setting options to python interpreter for a code block

setting options to python interpreter for a code block

[John Kitchin]

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Hi,
I am looking at a new strategy to capture stderr and exceptions in python
code blocks. Right now exceptions are not captured in the output, and
neither is stderr.

I made a little sandbox module that captures stdout, stderr, and exceptions
and then prints them all to stdout with some minor formatting. Here is an
example.

Say test.py has this content

#+BEGIN_SRC python
print 'hello'

print 4 + 6

import sys

print >>sys.stderr, 'message to stderr'


raise Exception('baboom')
#+END_SRC

When I use the sandbox, I get all the output on stdout like this.

#+BEGIN_SRC sh
python -m sandbox < test.py
# or cat test.py | python -m sandbox
#+END_SRC

#+RESULTS:
#+begin_example

--------------------------------------------------------------
hello
10


--------------------------------------------------------------
stderr:
message to stderr


--------------------------------------------------------------
Traceback (most recent call last):
  File "/home/jkitchin/Dropbox/pycse/pycse/sandbox/sandbox.py", line 16, in
<module>
    exec(content, ns_globals, ns_locals)
  File "<string>", line 10, in <module>
Exception: baboom


#+end_example


So, I was wondering how to get this to happen in org-mode on a regular
python block. I think it could work if I could define a custom interpreter
for a particular block, e.g. python-sandbox that takes the codeblock on
stdin.

Is there some other way that I could do this? Thanks!

John

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

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Re: setting options to python interpreter for a code block

[Eric Schulte]

You could try setting org-babel-python-command to "python -m sandbox".

If that doesn't work we could add a cmdline header argument to python
code blocks pretty easily.

Cheers,

John Kitchin <jkitchin@andrew.cmu.edu> writes:

> Hi,
> I am looking at a new strategy to capture stderr and exceptions in python
> code blocks. Right now exceptions are not captured in the output, and
> neither is stderr.
>
> I made a little sandbox module that captures stdout, stderr, and exceptions
> and then prints them all to stdout with some minor formatting. Here is an
> example.
>
> Say test.py has this content
>
> #+BEGIN_SRC python
> print 'hello'
>
> print 4 + 6
>
> import sys
>
> print >>sys.stderr, 'message to stderr'
>
>
> raise Exception('baboom')
> #+END_SRC
>
> When I use the sandbox, I get all the output on stdout like this.
>
> #+BEGIN_SRC sh
> python -m sandbox < test.py
> # or cat test.py | python -m sandbox
> #+END_SRC
>
> #+RESULTS:
> #+begin_example
>
> --------------------------------------------------------------
> hello
> 10
>
>
> --------------------------------------------------------------
> stderr:
> message to stderr
>
>
> --------------------------------------------------------------
> Traceback (most recent call last):
>   File "/home/jkitchin/Dropbox/pycse/pycse/sandbox/sandbox.py", line 16, in
> <module>
>     exec(content, ns_globals, ns_locals)
>   File "<string>", line 10, in <module>
> Exception: baboom
>
>
> #+end_example
>
>
> So, I was wondering how to get this to happen in org-mode on a regular
> python block. I think it could work if I could define a custom interpreter
> for a particular block, e.g. python-sandbox that takes the codeblock on
> stdin.
>
> Is there some other way that I could do this? Thanks!
>
> John
>
> -----------------------------------
> John Kitchin
> Associate Professor
> Doherty Hall A207F
> Department of Chemical Engineering
> Carnegie Mellon University
> Pittsburgh, PA 15213
> 412-268-7803
> http://kitchingroup.cheme.cmu.edu

-- 
Eric Schulte
https://cs.unm.edu/~eschulte
PGP: 0x614CA05D

Re: setting options to python interpreter for a code block

[John Kitchin]

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cool! this worked wonderfully:


(setq org-babel-python-command "python -m sandbox")
#+BEGIN_SRC python
print 'hello'

print 4 + 6

import sys

print >>sys.stderr, 'message to stderr'


raise Exception('baboom')
#+END_SRC

#+RESULTS:
#+begin_example

    --------------------------------------------------------------
    hello
10


    --------------------------------------------------------------
    stderr:
    message to stderr


    --------------------------------------------------------------
    Traceback (most recent call last):
  File "/home/jkitchin/Dropbox/pycse/pycse/sandbox/sandbox.py", line 19, in
<module>
    exec(content, ns_globals, ns_locals)
  File "<string>", line 10, in <module>
Exception: baboom


#+end_example

If anyone is interested, here is the sandbox module:
#!/usr/bin/env python
from cStringIO import StringIO
import os, sys

old_stdout = sys.stdout
old_stderr = sys.stderr
redirected_output = sys.stdout = StringIO()
redirected_error = sys.stderr = StringIO()

ns_globals = {}
ns_locals = {}


if __name__ == '__main__':
    content = sys.stdin.read()
    out, err, exc = None, None, None

    try:
        exec(content, ns_globals, ns_locals)
    except:
        import traceback
        exc = traceback.format_exc()

    out = redirected_output.getvalue()
    err = redirected_error.getvalue()

    sys.stdout = old_stdout
    sys.stderr = old_stderr

    s = '''
    --------------------------------------------------------------
    {0}
    '''.format(out)

    if err:
        s += '''
    --------------------------------------------------------------
    stderr:
    {0}
    '''.format(err)

    if exc:
        s += '''
    --------------------------------------------------------------
    {0}
    '''.format(exc)

    print s


John

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



On Wed, Sep 11, 2013 at 2:17 PM, Eric Schulte <schulte.eric@gmail.com>wrote:

> You could try setting org-babel-python-command to "python -m sandbox".
>
> If that doesn't work we could add a cmdline header argument to python
> code blocks pretty easily.
>
> Cheers,
>
> John Kitchin <jkitchin@andrew.cmu.edu> writes:
>
> > Hi,
> > I am looking at a new strategy to capture stderr and exceptions in python
> > code blocks. Right now exceptions are not captured in the output, and
> > neither is stderr.
> >
> > I made a little sandbox module that captures stdout, stderr, and
> exceptions
> > and then prints them all to stdout with some minor formatting. Here is an
> > example.
> >
> > Say test.py has this content
> >
> > #+BEGIN_SRC python
> > print 'hello'
> >
> > print 4 + 6
> >
> > import sys
> >
> > print >>sys.stderr, 'message to stderr'
> >
> >
> > raise Exception('baboom')
> > #+END_SRC
> >
> > When I use the sandbox, I get all the output on stdout like this.
> >
> > #+BEGIN_SRC sh
> > python -m sandbox < test.py
> > # or cat test.py | python -m sandbox
> > #+END_SRC
> >
> > #+RESULTS:
> > #+begin_example
> >
> > --------------------------------------------------------------
> > hello
> > 10
> >
> >
> > --------------------------------------------------------------
> > stderr:
> > message to stderr
> >
> >
> > --------------------------------------------------------------
> > Traceback (most recent call last):
> >   File "/home/jkitchin/Dropbox/pycse/pycse/sandbox/sandbox.py", line 16,
> in
> > <module>
> >     exec(content, ns_globals, ns_locals)
> >   File "<string>", line 10, in <module>
> > Exception: baboom
> >
> >
> > #+end_example
> >
> >
> > So, I was wondering how to get this to happen in org-mode on a regular
> > python block. I think it could work if I could define a custom
> interpreter
> > for a particular block, e.g. python-sandbox that takes the codeblock on
> > stdin.
> >
> > Is there some other way that I could do this? Thanks!
> >
> > John
> >
> > -----------------------------------
> > John Kitchin
> > Associate Professor
> > Doherty Hall A207F
> > Department of Chemical Engineering
> > Carnegie Mellon University
> > Pittsburgh, PA 15213
> > 412-268-7803
> > http://kitchingroup.cheme.cmu.edu
>
> --
> Eric Schulte
> https://cs.unm.edu/~eschulte
> PGP: 0x614CA05D
>

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