bug: anndata 0.11.0 breaking CLI

[Bento007]

Description

anndata 0.11.0 changes the way it handles sparsedata and this has caused the CLI to break

Run make unit-test
cd cellxgene_schema_cli \
&& coverage run --data-file=.coverage.6808a3e --parallel-mode --source=cellxgene_schema -m pytest --log-level=INFO ./tests
============================= test session starts ==============================
platform linux -- Python 3.10.15, pytest-8.3.3, pluggy-1.5.0
rootdir: /home/runner/work/single-cell-curation/single-cell-curation
configfile: pyproject.toml
collected 29 items / 2 errors

==================================== ERRORS ====================================
____ ERROR collecting cellxgene_schema_cli/tests/test_schema_compliance.py _____
ImportError while importing test module '/home/runner/work/single-cell-curation/single-cell-curation/cellxgene_schema_cli/tests/test_schema_compliance.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/opt/hostedtoolcache/Python/3.10.15/x64/lib/python3.10/importlib/__init__.py:[12](https://github.com/chanzuckerberg/single-cell-curation/actions/runs/11827884213/job/32956896561#step:6:13)6: in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
tests/test_schema_compliance.py:16: in <module>
    from cellxgene_schema.validate import (
cellxgene_schema/validate.py:14: in <module>
    from anndata._core.sparse_dataset import SparseDataset
E   ImportError: cannot import name 'SparseDataset' from 'anndata._core.sparse_dataset' (/opt/hostedtoolcache/Python/3.10.15/x64/lib/python3.10/site-packages/anndata/_core/sparse_dataset.py)
_________ ERROR collecting cellxgene_schema_cli/tests/test_validate.py _________
ImportError while importing test module '/home/runner/work/single-cell-curation/single-cell-curation/cellxgene_schema_cli/tests/test_validate.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/opt/hostedtoolcache/Python/3.10.15/x64/lib/python3.10/importlib/__init__.py:126: in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
tests/test_validate.py:[13](https://github.com/chanzuckerberg/single-cell-curation/actions/runs/11827884213/job/32956896561#step:6:14): in <module>
    from cellxgene_schema.validate import (
cellxgene_schema/validate.py:[14](https://github.com/chanzuckerberg/single-cell-curation/actions/runs/11827884213/job/32956896561#step:6:15): in <module>
    from anndata._core.sparse_dataset import SparseDataset
E   ImportError: cannot import name 'SparseDataset' from 'anndata._core.sparse_dataset' (/opt/hostedtoolcache/Python/3.10.[15](https://github.com/chanzuckerberg/single-cell-curation/actions/runs/11827884213/job/32956896561#step:6:16)/x64/lib/python3.10/site-packages/anndata/_core/sparse_dataset.py)
=========================== short test summary info ============================
ERROR tests/test_schema_compliance.py
ERROR tests/test_validate.py
!!!!!!!!!!!!!!!!!!! Interrupted: 2 errors during collection !!!!!!!!!!!!!!!!!!!!
============================== 2 errors in 2.01s ===============================
make: *** [Makefile:[20](https://github.com/chanzuckerberg/single-cell-curation/actions/runs/11827884213/job/32956896561#step:6:21): unit-test] Error 2

Version

This is on cellxgene-schema-cli 5.2.0

Fix

• Pin the version of anndata to <0.11.0 and release a patch
• Upgrade to 0.11.0 in the future.