On Wed, Oct 11, 2017 at 11:26 AM Roger Mason <rmason@mun.ca> wrote:

> 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
>

I cannot recreate that, though I am on different versions for everything:

- Emacs: 26.0.60 built from emacs-26 branch <-- This might be what actually
matters as I know that there were quite a few python.el commits in this
branch (
http://git.savannah.gnu.org/cgit/emacs.git/log/?h=emacs-26&qt=grep&q=python
 ).
- Org: built from Org master branch
- Python 3.6.2

I haven't used numpy or ase/scipy, so after:

> pip3 install --user numpy
> pip3 install --user scipy

I get:

#+PROPERTY: header-args:python :exports both :results output
#+BEGIN_SRC python
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]]))
print(quartz)
#+END_SRC

#+RESULTS:
: Atoms(symbols='Si3O6', pbc=True, cell=[[4.916, 0.0, 0.0],
[-2.4579999999999993, 4.257380885004301, 0.0], [0.0, 0.0, 5.4054]])


Is that what you expected in the RESULTS?

Here is my relatively simply python setup where I default the interpreter
to python3:
https://github.com/kaushalmodi/.emacs.d/blob/master/setup-files/setup-python.el

and my minimal ob-python setup:

(use-package ob-python
  :defer t
  :config
  (progn
    (setq org-babel-python-command "python3"))) ;Default to python 3.x

-- 

Kaushal Modi