Tests fail with pytest 8.1 when a `data` dir exists

[ivirshup]

First reported by @lazappi, but now confirmed by me.

Tests error during collection for a fresh dev install.

mamba create -yn scanpy-dev "python=3.12"
conda activate scanpy-dev
pip install -e ".[dev,test]" pytest-xdist  # pytest-xdist isn't required, but makes this faster
conda deactivate scanpy-dev
conda activate scanpy-dev
pytest -n auto

First everything fails since dask-expr isn't installed. This must be someone upstream pinning dask, but is easily solvable by adding dask-expr to the environment.

pip install dask-expr
pytest -n auto

Failures

FAILED scanpy/tests/test_score_genes.py::test_score_with_reference - TypeError: 'module' object is not callable
FAILED scanpy/tests/test_scrublet.py::test_scrublet[True-sparse] - ImportError: cannot import name '_pbmc3k' from 'scanpy.testing._helpers.data' (unknown location)
FAILED scanpy/tests/test_scrublet.py::test_scrublet[True-dense] - ImportError: cannot import name '_paul15' from 'scanpy.testing._helpers.data' (unknown location)
FAILED scanpy/tests/test_scrublet.py::test_scrublet[False-sparse] - ImportError: cannot import name '_pbmc3k' from 'scanpy.testing._helpers.data' (unknown location)
FAILED scanpy/tests/test_scrublet.py::test_scrublet[False-dense] - ImportError: cannot import name '_paul15' from 'scanpy.testing._helpers.data' (unknown location)
FAILED scanpy/tests/test_scrublet.py::test_scrublet_batched - ImportError: cannot import name '_pbmc3k' from 'scanpy.testing._helpers.data' (unknown location)
FAILED scanpy/tests/test_scrublet.py::test_scrublet_data - ImportError: cannot import name '_pbmc3k' from 'scanpy.testing._helpers.data' (unknown location)
FAILED scanpy/tests/test_scrublet.py::test_scrublet_simulate_doublets - ImportError: cannot import name '_pbmc3k' from 'scanpy.testing._helpers.data' (unknown location)
ERROR scanpy/tests/external/test_harmony_integrate.py
ERROR scanpy/tests/external/test_harmony_timeseries.py
ERROR scanpy/tests/external/test_palantir.py
ERROR scanpy/tests/external/test_sam.py
ERROR scanpy/tests/external/test_scanorama_integrate.py
ERROR scanpy/tests/external/test_wishbone.py
ERROR scanpy/tests/test_aggregated.py
ERROR scanpy/tests/test_clustering.py
ERROR scanpy/tests/test_dendrogram.py
ERROR scanpy/tests/test_deprecations.py
ERROR scanpy/tests/test_embedding.py
ERROR scanpy/tests/test_embedding_density.py
ERROR scanpy/tests/test_embedding_plots.py
ERROR scanpy/tests/test_filter_rank_genes_groups.py
ERROR scanpy/tests/test_get.py
ERROR scanpy/tests/test_highly_variable_genes.py
ERROR scanpy/tests/test_ingest.py
ERROR scanpy/tests/test_metrics.py
ERROR scanpy/tests/test_neighbors_key_added.py
ERROR scanpy/tests/test_paga.py
ERROR scanpy/tests/test_pca.py
ERROR scanpy/tests/test_plotting.py
ERROR scanpy/tests/test_preprocessing.py
ERROR scanpy/tests/test_queries.py
ERROR scanpy/tests/test_rank_genes_groups.py
ERROR scanpy/tests/test_normalization.py::test_normalize_pearson_residuals_warnings[toarray-float32] - ImportError: cannot import name 'pbmc3k' from 'scanpy.testing._helpers.data' (unknown location)
ERROR scanpy/tests/test_normalization.py::test_normalize_pearson_residuals_errors[toarray-float32-theta0] - ImportError: cannot import name 'pbmc3k' from 'scanpy.testing._helpers.data' (unknown location)
ERROR scanpy/tests/test_normalization.py::test_normalize_pearson_residuals_errors[toarray-float32-theta1] - ImportError: cannot import name 'pbmc3k' from 'scanpy.testing._helpers.data' (unknown location)
ERROR scanpy/tests/test_normalization.py::test_normalize_pearson_residuals_errors[toarray-float32-params2-Pearson residuals require `clip>=0` or `clip=None`.] - ImportError: cannot import name 'pbmc3k' from 'scanpy.testing._helpers.data' (unknown location)
ERROR scanpy/tests/test_normalization.py::test_normalize_pearson_residuals_pca[toarray-float32-no_hvg-30-100] - ImportError: cannot import name 'pbmc3k' from 'scanpy.testing._helpers.data' (unknown location)
ERROR scanpy/tests/test_normalization.py::test_normalize_pearson_residuals_pca[toarray-float32-no_hvg-30-200] - ImportError: cannot import name 'pbmc3k' from 'scanpy.testing._helpers.data' (unknown location)
ERROR scanpy/tests/test_normalization.py::test_normalize_pearson_residuals_pca[toarray-float32-no_hvg-50-100] - ImportError: cannot import name 'pbmc3k' from 'scanpy.testing._helpers.data' (unknown location)
ERROR scanpy/tests/test_normalization.py::test_normalize_pearson_residuals_pca[toarray-float32-no_hvg-50-200] - ImportError: cannot import name 'pbmc3k' from 'scanpy.testing._helpers.data' (unknown location)
ERROR scanpy/tests/test_normalization.py::test_normalize_pearson_residuals_pca[toarray-float32-hvg_default-30-100] - ImportError: cannot import name 'pbmc3k' from 'scanpy.testing._helpers.data' (unknown location)
ERROR scanpy/tests/test_normalization.py::test_normalize_pearson_residuals_pca[toarray-float32-hvg_default-30-200] - ImportError: cannot import name 'pbmc3k' from 'scanpy.testing._helpers.data' (unknown location)
