ITADN

Not compatible with numpy >= 2.0.0

#186Closedkverstae 创建于 2024-07-23
K
kverstaecommented
When trying to convert an AnnData object to a loom file, I get following error: ``` adata.write_loom(par["output"], write_obsm_varm=True) File "/usr/local/lib/python3.12/site-packages/anndata/_core/anndata.py", line 1973, in write_loom write_loom(filename, self, write_obsm_varm=write_obsm_varm) File "/usr/local/lib/python3.12/site-packages/anndata/_io/write.py", line 110, in write_loom create(fspath(filename), layers, row_attrs=row_attrs, col_attrs=col_attrs) File "/usr/local/lib/python3.12/site-packages/loompy/loompy.py", line 1065, in create with new(filename, file_attrs=file_attrs) as ds: ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/local/lib/python3.12/site-packages/loompy/loompy.py", line 1008, in new ds.attrs['CreationDate'] = timestamp() ~~~~~~~~^^^^^^^^^^^^^^^^ File "/usr/local/lib/python3.12/site-packages/loompy/global_attribute_manager.py", line 66, in __setitem__ return self.__setattr__(name, val) ^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/local/lib/python3.12/site-packages/loompy/global_attribute_manager.py", line 94, in __setattr__ normalized = loompy.materialize_attr_values(val) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/local/lib/python3.12/site-packages/loompy/normalize.py", line 91, in materialize_attr_values if np.issubdtype(a.dtype, np.string_) or np.issubdtype(a.dtype, np.object_): ^^^^^^^^^^ File "/usr/local/lib/python3.12/site-packages/numpy/__init__.py", line 397, in __getattr__ raise AttributeError( AttributeError: `np.string_` was removed in the NumPy 2.0 release. Use `np.bytes_` instead.. Did you mean: 'strings'? ```
关闭于 2024-12-16 1 条评论