* Troublesome python block @ 2017-10-11 15:25 Roger Mason 2017-10-11 16:13 ` Kyle Meyer 2017-10-11 16:35 ` Kaushal Modi 0 siblings, 2 replies; 3+ messages in thread From: Roger Mason @ 2017-10-11 15:25 UTC (permalink / raw) To: Org-Mode 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 ^ permalink raw reply [flat|nested] 3+ messages in thread
* Re: Troublesome python block 2017-10-11 15:25 Troublesome python block Roger Mason @ 2017-10-11 16:13 ` Kyle Meyer 2017-10-11 16:35 ` Kaushal Modi 1 sibling, 0 replies; 3+ messages in thread From: Kyle Meyer @ 2017-10-11 16:13 UTC (permalink / raw) To: Roger Mason, Org-Mode Hello, Roger Mason <rmason@mun.ca> writes: > This python block: [...] > 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 [...] > Any help in debugging this will be much appreciated. ob-python sessions have been broken to some degree for quite some time. See, e.g., https://lists.gnu.org/archive/html/emacs-orgmode/2015-03/msg00540.html I dropped my attempt to fix it because 1) I was still having trouble getting a complete understanding of what the issue was and 2) I didn't have the motivation to spend time digging deeper because I don't use ob-python (and in general am not a heavy Org-Babel user). Perhaps you or some other ob-python user could help make ob-python sessions more robust? In the meantime, you could try ob-ipython (https://github.com/gregsexton/ob-ipython). Looking at the README, it sounds like ob-python's problems were one of the author's motivations for writing the library. -- Kyle ^ permalink raw reply [flat|nested] 3+ messages in thread
* Re: Troublesome python block 2017-10-11 15:25 Troublesome python block Roger Mason 2017-10-11 16:13 ` Kyle Meyer @ 2017-10-11 16:35 ` Kaushal Modi 1 sibling, 0 replies; 3+ messages in thread From: Kaushal Modi @ 2017-10-11 16:35 UTC (permalink / raw) To: Roger Mason, Org-Mode [-- Attachment #1: Type: text/plain, Size: 4035 bytes --] 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 [-- Attachment #2: Type: text/html, Size: 5657 bytes --] ^ permalink raw reply [flat|nested] 3+ messages in thread
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