ERROR scanpy/tests/test_normalization.py::test_normalize_pearson_residuals_errors[csr_matrix-float32-params2-Pearson residuals require `clip>=0` or `clip=None`.] - ImportError: cannot import name 'pbmc3k' from 'scanpy.testing._helpers.data' (unknown location)
ERROR scanpy/tests/test_normalization.py::test_normalize_pearson_residuals_pca[csr_matrix-float32-no_hvg-30-100] - ImportError: cannot import name 'pbmc3k' from 'scanpy.testing._helpers.data' (unknown location)
ERROR scanpy/tests/test_normalization.py::test_normalize_pearson_residuals_pca[csr_matrix-float32-no_hvg-30-200] - ImportError: cannot import name 'pbmc3k' from 'scanpy.testing._helpers.data' (unknown location)
ERROR scanpy/tests/test_normalization.py::test_normalize_pearson_residuals_pca[csr_matrix-float32-no_hvg-50-100] - ImportError: cannot import name 'pbmc3k' from 'scanpy.testing._helpers.data' (unknown location)
ERROR scanpy/tests/test_normalization.py::test_normalize_pearson_residuals_pca[csr_matrix-float32-no_hvg-50-200] - ImportError: cannot import name 'pbmc3k' from 'scanpy.testing._helpers.data' (unknown location)
ERROR scanpy/tests/test_normalization.py::test_normalize_pearson_residuals_pca[csr_matrix-float32-hvg_default-30-100] - ImportError: cannot import name 'pbmc3k' from 'scanpy.testing._helpers.data' (unknown location)
ERROR scanpy/tests/test_normalization.py::test_normalize_pearson_residuals_pca[csr_matrix-float32-hvg_default-30-200] - ImportError: cannot import name 'pbmc3k' from 'scanpy.testing._helpers.data' (unknown location)
ERROR scanpy/tests/test_normalization.py::test_normalize_pearson_residuals_pca[csr_matrix-float32-hvg_default-50-100] - ImportError: cannot import name 'pbmc3k' from 'scanpy.testing._helpers.data' (unknown location)
ERROR scanpy/tests/test_normalization.py::test_normalize_pearson_residuals_pca[csr_matrix-float32-hvg_default-50-200] - ImportError: cannot import name 'pbmc3k' from 'scanpy.testing._helpers.data' (unknown location)
ERROR scanpy/tests/test_normalization.py::test_normalize_pearson_residuals_pca[csr_matrix-float32-hvg_opt_out-30-100] - ImportError: cannot import name 'pbmc3k' from 'scanpy.testing._helpers.data' (unknown location)
ERROR scanpy/tests/test_normalization.py::test_normalize_pearson_residuals_recipe[csr_matrix-float32-50-100] - ImportError: cannot import name 'pbmc3k' from 'scanpy.testing._helpers.data' (unknown location)
ERROR scanpy/tests/test_normalization.py::test_normalize_pearson_residuals_recipe[csr_matrix-float32-50-200] - ImportError: cannot import name 'pbmc3k' from 'scanpy.testing._helpers.data' (unknown location)
ERROR scanpy/tests/test_normalization.py::test_normalize_pearson_residuals_warnings[csr_matrix-int64] - ImportError: cannot import name 'pbmc3k' from 'scanpy.testing._helpers.data' (unknown location)
ERROR scanpy/tests/test_normalization.py::test_normalize_pearson_residuals_pca[csr_matrix-float32-hvg_opt_out-30-200] - ImportError: cannot import name 'pbmc3k' from 'scanpy.testing._helpers.data' (unknown location)
ERROR scanpy/tests/test_normalization.py::test_normalize_pearson_residuals_errors[csr_matrix-int64-theta0] - ImportError: cannot import name 'pbmc3k' from 'scanpy.testing._helpers.data' (unknown location)
ERROR scanpy/tests/test_normalization.py::test_normalize_pearson_residuals_errors[csr_matrix-int64-theta1] - ImportError: cannot import name 'pbmc3k' from 'scanpy.testing._helpers.data' (unknown location)
ERROR scanpy/tests/test_normalization.py::test_normalize_pearson_residuals_errors[csr_matrix-int64-params2-Pearson residuals require `clip>=0` or `clip=None`.] - ImportError: cannot import name 'pbmc3k' from 'scanpy.testing._helpers.data' (unknown location)
ERROR scanpy/tests/test_normalization.py::test_normalize_pearson_residuals_pca[csr_matrix-float32-hvg_opt_out-50-100] - ImportError: cannot import name 'pbmc3k' from 'scanpy.testing._helpers.data' (unknown location)
ERROR scanpy/tests/test_normalization.py::test_normalize_pearson_residuals_pca[csr_matrix-int64-no_hvg-30-100] - ImportError: cannot import name 'pbmc3k' from 'scanpy.testing._helpers.data' (unknown location)
ERROR scanpy/tests/test_normalization.py::test_normalize_pearson_residuals_pca[csr_matrix-int64-no_hvg-30-200] - ImportError: cannot import name 'pbmc3k' from 'scanpy.testing._helpers.data' (unknown location)
ERROR scanpy/tests/test_normalization.py::test_normalize_pearson_residuals_pca[csr_matrix-float32-hvg_opt_out-50-200] - ImportError: cannot import name 'pbmc3k' from 'scanpy.testing._helpers.data' (unknown location)
ERROR scanpy/tests/test_normalization.py::test_normalize_pearson_residuals_pca[csr_matrix-int64-no_hvg-50-100] - ImportError: cannot import name 'pbmc3k' from 'scanpy.testing._helpers.data' (unknown location)
ERROR scanpy/tests/test_normalization.py::test_normalize_pearson_residuals_pca[csr_matrix-float32-mask-30-100] - ImportError: cannot import name 'pbmc3k' from 'scanpy.testing._helpers.data' (unknown location)
