Develop Reference

Google Collab How to show value of assignments?

I am working on this python notebook in Google Collab:
https://github.com/AllenDowney/ModSimPy/blob/master/notebooks/chap01.ipynb
I had to change the configuration line because the one stated in the original was erroring out:
# Configure Jupyter to display the assigned value after an assignment
# Line commented below because errors out
# %config InteractiveShell.ast_node_interactivity='last_expr_or_assign'
# Edit solution given below
%config InteractiveShell.ast_node_interactivity='last_expr'
However, I think the original statement was meant to show values of assignments (if I'm not mistaken), so that when I run the following cell in the notebook, I should see an output:
meter = UNITS.meter
second = UNITS.second
a = 9.8 * meter / second**2
If so how can I make the notebook on google collab show output of assignments?

The short answer is: you can not show output of assignments in Colab.
Your confusion comes from how Google Colab works. The original script is meant to run in IPython. But Colab is not a regular IPython. When you run IPython shell, your %config InteractiveShell.ast_node_interactivity options are (citing documentation)
‘all’, ‘last’, ‘last_expr’ , ‘last_expr_or_assign’ or ‘none’,
specifying which nodes should be run interactively (displaying output
from expressions). ‘last_expr’ will run the last node interactively
only if it is an expression (i.e. expressions in loops or other blocks
are not displayed) ‘last_expr_or_assign’ will run the last expression
or the last assignment. Other values for this parameter will raise a
ValueError.
all will display all the variables, but not the assignments, for example
x = 5
x
y = 7
y
Out[]:
5
7
The differences between the options become more significant when you want to display variables in the loop.
In Colab your options are restricted to ['all', 'last', 'last_expr', 'none']. If you select all, the result for the above cell will be
Out[]:
57
Summarizing all that, there is no way of showing the result of assignment in Colab. Your only option (AFAIK) is to add the variable you want to see to the cell where it is assigned (which is similar to regular print):
meter = UNITS.meter
second = UNITS.second
a = 9.8 * meter / second**2
a

Google Colab has not yet been upgraded to the latest IPython version- if you explicitly upgrade with
!pip install -U ipython
then last_expr_or_assign will work.

Well the easy way is to just wrap your values in print statements like:
print(meter)
print(second)
print(a)
However, if you want to do it the jupyter way, looks like the answer is
from IPython.core.interactiveshell import InteractiveShell
InteractiveShell.ast_node_interactivity = "all"
Found the above from this link: https://stackoverflow.com/a/36835741/7086982

As mentioned by others, it doesn't work as last_expr_or_assign was introduced in juptyer v6.1, and colab is using v5.x. Upgrading the jupyter version on colab might cause some instability (warning shown by colab):
WARNING: Upgrading ipython, ipykernel, tornado, prompt-toolkit or pyzmq can
cause your runtime to repeatedly crash or behave in unexpected ways and is not
recommended
One other solution is to use an extension such as ipydex, which provides magic comments (like ##:, ##:T, ##:S) which cause that either the return value or the right hand side of an assignment of a line is displayed.
!pip install ipydex
%load_ext ipydex.displaytools
e.g.
a = 4
c = 5 ##:
output
c := 5
---

Codes in Ipython vs Pycharm

I am a newbie and the following question may be dumb and not well written.
I tried the following block of codes in Ipython:
%pylab qt5
x = randn(100,100)
y = mean(x,0)
import seaborn
plot(y)
And it delivered a plot. Everything was fine.
However, when I copied and pasted those same lines of codes to Pycharm and tried running, syntax error messages appeared.
For instance,
%pylab was not recognized.
Then I tried to import numpy and matplotlib one by one. But then,
randn(.,.) was not recognized.

You can use IPython/Jupyter notebooks in PyCharm by following this guide:
https://www.jetbrains.com/help/pycharm/using-ipython-jupyter-notebook-with-pycharm.html
You may modify code like the snippet below in order to run in PyCharm:
from numpy.random import randn
from numpy import mean
import seaborn
x = randn(10, 10)
y = mean(x, 0)
seaborn.plt.plot(x)
seaborn.plt.show()

IPython InteractiveShell fails to yield rich output when using `%matplotlib inline`

