Problem to install sparrow mesmer env

[Lucas-Maciel]

Hi,

I tried to install sparrow mesmer env but I had poblems. I'm using a windows machine and mamba.

First I tried the yaml file, just commented the jax part.

mamba env update -n sparrow-mesmer --file environment_mesmer.yml --prune
conda-forge/win-64                                          Using cache
conda-forge/noarch                                          Using cache
pkgs/main/noarch                                              No change
pkgs/r/win-64                                                 No change
pkgs/main/win-64                                              No change
pkgs/msys2/noarch                                             No change
pkgs/r/noarch                                                 No change
pkgs/msys2/win-64                                             No change
tensorflow/win-64                                             No change
tensorflow/noarch                                             No change

Looking for: ['geopandas=0.12.2', 'leidenalg=0.9.1', 'napari=0.4.18', 'pyqt', 'opencv=4.5.5', 'pip=22.2.2', 'python=3.9', 'rasterio=1.3.2', 'scanpy=1.9.4', 'scipy=1.8.0', 'seaborn=0.11.2', 'fsspec=2023.6.0', 'tensorflow=2.8']

Could not solve for environment specs
The following packages are incompatible
Γö£ΓöÇ python 3.9**  is installable with the potential options
Γöé  Γö£ΓöÇ python [3.9.0|3.9.1|...|3.9.7], which can be installed;
Γöé  ΓööΓöÇ python [3.9.0|3.9.1|...|3.9.9] would require
Γöé     ΓööΓöÇ python_abi 3.9.* *_cp39, which can be installed;
Γö£ΓöÇ rasterio 1.3.2**  is installable with the potential options
Γöé  Γö£ΓöÇ rasterio 1.3.2 would require
Γöé  Γöé  ΓööΓöÇ libgdal >=3.5.1,<3.6.0a0  with the potential options
Γöé  Γöé     Γö£ΓöÇ libgdal [3.5.1|3.5.2|3.5.3] would require
Γöé  Γöé     Γöé  ΓööΓöÇ icu >=70.1,<71.0a0 , which can be installed;
Γöé  Γöé     ΓööΓöÇ libgdal 3.5.3 would require
Γöé  Γöé        ΓööΓöÇ libjpeg-turbo >=2.1.5.1,<3.0a0 , which requires
Γöé  Γöé           ΓööΓöÇ jpeg <0.0.0a , which can be installed;
Γöé  Γö£ΓöÇ rasterio 1.3.2 would require
Γöé  Γöé  Γö£ΓöÇ python >=3.10,<3.11.0a0 , which conflicts with any installable versions previously reported;
Γöé  Γöé  ΓööΓöÇ python_abi 3.10.* *_cp310, which conflicts with any installable versions previously reported;
Γöé  ΓööΓöÇ rasterio 1.3.2 would require
Γöé     Γö£ΓöÇ python >=3.8,<3.9.0a0 , which conflicts with any installable versions previously reported;
Γöé     ΓööΓöÇ python_abi 3.8.* *_cp38, which conflicts with any installable versions previously reported;
ΓööΓöÇ tensorflow 2.8**  is uninstallable because it requires
   ΓööΓöÇ tensorflow-base [2.8.2 eigen_py310he3c91d7_0|2.8.2 eigen_py37he3c91d7_0|...|2.8.2 mkl_py39h6a7f48e_0], which requires
      Γö£ΓöÇ icu >=58.2,<59.0a0 , which conflicts with any installable versions previously reported;
      ΓööΓöÇ jpeg >=9e,<10a , which conflicts with any installable versions previously reported.

I also tried to change to python 3.10.08, the same as the cellpose env.