ERROR scanpy/tests/test_normalization.py::test_normalize_pearson_residuals_pca[csr_matrix-int64-no_hvg-50-200] - ImportError: cannot import name 'pbmc3k' from 'scanpy.testing._helpers.data' (unknown location)
ERROR scanpy/tests/test_normalization.py::test_normalize_pearson_residuals_pca[csr_matrix-int64-hvg_default-30-100] - ImportError: cannot import name 'pbmc3k' from 'scanpy.testing._helpers.data' (unknown location)
ERROR scanpy/tests/test_normalization.py::test_normalize_pearson_residuals_pca[csr_matrix-float32-mask-30-200] - ImportError: cannot import name 'pbmc3k' from 'scanpy.testing._helpers.data' (unknown location)
ERROR scanpy/tests/test_normalization.py::test_normalize_pearson_residuals_pca[csr_matrix-int64-hvg_default-30-200] - ImportError: cannot import name 'pbmc3k' from 'scanpy.testing._helpers.data' (unknown location)
ERROR scanpy/tests/test_normalization.py::test_normalize_pearson_residuals_pca[csr_matrix-float32-mask-50-100] - ImportError: cannot import name 'pbmc3k' from 'scanpy.testing._helpers.data' (unknown location)
ERROR scanpy/tests/test_normalization.py::test_normalize_pearson_residuals_pca[csr_matrix-int64-hvg_default-50-100] - ImportError: cannot import name 'pbmc3k' from 'scanpy.testing._helpers.data' (unknown location)
ERROR scanpy/tests/test_normalization.py::test_normalize_pearson_residuals_pca[csr_matrix-int64-hvg_default-50-200] - ImportError: cannot import name 'pbmc3k' from 'scanpy.testing._helpers.data' (unknown location)
ERROR scanpy/tests/test_normalization.py::test_normalize_pearson_residuals_pca[csr_matrix-float32-mask-50-200] - ImportError: cannot import name 'pbmc3k' from 'scanpy.testing._helpers.data' (unknown location)
ERROR scanpy/tests/test_normalization.py::test_normalize_pearson_residuals_pca[csr_matrix-int64-hvg_opt_out-30-100] - ImportError: cannot import name 'pbmc3k' from 'scanpy.testing._helpers.data' (unknown location)
ERROR scanpy/tests/test_normalization.py::test_normalize_pearson_residuals_pca[csr_matrix-int64-mask-30-200] - ImportError: cannot import name 'pbmc3k' from 'scanpy.testing._helpers.data' (unknown location)
ERROR scanpy/tests/test_normalization.py::test_normalize_pearson_residuals_recipe[csr_matrix-float32-30-100] - ImportError: cannot import name 'pbmc3k' from 'scanpy.testing._helpers.data' (unknown location)
ERROR scanpy/tests/test_normalization.py::test_normalize_pearson_residuals_pca[csr_matrix-int64-mask-50-100] - ImportError: cannot import name 'pbmc3k' from 'scanpy.testing._helpers.data' (unknown location)
ERROR scanpy/tests/test_normalization.py::test_normalize_pearson_residuals_pca[csr_matrix-int64-mask-50-200] - ImportError: cannot import name 'pbmc3k' from 'scanpy.testing._helpers.data' (unknown location)
ERROR scanpy/tests/test_normalization.py::test_normalize_pearson_residuals_pca[csr_matrix-int64-hvg_opt_out-30-200] - ImportError: cannot import name 'pbmc3k' from 'scanpy.testing._helpers.data' (unknown location)
ERROR scanpy/tests/test_normalization.py::test_normalize_pearson_residuals_recipe[csr_matrix-int64-30-100] - ImportError: cannot import name 'pbmc3k' from 'scanpy.testing._helpers.data' (unknown location)
ERROR scanpy/tests/test_normalization.py::test_normalize_pearson_residuals_recipe[csr_matrix-float32-30-200] - ImportError: cannot import name 'pbmc3k' from 'scanpy.testing._helpers.data' (unknown location)
ERROR scanpy/tests/test_normalization.py::test_normalize_pearson_residuals_recipe[csr_matrix-int64-30-200] - ImportError: cannot import name 'pbmc3k' from 'scanpy.testing._helpers.data' (unknown location)
ERROR scanpy/tests/test_normalization.py::test_normalize_pearson_residuals_pca[csr_matrix-int64-hvg_opt_out-50-100] - ImportError: cannot import name 'pbmc3k' from 'scanpy.testing._helpers.data' (unknown location)
ERROR scanpy/tests/test_normalization.py::test_normalize_pearson_residuals_recipe[csr_matrix-int64-50-100] - ImportError: cannot import name 'pbmc3k' from 'scanpy.testing._helpers.data' (unknown location)
ERROR scanpy/tests/test_normalization.py::test_normalize_pearson_residuals_recipe[csr_matrix-int64-50-200] - ImportError: cannot import name 'pbmc3k' from 'scanpy.testing._helpers.data' (unknown location)
ERROR scanpy/tests/test_normalization.py::test_normalize_pearson_residuals_pca[csr_matrix-int64-hvg_opt_out-50-200] - ImportError: cannot import name 'pbmc3k' from 'scanpy.testing._helpers.data' (unknown location)
ERROR scanpy/tests/test_normalization.py::test_normalize_pearson_residuals_pca[csr_matrix-int64-mask-30-100] - ImportError: cannot import name 'pbmc3k' from 'scanpy.testing._helpers.data' (unknown location)
ERROR scanpy/tests/test_normalization.py::test_normalize_pearson_residuals_pca[toarray-float32-hvg_default-50-100] - ImportError: cannot import name 'pbmc3k' from 'scanpy.testing._helpers.data' (unknown location)
ERROR scanpy/tests/test_normalization.py::test_normalize_pearson_residuals_pca[toarray-float32-hvg_default-50-200] - ImportError: cannot import name 'pbmc3k' from 'scanpy.testing._helpers.data' (unknown location)
