Error installing models with kipoi ls

[Al-Murphy]

I get an error when using kipoi ls.

So I went back and followed the documented steps in the README and used a clean conda env with python 3.10 on a linux machine but still get the same issue:

conda create -n "kipoi" python=3.10.0
conda activate kipoi
pip install kipoi

The error:

$ kipoi ls
INFO [kipoi.sources] Cloning https://github.com/kipoi/models.git into /home/aemurphy/.kipoi/models/
Cloning into '/home/aemurphy/.kipoi/models'...
remote: Enumerating objects: 553, done.
remote: Counting objects: 100% (553/553), done.
remote: Compressing objects: 100% (389/389), done.
error: RPC failed; curl 56 GnuTLS recv error (-9): Error decoding the received TLS packet.
fatal: the remote end hung up unexpectedly
fatal: early EOF
fatal: index-pack failed
Traceback (most recent call last):
  File "/home/aemurphy/anaconda3/envs/kipoi/bin/kipoi", line 8, in <module>
    sys.exit(main())
  File "/home/aemurphy/anaconda3/envs/kipoi/lib/python3.10/site-packages/kipoi/__main__.py", line 107, in main
    command_fn(args.command, sys.argv[2:])
  File "/home/aemurphy/anaconda3/envs/kipoi/lib/python3.10/site-packages/kipoi/cli/main.py", line 433, in cli_ls
    ls_helper(df, args.group_filter, args.tsv)
  File "/home/aemurphy/anaconda3/envs/kipoi/lib/python3.10/site-packages/kipoi/cli/main.py", line 444, in ls_helper
    dfg = list_models_by_group(df, group_filter)
  File "/home/aemurphy/anaconda3/envs/kipoi/lib/python3.10/site-packages/kipoi/sources.py", line 137, in list_models_by_group
    df = df[df.model.str.contains("^" + group[1:])].copy()
  File "/home/aemurphy/anaconda3/envs/kipoi/lib/python3.10/site-packages/pandas/core/generic.py", line 6299, in __getattr__
    return object.__getattribute__(self, name)
AttributeError: 'DataFrame' object has no attribute 'model'. Did you mean: 'mode'?

I also tried deleting the cached folder ~/.kipoi/ but this had no effect.

Package versions

# Name                    Version                   Build  Channel
_libgcc_mutex             0.1                        main  
_openmp_mutex             5.1                       1_gnu  
arrow                     1.3.0                    pypi_0    pypi
attrs                     21.4.0                   pypi_0    pypi
binaryornot               0.4.4                    pypi_0    pypi
bzip2                     1.0.8                h5eee18b_6  
ca-certificates           2024.7.2             h06a4308_0  
certifi                   2024.8.30                pypi_0    pypi
chardet                   5.2.0                    pypi_0    pypi
charset-normalizer        3.3.2                    pypi_0    pypi
click                     8.1.7                    pypi_0    pypi
colorlog                  6.8.2                    pypi_0    pypi
cookiecutter              2.6.0                    pypi_0    pypi
deprecation               2.1.0                    pypi_0    pypi
future                    1.0.0                    pypi_0    pypi
h5py                      3.11.0                   pypi_0    pypi
idna                      3.10                     pypi_0    pypi
jinja2                    3.1.4                    pypi_0    pypi
kipoi                     0.8.6                    pypi_0    pypi
kipoi-conda               0.3.1                    pypi_0    pypi
kipoi-utils               0.7.7                    pypi_0    pypi
ld_impl_linux-64          2.38                 h1181459_1  
libffi                    3.3                  he6710b0_2  
libgcc-ng                 11.2.0               h1234567_1  
libgomp                   11.2.0               h1234567_1  
libstdcxx-ng              11.2.0               h1234567_1  
libuuid                   1.41.5               h5eee18b_0  
markdown-it-py            3.0.0                    pypi_0    pypi
markupsafe                2.1.5                    pypi_0    pypi
mdurl                     0.1.2                    pypi_0    pypi
ncurses                   6.4                  h6a678d5_0  
numpy                     2.1.1                    pypi_0    pypi
openssl                   1.1.1w               h7f8727e_0  
packaging                 24.1                     pypi_0    pypi
pandas                    2.2.2                    pypi_0    pypi
pip                       24.2            py310h06a4308_0  
pygments                  2.18.0                   pypi_0    pypi
python                    3.10.0               h12debd9_5  
python-dateutil           2.9.0.post0              pypi_0    pypi
python-slugify            8.0.4                    pypi_0    pypi
pytz                      2024.2                   pypi_0    pypi
pyyaml                    6.0.2                    pypi_0    pypi
readline                  8.2                  h5eee18b_0  
related                   0.7.3                    pypi_0    pypi
requests                  2.32.3                   pypi_0    pypi
rich                      13.8.1                   pypi_0    pypi
setuptools                72.1.0          py310h06a4308_0  
six                       1.16.0                   pypi_0    pypi
sqlite                    3.45.3               h5eee18b_0  
text-unidecode            1.3                      pypi_0    pypi
tinydb                    4.8.0                    pypi_0    pypi
tk                        8.6.14               h39e8969_0  
tqdm                      4.66.5                   pypi_0    pypi
types-python-dateutil     2.9.0.20240906           pypi_0    pypi
tzdata                    2024.1                   pypi_0    pypi
urllib3                   2.2.3                    pypi_0    pypi
wheel                     0.44.0          py310h06a4308_0  
xz                        5.4.6                h5eee18b_1  
zlib                      1.2.13               h5eee18b_1  

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