  • Seurat PCA loadings only contain variable features, not all genes
  • {anndataR} now properly expands loadings matrix to include all genes with zeros for non-variable features
  • Adds a warning when rownames don't match var_names during conversion
• Directly use obs_names and var_names properties instead of corresponding indirect S3 methods rownames and colnames inside the package (PR #328)
• Fix the error message variable name in .validate_aligned_array() method (expected_colnames → expected_rownames) (PR #328)

Documentation

• Add a citation file, citation("anndataR") now returns details of the {anndataR} preprint (PR #351)
• Update vignettes to clarify and expand text and improve formatting, including adding mapping figures to conversion vignettes (PR #360, PR #372)
• Minor updates to function documentation (PR #319)
• Add explanatory comments for matrix generation alignment with Python dummy-anndata (PR #328)
• Replace \donttrun with \donttest in man pages (PR #371)

Development

• Add an AGENTS.md with instructions for AI agents used during development (PR #367)

Full Changelog: v0.99.0...v1.0.0

Version 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 #312, PR #313).
• Add more tests to increase coverage (PR #315)
• Clean up test output (PR #316)
• Minor updates to documentation (PR #310)

Full Changelog: v0.2.0...v0.99.0

Version 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

Full Changelog: v0.1.0...v0.2.0

Version 0.1.0

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

Contributors

• @rcannood
• @LouiseDck
• @lazappi
• @mtmorgan
• @csangara
• @ivirshup
• @melonora
• @SZhengP
• @dorien-er
• @gtca
• @bschilder

Full Changelog: https://github.com/scverse/anndataR/commits/v0.1.0