Re: [O] Problem with python session

[William Henney]

Yep, I agree. This is a wart in the vanilla python REPL, and org-mode can't
really do much about it.  Except maybe warn people.

As John noted, this is less of a problem if you use ipython as your REPL.
I think it is enough to just do

#+BEGIN_SRC emacs-lisp
(setq org-babel-python-command "ipython")
#+END_SRC

but I haven't tested this extensively since,  as I mentioned, I prefer to
use Greg Sexton's ob-ipython instead.  This integrates with the Jupyter
kernel by sending JSON to a web socket, rather than just pasting the source
block into a buffer, and that seems to be a more robust approach.

Will


On Tue, Oct 11, 2016 at 10:53 AM, Nicolas Goaziou 
wrote:

> Hello,
>
> John Kitchin  writes:
>
> > I am not sure it makes sense to change anything for this.
>
> Noted. Thank you for the feedback.
>
> Regards,
>
> --
> Nicolas Goaziou
>
>


-- 

  Dr William Henney, Instituto de Radioastronomía y Astrofísica,
  Universidad Nacional Autónoma de México, Campus Morelia

Re: [O] Problem with python session

[Nicolas Goaziou]

Hello,

John Kitchin  writes:

> I am not sure it makes sense to change anything for this.

Noted. Thank you for the feedback.

Regards,

-- 
Nicolas Goaziou

Re: [O] Problem with python session

[John Kitchin]

I am not sure it makes sense to change anything for this. There is
different behavior with scripts and the interpreter independently of
org-mode, e.g. with python -i:

>>> for i in range(3):
... print(i)
... i
  File "", line 3
i
^
SyntaxError: invalid syntax

Vanilla python sessions are kind of maddening. These seemingly identical blocks
are different, i.e. one works and one doesn't! Spoiler alert, they are not 
identical.

#+BEGIN_SRC python :results output org drawer :session
for i in range(3):
for j in range(3):

pass

print(i)
#+END_SRC

#+RESULTS:
:RESULTS:

...   File "", line 3

^
IndentationError: expected an indented block
File "", line 1
pass
^
IndentationError: unexpected indent
>>>   File "", line 1
print(i)
^
IndentationError: unexpected indent
:END:

This block which works has one space at the beginning of the blank lines.

#+BEGIN_SRC python :results output org drawer :session
for i in range(3):
for j in range(3):
 
pass
 
print(i)
#+END_SRC

#+RESULTS:
:RESULTS:

... ... ... ... ... 0
1
2
:END:

This kind of error would be hard to reliably fix IMHO since it would
rely on replacing blank lines with at least a space, and adding a blank
line after indentation changes, except they can not be empty, they need
at least a space in them. It is not clear that is a good idea. Maybe a
test that replaces "\n" with "\n \n" might clear it up, but might also
add a bunch of the ... >>> characters in the output? 

This is not an issue with python scripts or ipython, however.





Nicolas Goaziou writes:

> Hello,
>
> William Henney  writes:
>
>> I can reproduce your problem.  This is (arguably) a bug in ob-python when
>> using the vanilla python interpreter together with the :session argument.
>> You can work around it by putting a blank line after the for-loop in your
>> second code block.
>>
>> I say that it is arguable that this is a bug or not since you would have
>> exactly the same error if you were to literally type your code block in at
>> the python interactive prompt.  That is, you have to give a second newline
>> in order to close the loop and return to the top-level prompt.  However, it
>> is admittedly confusing to have different behavior with and without the
>> ":session" argument.
>
> Thank you for the analysis. Would you have a suggestion on how to
> improve the situation?
>
> Regards,


-- 
Professor John Kitchin
Doherty Hall A207F
Department of Chemical Engineering
Carnegie Mellon University
Pittsburgh, PA 15213
412-268-7803
@johnkitchin
http://kitchingroup.cheme.cmu.edu

Re: [O] Problem with python session

[Nicolas Goaziou]

Hello,

William Henney  writes:

> I can reproduce your problem.  This is (arguably) a bug in ob-python when
> using the vanilla python interpreter together with the :session argument.
> You can work around it by putting a blank line after the for-loop in your
> second code block.
>
> I say that it is arguable that this is a bug or not since you would have
> exactly the same error if you were to literally type your code block in at
> the python interactive prompt.  That is, you have to give a second newline
> in order to close the loop and return to the top-level prompt.  However, it
> is admittedly confusing to have different behavior with and without the
> ":session" argument.

Thank you for the analysis. Would you have a suggestion on how to
improve the situation?

Regards,

-- 
Nicolas Goaziou

Re: [O] Problem with python session

[William Henney]

Hi Florian

I can reproduce your problem.  This is (arguably) a bug in ob-python when
using the vanilla python interpreter together with the :session argument.
You can work around it by putting a blank line after the for-loop in your
second code block.

I say that it is arguable that this is a bug or not since you would have
exactly the same error if you were to literally type your code block in at
the python interactive prompt.  That is, you have to give a second newline
in order to close the loop and return to the top-level prompt.  However, it
is admittedly confusing to have different behavior with and without the
":session" argument.

