kr-colab / popvae

genotype dimensionality reduction with a VAE
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issue in istalling #20

Open raveancic opened 1 year ago

raveancic commented 1 year ago

Dear all, thank you very much for this tool. Unfortunately I am finding many issues in installing this tool on a conda env with ptyhon=3.7.7. The final issue I encountered is the python version, it says that python=3.8 is required. I was wondering if you pushed a new version and other requirments are needed. Thank you very much in advance. Alessandro

andrewkern commented 1 year ago

Hi there- just to be clear, is the package working okay for you with Python 3.8?

raveancic commented 1 year ago

Hi, thank you for you super fast response. The error was caused by scipy, since the version was not indicated in the setup.py. At the end, to get it installed and running, beside python==3.7.7 and tensorflow==1.15.4 I needed to manually install (trhu pip) first cython==0.29.32 then scipy==1.7.3 and finally protobuf==3.19.0

Attached the whole list of pakcages and their version, I do not know if can help someone else.

contourpy                 1.0.6                    pypi_0    pypi
cycler                    0.11.0                   pypi_0    pypi
cython                    0.29.32                  pypi_0    pypi
dask                      2022.2.0                 pypi_0    pypi
entrypoints               0.4                      pypi_0    pypi
fasteners                 0.18                     pypi_0    pypi
fftw                      3.3.9                h27cfd23_1
fonttools                 4.38.0                   pypi_0    pypi
fsspec                    2022.11.0                pypi_0    pypi
gast                      0.2.2                    pypi_0    pypi
google-pasta              0.2.0                    pypi_0    pypi
grpcio                    1.51.1                   pypi_0    pypi
h5py                      2.10.0                   pypi_0    pypi
importlib-metadata        5.2.0                    pypi_0    pypi
intel-openmp              2021.4.0          h06a4308_3561
jinja2                    3.1.2                    pypi_0    pypi
keras                     2.3.1                    pypi_0    pypi
keras-applications        1.0.8                    pypi_0    pypi
keras-preprocessing       1.1.2                    pypi_0    pypi
kiwisolver                1.4.4                    pypi_0    pypi
ld_impl_linux-64          2.38                 h1181459_1
libffi                    3.3                  he6710b0_2
libgcc-ng                 11.2.0               h1234567_1
libgfortran-ng            11.2.0               h00389a5_1
libgfortran5              11.2.0               h1234567_1
libgomp                   11.2.0               h1234567_1
libstdcxx-ng              11.2.0               h1234567_1
locket                    1.0.0                    pypi_0    pypi
markdown                  3.4.1                    pypi_0    pypi
markupsafe                2.1.1                    pypi_0    pypi
matplotlib                3.5.3                    pypi_0    pypi
mkl                       2021.4.0           h06a4308_640
mkl-service               2.4.0            py37h7f8727e_0
mkl_fft                   1.3.1            py37hd3c417c_0
mkl_random                1.2.2            py37h51133e4_0
ncurses                   6.3                  h5eee18b_3
numcodecs                 0.10.2                   pypi_0    pypi
numpy                     1.18.1                   pypi_0    pypi
numpy-base                1.21.5           py37ha15fc14_3
openssl                   1.1.1s               h7f8727e_0
opt-einsum                3.3.0                    pypi_0    pypi
packaging                 22.0                     pypi_0    pypi
pandas                    1.3.5                    pypi_0    pypi
partd                     1.3.0                    pypi_0    pypi
pillow                    9.3.0                    pypi_0    pypi
pip                       22.3.1           py37h06a4308_0
popvae                    0.1                      pypi_0    pypi
protobuf                  3.19.0                   pypi_0    pypi
pyparsing                 3.0.9                    pypi_0    pypi
python                    3.7.7                hcff3b4d_5
python-dateutil           2.8.2                    pypi_0    pypi
pytz                      2022.7                   pypi_0    pypi
pyyaml                    6.0                      pypi_0    pypi
readline                  8.2                  h5eee18b_0
scikit-allel              1.3.5                    pypi_0    pypi
scipy                     1.7.3            py37h6c91a56_2
setuptools                65.5.0           py37h06a4308_0
six                       1.16.0             pyhd3eb1b0_1
sqlite                    3.40.0               h5082296_0
tensorboard               1.15.0                   pypi_0    pypi
tensorflow                1.15.4                   pypi_0    pypi
tensorflow-estimator      1.15.1                   pypi_0    pypi
termcolor                 2.1.1                    pypi_0    pypi
tk                        8.6.12               h1ccaba5_0
toolz                     0.12.0                   pypi_0    pypi
tornado                   6.2                      pypi_0    pypi
tqdm                      4.64.1                   pypi_0    pypi
typing-extensions         4.4.0                    pypi_0    pypi
werkzeug                  2.2.2                    pypi_0    pypi
wheel                     0.38.4                   pypi_0    pypi
wrapt                     1.14.1                   pypi_0    pypi
xyzservices               2022.9.0                 pypi_0    pypi
xz                        5.2.8                h5eee18b_0
zarr                      2.13.3                   pypi_0    pypi
zipp                      3.11.0                   pypi_0    pypi
zlib                      1.2.13               h5eee18b_0

Cheers