scverse / scverse/anndata

Test failures as of 0.11.4 on NixOS

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Description

Please make sure these conditions are met
  • I have checked that this issue has not already been reported.
  • I have confirmed this bug exists on the latest version of anndata.
  • (optional) I have confirmed this bug exists on the master branch of anndata.
Report

I'm seeing a number of test failures as of the latest version, 0.11.4,

=========================== short test summary info ============================
FAILED tests/test_concatenate.py::test_concat_dask_sparse_matches_memory[outer-only] - AssertionError:
FAILED tests/test_concatenate.py::test_concat_dask_sparse_matches_memory[outer-first] - AssertionError:
FAILED tests/test_concatenate.py::test_concat_dask_sparse_matches_memory[outer-same] - AssertionError:
FAILED tests/test_concatenate.py::test_concat_dask_sparse_matches_memory[outer-unique] - AssertionError:
FAILED tests/test_concatenate.py::test_concat_dask_sparse_matches_memory[outer-None] - AssertionError:
= 5 failed, 3265 passed, 23 skipped, 74 xfailed, 324 warnings in 89.90s (0:01:29) =

Full logs available here: https://gist.github.com/samuela/cb1e21408c78ff89726fcb2caf213532

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Contributor guide

Open the contributing guide

First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

Research direction

Start with the five failing cases in tests/test_concatenate.py::test_concat_dask_sparse_matches_memory and compare their NixOS failures with the full logs in the linked gist. Investigate why the dask sparse and in-memory concatenation results differ in each parameterization. Done means the reported failures pass without regressing the existing test suite.

Written by the indexing model from the issue text.

Assessment

Tech stack
python
Domain
data, testing-qa
Issue type
Bug
Difficulty
4/5
Estimated time
3-5 days
Activity status
Stale
Clarity
Needs clarification
Newbie friendliness
25/100

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