On Wed, Oct 11, 2017 at 11:26 AM Roger Mason <rma...@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