I had never come across this bug myself, since I use ob-ipython for
interactive python sessions (https://github.com/gregsexton/ob-ipython)

Here is a minimal example that shows the problem.

Cheers

Will

* Test of ob-python in session mode with vanilla python interpreter

** FAILS: Without blank line after indented loop
#+BEGIN_SRC python :session *ob-python session*
for x in 1, 2:
pass
x
#+END_SRC

#+RESULTS:

An error message appears in the =*ob-python session*= buffer, which can be
visited via =C-c C-v C-z= with point inside the code block.

#+BEGIN_EXAMPLE
>>> 'org_babel_python_eoe'
>>> 'org_babel_python_eoe'
>>> for x in 1, 2:
... pass
... x
  File "", line 3
x
^
SyntaxError: invalid syntax
#+END_EXAMPLE

** SUCCEEDS: With blank line after indented loop
#+BEGIN_SRC python :session *ob-python session*
for x in 1, 2:
pass

x
#+END_SRC

#+RESULTS:
: 2

** SUCCEEDS: Without using a session
#+BEGIN_SRC python :return x
for x in 1, 2:
pass
x
#+END_SRC

#+RESULTS:
: 2

** SUCCEEDS: Using ob-ipython instead of ob-python
#+BEGIN_SRC ipython :session
for x in 1, 2:
pass
x
#+END_SRC

#+RESULTS:
: 2


On Thu, Oct 6, 2016 at 7:41 AM, Florian Lindner  wrote:

> Hello,
>
> I have an org file:
>
> * Overview of available basis functions
> #+BEGIN_SRC python :session generateBFpics :exports results :results file
>   import matplotlib.pyplot as plt
>   import numpy as np
>
>   def set_plotoptions():
>   plt.xlabel("x")
>   plt.ylabel("$\phi(x)$")
>   plt.grid()
>
>
>   np.seterr(invalid='ignore')
>
>   x = np.linspace(-3, 3, 1000)
>
>   plt.plot(x,  np.log(abs(x))*np.power(x, 2))
>   plt.suptitle("Thin Plate Splines")
>   plt.title("$\phi(|x|) = \log(x) \cdot x^2$")
>   set_plotoptions()
>   plt.savefig("bf-tps.pdf")
>   plt.close()
>   "bf-tps.pdf"
> #+END_SRC
>
> #+RESULTS:
> [[file:bf-tps.pdf]]
>
> #+BEGIN_SRC python :session generateBFpics :exports results :results file
>   for shape in [1, 2, 3, 4]:
>   plt.plot(x, np.power(shape, 2) + np.power(x,2), label = "s = %i" %
> shape)
>   plt.suptitle("Multi Quadrics")
>   plt.title("$\phi(|x|) = s^2 + x^2$")
>   plt.legend()
>   set_plotoptions()
>   plt.savefig("bf-multiquadrics.pdf")
>   plt.close()
>   "bf-multiquadrics.pdf"
> #+END_SRC
>
> #+RESULTS:
> [[file:bf-multiquadrics.pdf]]
>
>
>
> Both PDFs are generated. But only the first one has the content I expect,
> the othe one is an empty plot (it's a plot,
> yes, but empty axes.
>
> When I copy these pieces of code into on .py file it works just great. To
> my understanding that just how session mode works.
>
> What could be the problem here?
>
> Thanks,
> Florian
>
>
>


-- 

  Dr William Henney, Instituto de Radioastronomía y Astrofísica,
  Universidad Nacional Autónoma de México, Campus Morelia

[O] Problem with python session

[Florian Lindner]

Hello,

I have an org file:

* Overview of available basis functions
#+BEGIN_SRC python :session generateBFpics :exports results :results file
  import matplotlib.pyplot as plt
  import numpy as np

  def set_plotoptions():
  plt.xlabel("x")
  plt.ylabel("$\phi(x)$")
  plt.grid()


  np.seterr(invalid='ignore')

  x = np.linspace(-3, 3, 1000)

  plt.plot(x,  np.log(abs(x))*np.power(x, 2))
  plt.suptitle("Thin Plate Splines")
  plt.title("$\phi(|x|) = \log(x) \cdot x^2$")
  set_plotoptions()
  plt.savefig("bf-tps.pdf")
  plt.close()
  "bf-tps.pdf"
#+END_SRC

#+RESULTS:
[[file:bf-tps.pdf]]

#+BEGIN_SRC python :session generateBFpics :exports results :results file
  for shape in [1, 2, 3, 4]:
  plt.plot(x, np.power(shape, 2) + np.power(x,2), label = "s = %i" % shape)
  plt.suptitle("Multi Quadrics")
  plt.title("$\phi(|x|) = s^2 + x^2$")
  plt.legend()
  set_plotoptions()
  plt.savefig("bf-multiquadrics.pdf")
  plt.close()
  "bf-multiquadrics.pdf"
#+END_SRC

#+RESULTS:
[[file:bf-multiquadrics.pdf]]



Both PDFs are generated. But only the first one has the content I expect, the 
othe one is an empty plot (it's a plot,
yes, but empty axes.

When I copy these pieces of code into on .py file it works just great. To my 
understanding that just how session mode works.

What could be the problem here?

Thanks,
Florian