Changelog

Source: NEWS.md

anndataR 1.3.1

• Add support for reading backed objects using DelayedArray matrices, including a backed argument for HDF5AnnData and InMemoryAnnData, and conversion of backed AnnData objects to SingleCellExperiment/Seurat (PR #387).
• Add support for writing Zarr v3 stores, using (i) zarr_format argument of write_zarr()/as_ZarrAnnData() or (ii) the anndataR.zarr_format option. New stores are written as Zarr v3 by default (PR #455).
• Write strings as VLen-UTF8 rather than as fixed-width, so that string arrays read back as variable length strings in Python anndata (PR #455).
• Use the format of an existing Zarr store when writing to it and truncate the store when mode = "w", so that a store can no longer end up with a mix of Zarr v2 and v3 nodes (PR #455).
• Enable additional linters and optimise several suboptimal code patterns (PR #453).
• Fix create_zarr() so that Zarr stores can be created at relative paths and at paths containing regex metacharacters (PR #478).
• Fix use of & instead of && when validating column names in AbstractAnnData (PR #487).
• Update tests to take into account the Rarr structured datatype breaking change (PR #462).
• Temporarily require Python anndata < 0.13.0 in tests, workflows and the Python usage vignette (PR #481).
• Add Zarr to the benchmarks (PR #446).
• Add Bioconductor R-universe checks (PR #470).
• Fix CI runners (PR #457).
• Upgrade to roxygen2 8.0.0.
• Simplify roxygen documentation for the H5AD and Zarr helpers by using @inheritParams (PR #479).
• Update CITATION with the published paper (PR #464).
• Mark Zarr support as implemented in the class diagram (PR #460).

anndataR 1.3.0

• Bioconductor 3.24 devel

anndataR 1.2.0

• Bioconductor 3.23 release

anndataR 1.1.3

• Prepare for Bioconductor 3.23 release (PR #449).
• Add initial Zarr support for reading and writing .zarr stores (PR #190).

anndataR 1.1.2

• Fix broken links (PR #429).
• Fix the software design vignette (PR #438).
• Fix GitHub Actions MacOS/Windows setup issue (PR #447).

anndataR 1.1.1

• 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).

anndataR 1.1.0

• Bioconductor 3.23 devel
• Separate reading and writing keys in HDF5AnnData (PR #392).
• Add a check for 0 dimensions when converting to Seurat (PR #393).
• Warn that matrix dim names will not be written to H5AD files (PR #396).
• Add a warning to .from_SCE_convert() (PR #402).
• Warn when a rotation is provided but not stored in a LinearEmbeddingMatrix (PR #407).
• Fix linting issues (PR #389).
• Add Bioconductor badges (PR #375).
• Update {pkgdown} rendering (PR #379).
• Force loading the environment in the Python vignette (PR #394).
• Add issue templates (PR #395).
• Update GitHub Actions based on those used by {rhdf5} (PR #378).
• Set different cache versions in GitHub Actions (PR #403).
• Update CI (PR #416).

anndataR 1.0.2

• Fix broken links (PR #430).

anndataR 1.0.1

• 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).

anndataR 1.0.0

• Bioconductor 3.22 release (October 2025)

anndataR 0.99.6

• Use the correct mapping figure in the SingleCellExperiment usage vignette (PR #372)
• Fix accessing layers keys for ReticulateAnnData (PR #372)
• Minor updates to the Python usage vignette (PR #372)
• Add the Python vignette to the {pkgdown} index (PR #372)

anndataR 0.99.4

• Address minor issues from Bioconductor checks (PR #371)
  • Combine the opts_chunks$set() calls in the Python usage vignette
  • Replace \donttrun with \donttest in man pages

anndataR 0.99.3

New functionality

• 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 ReticulateAnnData class for seamless Python integration via {reticulate} (PR #322)
• Add AGENTS.md with instructions for developers (PR #367).

Major changes

• Refactor obs/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 dimnames
  • All matrix data (X, layers, obsm, varm, obsp, varp) is now stored internally without dimnames for consistency
  • Dimnames are added on-the-fly when users access data, ensuring proper obs/var name display

Minor changes

• Refactor setter methods in HDF5AnnData and InMemoryAnnData to use pipe operators for cleaner code (PR #328)
• Add explanatory comments for matrix generation alignment with Python dummy-anndata (PR #328)
• Add get_generator_types() function return allowed/example types for generate_dataset() (PR #354)
• Add checks for type arguments to generate_dataset() (PR #354)
• Generalise the layers created by generate_dataset() when format = "Seurat" (PR #354)

Bug fixes

• Add compression parameter to additional write operations in HDF5AnnData for consistency (PR #328)
• Directly use obs_names and var_names properties instead of corresponding indirect S3 methods rownames and colnames (PR #328)
• Fix error message variable name in .validate_aligned_array() method (expected_colnames → expected_rownames) (PR #328)
• Fix Seurat conversion for PCA loadings with variable feature subsets (PR #328)
  • Seurat PCA loadings only contain variable features, not all genes
  • Now properly expands loadings matrix to include all genes with zeros for non-variable features
  • Adds warning when rownames don’t match var_names during conversion
• Avoid writing character datasets to H5AD files with LZF compression as it causes R to crash (PR #356)
• 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)

Documentation

• citation("anndataR") now returns details of the {anndataR} preprint (PR #351)
• Update vignettes to clarify and expand text and improve formatting (PR #360)

anndataR 0.99.2

• Add @return to R6 object man pages to address {BiocCheck} warning (PR #319)

anndataR 0.99.1

• Resubmit because of failing Bioc checks (PR #318)

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 clean-ups 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 (initial 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