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Somewhere, we broke zappy tests.
This diff is the start of fixing this: https://github.com/scverse/scanpy/compare/d3a8c7981321e4f0afa3290dd84c06fed3654b0a..fd90edb71b6f5fc4cc58638583ea4ff37b34e660
pip install zappy pytest scanpy/tests/test_preprocessing_distributed.py
____________________________________________________________________________________________________________________________________ test_normalize_total[direct] ____________________________________________________________________________________________________________________________________ adata = AnnData object with n_obs × n_vars = 10000 × 1000 var: 'gene_ids', adata_dist = AnnData object with n_obs × n_vars = 10000 × 1000 var: 'gene_ids' uns: 'dist-mode' def test_normalize_total(adata: AnnData, adata_dist: AnnData): > normalize_total(adata_dist) scanpy/tests/test_preprocessing_distributed.py:93: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ /home/phil/.local/share/hatch/env/virtual/scanpy/q4In3tK-/hatch-test.stable/lib/python3.12/site-packages/legacy_api_wrap/__init__.py:80: in fn_compatible return fn(*args_all, **kw) scanpy/preprocessing/_normalization.py:240: in normalize_total adata, _normalize_data(X, counts_per_cell, target_sum), layer=layer scanpy/preprocessing/_normalization.py:49: in _normalize_data return axis_mul_or_truediv( /usr/lib/python3.12/functools.py:909: in wrapper return dispatch(args[0].__class__)(*args, **kw) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ X = <zappy.direct.array.DirectZappyArray object at 0x7f06eb607a40>, scaling_array = array([0.9270073, 0.4379562, 1.5985402, ..., 0.8540146, 1.5109489, 0.8978102], dtype=float32), axis = 0, op = <built-in function truediv> @singledispatch def axis_mul_or_truediv( X: sparse.spmatrix, scaling_array, axis: Literal[0, 1], op: Callable[[Any, Any], Any], *, allow_divide_by_zero: bool = True, out: sparse.spmatrix | None = None, ) -> sparse.spmatrix: check_op(op) if out is not None: if X.data is not out.data: raise ValueError( "`out` argument provided but not equal to X. This behavior is not supported for sparse matrix scaling." ) if not allow_divide_by_zero and op is truediv: scaling_array = scaling_array.copy() + (scaling_array == 0) row_scale = axis == 0 column_scale = axis == 1 if row_scale: def new_data_op(x): return op(x.data, np.repeat(scaling_array, np.diff(x.indptr))) elif column_scale: def new_data_op(x): return op(x.data, scaling_array.take(x.indices, mode="clip")) > if X.format == "csr": E AttributeError: 'DirectZappyArray' object has no attribute 'format' scanpy/_utils/__init__.py:612: AttributeError
----- anndata 0.10.7 scanpy 1.10.0rc2.dev61+g874d99b3 ----- PIL 10.3.0 asciitree NA cloudpickle 3.0.0 coverage 7.5.3 cycler 0.12.1 cython_runtime NA dask 2024.5.2 dateutil 2.9.0.post0 distutils 3.12.3 h5py 3.11.0 igraph 0.11.5 joblib 1.4.2 kiwisolver 1.4.5 legacy_api_wrap NA leidenalg 0.10.2 llvmlite 0.42.0 matplotlib 3.9.0 mpl_toolkits NA natsort 8.4.0 numba 0.59.1 numcodecs 0.12.1 numpy 1.26.4 packaging 24.0 pandas 2.2.2 psutil 5.9.8 pyparsing 3.1.2 pytz 2024.1 scipy 1.13.1 session_info 1.0.0 setuptools 70.0.0 setuptools_scm NA six 1.16.0 sklearn 1.5.0 texttable 1.7.0 threadpoolctl 3.5.0 tlz 0.12.1 toolz 0.12.1 yaml 6.0.1 zappy NA zarr 2.18.2 ----- Python 3.12.3 (main, Apr 23 2024, 09:16:07) [GCC 13.2.1 20240417] Linux-6.9.3-zen1-1-zen-x86_64-with-glibc2.39 ----- Session information updated at 2024-06-03 11:27
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What happened?
Somewhere, we broke zappy tests.
This diff is the start of fixing this: https://github.com/scverse/scanpy/compare/d3a8c7981321e4f0afa3290dd84c06fed3654b0a..fd90edb71b6f5fc4cc58638583ea4ff37b34e660
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The text was updated successfully, but these errors were encountered: