A very very common source of confusion when using python interactively is that warnings disappear. Specifically, they show up the first time they might appear, but then never again after that...:
In [14]: np.zeros(10) / 0
/usr/bin/ipython3:1: RuntimeWarning: invalid value encountered in true_divide
#!/usr/bin/env python3
Out[14]: array([ nan, nan, nan, nan, nan, nan, nan, nan, nan, nan])
In [15]: 0 / np.zeros(5)
Out[15]: array([ nan, nan, nan, nan, nan])
This is because by default, the warnings module attempts to only show each warning once per "source"; the idea is that if you write something like
for i in xrange(10000):
np.log(0) # **
then you really only need to hear about the problem on line ** once, not 10,000 times.
But this interacts badly with interactive usage, because the warnings module has a bug: it thinks that the first line of one interactive cell is the same line as the first line of another interactive cell, so if np.zeros(10) / 0 has raised a warning then it thinks 0 / np.zeros(5) has as well. Because they are the same line. Oops.
Specifically, the way the warnings module keeps track of these things is with a really weird hack: whenever it issues a warning, it reaches into the execution environment of the code issuing the warning, and creates a global variable called __warningregistry__. For example:
In [1]: __warningregistry__
---------------------------------------------------------------------------
NameError Traceback (most recent call last)
<ipython-input-1-41b71685b3a2> in <module>()
----> 1 __warningregistry__
NameError: name '__warningregistry__' is not defined
In [2]: np.zeros(10) / 0
/home/njs/.user-python2.7-64bit-3/bin/ipython:1: RuntimeWarning: invalid value encountered in divide
#!/home/njs/.user-python2.7-64bit-3/bin/python
Out[2]: array([ nan, nan, nan, nan, nan, nan, nan, nan, nan, nan])
In [3]: __warningregistry__
Out[3]: {('invalid value encountered in divide', RuntimeWarning, 1): True}
This __warningregistry__ value says that line 1 of the code in this namespace has already issued the given warning, so if you ever see another piece of code whose line number is 1, and which is executing in this namespace, try to issue this warning, then that warning should not be displayed.
However, in the interactive case, we know that every time we execute a new cell, the line numbers are effectively reset -- line 1 of this cell is totally different from line 1 of the previous cell. Ipython should take care of informing the warnings module of this fact.
This can be done very simply: just delete the __warningregistry__ variable from the interactive namespace after each time a cell finishes executing. This will cause the warnings module to treat each new block of code as a new block of code.
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