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Actions had no HDF5 input, so load_input's Cell Ranger /matrix reader never ran. Commit a synthetic 80x2120 filtered_feature_bc_matrix.h5 (plus generator) that survives default QC/HVG, enable --features hdf5 with libhdf5-dev, and require PACKET.md artifacts. Co-authored-by: Josh Garton <jwg054000@users.noreply.github.com>
jwg054000
marked this pull request as ready for review
September 2, 2026 19:24
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Closes the “no H5 in Actions” gap on #3. GitHub Actions previously ran
cargo testwithout--features hdf5and without a Cell Ranger matrix, soload_inputnever hitread_10x_h5.What
testdata/filtered_feature_bc_matrix.h5(80 cells × 2120 genes, ~275 KB). Real HDF5/matrixlayout (data/indices/indptr/shape/barcodes/features/name). Not a public PBMC file.scripts/gen_10x_ci_fixture.py--min-genes 200,--max-pct-mt 5(MT-*genes, low mito %),--n-hvg 2000,--n-pcs 50(rank clamp already on main from Clamp n_pcs so default H5 pipeline does not panic #7),--knn-k 15libhdf5-dev, runscargo test(unchanged, no HDF5), thencargo test --features hdf5, thenrustpipe-sc pipeline --input testdata/filtered_feature_bc_matrix.h5and requires PACKET.md files:qc_metrics.csvpca_scores.csvclusters.csvmarkers.csvpipeline_timings.jsonNot in this PR
--qc-bamsmoke--inputremains H5 / H5AD / CSV only (never rustqc featureCounts)Related: #3