I am writing a custom client (a web-based graph representation of an IPython Notebook) for an IPython application and the easiest way to manage IPython programmatically seems to be using the IPython.core.InteractiveShell instance.
Consider this example: when a Jupyter Notebook cell that uses rich output is executed with inline magic, Notebook shows the appropriate rich representation (a plotted image) of plt.show() inline:
%matplotlib inline
import matplotlib.pyplot as plt
import numpy as np
t = np.arange(0.0, 2.0, 0.01)
s = np.sin(2*np.pi*t)
plt.plot(t, s)
plt.xlabel('time (s)')
plt.ylabel('voltage (mV)')
plt.title('About as simple as it gets, folks')
plt.grid(True)
plt.show()
I want to be able to retrieve the image when using IPython programmatically via its API, namely InteractiveShell, like this:
from IPython.core.interactiveshell import InteractiveShell
shell = InteractiveShell()
result = shell.run_cell("...above code of the cell here...")
# result either gives an error when using %matplotlib inline or retrieves
# no useful info if no line magic is present
Problem is that InteractiveShell instance will not accept the %matplotlib inline magic, giving a NotImplementedError in its enable_gui method which is, wll, not implemented. I found very few information about this apart from a single issue on IPython's Github.
I know I can do this manually by using plt.save() but that doesn't seem right to me as I don't want to write manual interpretations each time I need another rich representation of the result. I feel like I'm missing a lot here in the way IPython works, so I'm asking for help in retrieving the results. What exactly does Jupyter Notebook do to retrieve the rich representation and perhaps can it be done painlessly via other means? I'm looking at using jupyter_client but for now that seems to be even more confusing.
UPDATE:
The io.capture_output context manager seems to be the way to go but I've been able to capture string outputs only (pretty much the same as using %%capture cell magic):
with io.capture_output() as captured:
result = shell.run_cell(cell)
#captures strings only:
captured.stdout = {str} '<matplotlib.figure.Figure at 0x4f486d8>'

Error using LaTeX for plot rendering in MacOS 10.11

I recently made a clean install of OSX 10.11, installed Anaconda with python 3.5, Xcode, MacTex 2015 and updated all of these.
I have a problem when I want to use LaTeX in matplotlib.
Here is a short example:
import numpy as np
import matplotlib.pyplot as plt
from matplotlib import rc
rc('font', **{'family': 'serif', 'serif': ['Computer Modern']})
rc('text', usetex=True)
b = np.array([10, 11, 12, 13],dtype=np.float)
bStd = np.array([1.4, 0.6, 0.3, 1.1],dtype=np.float)
N = len(b)
ind = np.arange(N,dtype=np.float)
width = 0.8
FS=11
fig, ax = plt.subplots(figsize=(5.9055, 3.937))
Test = ax.plot(ind,b)
yerr = plt.errorbar(ind,b,bStd)
ax.set_title('Lorem ipsum dolor sit amet...', fontsize = FS, family = ['serif'])
ax.set_xticks(ind)
ax.set_xlim([-width, N-1+width])
ax.set_xticklabels( ('A','B','C','D'), fontsize = FS, family = ['serif'])
ax.set_ylabel('Value / $X/yy^2$',multialignment="center",fontsize = FS, family = ['serif'])
ax.set_ylim(0,20)
plt.tight_layout()
plt.savefig('Test.pdf', format='pdf',bbox_inches='tight')
When I try to use TeX in matplotlib, I receive the following:
RuntimeError: LaTeX was not able to process the following string:
b'lp'
Here is the full report generated by LaTeX:
I think that Spyder does not know how to access LaTeX. May this be a problem of the new rootless feature in El Capitan?
I already searched the web and of course Stackoverflow, but none of the suggestions, I found there, helped me.
Do you have any idea?
I just started to learn how to work with python, therefore I am really inexperienced, which might be visible in my example.
Thank you for your time.

Using Spyder as installed with MacPorts, I have the very same problems, but using Python3 as installed by MacPorts on a Mac OS Terminal, everything compiles fine (which seems strange since Spyder relies on this version of Python...).
As a workaround, if using the Terminal is fine for you, you may run directly your script from the Terminal (however, make sure that you use python as installed by anaconda by giving the explicit path to the executable), but this defeats the purpose of installing a nice GUI such as Spyder.

Differences between ipython %run and promt

I've the following simple erroneous code
from numpy import random, sqrt
points = random.randn(20,3);
points = points / sqrt(sum(points**2,1))
In ipython (with %autoreload 2) if I copy and paste it into the terminal I get a ValueError as one would expect. If I save this as a file and use %run then it runs without error (it shouldn't).
What's going on here?

I just figured it out, but I had written the question and it might be useful to someone else.
It is a difference between the numpy sum and the native sum. Changing the first line to
from numpy import random, sqrt, sum
fixes it as %run uses the native version by default (at least with my settings). The native run does not take an axis parameter, but does not throw an error either, because it is a start parameter, which is in effect just an offset to the sum. So,
>>> sum([1,2,3],10000)
10006
for the native version. And "axis out of bounds" for the numpy one.