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theislab / diffxpy

Differential expression analysis for single-cell RNA-seq data.
https://diffxpy.rtfd.io
BSD 3-Clause "New" or "Revised" License
191 stars 23 forks source link

import error with tensorflow #158

Open z5ouyang opened 4 years ago

z5ouyang commented 4 years ago

I just installed diffxpy followed the installation instructions: pip install tf-nightly pip install tfp-nightly pip install tensorflow pip install tensorflow-probability git clone https://github.com/theislab/batchglm.git cd batchglm;pip install -e .;cd .. git clone https://github.com/theislab/diffxpy.git cd diffxpy;pip install -e .;cd ..

then when I "import diffxpy.api as de", error: generic_utils.populate_dict_with_module_objects( AttributeError: module 'tensorflow.python.keras.utils.generic_utils' has no attribute 'populate_dict_with_module_objects'

Env info: Python 3.8.2 (default, Mar 26 2020, 15:53:00) [GCC 7.3.0] :: Anaconda, Inc. on linux Name: tf-nightly; Version: 2.3.0.dev20200512 Name: tfp-nightly; Version: 0.11.0.dev20200512 Name: tensorflow; Version: 2.2.0 Name: tensorflow-probability; Version: 0.9.0

Thank you!

baohongz commented 4 years ago

$ pip install diffxpy

(test) [bzhang1@omicsoft01 app]$ pip show diffxpy Name: diffxpy Version: 0.7.4 Summary: Fast and scalable differential expression analysis on single-cell RNA-seq data Home-page: UNKNOWN Author: David S. Fischer, Florian R. Hölzlwimmer Author-email: david.fischer@helmholtz-muenchen.de, diffxpy@frhoelzlwimmer.de License: UNKNOWN Location: /opt/anaconda3/envs/test/lib/python3.7/site-packages Requires: numpy, scipy, pandas, statsmodels, patsy, batchglm Required-by:

z5ouyang commented 4 years ago

After uninstalling everything, and reinstall the following it works now: pip install tensorflow pip install diffxpy

Please update the documentation. Thanks

davidsebfischer commented 4 years ago

Thanks @z5ouyang, will do that!