Tags: scverse/spatialdata
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Fix numba JIT configuration failing on airflow runner (#1117) fix: prevent numba JIT errors during test collection on runner envs Two issues caused collection-time failures when running tests in runner environments (e.g. the ome_sdc conda env where Airflow is used): 1. os.environ.setdefault("NUMBA_DISABLE_JIT", "1") is a no-op if the environment already exports NUMBA_DISABLE_JIT=0. Switched to a force-set assignment, and added a sys.modules patch for the case where a pytest plugin (fast-array-utils, npe2, napari-plugin-engine) has already imported numba before conftest.py runs — numba reads its config once at import time, so the env var alone is too late. 2. Module-level blobs() calls in four test files executed during pytest collection, before conftest.py had taken effect. Replaced each with a @pytest.fixture(scope="module"), which fires during test execution. No performance change — blobs() is still called once per file. refactor: consolidate numba JIT disable into root conftest only The sub-conftest files in core/operations/ and dataloader/ duplicated the same NUMBA_DISABLE_JIT logic already present in the root tests/conftest.py. Removed the duplicates. --------- Co-authored-by: Claude Sonnet 4.6 <noreply@anthropic.com>
Fix numba JIT configuration failing on airflow runner (#1117) fix: prevent numba JIT errors during test collection on runner envs Two issues caused collection-time failures when running tests in runner environments (e.g. the ome_sdc conda env where Airflow is used): 1. os.environ.setdefault("NUMBA_DISABLE_JIT", "1") is a no-op if the environment already exports NUMBA_DISABLE_JIT=0. Switched to a force-set assignment, and added a sys.modules patch for the case where a pytest plugin (fast-array-utils, npe2, napari-plugin-engine) has already imported numba before conftest.py runs — numba reads its config once at import time, so the env var alone is too late. 2. Module-level blobs() calls in four test files executed during pytest collection, before conftest.py had taken effect. Replaced each with a @pytest.fixture(scope="module"), which fires during test execution. No performance change — blobs() is still called once per file. refactor: consolidate numba JIT disable into root conftest only The sub-conftest files in core/operations/ and dataloader/ duplicated the same NUMBA_DISABLE_JIT logic already present in the root tests/conftest.py. Removed the duplicates. --------- Co-authored-by: Claude Sonnet 4.6 <noreply@anthropic.com>
ome zarr chunks (#1092) * ome zarr chunks * set scale factors to emtpy list + fix unit tests * mypy * lowercase to fix unit test linux * bump ome zarr in pyproject toml * dask accessor is now always loaded * deduplicate storage option util; use chunks from data when not specified in storage options * simplify, document and test the chunk helper functions * guard against storage_options["chunks"]="" + Change ValueError * remove data argument from _prepare_storage_options() * remove data argument from _prepare_storage_options() --------- Co-authored-by: Luca Marconato <m.lucalmer@gmail.com>
Remove xarray-schema; validate() are now class methods (#1066) * remove xarray-schema; validate() are now class methods * small code cleanup * remove unused model instances; fix validation for table (should not modify the object) * fix test_set_table_annotates_spatialelement * remove deprecation warning for raster and table model __init__
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