ERROR scanpy/tests/test_normalization.py::test_normalize_pearson_residuals_pca[toarray-float32-hvg_opt_out-30-100] - ImportError: cannot import name 'pbmc3k' from 'scanpy.testing._helpers.data' (unknown location)
ERROR scanpy/tests/test_normalization.py::test_normalize_pearson_residuals_pca[toarray-float32-hvg_opt_out-30-200] - ImportError: cannot import name 'pbmc3k' from 'scanpy.testing._helpers.data' (unknown location)
ERROR scanpy/tests/test_normalization.py::test_normalize_pearson_residuals_pca[toarray-float32-hvg_opt_out-50-100] - ImportError: cannot import name 'pbmc3k' from 'scanpy.testing._helpers.data' (unknown location)
ERROR scanpy/tests/test_normalization.py::test_normalize_pearson_residuals_pca[toarray-float32-hvg_opt_out-50-200] - ImportError: cannot import name 'pbmc3k' from 'scanpy.testing._helpers.data' (unknown location)
ERROR scanpy/tests/test_normalization.py::test_normalize_pearson_residuals_pca[toarray-float32-mask-30-100] - ImportError: cannot import name 'pbmc3k' from 'scanpy.testing._helpers.data' (unknown location)
ERROR scanpy/tests/test_normalization.py::test_normalize_pearson_residuals_pca[toarray-float32-mask-30-200] - ImportError: cannot import name 'pbmc3k' from 'scanpy.testing._helpers.data' (unknown location)
ERROR scanpy/tests/test_normalization.py::test_normalize_pearson_residuals_pca[toarray-float32-mask-50-100] - ImportError: cannot import name 'pbmc3k' from 'scanpy.testing._helpers.data' (unknown location)
ERROR scanpy/tests/test_normalization.py::test_normalize_pearson_residuals_pca[toarray-float32-mask-50-200] - ImportError: cannot import name 'pbmc3k' from 'scanpy.testing._helpers.data' (unknown location)
ERROR scanpy/tests/test_normalization.py::test_normalize_pearson_residuals_recipe[toarray-float32-30-100] - ImportError: cannot import name 'pbmc3k' from 'scanpy.testing._helpers.data' (unknown location)
ERROR scanpy/tests/test_normalization.py::test_normalize_pearson_residuals_recipe[toarray-float32-30-200] - ImportError: cannot import name 'pbmc3k' from 'scanpy.testing._helpers.data' (unknown location)
ERROR scanpy/tests/test_normalization.py::test_normalize_pearson_residuals_recipe[toarray-float32-50-100] - ImportError: cannot import name 'pbmc3k' from 'scanpy.testing._helpers.data' (unknown location)
ERROR scanpy/tests/test_normalization.py::test_normalize_pearson_residuals_recipe[toarray-float32-50-200] - ImportError: cannot import name 'pbmc3k' from 'scanpy.testing._helpers.data' (unknown location)
ERROR scanpy/tests/test_normalization.py::test_normalize_pearson_residuals_warnings[toarray-int64] - ImportError: cannot import name 'pbmc3k' from 'scanpy.testing._helpers.data' (unknown location)
ERROR scanpy/tests/test_normalization.py::test_normalize_pearson_residuals_errors[toarray-int64-theta0] - ImportError: cannot import name 'pbmc3k' from 'scanpy.testing._helpers.data' (unknown location)
ERROR scanpy/tests/test_normalization.py::test_normalize_pearson_residuals_errors[toarray-int64-theta1] - ImportError: cannot import name 'pbmc3k' from 'scanpy.testing._helpers.data' (unknown location)
ERROR scanpy/tests/test_normalization.py::test_normalize_pearson_residuals_errors[toarray-int64-params2-Pearson residuals require `clip>=0` or `clip=None`.] - ImportError: cannot import name 'pbmc3k' from 'scanpy.testing._helpers.data' (unknown location)
ERROR scanpy/tests/test_normalization.py::test_normalize_pearson_residuals_pca[toarray-int64-no_hvg-30-100] - ImportError: cannot import name 'pbmc3k' from 'scanpy.testing._helpers.data' (unknown location)
ERROR scanpy/tests/test_normalization.py::test_normalize_pearson_residuals_pca[toarray-int64-no_hvg-30-200] - ImportError: cannot import name 'pbmc3k' from 'scanpy.testing._helpers.data' (unknown location)
ERROR scanpy/tests/test_normalization.py::test_normalize_pearson_residuals_pca[toarray-int64-no_hvg-50-100] - ImportError: cannot import name 'pbmc3k' from 'scanpy.testing._helpers.data' (unknown location)
ERROR scanpy/tests/test_scrublet.py::test_scrublet_params[expected_doublet_rate-0.1] - ImportError: cannot import name '_pbmc3k' from 'scanpy.testing._helpers.data' (unknown location)
ERROR scanpy/tests/test_scrublet.py::test_scrublet_params[synthetic_doublet_umi_subsampling-0.8] - ImportError: cannot import name '_pbmc3k' from 'scanpy.testing._helpers.data' (unknown location)
ERROR scanpy/tests/test_scrublet.py::test_scrublet_params[knn_dist_metric-manhattan] - ImportError: cannot import name '_pbmc3k' from 'scanpy.testing._helpers.data' (unknown location)
ERROR scanpy/tests/test_scrublet.py::test_scrublet_params[normalize_variance-False] - ImportError: cannot import name '_pbmc3k' from 'scanpy.testing._helpers.data' (unknown location)
ERROR scanpy/tests/test_scrublet.py::test_scrublet_params[log_transform-True] - ImportError: cannot import name '_pbmc3k' from 'scanpy.testing._helpers.data' (unknown location)
