scipy.weave depreacted

[hkennyv]

It looks like weave was deprecated in scipy and moved to its own project.

  File "/Users/khuynh/stackoverflow/pyi/venv/lib/python2.7/site-packages/MDAnalysis/analysis/distances.py", line 31, in <module>
    from scipy import weave
ImportError: cannot import name weave

I was able to resolve this quickly by

1. installing weave via pip install weave
2. editing the file in scipy at venv/lib/python2.7/site-packages/MDAnalysis/analysis/distances.py

and changing:

import numpy
from scipy import sparse
from scipy import weave
from scipy.weave import converters

to:

import numpy
from scipy import sparse
#  from scipy import weave
#  from scipy.weave import converters

import weave
from weave import converters

is there a more elegant way to do this? i don't think modifying the source of scipy is the most graceful way.. open to suggestions? :)

I've also written a stackoverflow answer for this here.

[mtiberti]

Hi,
thanks for your efforts! Alternatively, you can simply comment out the offending line in libinteract (line 2), I just realised it's a stray import and imported function is not actually used in the code. I'll add this to the list of fixes - we are planning on releasing a Py3 compatible version which uses the latest MDAnalysis as well and will make things much simpler - stay tuned!

[hkennyv]

Thank you and thanks for your work too, I look forward to seeing the py3 release! Is it worth submitting a PR to fix this in the 2.7 version or is development here halted?

[elenapapaleo]

We have now the py3 release here: https://github.com/ELELAB/pyinteraph2