Equality comparisons are not supported for AnnData objects, instead compare the desired attributes.

[zhongzheng1999]

counts_file_path must is a path to the normalized count matrix, or an in-memory AnnData object, but when you make an Anndata object, cellphonedb doesn't work!

---

NotImplementedError Traceback (most recent call last) Cell In[21], line 1 ----> 1 cpdb_results = cpdb_analysis_method.call( 2 cpdb_file_path=cpdb_file_path, 3 meta_file_path=meta_file_path, 4 counts_file_path=adata_count, 5 counts_data='hgnc_symbol', 6 score_interactions=True, 7 output_path=out_path, 8 separator='|', 9 threads=5, 10 threshold=0.1, 11 result_precision=3, 12 debug=False, 13 output_suffix='M1' 14 )

File ~/mambaforge/envs/scanpy/lib/python3.11/site-packages/cellphonedb/src/core/methods/cpdb_analysis_method.py:79, in call(cpdb_file_path, meta_file_path, counts_file_path, counts_data, output_path, microenvs_file_path, separator, threshold, result_precision, debug, output_suffix, score_interactions, threads) 77 # Report error unless the required arguments have been provided 78 required_arguments = [cpdb_file_path, meta_file_path, counts_file_path, counts_data, output_path] ---> 79 if None in required_arguments or '' in required_arguments: 80 raise MissingRequiredArgumentsException(description="All of the following arguments need to be provided: {}".format( 81 "cpdb_file_path, meta_file_path, counts_file_path, counts_data, output_path")) 83 # Load into memory CellphoneDB data

File ~/mambaforge/envs/scanpy/lib/python3.11/site-packages/anndata/_core/anndata.py:656, in AnnData.eq(self, other) 654 def eq(self, other): 655 """Equality testing""" --> 656 raise NotImplementedError( 657 "Equality comparisons are not supported for AnnData objects, " 658 "instead compare the desired attributes." 659 )

NotImplementedError: Equality comparisons are not supported for AnnData objects, instead compare the desired attributes. Selection deleted

[Roger-GOAT]

get the same error. Anyone solve it?

[cakirb]

Hello,

Sorry for the late reply!! This problem was fixed previously, you should install CellPhoneDB from GitHub to fix on your side: pip install --force-reinstall "git+https://github.com/ventolab/CellphoneDB.git"

Please let us know if this helps you!

Best, Batu

[zhongzheng1999]

Hi @cakirb ！ I wanted to let you know that I have successfully resolved the issue and managed to run cpdb_statistical_analysis_method.call as you suggested. However, I encountered the following error during installation: ERROR: pip's dependency resolver does not currently take into account all the packages that are installed. This behaviour is the source of the following dependency conflicts.

chex 0.1.85 requires jax>=0.4.16, but you have jax 0.4.4 which is incompatible. torchvision 0.17.1 requires torch==2.2.1, but you have torch 2.3.0 which is incompatible. orbax-checkpoint 0.5.3 requires jax>=0.4.9, but you have jax 0.4.4 which is incompatible. scikit-bio 0.5.9 requires scipy<=1.10.1, but you have scipy 1.13.0 which is incompatible. scanorama 1.7.4 requires intervaltree>=3.1.0, but you have intervaltree 2.1.0 which is incompatible. numpyro 0.13.2 requires jax>=0.4.14, but you have jax 0.4.4 which is incompatible. botocore 1.32.1 requires urllib3<2.1,>=1.25.4; python_version >= "3.10", but you have urllib3 2.2.1 which is incompatible.

I understand that this might be due to incorrect dependency versions. Despite this, I was still able to get the results. Perhaps loosening the dependency version requirements could help reduce the anxiety caused by these errors, haha. Thank you very much for your help!

[cakirb]

Hi @zhongzheng1999,

Glad this worked well for you! Also thanks for your feedback on dependency error, we will look into loosening the version requirements.

Best, Batu