ERROR scanpy/tests/test_scrublet.py::test_scrublet_params[mean_center-False] - ImportError: cannot import name '_pbmc3k' from 'scanpy.testing._helpers.data' (unknown location)
ERROR scanpy/tests/test_scrublet.py::test_scrublet_params[n_prin_comps-10] - ImportError: cannot import name '_pbmc3k' from 'scanpy.testing._helpers.data' (unknown location)
ERROR scanpy/tests/test_scrublet.py::test_scrublet_params[n_neighbors-2] - ImportError: cannot import name '_pbmc3k' from 'scanpy.testing._helpers.data' (unknown location)
ERROR scanpy/tests/test_scrublet.py::test_scrublet_params[threshold-0.1] - ImportError: cannot import name '_pbmc3k' from 'scanpy.testing._helpers.data' (unknown location)
ERROR scanpy/tests/test_normalization.py::test_normalize_pearson_residuals_pca[toarray-int64-no_hvg-50-200] - ImportError: cannot import name 'pbmc3k' from 'scanpy.testing._helpers.data' (unknown location)
ERROR scanpy/tests/test_normalization.py::test_normalize_pearson_residuals_pca[toarray-int64-hvg_default-30-100] - ImportError: cannot import name 'pbmc3k' from 'scanpy.testing._helpers.data' (unknown location)
ERROR scanpy/tests/test_normalization.py::test_normalize_pearson_residuals_pca[toarray-int64-hvg_default-30-200] - ImportError: cannot import name 'pbmc3k' from 'scanpy.testing._helpers.data' (unknown location)
ERROR scanpy/tests/test_normalization.py::test_normalize_pearson_residuals_pca[toarray-int64-hvg_default-50-100] - ImportError: cannot import name 'pbmc3k' from 'scanpy.testing._helpers.data' (unknown location)
ERROR scanpy/tests/test_normalization.py::test_normalize_pearson_residuals_pca[toarray-int64-hvg_default-50-200] - ImportError: cannot import name 'pbmc3k' from 'scanpy.testing._helpers.data' (unknown location)
ERROR scanpy/tests/test_normalization.py::test_normalize_pearson_residuals_pca[toarray-int64-hvg_opt_out-30-100] - ImportError: cannot import name 'pbmc3k' from 'scanpy.testing._helpers.data' (unknown location)
ERROR scanpy/tests/test_normalization.py::test_normalize_pearson_residuals_pca[toarray-int64-hvg_opt_out-30-200] - ImportError: cannot import name 'pbmc3k' from 'scanpy.testing._helpers.data' (unknown location)
ERROR scanpy/tests/test_normalization.py::test_normalize_pearson_residuals_pca[toarray-int64-hvg_opt_out-50-100] - ImportError: cannot import name 'pbmc3k' from 'scanpy.testing._helpers.data' (unknown location)
ERROR scanpy/tests/test_normalization.py::test_normalize_pearson_residuals_pca[toarray-int64-hvg_opt_out-50-200] - ImportError: cannot import name 'pbmc3k' from 'scanpy.testing._helpers.data' (unknown location)
ERROR scanpy/tests/test_normalization.py::test_normalize_pearson_residuals_pca[toarray-int64-mask-30-100] - ImportError: cannot import name 'pbmc3k' from 'scanpy.testing._helpers.data' (unknown location)
ERROR scanpy/tests/test_normalization.py::test_normalize_pearson_residuals_pca[toarray-int64-mask-30-200] - ImportError: cannot import name 'pbmc3k' from 'scanpy.testing._helpers.data' (unknown location)
ERROR scanpy/tests/test_normalization.py::test_normalize_pearson_residuals_pca[toarray-int64-mask-50-100] - ImportError: cannot import name 'pbmc3k' from 'scanpy.testing._helpers.data' (unknown location)
ERROR scanpy/tests/test_normalization.py::test_normalize_pearson_residuals_pca[toarray-int64-mask-50-200] - ImportError: cannot import name 'pbmc3k' from 'scanpy.testing._helpers.data' (unknown location)
ERROR scanpy/tests/test_normalization.py::test_normalize_pearson_residuals_recipe[toarray-int64-30-100] - ImportError: cannot import name 'pbmc3k' from 'scanpy.testing._helpers.data' (unknown location)
ERROR scanpy/tests/test_normalization.py::test_normalize_pearson_residuals_recipe[toarray-int64-30-200] - ImportError: cannot import name 'pbmc3k' from 'scanpy.testing._helpers.data' (unknown location)
ERROR scanpy/tests/test_normalization.py::test_normalize_pearson_residuals_recipe[toarray-int64-50-100] - ImportError: cannot import name 'pbmc3k' from 'scanpy.testing._helpers.data' (unknown location)
ERROR scanpy/tests/test_normalization.py::test_normalize_pearson_residuals_recipe[toarray-int64-50-200] - ImportError: cannot import name 'pbmc3k' from 'scanpy.testing._helpers.data' (unknown location)
ERROR scanpy/tests/test_normalization.py::test_normalize_pearson_residuals_warnings[csr_matrix-float32] - ImportError: cannot import name 'pbmc3k' from 'scanpy.testing._helpers.data' (unknown location)
ERROR scanpy/tests/test_normalization.py::test_normalize_pearson_residuals_errors[csr_matrix-float32-theta0] - ImportError: cannot import name 'pbmc3k' from 'scanpy.testing._helpers.data' (unknown location)
ERROR scanpy/tests/test_normalization.py::test_normalize_pearson_residuals_errors[csr_matrix-float32-theta1] - ImportError: cannot import name 'pbmc3k' from 'scanpy.testing._helpers.data' (unknown location)
=========================================================== 8 failed, 670 passed, 40 skipped, 3 xfailed, 400 warnings, 130 errors in 44.70s ============================================================

