Re: bug#58678: 28.2; :session in org-babel for python unexpected output

Re: bug#58678: 28.2; :session in org-babel for python unexpected output

[Ihor Radchenko]

[Redirecting from Emacs bugs]
[See the quote below for the original report]

> #+RESULTS:
> : >>> __PYTHON_EL_eval("try:\nwith open('/var/folders/dk/3btmprj123b_31jsp30thzrm0000gq/T/babel-9tY6uv/python-92ZLVe') as __org_babel_python_tmpfile:\nexec(compile(__org_babel_python_tmpfile.read(), __org_babel_python_tmpfile.name, 'exec'))\nexcept:\nraise\nfinally:\nprint('
> ```

I am unable to reproduce with the latest main on Linux.
Sergey, could you please try to reproduce with the latest Org version
from Git? See https://orgmode.org/manual/Feedback.html#Feedback

Best,
Ihor

Sergey via "Bug reports for GNU Emacs, the Swiss army knife of text
editors" <bug-gnu-emacs@gnu.org> writes:

> Running the following org file in 'emacs -Q' leads to an unexpected
> output as demonstrated below:
> ```
> #+begin_src elisp
> (setq org-babel-python-command "python3")
> (setq python-shell-interpreter "/usr/bin/python3")
> (org-babel-do-load-languages
> 'org-babel-load-languages
> '(
> (python . t)))
> #+end_src
>
> #+begin_src python :results output
> print(2)
> #+end_src
>
> #+RESULTS:
> : 2
>
> #+begin_src python :results output :session *python-test*
> print(2)
> #+end_src
>
> #+RESULTS:
> : >>> __PYTHON_EL_eval("try:\nwith open('/var/folders/dk/3btmprj123b_31jsp30thzrm0000gq/T/babel-9tY6uv/python-92ZLVe') as __org_babel_python_tmpfile:\nexec(compile(__org_babel_python_tmpfile.read(), __org_babel_python_tmpfile.name, 'exec'))\nexcept:\nraise\nfinally:\nprint('
> ```
>
> In GNU Emacs 28.2 (build 1, aarch64-apple-darwin21.6.0, NS appkit-2113.60 Version 12.6 (Build 21G115))
> of 2022-10-12 built on MAC-140754
> Windowing system distributor 'Apple', version 10.3.2113
> System Description:macOS 12.6
>
> Configured using:
> 'configure --disable-dependency-tracking --disable-silent-rules
> --enable-locallisppath=/opt/homebrew/share/emacs/site-lisp
> --infodir=/opt/homebrew/Cellar/emacs-plus@28/28.2/share/info/emacs
> --prefix=/opt/homebrew/Cellar/emacs-plus@28/28.2 --with-xml2
> --with-gnutls --without-dbus --without-imagemagick --with-modules
> --with-rsvg --with-ns --disable-ns-self-contained 'CFLAGS=-Os -w -pipe
> -mmacosx-version-min=12
> -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk
> -DFD_SETSIZE=10000 -DDARWIN_UNLIMITED_SELECT'
> 'CPPFLAGS=-I/opt/homebrew/opt/icu4c/include
> -I/opt/homebrew/opt/openssl@1.1/include
> -I/opt/homebrew/opt/readline/include -isystem/opt/homebrew/include
> -F/opt/homebrew/Frameworks
> -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk'
> 'LDFLAGS=-L/opt/homebrew/opt/icu4c/lib
> -L/opt/homebrew/opt/openssl@1.1/lib -L/opt/homebrew/opt/readline/lib
> -L/opt/homebrew/lib -F/opt/homebrew/Frameworks
> -Wl,-headerpad_max_install_names
> -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk''
>
> Configured features:
> ACL GLIB GMP GNUTLS JPEG JSON LCMS2 LIBXML2 MODULES NOTIFY KQUEUE NS
> PDUMPER PNG RSVG THREADS TIFF TOOLKIT_SCROLL_BARS XIM ZLIB
>
> Important settings:
> value of $LANG: en_US.UTF-8
> locale-coding-system: utf-8-unix
>
> Major mode: Info
>
> Minor modes in effect:
> shell-dirtrack-mode: t
> tooltip-mode: t
> global-eldoc-mode: t
> show-paren-mode: t
> electric-indent-mode: t
> mouse-wheel-mode: t
> tool-bar-mode: t
> menu-bar-mode: t
> file-name-shadow-mode: t
> global-font-lock-mode: t
> font-lock-mode: t
> blink-cursor-mode: t
> auto-composition-mode: t
> auto-encryption-mode: t
> auto-compression-mode: t
> buffer-read-only: t
> line-number-mode: t
> indent-tabs-mode: t
> transient-mark-mode: t
>
> Load-path shadows:
> None found.
>
> Features:
> (shadow sort mail-extr emacsbug sendmail info warnings compile ob-python
> python tramp-sh tramp tramp-loaddefs trampver tramp-integration files-x
> tramp-compat shell ls-lisp vc-git diff-mode vc-dispatcher org-element
> avl-tree generator ol-eww eww xdg url-queue thingatpt mm-url ol-rmail
> ol-mhe ol-irc ol-info ol-gnus nnselect gnus-search eieio-opt cl-extra
> help-mode speedbar ezimage dframe gnus-art mm-uu mml2015 mm-view
> mml-smime smime dig gnus-sum shr kinsoku svg dom browse-url url
> url-proxy url-privacy url-expand url-methods url-history url-cookie
> url-domsuf url-util url-parse url-vars mailcap gnus-group gnus-undo
> gnus-start gnus-dbus dbus xml gnus-cloud nnimap nnmail mail-source utf7
> netrc nnoo parse-time gnus-spec gnus-int gnus-range message rmc puny
> rfc822 mml mml-sec epa derived epg rfc6068 epg-config mm-decode
> mm-bodies mm-encode mail-parse rfc2231 mailabbrev gmm-utils mailheader
> gnus-win gnus nnheader gnus-util rmail rmail-loaddefs auth-source cl-seq
> eieio eieio-core cl-macs eieio-loaddefs password-cache rfc2047 rfc2045
> ietf-drums text-property-search mail-utils mm-util mail-prsvr wid-edit
> ol-docview doc-view jka-compr image-mode exif dired dired-loaddefs
> ol-bibtex ol-bbdb ol-w3m ol-doi org-link-doi org ob ob-tangle ob-ref
> ob-lob ob-table ob-exp org-macro org-footnote org-src ob-comint
> org-pcomplete pcomplete comint ansi-color ring org-list org-faces
> org-entities noutline outline easy-mmode org-version ob-emacs-lisp
> ob-core ob-eval org-table oc-basic json map bibtex iso8601 time-date
> subr-x ol rx org-keys oc seq byte-opt gv bytecomp byte-compile cconv
> org-compat advice org-macs org-loaddefs format-spec find-func cal-menu
> calendar cal-loaddefs cl-loaddefs cl-lib iso-transl tooltip eldoc paren
> electric uniquify ediff-hook vc-hooks lisp-float-type elisp-mode mwheel
> term/ns-win ns-win ucs-normalize mule-util term/common-win tool-bar dnd
> fontset image regexp-opt fringe tabulated-list replace newcomment
> text-mode lisp-mode prog-mode register page tab-bar menu-bar rfn-eshadow
> isearch easymenu timer select scroll-bar mouse jit-lock font-lock syntax
> font-core term/tty-colors frame minibuffer cl-generic cham georgian
> utf-8-lang misc-lang vietnamese tibetan thai tai-viet lao korean
> japanese eucjp-ms cp51932 hebrew greek romanian slovak czech european
> ethiopic indian cyrillic chinese composite emoji-zwj charscript charprop
> case-table epa-hook jka-cmpr-hook help simple abbrev obarray
> cl-preloaded nadvice button loaddefs faces cus-face macroexp files
> window text-properties overlay sha1 md5 base64 format env code-pages
> mule custom widget hashtable-print-readable backquote threads kqueue
> cocoa ns lcms2 multi-tty make-network-process emacs)
>
> Memory information:
> ((conses 16 217410 17812)
> (symbols 48 22121 1)
> (strings 32 80449 5421)
> (string-bytes 1 2659099)
> (vectors 16 40607)
> (vector-slots 8 454675 43035)
> (floats 8 276 108)
> (intervals 56 1253 0)
> (buffers 992 19))
>
> Sent with [Proton Mail](https://proton.me/) secure email.

