Changelog • anndataR

anndataR 1.1.0

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)

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

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).

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

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)

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)

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

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

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)

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!

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

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)

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)

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

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

Initial release candidate of {anndataR} including: