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pirl-unc / tcrsift / 25752941312
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DEFAULT BRANCH: main
Ran 12 May 2026 06:06PM UTC
Jobs 4
Files 25
Run time 1min
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12 May 2026 06:05PM UTC coverage: 70.847% (+0.009%) from 70.838%
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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.

4644 of 6555 relevant lines covered (70.85%)

2.83 hits per line

Coverage Regressions

Lines Coverage ∆ File
15
89.0
0.07% loader.py
Jobs
ID Job ID Ran Files Coverage
1 python-3.11 - 25752941312.1 12 May 2026 06:06PM UTC 25
70.84
GitHub Action Run
2 python-3.10 - 25752941312.2 12 May 2026 06:06PM UTC 25
70.84
GitHub Action Run
3 python-3.12 - 25752941312.3 12 May 2026 06:06PM UTC 25
70.84
GitHub Action Run
4 python-3.9 - 25752941312.4 12 May 2026 06:06PM UTC 25
70.81
GitHub Action Run
Source Files on build 25752941312
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