Now we get a ton of failures due to a failure to import test dataset helpers

---

Pinning pytest<8 seems to resolve the issue.

@flying-sheep any ideas? Any idea why CI is working with pytest 8.1.1 while we get failures locally?

Environment info

My environments are both using ubuntu

My working env

# packages in environment at /mnt/workspace/mambaforge/envs/scanpy-dev2:
#
# Name                    Version                   Build  Channel
_libgcc_mutex             0.1                 conda_forge    conda-forge
_openmp_mutex             4.5                       2_gnu    conda-forge
anndata                   0.10.7                   pypi_0    pypi
array-api-compat          1.6                      pypi_0    pypi
asciitree                 0.3.3                    pypi_0    pypi
attrs                     23.2.0                   pypi_0    pypi
bzip2                     1.0.8                hd590300_5    conda-forge
ca-certificates           2024.2.2             hbcca054_0    conda-forge
cfgv                      3.4.0                    pypi_0    pypi
click                     8.1.7                    pypi_0    pypi
cloudpickle               3.0.0                    pypi_0    pypi
contourpy                 1.2.1                    pypi_0    pypi
coverage                  7.4.4                    pypi_0    pypi
cycler                    0.12.1                   pypi_0    pypi
dask                      2024.4.1                 pypi_0    pypi
dask-expr                 1.0.10                   pypi_0    pypi
distlib                   0.3.8                    pypi_0    pypi
execnet                   2.1.1                    pypi_0    pypi
fasteners                 0.19                     pypi_0    pypi
filelock                  3.13.3                   pypi_0    pypi
fonttools                 4.51.0                   pypi_0    pypi
fsspec                    2024.3.1                 pypi_0    pypi
h5py                      3.10.0                   pypi_0    pypi
identify                  2.5.35                   pypi_0    pypi
igraph                    0.11.4                   pypi_0    pypi
imageio                   2.34.0                   pypi_0    pypi
iniconfig                 2.0.0                    pypi_0    pypi
joblib                    1.4.0                    pypi_0    pypi
kiwisolver                1.4.5                    pypi_0    pypi
lazy-loader               0.4                      pypi_0    pypi
ld_impl_linux-64          2.40                 h41732ed_0    conda-forge
legacy-api-wrap           1.4                      pypi_0    pypi
leidenalg                 0.10.2                   pypi_0    pypi
libexpat                  2.6.2                h59595ed_0    conda-forge
libffi                    3.4.2                h7f98852_5    conda-forge
libgcc-ng                 13.2.0               h807b86a_5    conda-forge
libgomp                   13.2.0               h807b86a_5    conda-forge
libnsl                    2.0.1                hd590300_0    conda-forge
libsqlite                 3.45.2               h2797004_0    conda-forge
libuuid                   2.38.1               h0b41bf4_0    conda-forge
libxcrypt                 4.4.36               hd590300_1    conda-forge
libzlib                   1.2.13               hd590300_5    conda-forge
llvmlite                  0.42.0                   pypi_0    pypi
locket                    1.0.0                    pypi_0    pypi
matplotlib                3.8.4                    pypi_0    pypi
natsort                   8.4.0                    pypi_0    pypi
ncurses                   6.4.20240210         h59595ed_0    conda-forge
networkx                  3.3                      pypi_0    pypi
nodeenv                   1.8.0                    pypi_0    pypi
numba                     0.59.1                   pypi_0    pypi
numcodecs                 0.12.1                   pypi_0    pypi
numpy                     1.26.4                   pypi_0    pypi
openssl                   3.2.1                hd590300_1    conda-forge
packaging                 24.0                     pypi_0    pypi
pandas                    2.2.1                    pypi_0    pypi
partd                     1.4.1                    pypi_0    pypi
patsy                     0.5.6                    pypi_0    pypi
pbr                       6.0.0                    pypi_0    pypi
pillow                    10.3.0                   pypi_0    pypi
pip                       24.0               pyhd8ed1ab_0    conda-forge
platformdirs              4.2.0                    pypi_0    pypi
pluggy                    1.4.0                    pypi_0    pypi
pre-commit                3.7.0                    pypi_0    pypi
profimp                   0.1.0                    pypi_0    pypi
pyarrow                   15.0.2                   pypi_0    pypi
pynndescent               0.5.12                   pypi_0    pypi
pyparsing                 3.1.2                    pypi_0    pypi
pytest                    7.4.4                    pypi_0    pypi
pytest-cov                5.0.0                    pypi_0    pypi
pytest-mock               3.14.0                   pypi_0    pypi
pytest-nunit              1.0.7                    pypi_0    pypi
pytest-xdist              3.5.0                    pypi_0    pypi
python                    3.12.2          hab00c5b_0_cpython    conda-forge
python-dateutil           2.9.0.post0              pypi_0    pypi
pytz                      2024.1                   pypi_0    pypi
pyyaml                    6.0.1                    pypi_0    pypi
readline                  8.2                  h8228510_1    conda-forge
scanpy                    1.10.0rc2.dev33+g9c8c095d          pypi_0    pypi
scikit-image              0.22.0                   pypi_0    pypi
scikit-learn              1.4.1.post1              pypi_0    pypi
scipy                     1.13.0                   pypi_0    pypi
seaborn                   0.13.2                   pypi_0    pypi
session-info              1.0.0                    pypi_0    pypi
setuptools                69.2.0             pyhd8ed1ab_0    conda-forge
setuptools-scm            8.0.4                    pypi_0    pypi
six                       1.16.0                   pypi_0    pypi
statsmodels               0.14.1                   pypi_0    pypi
stdlib-list               0.10.0                   pypi_0    pypi
texttable                 1.7.0                    pypi_0    pypi
threadpoolctl             3.4.0                    pypi_0    pypi
tifffile                  2024.2.12                pypi_0    pypi
tk                        8.6.13          noxft_h4845f30_101    conda-forge
toolz                     0.12.1                   pypi_0    pypi
tqdm                      4.66.2                   pypi_0    pypi
typing-extensions         4.11.0                   pypi_0    pypi
tzdata                    2024.1                   pypi_0    pypi
umap-learn                0.5.6                    pypi_0    pypi
virtualenv                20.25.1                  pypi_0    pypi
wheel                     0.43.0             pyhd8ed1ab_1    conda-forge
xz                        5.2.6                h166bdaf_0    conda-forge
zarr                      2.17.2                   pypi_0    pypi

