From mboxrd@z Thu Jan  1 00:00:00 1970
From: Roger Mason <rmason@mun.ca>
Subject: Troublesome python block
Date: Wed, 11 Oct 2017 12:55:35 -0230
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To: Org-Mode <emacs-orgmode@gnu.org>

hello,

This python block:

#+BEGIN_SRC python :session true :results output
  import numpy as np
  from ase import Atoms
  from ase.calculators.gulp import GULP, Conditions

  quartz = Atoms(symbols='Si3O6', pbc=np.array([True,True,True], dtype=bool),
           cell=np.array([[4.916, 0.0, 0.0], [-2.4579999999999993, 4.257380885004301, 0.0], [0.0, 0.0, 5.4054]]),
	   positions=np.array([[ 2.3016712,   0.,      1.80161982],
                      [-1.1508356, 1.99330573, 3.60341982],
                      [ 1.3071644, 2.26407515, 5.40521982],
                      [ 1.3767258, 1.13288905, 1.15189074],
                      [ 3.2465264, 0.62583499, 2.95369074],
                      [ 2.7507478, 2.49865684, 4.75549074],
                      [ 0.2927478, 1.75872404, 4.25350926],
                      [-1.0812742, 3.12449183, 2.45170926],
                      [ 0.7885264, 3.63154589, 0.64990926]]))
#+END_SRC

produces this output:

#+RESULTS:
#+begin_example
Python 2.7.13 (default, Jul  2 2017, 01:20:25) 
[GCC 4.2.1 Compatible FreeBSD Clang 3.4.1 (tags/RELEASE_34/dot1-final 208032)] on freebsd10
Type "help", "copyright", "credits" or "license" for more information.
python.el: native completion setup loaded
and
as
assert
break
class
continue
def
del
elif
else
....[SNIPPED]....
AttributeError
OverflowError

0__dummy_completion__  1__dummy_completion__
#+end_example

The same python script produces no errors in a python interpreter
started from the command line and it reports no errors when run as
'python twaddle.py'.

Any help in debugging this will be much appreciated.

Roger

Org mode version 9.0.3 (release_9.0.3-170-gfed1cf @
/home/rmason/.emacs.d/org-git/org-mode/lisp/)
GNU Emacs 25.2.1 (i386-portbld-freebsd10.3, GTK+ Version 3.22.15) of 2017-07-03
Python 2.7.13 (default, Jul  2 2017, 01:20:25) 
[GCC 4.2.1 Compatible FreeBSD Clang 3.4.1 (tags/RELEASE_34/dot1-final 208032)] on freebsd10