-- 
Ihor Radchenko // yantar92,
Org mode contributor,
Learn more about Org mode at <https://orgmode.org/>.
Support Org development at <https://liberapay.com/org-mode>,
or support my work at <https://liberapay.com/yantar92>

Re: bug#58678: 28.2; :session in org-babel for python unexpected output

[Sergey]

I have traced this to org-bable issue with MacOS python readline and native completion. Similar issues discussed in 
https://github.com/jorgenschaefer/elpy/issues/887
and 
https://debbugs.gnu.org/cgi/bugreport.cgi?bug=25753

The solution proposed in those threads, i.e., installing python from homebrew, which has gnureadline, helps for emacs 27 but causes freezing in emacs 28 after displaying following message:
```
Warning (python): Your ‘python-shell-interpreter’ doesn’t seem to support readline, yet ‘python-shell-completion-native-enable’ was t and "python3" is not part of the ‘python-shell-completion-native-disabled-interpreters’ list. Native completions have been disabled locally.
```

Setting ~python-shell-completion-native-enable~ to nil removes the warning but doesn't prevent freezing. This behaviour persists with minimal org setup as well (although, I believe my emacs comes with org pre-packaged).

Cheers,
Sergey.


------- Original Message -------
On Saturday, October 22nd, 2022 at 12:58 AM, Ihor Radchenko <yantar92@posteo.net> wrote:


> [Redirecting from Emacs bugs]
> [See the quote below for the original report]
> 
> > #+RESULTS:
> > : >>> __PYTHON_EL_eval("try:\nwith open('/var/folders/dk/3btmprj123b_31jsp30thzrm0000gq/T/babel-9tY6uv/python-92ZLVe') as __org_babel_python_tmpfile:\nexec(compile(__org_babel_python_tmpfile.read(), __org_babel_python_tmpfile.name, 'exec'))\nexcept:\nraise\nfinally:\nprint('
> > ```
> 
> 
> I am unable to reproduce with the latest main on Linux.
> Sergey, could you please try to reproduce with the latest Org version
> from Git? See https://orgmode.org/manual/Feedback.html#Feedback
> 
> Best,
> Ihor
> 
> Sergey via "Bug reports for GNU Emacs, the Swiss army knife of text
> editors" bug-gnu-emacs@gnu.org writes:
> 
> > Running the following org file in 'emacs -Q' leads to an unexpected
> > output as demonstrated below:
> > ```
> > #+begin_src elisp
> > (setq org-babel-python-command "python3")
> > (setq python-shell-interpreter "/usr/bin/python3")
> > (org-babel-do-load-languages
> > 'org-babel-load-languages
> > '(
> > (python . t)))
> > #+end_src
> > 
> > #+begin_src python :results output
> > print(2)
> > #+end_src
> > 
> > #+RESULTS:
> > : 2
> > 
> > #+begin_src python :results output :session python-test
> > print(2)
> > #+end_src
> > 
> > #+RESULTS:
> > : >>> __PYTHON_EL_eval("try:\nwith open('/var/folders/dk/3btmprj123b_31jsp30thzrm0000gq/T/babel-9tY6uv/python-92ZLVe') as __org_babel_python_tmpfile:\nexec(compile(__org_babel_python_tmpfile.read(), __org_babel_python_tmpfile.name, 'exec'))\nexcept:\nraise\nfinally:\nprint('
> > ```
> > 
> > In GNU Emacs 28.2 (build 1, aarch64-apple-darwin21.6.0, NS appkit-2113.60 Version 12.6 (Build 21G115))
> > of 2022-10-12 built on MAC-140754
> > Windowing system distributor 'Apple', version 10.3.2113
> > System Description:macOS 12.6
> > 
> > Configured using:
> > 'configure --disable-dependency-tracking --disable-silent-rules
> > --enable-locallisppath=/opt/homebrew/share/emacs/site-lisp
> > --infodir=/opt/homebrew/Cellar/emacs-plus@28/28.2/share/info/emacs
> > --prefix=/opt/homebrew/Cellar/emacs-plus@28/28.2 --with-xml2
> > --with-gnutls --without-dbus --without-imagemagick --with-modules
> > --with-rsvg --with-ns --disable-ns-self-contained 'CFLAGS=-Os -w -pipe
> > -mmacosx-version-min=12
> > -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk
> > -DFD_SETSIZE=10000 -DDARWIN_UNLIMITED_SELECT'
> > 'CPPFLAGS=-I/opt/homebrew/opt/icu4c/include
> > -I/opt/homebrew/opt/openssl@1.1/include
> > -I/opt/homebrew/opt/readline/include -isystem/opt/homebrew/include
> > -F/opt/homebrew/Frameworks
> > -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk'
> > 'LDFLAGS=-L/opt/homebrew/opt/icu4c/lib
> > -L/opt/homebrew/opt/openssl@1.1/lib -L/opt/homebrew/opt/readline/lib
> > -L/opt/homebrew/lib -F/opt/homebrew/Frameworks
> > -Wl,-headerpad_max_install_names
> > -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk''
> > 
> > Configured features:
> > ACL GLIB GMP GNUTLS JPEG JSON LCMS2 LIBXML2 MODULES NOTIFY KQUEUE NS
> > PDUMPER PNG RSVG THREADS TIFF TOOLKIT_SCROLL_BARS XIM ZLIB
> > 
> > Important settings:
> > value of $LANG: en_US.UTF-8
> > locale-coding-system: utf-8-unix
> > 
> > Major mode: Info
> > 
> > Minor modes in effect:
> > shell-dirtrack-mode: t
> > tooltip-mode: t
> > global-eldoc-mode: t
> > show-paren-mode: t
> > electric-indent-mode: t
> > mouse-wheel-mode: t
> > tool-bar-mode: t
> > menu-bar-mode: t
> > file-name-shadow-mode: t
> > global-font-lock-mode: t
> > font-lock-mode: t
> > blink-cursor-mode: t
> > auto-composition-mode: t
> > auto-encryption-mode: t