My failing env

# packages in environment at /mnt/workspace/mambaforge/envs/scanpy-dev2:
#
# Name                    Version                   Build  Channel
_libgcc_mutex             0.1                 conda_forge    conda-forge
_openmp_mutex             4.5                       2_gnu    conda-forge
anndata                   0.10.7                   pypi_0    pypi
array-api-compat          1.6                      pypi_0    pypi
asciitree                 0.3.3                    pypi_0    pypi
attrs                     23.2.0                   pypi_0    pypi
bzip2                     1.0.8                hd590300_5    conda-forge
ca-certificates           2024.2.2             hbcca054_0    conda-forge
cfgv                      3.4.0                    pypi_0    pypi
click                     8.1.7                    pypi_0    pypi
cloudpickle               3.0.0                    pypi_0    pypi
contourpy                 1.2.1                    pypi_0    pypi
coverage                  7.4.4                    pypi_0    pypi
cycler                    0.12.1                   pypi_0    pypi
dask                      2024.4.1                 pypi_0    pypi
dask-expr                 1.0.10                   pypi_0    pypi
distlib                   0.3.8                    pypi_0    pypi
execnet                   2.1.1                    pypi_0    pypi
fasteners                 0.19                     pypi_0    pypi
filelock                  3.13.3                   pypi_0    pypi
fonttools                 4.51.0                   pypi_0    pypi
fsspec                    2024.3.1                 pypi_0    pypi
h5py                      3.10.0                   pypi_0    pypi
identify                  2.5.35                   pypi_0    pypi
igraph                    0.11.4                   pypi_0    pypi
imageio                   2.34.0                   pypi_0    pypi
iniconfig                 2.0.0                    pypi_0    pypi
joblib                    1.4.0                    pypi_0    pypi
kiwisolver                1.4.5                    pypi_0    pypi
lazy-loader               0.4                      pypi_0    pypi
ld_impl_linux-64          2.40                 h41732ed_0    conda-forge
legacy-api-wrap           1.4                      pypi_0    pypi
leidenalg                 0.10.2                   pypi_0    pypi
libexpat                  2.6.2                h59595ed_0    conda-forge
libffi                    3.4.2                h7f98852_5    conda-forge
libgcc-ng                 13.2.0               h807b86a_5    conda-forge
libgomp                   13.2.0               h807b86a_5    conda-forge
libnsl                    2.0.1                hd590300_0    conda-forge
libsqlite                 3.45.2               h2797004_0    conda-forge
libuuid                   2.38.1               h0b41bf4_0    conda-forge
libxcrypt                 4.4.36               hd590300_1    conda-forge
libzlib                   1.2.13               hd590300_5    conda-forge
llvmlite                  0.42.0                   pypi_0    pypi
locket                    1.0.0                    pypi_0    pypi
matplotlib                3.8.4                    pypi_0    pypi
natsort                   8.4.0                    pypi_0    pypi
ncurses                   6.4.20240210         h59595ed_0    conda-forge
networkx                  3.3                      pypi_0    pypi
nodeenv                   1.8.0                    pypi_0    pypi
numba                     0.59.1                   pypi_0    pypi
numcodecs                 0.12.1                   pypi_0    pypi
numpy                     1.26.4                   pypi_0    pypi
openssl                   3.2.1                hd590300_1    conda-forge
packaging                 24.0                     pypi_0    pypi
pandas                    2.2.1                    pypi_0    pypi
partd                     1.4.1                    pypi_0    pypi
patsy                     0.5.6                    pypi_0    pypi
pbr                       6.0.0                    pypi_0    pypi
pillow                    10.3.0                   pypi_0    pypi
pip                       24.0               pyhd8ed1ab_0    conda-forge
platformdirs              4.2.0                    pypi_0    pypi
pluggy                    1.4.0                    pypi_0    pypi
pre-commit                3.7.0                    pypi_0    pypi
profimp                   0.1.0                    pypi_0    pypi
pyarrow                   15.0.2                   pypi_0    pypi
pynndescent               0.5.12                   pypi_0    pypi
pyparsing                 3.1.2                    pypi_0    pypi
pytest                    8.1.1                    pypi_0    pypi
pytest-cov                5.0.0                    pypi_0    pypi
pytest-mock               3.14.0                   pypi_0    pypi
pytest-nunit              1.0.7                    pypi_0    pypi
pytest-xdist              3.5.0                    pypi_0    pypi
python                    3.12.2          hab00c5b_0_cpython    conda-forge
python-dateutil           2.9.0.post0              pypi_0    pypi
pytz                      2024.1                   pypi_0    pypi
pyyaml                    6.0.1                    pypi_0    pypi
readline                  8.2                  h8228510_1    conda-forge
scanpy                    1.10.0rc2.dev33+g9c8c095d          pypi_0    pypi
scikit-image              0.22.0                   pypi_0    pypi
scikit-learn              1.4.1.post1              pypi_0    pypi
scipy                     1.13.0                   pypi_0    pypi
seaborn                   0.13.2                   pypi_0    pypi
session-info              1.0.0                    pypi_0    pypi
setuptools                69.2.0             pyhd8ed1ab_0    conda-forge
setuptools-scm            8.0.4                    pypi_0    pypi
six                       1.16.0                   pypi_0    pypi
statsmodels               0.14.1                   pypi_0    pypi
stdlib-list               0.10.0                   pypi_0    pypi
texttable                 1.7.0                    pypi_0    pypi
threadpoolctl             3.4.0                    pypi_0    pypi
tifffile                  2024.2.12                pypi_0    pypi
tk                        8.6.13          noxft_h4845f30_101    conda-forge
toolz                     0.12.1                   pypi_0    pypi
tqdm                      4.66.2                   pypi_0    pypi
typing-extensions         4.11.0                   pypi_0    pypi
tzdata                    2024.1                   pypi_0    pypi
umap-learn                0.5.6                    pypi_0    pypi
virtualenv                20.25.1                  pypi_0    pypi
wheel                     0.43.0             pyhd8ed1ab_1    conda-forge
xz                        5.2.6                h166bdaf_0    conda-forge
zarr                      2.17.2                   pypi_0    pypi

