From: Kaushal Modi <kaushal.modi@gmail.com>
To: Roger Mason <rmason@mun.ca>, Org-Mode <emacs-orgmode@gnu.org>
Subject: Re: Troublesome python block
Date: Wed, 11 Oct 2017 16:35:15 +0000 [thread overview]
Message-ID: <CAFyQvY3Jbm4=RjEjQpAs6TOhGePEAV0x5fwdR+4hD1f6rrTaOQ@mail.gmail.com> (raw)
In-Reply-To: <y65vajlk8pc.fsf@mun.ca>
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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
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prev parent reply other threads:[~2017-10-11 16:35 UTC|newest]
Thread overview: 3+ messages / expand[flat|nested] mbox.gz Atom feed top
2017-10-11 15:25 Troublesome python block Roger Mason
2017-10-11 16:13 ` Kyle Meyer
2017-10-11 16:35 ` Kaushal Modi [this message]
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