Re: [O] Troublesome python block

[Kaushal Modi]

On Wed, Oct 11, 2017 at 11:26 AM Roger Mason <address@hidden> 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