> > auto-compression-mode: t
> > buffer-read-only: t
> > line-number-mode: t
> > indent-tabs-mode: t
> > transient-mark-mode: t
> > 
> > Load-path shadows:
> > None found.
> > 
> > Features:
> > (shadow sort mail-extr emacsbug sendmail info warnings compile ob-python
> > python tramp-sh tramp tramp-loaddefs trampver tramp-integration files-x
> > tramp-compat shell ls-lisp vc-git diff-mode vc-dispatcher org-element
> > avl-tree generator ol-eww eww xdg url-queue thingatpt mm-url ol-rmail
> > ol-mhe ol-irc ol-info ol-gnus nnselect gnus-search eieio-opt cl-extra
> > help-mode speedbar ezimage dframe gnus-art mm-uu mml2015 mm-view
> > mml-smime smime dig gnus-sum shr kinsoku svg dom browse-url url
> > url-proxy url-privacy url-expand url-methods url-history url-cookie
> > url-domsuf url-util url-parse url-vars mailcap gnus-group gnus-undo
> > gnus-start gnus-dbus dbus xml gnus-cloud nnimap nnmail mail-source utf7
> > netrc nnoo parse-time gnus-spec gnus-int gnus-range message rmc puny
> > rfc822 mml mml-sec epa derived epg rfc6068 epg-config mm-decode
> > mm-bodies mm-encode mail-parse rfc2231 mailabbrev gmm-utils mailheader
> > gnus-win gnus nnheader gnus-util rmail rmail-loaddefs auth-source cl-seq
> > eieio eieio-core cl-macs eieio-loaddefs password-cache rfc2047 rfc2045
> > ietf-drums text-property-search mail-utils mm-util mail-prsvr wid-edit
> > ol-docview doc-view jka-compr image-mode exif dired dired-loaddefs
> > ol-bibtex ol-bbdb ol-w3m ol-doi org-link-doi org ob ob-tangle ob-ref
> > ob-lob ob-table ob-exp org-macro org-footnote org-src ob-comint
> > org-pcomplete pcomplete comint ansi-color ring org-list org-faces
> > org-entities noutline outline easy-mmode org-version ob-emacs-lisp
> > ob-core ob-eval org-table oc-basic json map bibtex iso8601 time-date
> > subr-x ol rx org-keys oc seq byte-opt gv bytecomp byte-compile cconv
> > org-compat advice org-macs org-loaddefs format-spec find-func cal-menu
> > calendar cal-loaddefs cl-loaddefs cl-lib iso-transl tooltip eldoc paren
> > electric uniquify ediff-hook vc-hooks lisp-float-type elisp-mode mwheel
> > term/ns-win ns-win ucs-normalize mule-util term/common-win tool-bar dnd
> > fontset image regexp-opt fringe tabulated-list replace newcomment
> > text-mode lisp-mode prog-mode register page tab-bar menu-bar rfn-eshadow
> > isearch easymenu timer select scroll-bar mouse jit-lock font-lock syntax
> > font-core term/tty-colors frame minibuffer cl-generic cham georgian
> > utf-8-lang misc-lang vietnamese tibetan thai tai-viet lao korean
> > japanese eucjp-ms cp51932 hebrew greek romanian slovak czech european
> > ethiopic indian cyrillic chinese composite emoji-zwj charscript charprop
> > case-table epa-hook jka-cmpr-hook help simple abbrev obarray
> > cl-preloaded nadvice button loaddefs faces cus-face macroexp files
> > window text-properties overlay sha1 md5 base64 format env code-pages
> > mule custom widget hashtable-print-readable backquote threads kqueue
> > cocoa ns lcms2 multi-tty make-network-process emacs)
> > 
> > Memory information:
> > ((conses 16 217410 17812)
> > (symbols 48 22121 1)
> > (strings 32 80449 5421)
> > (string-bytes 1 2659099)
> > (vectors 16 40607)
> > (vector-slots 8 454675 43035)
> > (floats 8 276 108)
> > (intervals 56 1253 0)
> > (buffers 992 19))
> > 
> > Sent with Proton Mail secure email.
> 
> 
> --
> Ihor Radchenko // yantar92,
> Org mode contributor,
> Learn more about Org mode at https://orgmode.org/.
> 
> Support Org development at https://liberapay.com/org-mode,
> 
> or support my work at https://liberapay.com/yantar92

