py_eddy_tracker.dataset.grid issue about py-eddy-tracker

[AntSimi]

Did you get same error when you do an import netCDF4?
How did you install py eddy tracker?

[emma97956461]

No I didn't get any error when importing netcdf4, I tried installing pyeddytracker in multiple ways:
on my local machine, both from terminal with pip and homebrew, and directly from jupyterlab.
I also work on remote machines and tried there, in the same ways. I always encountered some kind of issue when importing the dataset.grid, which is either related to numpy or netcdf4. Today I thought the problem was solved, but after restarting my kernel I find that I can't even import py_eddy_tracker anymore, because of numpy; I get the error:
AttributeError: module 'numpy' has no attribute 'ndarray'
Thank you for the help

[marimpacheco]

I am having an issue with py_eddy_tracker.dataset.grid as well.

I had to recreate the py-eddy-tracker environment after a system upgrade in the remote machine.
I created the environment from the environment.yml file:

conda env create --file environment.yml
conda activate binder-pyeddytracker
python setup.py install

The error that comes for me:

ImportError                               Traceback (most recent call last)
Cell In[2], line 23
     21 from py_eddy_tracker.gui import GUI
     22 from py_eddy_tracker.tracking import Correspondances
---> 23 from py_eddy_tracker.dataset.grid import UnRegularGridDataset
     24 from py_eddy_tracker.eddy_feature import Contours

File ~/miniconda3/envs/binder-pyeddytracker/lib/python3.10/site-packages/py_eddy_tracker/dataset/grid.py:8
      5 from datetime import datetime
      6 import logging
----> 8 from cv2 import filter2D
      9 from matplotlib.path import Path as BasePath
     10 from netCDF4 import Dataset

File ~/miniconda3/envs/binder-pyeddytracker/lib/python3.10/site-packages/cv2/__init__.py:181
    176             if DEBUG: print("Extra Python code for", submodule, "is loaded")
    178     if DEBUG: print('OpenCV loader: DONE')
--> 181 bootstrap()

File ~/miniconda3/envs/binder-pyeddytracker/lib/python3.10/site-packages/cv2/__init__.py:153, in bootstrap()
    149 if DEBUG: print("Relink everything from native cv2 module to cv2 package")
    151 py_module = sys.modules.pop("cv2")
--> 153 native_module = importlib.import_module("cv2")
    155 sys.modules["cv2"] = py_module
    156 setattr(py_module, "_native", native_module)

File ~/miniconda3/envs/binder-pyeddytracker/lib/python3.10/importlib/__init__.py:126, in import_module(name, package)
    124             break
    125         level += 1
--> 126 return _bootstrap._gcd_import(name[level:], package, level)

ImportError: libGL.so.1: cannot open shared object file: No such file or directory 

[AntSimi]

Did you have same error if you only do (env creation must install also py eddy tracker package):

conda env create --file environment.yml
conda activate binder-pyeddytracker

[marimpacheco]

Yes

[AntSimi]

I don't know how to solve cv2 install problem, i am not able to reproduce this pb on several platform