Test issue 2271 - #2277
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katosh wants to merge 18 commits into
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Test issue 2271#2277katosh wants to merge 18 commits into
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This test demonstrates the bug where read_lazy() returns obs_names/var_names
as byte-string representations ("b'cell_A'") instead of decoded strings.
See: scverse#2271
- Skip full CI for test-issue-* branches - Add dedicated workflow that only runs the specific regression test
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Note on version requirementsThe regression test initially passed in CI due to version dependencies. This bug only manifests with pandas 3.0+ AND numpy < 2.2.3. See failed test in https://github.com/scverse/anndata/actions/runs/20719835864/job/59480330959 Why these versions matter
Version matrix
Why the fix in #2272 is still neededEven though numpy 2.2.3+ masks this bug, the fix in #2272 may still be the correct solution because:
Reproducing the bugTo demonstrate the bug exists on main, the test must run with:
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Add regression test for issue #2271 (expected to fail)
This PR adds a regression test that demonstrates the bug reported in #2271.
Purpose
This PR is intentionally expected to fail CI to confirm that issue #2271 exists on main and not just on my local machine. The fix is in PR #2272.
The Bug
read_lazy() returns obs_names/var_names as byte-string representations ("b'cell_A'") instead of properly decoded strings ("cell_A").
Test Output on main
FAILED tests/lazy/test_read.py::test_nullable_string_index_decoding assert obs_names == expected_obs E assert ["b'cell_A'", "b'cell_B'", ...] == ['cell_A', 'cell_B', ...] E At index 0 diff: "b'cell_A'" != 'cell_A'Related