Fix compatibility issues with Python 2 #1004
Conversation
hakonsbm
changed the title
| @@ -64,6 +64,7 @@ | |||
|
|
|||
| ''' | |||
|
|
|||
| from __future__ import print_function | |||
There was a problem hiding this comment.
Why do we need this future import?
There was a problem hiding this comment.
Because of the end=' ' here:
| @@ -1261,6 +1261,11 @@ | |||
| " self.hp = ht_params\n", | |||
| " \n", | |||
| " def m_inf(self, D):\n", | |||
| " # Workaround for handling complex numbers in Python 2\n", | |||
There was a problem hiding this comment.
Hm, I am not really happy with this work-around, it is a lot of distracting code for a notebook. And can D really become negative? From the math, we should always have D>0 strictly.
There was a problem hiding this comment.
I agree that it's not an elegant work-around. m_inf is called from voltage_clamp like this
m_old = channel.m_inf(DT_V_seq[0][1])where channel is iDK and DT_V_seq is the list in
nr, cr = voltage_clamp(iDK, [(500, -65.), (500, -35.), (500, -25.), (500, 0.), (5000, -70.)],
nest_dt=1.)There was a problem hiding this comment.
So I guess the problem is that in
def compute_I(self, t, V, m0, h0, D0):
self.D = si.odeint(self.dD, D0, t, args=(V,))
self.m = self.m_inf(self.D)
return - self.hp['g_peak_KNa'] * self.m * (V - self.hp['E_rev_KNa'])self.D may contain negative values (numerical error from odeint). But we know that D must always be strictly positive, so we should (i) check that we only get numerical noise below zero and then (ii) replace negative values in the result of odeint() with the smallest possible positive number.
There was a problem hiding this comment.
I think you misunderstood my previous comment. voltage_clamp() is called with a channel, and a list of interval-voltage pairs referred to as DT_V_seq. In voltage_clamp we have
# Control part
t_old = 0.
try:
m_old = channel.m_inf(DT_V_seq[0][1])
except NotImplementedError:
m_old = Nonewhere DT_V_seq[0][1] is the voltage of the first interval-voltage pair, i.e. -65.0.
This is before it calls compute_I(). And I checked the values for self.D, they are all positive.
heplesser
added
ZC: Documentation
Corrected implementation in pure-python version of I_DK
This PR contains some fixes for compatibility issues when using Python 2 when running examples and model_details scripts.
Python 2 doesn't handle complex numbers as elegantly as Python 3, which led to an error when running
HillTononiModels.ipynbusing Python 2. The problematic variable is now explicitly converted to a complex number if needed. There were also some minor issues in the PyNEST examples.