Backport fixes to Bioc 3.23 - anndataR 1.2.2 - #503
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* check RELEASE_ branches against bioc release * Drop the `ubuntu-latest` Bioconductor release leg from the matrix * Derive `bioc-version` from the target branch instead of the matrix * Run the workflow on pushes to `RELEASE_**` as well as `devel` * add NEWS entry * pin each RELEASE_ branch to its own bioc version `RELEASE_3_22` needs Bioconductor 3.22 and R 4.5, not whichever release happens to be current. Derive the version from the branch name in a small `bioc-version` job and feed it to the matrix. (cherry picked from commit 8320a69)
* Add read_h5ad_nullable_string() helper * Add read_zarr_nullable_string() * Add write_h5ad_nullable_string() * Add write_zarr_nullable_string() * Update example files * Update example data files * Add tests for nullable strings * Use zarr_format * Add nullable string roundtrip tests * Style * Update NEWS --------- Co-authored-by: Robrecht Cannoodt <rcannood@gmail.com> (cherry picked from commit c5cf4be)
PR #502 dropped the `ubuntu-latest` + Bioconductor devel matrix leg and gated BiocCheck on the resolved version being `devel`. On a `RELEASE_*` branch that version is now `3.23`, so BiocCheck stopped running there entirely. Run it on `ubuntu-latest` regardless of the resolved version; every branch is checked against the Bioconductor version it targets, so BiocCheck is meaningful on both. `devel` needs the same change.
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Bencher Report| Project | anndataR |
| Branch | backport-release-3-23-1.2.2 |
| Testbed | ubuntu-latest |
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hdf5_write_boolean_dataset() called as.integer(value) before checking dim(value) to compute the dataspace shape. as.integer() drops the dim attribute, so the check always fell through to the flat-vector branch, and any 2D+ logical matrix (X/layers/obsm/varm) was written as a 1D dataset. Reading it back then failed since the shape no longer matched (n_obs, n_var). Capture dims before the conversion, and align H5Screate_simple()'s native argument with hdf5_write_dataset() a few lines above (native = FALSE), which is what write_h5ad_dense_array() already transposes values for. Fixes #495 (cherry picked from commit fa91217)
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Backports fixes from
develtoRELEASE_3_23, following the same rule as #489: no new features beyond what fixes compatibility with files Python anndata already writes.nullable-string-array#480Not backported:
hdf5_write_boolean_dataset()) #495DelayedArrayreading #387