Recommended python version?

[smazurchuk]

Hi!

Thanks for making this available. I was wondering if there is a preferred way to demo these scripts?

I'm using anaconda to manage environments. If you create a fresh/clean environment with python 2.7 (e.g. conda create --name vl_interface python=2.7) , cloning this repo, and try to setup the packages, it throws an error (using pip install e .)

On the flip side, using python 3.9, you can install the required packages, but all of the scripts fail out of the box

(vl_interface) smazurchuk@noether:~/Desktop/projects/vl_interface/scripts/plotting$ ipython
Python 3.9.7 (default, Sep 16 2021, 13:09:58)
Type 'copyright', 'credits' or 'license' for more information
IPython 7.29.0 -- An enhanced Interactive Python. Type '?' for help.

In [1]: import cortex
---------------------------------------------------------------------------
ValueError                                Traceback (most recent call last)
<ipython-input-1-abeddb261fa9> in <module>
----> 1 import cortex

~/anaconda3/envs/vl_interface/lib/python3.9/site-packages/cortex/__init__.py in <module>
      2 # vi: set fileencoding=utf-8 ft=python sts=4 ts=4 sw=4 et:
      3 from cortex.dataset import Dataset, Volume, Vertex, VolumeRGB, VertexRGB, Volume2D, Vertex2D, Colors
----> 4 from cortex import align, volume, quickflat, webgl, segment, options
      5 from cortex.database import db
      6 from cortex.utils import *

~/anaconda3/envs/vl_interface/lib/python3.9/site-packages/cortex/quickflat/__init__.py in <module>
----> 1 from .view import make_figure, make_png, make_svg, make_movie, make_gif
      2 from .utils import make_flatmap_image
      3 from . import composite

~/anaconda3/envs/vl_interface/lib/python3.9/site-packages/cortex/quickflat/view.py in <module>
      5 import numpy as np
      6
----> 7 from .. import utils
      8 from .. import dataset
      9 from .utils import make_flatmap_image

~/anaconda3/envs/vl_interface/lib/python3.9/site-packages/cortex/utils.py in <module>
     21 from .options import config
     22 from .freesurfer import fs_aseg_dict
---> 23 from .polyutils import Surface
     24 from . import formats
     25 from .testing_utils import INKSCAPE_VERSION

~/anaconda3/envs/vl_interface/lib/python3.9/site-packages/cortex/polyutils/__init__.py in <module>
     18     marching_cubes,
     19 )
---> 20 from .surface import Surface, _ptset, _quadset

~/anaconda3/envs/vl_interface/lib/python3.9/site-packages/cortex/polyutils/surface.py in <module>
      9 import scipy.sparse.linalg
     10
---> 11 from . import exact_geodesic
     12 from . import subsurface
     13 from .misc import _memo

~/anaconda3/envs/vl_interface/lib/python3.9/site-packages/cortex/polyutils/exact_geodesic.py in <module>
      7
      8 from ..options import config
----> 9 from .. import formats
     10
     11

~/anaconda3/envs/vl_interface/lib/python3.9/site-packages/cortex/formats.pyx in init cortex.formats()

ValueError: numpy.ndarray size changed, may indicate binary incompatibility. Expected 96 from C header, got 88 from PyObject

In [2]:

Do you have any thoughts or recommendations for an environment to try out these functions?

Thanks