1

This worked seamlessly, but at some point, I lost the ability to pass string-type variable values between code blocks in Org Babel. Let’s take the following example:

#+begin_src python :session *PY* :exports code :results output
from sympy import *
x = Symbol('x')
f = x+x/2
a = 7

print(f)
print(latex(f))
print(a)
#+end_src

#+RESULTS:
: 3*x/2
: \frac{3 x}{2}
: 7

#+begin_src python :session *PY* :exports code :results output
print(latex(f))
print(f)
print(a)
#+end_src

#+RESULTS:
: \mathtt{\text{<\_io.TextIOWrapper name='/tmp/babel-KrI2mU/python-FVFmyv' mode='r' encoding='UTF-8'>}}
: <_io.TextIOWrapper name='/tmp/babel-KrI2mU/python-FVFmyv' mode='r' encoding='UTF-8'>
: 7

src_python[:session *PY* :results output]{print(x+x)} {{{results(=2*x=)}}}
src_python[:session *PY* :results output]{print(f)} {{{results(=<_io.TextIOWrapper name='/tmp/babel-KrI2mU/python-eN4EFB' mode='r' encoding='UTF-8'>=)}}}

It seems something must have changed in org-babel and now it's trying to read temporary files as strings. What should I do to localize the problem and restore the functionality? Software version: Emacs 30.1, org-mode 9.7.11

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3
  • It works here if I change f to e: it seems f has a special meaning for something (although I don't know what). Commented Jun 12 at 0:22
  • Indeed! I don't have much time to test it thoroughly but it seems everything but f works fine. Hmmm... maybe it has something to do with python f-strings? The variable named f could be misinterpreted at some point/ treated as f-string prefix or something...? Commented Jun 12 at 7:19
  • 3
    I’m voting to close this question because the problem was caused by a bug in Org mode that has since been fixed. Commented Jul 21 at 1:33

1 Answer 1

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1

As noted, the use of f in the code is triggering the problem (any identifier other than f works fine).

The problem is caused by a bug in org-babel-python-evaluate-session which saves the code in a temporary file and then evaluates it by constructing a string and sending it to the python interpreter:

    ...
    (let ((body (format "\
with open('%s') as f:
    exec(compile(f.read(), f.name, 'exec'))"
                   (org-babel-process-file-name
                    tmp-src-file 'noquote))))
         (org-babel-python-send-string session body))

The problem is the reuse of f as the file handle in the with statement: when the Python interpreter evaluates the code, the value of f is the file handle instead of the original string. Ideally, org-babel-python-evaluate-session should use, instead of f, an identifier that is not used by the user code that was squirreled into the temp file - that may be difficult to arrange, but an easy, and almost foolproof, workaround would be to construct a random identifier that would, in all likelihood, avoid the collision.[1]

Please report this (and reference this question) with M-x org-submit-bug-report.

The obvious workaround is to not use f for now, until the bug is fixed.

[1] Something like a concatenation of __file__handle__ with a UUID produced by org-id-uuid (with underscores instead of dashes) should work pretty well in virtually all cases.

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2
  • 1
    Bug reported here Commented Jun 13 at 8:32
  • The ob-python maintainer has pushed a fix into the bugfix branch and to the main branch. Commented Jun 15 at 1:39

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