ImportError when using dolfinx in PythonCall

[touste]

Affects: PythonCall

Describe the bug

using CondaPkg
]conda add fenics-dolfinx

using PythonCall
dolfinx = pyimport("dolfinx")

ERROR: LoadError: Python: ImportError: libdolfinx.so.0.10: cannot open shared object file: No such file or directory

What's strange is

using CondaPkg
]conda run python
>>> import dolfinx

works fine

Your system
Ubuntu 24.04, Julia 1.12.1, PythonCall 0.9.30. Python and Conda managed by CondaPkg (default environment).

[touste]

The issue somehow disappeared when I started from a clean environment, I'm not able to reproduce it anymore...

[aibiliGaferreira]

I'm having a similar issue, but only when using Ubuntu WSL. It works fine on Windows, but when I try running the same script on WSL I get the error:

julia> pyimport("fundus_image_toolbox")
ERROR: Python: OSError: libmkl_gnu_thread.so.2: cannot open shared object file: No such file or directory
Python stacktrace:
 [1] __init__
   @ ctypes /mnt/d/projects/FOCAL/.CondaPkg/.pixi/envs/default/lib/python3.12/ctypes/__init__.py:379
 [2] _load_global_deps
   @ /mnt/d/projects/FOCAL/.CondaPkg/.pixi/envs/default/lib/python3.12/site-packages/torch/__init__.py:366
 [3] _preload_cuda_deps
   @ /mnt/d/projects/FOCAL/.CondaPkg/.pixi/envs/default/lib/python3.12/site-packages/torch/__init__.py:344
 [4] _load_global_deps
   @ /mnt/d/projects/FOCAL/.CondaPkg/.pixi/envs/default/lib/python3.12/site-packages/torch/__init__.py:388
 [5] <module>
   @ /mnt/d/projects/FOCAL/.CondaPkg/.pixi/envs/default/lib/python3.12/site-packages/torch/__init__.py:430
 [6] <module>
   @ /mnt/d/projects/FOCAL/.CondaPkg/.pixi/envs/default/lib/python3.12/site-packages/fundus_image_toolbox/circle_crop/eyeq_preprocess.py:2
 [7] <module>
   @ /mnt/d/projects/FOCAL/.CondaPkg/.pixi/envs/default/lib/python3.12/site-packages/fundus_image_toolbox/circle_crop/__init__.py:1
 [8] <module>
   @ /mnt/d/projects/FOCAL/.CondaPkg/.pixi/envs/default/lib/python3.12/site-packages/fundus_image_toolbox/__init__.py:1
Stacktrace:
 [1] pythrow()
   @ PythonCall.Core ~/.julia/packages/PythonCall/83z4q/src/Core/err.jl:77
 [2] errcheck
   @ ~/.julia/packages/PythonCall/83z4q/src/Core/err.jl:10 [inlined]
 [3] pyimport(m::String)
   @ PythonCall.Core ~/.julia/packages/PythonCall/83z4q/src/Core/builtins.jl:1458
 [4] top-level scope
   @ REPL[7]:1

This is what my CondaPkg.toml looks like:

[deps]
pytorch = ""
numpy = ""
stringzilla = ""

[pip.deps]
fundus_image_toolbox = ""

I've tried adding the mkl packages to CondaPkg.toml, as well as fixing a python version (3.12), but none of those attempts solved the issue. However, if I run

julia> using CondaPkg
pkg> conda run python
>>> import fundus_image_toolbox as fit
Module missing, downloading it from https://github.com/berenslab/MIDL24-segmentation_quality_control...
Adjusting imports...
Done.
Module missing, downloading it from https://github.com/dsc/bunch...
>>> fit.__file__
'/mnt/d/projects/FOCAL/.CondaPkg/.pixi/envs/default/lib/python3.12/site-packages/fundus_image_toolbox/__init__.py'
>>> 

it works. I've also looked at .CondaPkg, at the file libmkl_gnu_thread.so.2 is there, so I'm not sure what the issue could be (.CondaPkg/.pixi/envs/default/lib/libmkl_intel_thread.so.2)