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Ran 12 May 2026 06:06PM UTC

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Committed 12 May 2026 06:05PM UTC coverage: 70.836% (+0.009%) from 70.827%

Job # 25752941312.1

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push

github

Committed by

web-flow

Commit Message

Fix #37: convert CSC→CSR in _ensure_x so concat_on_disk accepts CellRanger inputs (#38)

Closes #37. Regression introduced by PR #31 (concat_on_disk-based
load_samples, 0.7.6) that crashed `tcrsift run` on every multi-sample
CellRanger sheet.

CellRanger's filtered_feature_bc_matrix writes CSC sparse matrices.
anndata.experimental.concat_on_disk only supports CSR along the obs
axis and raises

  NotImplementedError: Concat of following not supported: ['csc', ...]

`_ensure_x` now converts CSC inputs to CSR before the spill (one
`.tocsr()` call per sample, cheap relative to the disk round-trip),
so all spilled h5ads have a concat-compatible layout. VDJ-only path
unchanged (synthesizes a CSR zero-column placeholder as before).

The reporter's suggested fix verbatim, plus the test that locks it
in. New `test_load_samples_handles_csc_inputs` builds two synthetic
samples with CSC X — verified to reproduce the original
NotImplementedError without the fix, passes with it.

Test gap that hid this: existing fixtures all use sp.random(...,
format="csr"). Adding a CSC fixture closes that gap.

Version 0.8.5.

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