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cistrome / MIRA

Python package for analysis of multiomic single cell RNA-seq and ATAC-seq.
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IndexError: Unknown indexer Ellipsis of type <class 'ellipsis'> #41

Closed WENHUAN22 closed 3 months ago

WENHUAN22 commented 5 months ago

The program reports an error when I try to run the coed from tutorial train, test = model.train_test_split(data) or tuner.fit(data)

Both the error messages show Traceback (most recent call last): File "/home/zeng/software/anaconda3/envs/mira/lib/python3.9/site-packages/IPython/core/interactiveshell.py", line 3505, in run_code exec(code_obj, self.user_global_ns, self.user_ns) File "", line 11, in tuner.fit(data) File "/home/zeng/software/anaconda3/envs/mira/lib/python3.9/site-packages/mira/topic_model/hyperparameter_optim/trainer.py", line 620, in fit train, test = cache.cache_data(overwrite=True) File "/home/zeng/software/anaconda3/envs/mira/lib/python3.9/site-packages/mira/topic_model/base.py", line 250, in cache_data train, test = self.model.train_test_split( File "/home/zeng/software/anaconda3/envs/mira/lib/python3.9/site-packages/mira/topic_model/base.py", line 494, in train_test_split return train_test_split(adata, File "/home/zeng/software/anaconda3/envs/mira/lib/python3.9/site-packages/sklearn/utils/_param_validation.py", line 213, in wrapper return func(*args, *kwargs) File "/home/zeng/software/anaconda3/envs/mira/lib/python3.9/site-packages/sklearn/model_selection/_split.py", line 2683, in train_test_split return list( File "/home/zeng/software/anaconda3/envs/mira/lib/python3.9/site-packages/sklearn/model_selection/_split.py", line 2685, in (_safe_indexing(a, train), _safe_indexing(a, test)) for a in arrays File "/home/zeng/software/anaconda3/envs/mira/lib/python3.9/site-packages/sklearn/utils/init.py", line 386, in _safe_indexing return _array_indexing(X, indices, indices_dtype, axis=axis) File "/home/zeng/software/anaconda3/envs/mira/lib/python3.9/site-packages/sklearn/utils/init.py", line 196, in _array_indexing return array[key, ...] if axis == 0 else array[:, key] File "/home/zeng/software/anaconda3/envs/mira/lib/python3.9/site-packages/anndata/_core/anndata.py", line 1177, in getitem oidx, vidx = self._normalize_indices(index) File "/home/zeng/software/anaconda3/envs/mira/lib/python3.9/site-packages/anndata/_core/anndata.py", line 1158, in _normalize_indices return _normalize_indices(index, self.obs_names, self.var_names) File "/home/zeng/software/anaconda3/envs/mira/lib/python3.9/site-packages/anndata/_core/index.py", line 36, in _normalize_indices ax1 = _normalize_index(ax1, names1) File "/home/zeng/software/anaconda3/envs/mira/lib/python3.9/site-packages/anndata/_core/index.py", line 116, in _normalize_index raise IndexError(f"Unknown indexer {indexer!r} of type {type(indexer)}") IndexError: Unknown indexer Ellipsis of type <class 'ellipsis'> train, test = model.train_test_split(data) Traceback (most recent call last): File "/home/zeng/software/anaconda3/envs/mira/lib/python3.9/site-packages/IPython/core/interactiveshell.py", line 3505, in run_code exec(code_obj, self.user_global_ns, self.user_ns) File "", line 1, in train, test = model.train_test_split(data) File "/home/zeng/software/anaconda3/envs/mira/lib/python3.9/site-packages/mira/topic_model/base.py", line 494, in train_test_split return train_test_split(adata, File "/home/zeng/software/anaconda3/envs/mira/lib/python3.9/site-packages/sklearn/utils/_param_validation.py", line 213, in wrapper return func(args, **kwargs) File "/home/zeng/software/anaconda3/envs/mira/lib/python3.9/site-packages/sklearn/model_selection/_split.py", line 2683, in train_test_split return list( File "/home/zeng/software/anaconda3/envs/mira/lib/python3.9/site-packages/sklearn/model_selection/_split.py", line 2685, in (_safe_indexing(a, train), _safe_indexing(a, test)) for a in arrays File "/home/zeng/software/anaconda3/envs/mira/lib/python3.9/site-packages/sklearn/utils/init.py", line 386, in _safe_indexing return _array_indexing(X, indices, indices_dtype, axis=axis) File "/home/zeng/software/anaconda3/envs/mira/lib/python3.9/site-packages/sklearn/utils/init.py", line 196, in _array_indexing return array[key, ...] if axis == 0 else array[:, key] File "/home/zeng/software/anaconda3/envs/mira/lib/python3.9/site-packages/anndata/_core/anndata.py", line 1177, in getitem oidx, vidx = self._normalize_indices(index) File "/home/zeng/software/anaconda3/envs/mira/lib/python3.9/site-packages/anndata/_core/anndata.py", line 1158, in _normalize_indices return _normalize_indices(index, self.obs_names, self.var_names) File "/home/zeng/software/anaconda3/envs/mira/lib/python3.9/site-packages/anndata/_core/index.py", line 36, in _normalize_indices ax1 = _normalize_index(ax1, names1) File "/home/zeng/software/anaconda3/envs/mira/lib/python3.9/site-packages/anndata/_core/index.py", line 116, in _normalize_index raise IndexError(f"Unknown indexer {indexer!r} of type {type(indexer)}") IndexError: Unknown indexer Ellipsis of type <class 'ellipsis'>

I am wondering if anyone has any idea about this error.

AllenWLynch commented 5 months ago

Hi, I saw another issue which reported this bug, and have found the issue. Anndata is no longer interoperable with scikit-learn's model selection API. A fix should be available early this week!