Question

I wrote this code to calculate the mode and standard deviation for a large sample:

import numpy as np
import csv
import scipy.stats as sp
import math

r=open('stats.txt', 'w') #file with results
r.write('Data File'+'\t'+ 'Mode'+'\t'+'Std Dev'+'\n')
f=open('data.ls', 'rb') #file with the data files

for line in f:
    dataf=line.strip()
    data=csv.reader(open(dataf, 'rb'))
    data.next()
    data_list=[]
    datacol=[]
    data_list.extend(data)
    for rows in data_list:
            datacol.append(math.log10(float(rows[73])))
    m=sp.mode(datacol)
    s=sp.std(datacol)
    r.write(dataf+'\t'+str(m)+'\t'+str(s)+'\n')
    del(datacol)
    del(data_list)

Which is working well -I think! However after I run the code there is an error message on my terminal and I am wondering if anybody can tell me what it means?

 /usr/lib/python2.6/dist-packages/scipy/stats/stats.py:1328: DeprecationWarning:     scipy.stats.std is deprecated; please update your code to use numpy.std.
    Please note that:
    - numpy.std axis argument defaults to None, not 0
    - numpy.std has a ddof argument to replace bias in a more general manner.
      scipy.stats.std(a, bias=True) can be replaced by numpy.std(x,
      axis=0, ddof=0), scipy.stats.std(a, bias=False) by numpy.std(x, axis=0,
      ddof=1).
  ddof=1).""", DeprecationWarning)
/usr/lib/python2.6/dist-packages/scipy/stats/stats.py:1304: DeprecationWarning: scipy.stats.var is deprecated; please update your code to use numpy.var.
Please note that:
    - numpy.var axis argument defaults to None, not 0
    - numpy.var has a ddof argument to replace bias in a more general manner.
      scipy.stats.var(a, bias=True) can be replaced by numpy.var(x,
      axis=0, ddof=0), scipy.stats.var(a, bias=False) by var(x, axis=0,
      ddof=1).
  ddof=1).""", DeprecationWarning)
/usr/lib/python2.6/dist-packages/scipy/stats/stats.py:420: DeprecationWarning: scipy.stats.mean is deprecated; please update your code to use numpy.mean.
Please note that:
    - numpy.mean axis argument defaults to None, not 0
    - numpy.mean has a ddof argument to replace bias in a more general manner.
      scipy.stats.mean(a, bias=True) can be replaced by numpy.mean(x,
axis=0, ddof=1).
  axis=0, ddof=1).""", DeprecationWarning)

Answer 1

Those are deprecation warnings, which usually mean that your code will work, but may stop working in a future release.

Currently you have this line s=sp.std(datacol). It looks like the warning suggests using numpy.std() instead of scipy.stats.std() Making this change could make this warning go away.

If you don’t care about the deprecation warning and want to use your code as is, you can suppress it with the warnings module. For example, if you have a function fxn() that generates a DeprecationWarning, you can wrap it like this:

with warnings.catch_warnings():
    warnings.simplefilter("ignore")
    fxn()  #this function generates DeprecationWarnings