bug#58678: 28.2; :session in org-babel for python unexpected output

[Ihor Radchenko]

Sergey <srg.koshelev@proton.me> writes:

> I have traced this to org-bable issue with MacOS python readline and native completion. Similar issues discussed in 
> https://github.com/jorgenschaefer/elpy/issues/887
> and 
> https://debbugs.gnu.org/cgi/bugreport.cgi?bug=25753
>
> The solution proposed in those threads, i.e., installing python from homebrew, which has gnureadline, helps for emacs 27 but causes freezing in emacs 28 after displaying following message:
> ```
> Warning (python): Your ‘python-shell-interpreter’ doesn’t seem to support readline, yet ‘python-shell-completion-native-enable’ was t and "python3" is not part of the ‘python-shell-completion-native-disabled-interpreters’ list. Native completions have been disabled locally.
> ```
>
> Setting ~python-shell-completion-native-enable~ to nil removes the warning but doesn't prevent freezing. This behaviour persists with minimal org setup as well (although, I believe my emacs comes with org pre-packaged).

So, it looks like Emacs bug then.
Let us see what Emacs devs can suggest.

-- 
Ihor Radchenko // yantar92,
Org mode contributor,
Learn more about Org mode at <https://orgmode.org/>.
Support Org development at <https://liberapay.com/org-mode>,
or support my work at <https://liberapay.com/yantar92>