Changelog

Source: NEWS.md

convert2anndata 0.3.0

Bidirectional conversion

convert2anndata is now a bidirectional converter. In addition to the existing SingleCellExperiment / Seurat → AnnData direction, it can convert AnnData (.h5ad) objects into Seurat or SingleCellExperiment objects:

• convert_anndata_to_seurat() — AnnData → Seurat.
• convert_anndata_to_sce() — AnnData → SingleCellExperiment.

Both accept either an in-memory AnnData object or a path to an .h5ad file. AnnData components are mapped as follows: X / layers → assays, obsm → dimensional reductions, obs / var → cell / feature metadata, and obsp → Seurat graphs (for the Seurat target).

Command-line interface

• cli_convert() now dispatches on the input file extension: .rds → .h5ad and .h5ad → .rds.
• The .h5ad → .rds direction supports -t seurat (default) or -t sce to choose the target object type.

Python / reticulate setup

New helpers make the reticulate ↔︎ Python anndata wiring explicit and easier to debug:

• setup_anndata_python() — resolve and activate a Python environment that has anndata installed.
• check_anndata_python() — fail fast with an actionable message when Python, anndata, or numpy are not reachable.
• diagnose_anndata_python() — print a full diagnostic of the active Python environment.

The path entry points to the converters call check_anndata_python() automatically.

Seurat 5 support and use_raw

• Conversions are robust across Seurat 4 / Seurat 5 layer and slot naming.
• use_raw = "auto" (the default) uses adata.raw as the counts matrix only when no requested counts_layer is present; "always" and "never" force the behaviour, and a logical value is still accepted for backward compatibility.

New exported helpers

The full extract_anndata_* family is now exported for building custom conversions: extract_anndata_X(), extract_anndata_layers(), extract_anndata_obsm(), extract_anndata_obsp(), and extract_anndata_raw(). Also new: attach_reductions_seurat().

Tests, evaluation harness, and validation

• About ten new test files cover the AnnData → Seurat / SCE direction, edge cases, sparse-matrix handling, raw / obsp, and realistic scanpy-style datasets. Tests that need Python anndata skip gracefully when it is unavailable.
• A standalone evaluation harness (eval/) exercises full roundtrips, edge cases, a real pbmc3k dataset, and a quantitative roundtrip-fidelity check.

Validation results (0.3.0)

Validated with R 4.4.1, Seurat 5.4.0, SingleCellExperiment 1.28.1, reticulate 1.45.0, and Python anndata 0.12.0:

• R CMD check: 0 errors, 0 warnings, 3 (benign) notes.
• testthat: 387 passing, 0 failing, 1 skipped (a CLI subprocess test that needs the package installed on the library path).
• Roundtrip fidelity: X, obs, var, obsm, and obsp roundtrip within numeric tolerance through the SCE-mediated path; obsp also roundtrips through the Seurat-mediated path.

Known limitations

• The Seurat-mediated path (AnnData → Seurat → ...) cannot preserve arbitrary extra layers or var (feature) metadata, because a Seurat assay only has counts / data / scale.data slots and no feature-metadata store. Use the SCE-mediated path when verbatim layers or var columns matter.
• convert_anndata_to_sce() does not yet attach obsp matrices as colPairs (the Seurat target does attach them as graphs). This is a planned follow-up.

Documentation

• README rewritten with a direction reference table, Python environment notes, and a troubleshooting section.
• _pkgdown.yml updated for bidirectional conversion with a grouped reference index.
• DESCRIPTION retitled and bumped to 0.3.0.