Incompatibility with Python 3.9x or Numpy versions.

[theholymath]

I am trying to explore the code and getting some incompatibility with python version 3.9 and/or my version of numpy 1.19.3

The trace:

---------------------------------------------------------------------------
ValueError                                Traceback (most recent call last)
<ipython-input-2-fab5524ebb5d> in <module>
----> 1 import pymde

/usr/local/lib/python3.9/site-packages/pymde/__init__.py in <module>
      5 from pymde.constraints import Centered, Anchored, Standardized
      6 
----> 7 from pymde import datasets
      8 
      9 from pymde.preprocess.graph import Graph

/usr/local/lib/python3.9/site-packages/pymde/datasets.py in <module>
     16 
     17 import numpy as np
---> 18 from pymde.preprocess.graph import Graph
     19 from pymde.problem import LOGGER
     20 import scipy.sparse as sp

/usr/local/lib/python3.9/site-packages/pymde/preprocess/__init__.py in <module>
      3 from pymde.preprocess.preprocess import scale
      4 
----> 5 from pymde.preprocess.generic import distances, k_nearest_neighbors
      6 
      7 from . import graph

/usr/local/lib/python3.9/site-packages/pymde/preprocess/generic.py in <module>
      3 import torch
      4 
----> 5 from pymde.preprocess import data_matrix
      6 from pymde.preprocess import graph
      7 

/usr/local/lib/python3.9/site-packages/pymde/preprocess/data_matrix.py in <module>
      4 
      5 from pymde import problem
----> 6 from pymde.preprocess.graph import Graph
      7 from pymde.preprocess.preprocess import sample_edges
      8 from pymde import util

/usr/local/lib/python3.9/site-packages/pymde/preprocess/graph.py in <module>
      9 from pymde import problem
     10 from pymde.functions import penalties, losses
---> 11 from pymde.preprocess import _graph
     12 
     13 

pymde/preprocess/_graph.pyx in init pymde.preprocess._graph()

ValueError: numpy.ndarray size changed, may indicate binary incompatibility. Expected 88 from C header, got 80 from PyObject

[theholymath]

Okay, upgraded to numpy==1.20 and it works now. Something weird with numpy 1.19 though.

[akshayka]

Thanks for reporting. It might be the case that the wheels are built with 1.20, instead of the oldest supported numpy version. The way the build handles the NumPy version dependency right now is not ideal.

[afrendeiro]

Can confirm the same using Python3.9 and numpy==1.19.5, solved with numpy upgrade to 1.21.0.

[akshayka]

PR #41 should fix this problem. I won't close this issue until a new version of PyMDE is deployed with the fix, though.