Looking for: ['geopandas=0.12.2', 'leidenalg=0.9.1', 'napari=0.4.18', 'pyqt', 'opencv=4.5.5', 'pip=22.2.2', 'python=3.10.8', 'rasterio=1.3.2', 'scanpy=1.9.4', 'scipy=1.8.0', 'seaborn=0.11.2', 'fsspec=2023.6.0', 'tensorflow=2.8']

Could not solve for environment specs
The following packages are incompatible
Γö£ΓöÇ python 3.10.8**  is installable with the potential options
Γöé  Γö£ΓöÇ python 3.10.8, which can be installed;
Γöé  ΓööΓöÇ python 3.10.8 would require
Γöé     ΓööΓöÇ python_abi 3.10.* *_cp310, which can be installed;
Γö£ΓöÇ rasterio 1.3.2**  is installable with the potential options
Γöé  Γö£ΓöÇ rasterio 1.3.2 would require
Γöé  Γöé  ΓööΓöÇ libgdal >=3.5.1,<3.6.0a0  with the potential options
Γöé  Γöé     Γö£ΓöÇ libgdal [3.5.1|3.5.2|3.5.3] would require
Γöé  Γöé     Γöé  ΓööΓöÇ icu >=70.1,<71.0a0 , which can be installed;
Γöé  Γöé     ΓööΓöÇ libgdal 3.5.3 would require
Γöé  Γöé        Γö£ΓöÇ icu >=72.1,<73.0a0 , which can be installed;
Γöé  Γöé        ΓööΓöÇ libjpeg-turbo >=2.1.5.1,<3.0a0 , which requires
Γöé  Γöé           ΓööΓöÇ jpeg <0.0.0a , which can be installed;
Γöé  Γö£ΓöÇ rasterio 1.3.2 would require
Γöé  Γöé  Γö£ΓöÇ python >=3.8,<3.9.0a0 , which conflicts with any installable versions previously reported;
Γöé  Γöé  ΓööΓöÇ python_abi 3.8.* *_cp38, which conflicts with any installable versions previously reported;
Γöé  ΓööΓöÇ rasterio 1.3.2 would require
Γöé     Γö£ΓöÇ python >=3.9,<3.10.0a0 , which conflicts with any installable versions previously reported;
Γöé     ΓööΓöÇ python_abi 3.9.* *_cp39, which conflicts with any installable versions previously reported;
ΓööΓöÇ tensorflow 2.8**  is uninstallable because there are no viable options
   Γö£ΓöÇ tensorflow 2.8.2 would require
   Γöé  ΓööΓöÇ tensorflow-base 2.8.2 gpu_py310h9761872_0, which requires
   Γöé     Γö£ΓöÇ icu >=58.2,<59.0a0 , which conflicts with any installable versions previously reported;
   Γöé     ΓööΓöÇ jpeg >=9e,<10a , which conflicts with any installable versions previously reported;
   Γö£ΓöÇ tensorflow 2.8.2 would require
   Γöé  ΓööΓöÇ tensorflow-base [2.8.2 eigen_py310he3c91d7_0|2.8.2 mkl_py310h6a7f48e_0], which requires
   Γöé     ΓööΓöÇ icu >=58.2,<59.0a0 , which conflicts with any installable versions previously reported;
   Γö£ΓöÇ tensorflow 2.8.2 would require
   Γöé  ΓööΓöÇ python 3.7.* , which conflicts with any installable versions previously reported;
   Γö£ΓöÇ tensorflow 2.8.2 would require
   Γöé  ΓööΓöÇ python 3.8.* , which conflicts with any installable versions previously reported;
   ΓööΓöÇ tensorflow 2.8.2 would require
      ΓööΓöÇ python 3.9.* , which conflicts with any installable versions previously reported.

Python 3.8 and 3.10.0 didn't work as well.

[ArneDefauw]

Hi Lucas, thanks for opening the issue, I will try to reproduce it

[ArneDefauw]

I could not reproduce this error on mac, I could build the environment and use sparrow. I guess the problem is tensorflow. Have you tried commenting tensorflow in the .yml, and then installing it via pip, e.g.

conda env create -f environment_mesmer.yml
conda activate mesmer_sparrow
pip install tensorflow=2.8

mesmer requires python 3.9 and tensorflow 2.8, so changing the python version or tensorflow version will not fix your issue