Error in py_module_import

Hi, I am running SAVERX with Rstudio, R3.6.2 under Ubuntu 16.04 and a Python 3.5 virtual environment with the sctransfer package v0.0.9. No error messages loading SAVERX or installing the python dependencies but I get this while running SAVERX:

> library("SAVERX")
> scFile <- saverx("./rawcounts.rds")
[1] "Input file is: ./rawcounts.rds"
[1] "Use a pretrained model: No"
[1] "Processed file saved as: 1582598887.77262/tmpdata.rds"
[1] "Data preprocessed ..."
Error in py_module_import(module, convert = convert) : 
  SyntaxError: invalid syntax (_settings.py, line 351)

Python packages available:

Package              Version   
-------------------- ----------
absl-py              0.9.0     
anndata              0.6.20    
astor                0.8.1     
cachetools           4.0.0     
certifi              2019.11.28
chardet              3.0.4     
cTPnet               0.2.6     
cycler               0.10.0    
decorator            4.4.1     
gast                 0.2.2     
google-auth          1.11.2    
google-auth-oauthlib 0.4.1     
google-pasta         0.1.8     
grpcio               1.27.2    
h5py                 2.10.0    
idna                 2.9       
joblib               0.14.1    
Keras                2.3.1     
Keras-Applications   1.0.8     
Keras-Preprocessing  1.1.0     
kiwisolver           1.1.0     
llvmlite             0.31.0    
Markdown             3.2.1     
matplotlib           3.0.3     
natsort              7.0.1     
networkx             2.4       
numba                0.47.0    
numexpr              2.7.1     
numpy                1.18.1    
oauthlib             3.1.0     
opt-einsum           3.1.0     
pandas               0.24.2    
patsy                0.5.1     
pip                  20.0.2    
pkg-resources        0.0.0     
protobuf             3.11.3    
pyasn1               0.4.8     
pyasn1-modules       0.2.8     
pyparsing            2.4.6     
python-dateutil      2.8.1     
pytz                 2019.3    
PyYAML               5.3       
requests             2.23.0    
requests-oauthlib    1.3.0     
rsa                  4.0       
scanpy               1.4.3     
scikit-learn         0.22.1    
scipy                1.4.1     
sctransfer           0.0.9     
seaborn              0.9.1     
setuptools           45.2.0    
six                  1.14.0    
statsmodels          0.11.1    
tables               3.6.1     
tensorboard          2.0.2     
tensorflow           2.0.0     
tensorflow-estimator 2.0.1     
termcolor            1.1.0     
torch                1.4.0     
tqdm                 4.43.0    
umap-learn           0.3.10    
urllib3              1.25.8    
Werkzeug             1.0.0     
wheel                0.34.2    
wrapt                1.12.0

I also tried with tensorflow 2.1 which produces the same error message with some GPU related warnings on top. Tracing those other warnings led me to this thread: https://github.com/tensorflow/tensorflow/issues/35968 However, whereas downgrading to 2.0.0 solved the issue for them it does not remove the error reported here.

Any ideas? Thanks in advance! Jerry

jingshuw / SAVERX

Error in py_module_import #13