Luke's environment: MacOS Ventura 13.4.1. Intel MacBook pro

Luke's failing env

# packages in environment at /Users/luke.zappia/miniconda3/envs/scanpy-dev:
#
# Name                    Version                   Build  Channel
anndata                   0.10.6                   pypi_0    pypi
array-api-compat          1.4.1                    pypi_0    pypi
asciitree                 0.3.3                    pypi_0    pypi
attrs                     23.2.0                   pypi_0    pypi
bzip2                     1.0.8                h10d778d_5    conda-forge
ca-certificates           2024.2.2             h8857fd0_0    conda-forge
cfgv                      3.4.0                    pypi_0    pypi
click                     8.1.7                    pypi_0    pypi
cloudpickle               3.0.0                    pypi_0    pypi
contourpy                 1.2.0                    pypi_0    pypi
coverage                  7.4.4                    pypi_0    pypi
cycler                    0.12.1                   pypi_0    pypi
dask                      2024.3.0                 pypi_0    pypi
distlib                   0.3.8                    pypi_0    pypi
execnet                   2.1.1                    pypi_0    pypi
fasteners                 0.19                     pypi_0    pypi
filelock                  3.13.3                   pypi_0    pypi
fonttools                 4.49.0                   pypi_0    pypi
fsspec                    2024.2.0                 pypi_0    pypi
h5py                      3.10.0                   pypi_0    pypi
identify                  2.5.35                   pypi_0    pypi
igraph                    0.11.4                   pypi_0    pypi
imageio                   2.34.0                   pypi_0    pypi
iniconfig                 2.0.0                    pypi_0    pypi
joblib                    1.3.2                    pypi_0    pypi
kiwisolver                1.4.5                    pypi_0    pypi
lazy-loader               0.3                      pypi_0    pypi
legacy-api-wrap           1.4                      pypi_0    pypi
leidenalg                 0.10.2                   pypi_0    pypi
libexpat                  2.6.2                h73e2aa4_0    conda-forge
libffi                    3.4.2                h0d85af4_5    conda-forge
libsqlite                 3.45.2               h92b6c6a_0    conda-forge
libzlib                   1.2.13               h8a1eda9_5    conda-forge
llvmlite                  0.42.0                   pypi_0    pypi
locket                    1.0.0                    pypi_0    pypi
matplotlib                3.8.3                    pypi_0    pypi
natsort                   8.4.0                    pypi_0    pypi
ncurses                   6.4                  h93d8f39_2    conda-forge
networkx                  3.2.1                    pypi_0    pypi
nodeenv                   1.8.0                    pypi_0    pypi
numba                     0.59.0                   pypi_0    pypi
numcodecs                 0.12.1                   pypi_0    pypi
numpy                     1.26.4                   pypi_0    pypi
openssl                   3.2.1                hd75f5a5_0    conda-forge
packaging                 24.0                     pypi_0    pypi
pandas                    2.2.1                    pypi_0    pypi
partd                     1.4.1                    pypi_0    pypi
patsy                     0.5.6                    pypi_0    pypi
pbr                       6.0.0                    pypi_0    pypi
pillow                    10.2.0                   pypi_0    pypi
pip                       24.0               pyhd8ed1ab_0    conda-forge
platformdirs              4.2.0                    pypi_0    pypi
pluggy                    1.4.0                    pypi_0    pypi
pre-commit                3.7.0                    pypi_0    pypi
profimp                   0.1.0                    pypi_0    pypi
pynndescent               0.5.11                   pypi_0    pypi
pyparsing                 3.1.2                    pypi_0    pypi
pytest                    8.1.1                    pypi_0    pypi
pytest-cov                4.1.0                    pypi_0    pypi
pytest-mock               3.12.0                   pypi_0    pypi
pytest-nunit              1.0.7                    pypi_0    pypi
pytest-xdist              3.5.0                    pypi_0    pypi
python                    3.12.2          h9f0c242_0_cpython    conda-forge
python-dateutil           2.9.0.post0              pypi_0    pypi
pytz                      2024.1                   pypi_0    pypi
pyyaml                    6.0.1                    pypi_0    pypi
readline                  8.2                  h9e318b2_1    conda-forge
scanpy                    1.10.0rc2.dev16+g60aa7180          pypi_0    pypi
scikit-image              0.22.0                   pypi_0    pypi
scikit-learn              1.4.1.post1              pypi_0    pypi
scipy                     1.12.0                   pypi_0    pypi
seaborn                   0.13.2                   pypi_0    pypi
session-info              1.0.0                    pypi_0    pypi
setuptools                69.2.0             pyhd8ed1ab_0    conda-forge
setuptools-scm            8.0.4                    pypi_0    pypi
six                       1.16.0                   pypi_0    pypi
statsmodels               0.14.1                   pypi_0    pypi
stdlib-list               0.10.0                   pypi_0    pypi
texttable                 1.7.0                    pypi_0    pypi
threadpoolctl             3.3.0                    pypi_0    pypi
tifffile                  2024.2.12                pypi_0    pypi
tk                        8.6.13               h1abcd95_1    conda-forge
toolz                     0.12.1                   pypi_0    pypi
tqdm                      4.66.2                   pypi_0    pypi
typing-extensions         4.11.0                   pypi_0    pypi
tzdata                    2024.1                   pypi_0    pypi
umap-learn                0.5.5                    pypi_0    pypi
virtualenv                20.25.1                  pypi_0    pypi
wheel                     0.42.0             pyhd8ed1ab_0    conda-forge
xz                        5.2.6                h775f41a_0    conda-forge
zarr                      2.17.1                   pypi_0    pypi

TODO:

• Unpin pytest

[ivirshup]

It looks like pinning pytest<8.1 and removing an auto import of dask.dataframe should fix this.

Would be nice to not pin pytest.

[ivirshup]

@flying-sheep does anndata need to have a pytest minimum bound of 8.1? It seems to run fine for me with 8.0.2, and scanpy is having problems with 8.1.1.

[flying-sheep]

What happens is

1. pip install -e adds the repo directory to sys.path, since we don‘t use a src directory

2. something imports the data directory instead of scanpy.testing._helpers.data and stores it in the wrong place in sys.modules:

   >>> sys.modules["scanpy.testing._helpers.data"]
   <module 'scanpy.testing._helpers.data' (namespace) from ['/home/phil/Dev/Python/Single Cell/scanpy/data']>
   

I assume that some of the attempts to fix our doctest woes in Pytest 8.1 led to this bug being introduced in Pytest 8.1.

But I’d like to figure out what exactly causes that bug before we do anything.

PS: Of course things like this are exactly why we switched anndata to a src layout: that way src can be in sys.path instead of a kitchen sink directory, and import <something> will only see directories that are meant to contain exclusively python packages. Pytest shouldn’t import data and then store the resulting module as sys.modules['scanpy.testing._helpers.data']

[ivirshup]

@flying-sheep do you want to use this issue to investigate why this doesn't work with pytest 8.1, or track that in a new issue for unpinning it?

If you want to track it here, feel free to edit the title

[flying-sheep]

Done. I think the difference between CI and local is that locally, the data dir exists for all of us

[ivirshup]

What's your proposed solution? It seems like that should be fine, so I'm imagining something needs to change in pytest?

[flying-sheep]

Still no clue: pytest-dev/pytest#12194 (comment)

I haven’t been able to create a minimal reproducer yet.

The problem is that the wrong module gets returned by a _frozen_importlib_external.PathFinder, so basically a blackbox.