Fix Blosc-compressed H5AD input and release 0.2.14 - #16
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QCatch fails while opening Blosc-compressed H5AD files produced by simpleaf because it neither installs nor registers the required HDF5 filters. Add
hdf5pluginas a runtime dependency and import it before the shared H5AD reader runs. Both direct-file input and directory discovery now work without copying plugins into a system directory.This prepares version 0.2.14 and documents a workaround for the existing Bioconda container. The Bioconda recipe must also explicitly include the runtime dependency because it installs QCatch with
--no-deps; that update will follow the PyPI release.Release validation also exposed an AnnData 0.13 compatibility issue:
.layersnow contains the primary matrix under theNonekey. Preserve that matrix while sorting named layers instead of comparingNonewith strings. A round-trip test verifies the primary matrix, named layers, and retained cells in both full and filtered outputs on AnnData 0.11 and 0.13.Validation: the original 22 local tests passed with Bioconda-aligned dependencies. Six compression regression cases cover Blosc/Zstd, gzip, and uncompressed input in fresh processes without a plugin directory; both Blosc cases fail against unmodified QCatch. An additional run on the official PBMC fixture recompressed with Blosc/Zstd successfully generated the report, H5AD, and CSV. Source and wheel builds pass. The inactivity-disabled Linux test workflow has been restored for release validation.
Fixes #15.