Jack Kamm 3ff21c7138 Add options to skip extra processing in org-babel-comint-with-output ... This patch adds options to org-babel-comint-with-output to skip prompt removal. Allowing individual languages to handle this cleanup can be more robust than relying on the generic ob-comint implementation. This allows ob-python to switch back to using `org-babel-comint-with-output' rather than its own bespoke reimplementation, reducing code duplication. Furthermore, this adds a new implementation of ob-R non-async session output evaluation, that is similar to the ob-python approach in that it avoids leaking prompts, rather than relying on the cleanup from `org-babel-comint-with-output'. A test is added to test-ob-R.el to demonstrate the improved robustness of the new approach; previously, this test would fail due to a false positive prompt, but now passes. * lisp/ob-comint.el (org-babel-comint--remove-prompts-p): New helper function to parse the prompt-handling argument in `org-babel-comint-with-output' and `org-babel-comint-async-register'. (org-babel-comint-with-output): Add a new argument to prevent extra processing for prompt cleanup. Also, search for the end-of-execution sentinel within the collected output rather than the comint buffer, which doesn't depend on the position of point during evaluation. (org-babel-comint-async-register): Move parsing of prompt-handling argument to `org-babel-comint--remove-prompts-p'. * lisp/ob-python.el: Require subr-x for Emacs 27 compatibility. (org-babel-python-send-string): Switch to using `org-babel-comint-with-output', rather than bespoke reimplementation. * lisp/ob-R.el: Require subr-x for Emacs 27 compatibility. (ess-send-string): Declare external function. (org-babel-R-evaluate-session): New implementation of output evaluation that avoids leaking prompts, by writing the code block to a tmp file and then sourcing it. * testing/lisp/test-ob-R.el (test-ob-r/session-output-with->-bol): New test for robustness against false positive prompts at the beginning of a line.		2024-11-12 19:54:28 -08:00
..
Makefile	Fix parallel execution of Makefiles	2024-06-20 18:27:04 +02:00
ob-awk.el	ob-*: Do not emit redundant messages about code block evaluation	2024-06-13 15:22:28 +02:00
ob-C.el	ob-*: Do not emit redundant messages about code block evaluation	2024-06-13 15:22:28 +02:00
ob-calc.el	Merge branch 'km/from-emacs-master'	2024-05-28 23:01:23 -04:00
ob-clojure.el	Replace use of if-let and when-let, obsolete in Emacs 31.0.50	2024-10-27 10:34:05 +08:00
ob-comint.el	Add options to skip extra processing in org-babel-comint-with-output	2024-11-12 19:54:28 -08:00
ob-core.el	Replace use of if-let and when-let, obsolete in Emacs 31.0.50	2024-10-27 10:34:05 +08:00
ob-css.el	Merge branch 'bugfix'	2024-01-06 16:02:02 -05:00
ob-ditaa.el	ob-*: Do not emit redundant messages about code block evaluation	2024-06-13 15:22:28 +02:00
ob-dot.el	Merge branch 'bugfix'	2024-01-06 16:02:02 -05:00
ob-emacs-lisp.el	fixup! lisp/ob-emacs-lisp.el: Throw an error when session is requested	2024-04-09 16:35:44 +03:00
ob-eshell.el	Merge branch 'km/from-emacs-master'	2024-05-28 23:01:23 -04:00
ob-eval.el	ob-core: Unify Org Babel related buffer names using constant variable	2024-07-16 19:09:45 +02:00
ob-exp.el	Replace use of if-let and when-let, obsolete in Emacs 31.0.50	2024-10-27 10:34:05 +08:00
ob-forth.el	Merge branch 'bugfix'	2024-01-06 16:02:02 -05:00
ob-fortran.el	Merge branch 'bugfix'	2024-01-06 16:02:02 -05:00
ob-gnuplot.el	Merge branch 'bugfix'	2024-08-22 14:37:15 +02:00
ob-groovy.el	ob-*: Do not emit redundant messages about code block evaluation	2024-06-13 15:22:28 +02:00
ob-haskell.el	Rename org-babel-comint-prompt-regexp-old' to ...-fallback'	2024-08-05 17:02:56 +02:00
ob-java.el	Merge branch 'bugfix'	2024-01-06 16:02:02 -05:00
ob-js.el	Merge branch 'bugfix'	2024-01-06 16:02:02 -05:00
ob-julia.el	Replace use of if-let and when-let, obsolete in Emacs 31.0.50	2024-10-27 10:34:05 +08:00
ob-latex.el	org-babel-latex-process-alist: Use latemk or run latex trice	2024-06-03 16:32:02 +02:00
ob-lilypond.el	Backport commit 45a20d781 from Emacs	2024-07-01 22:33:10 -04:00
ob-lisp.el	Merge branch 'bugfix'	2024-01-06 16:02:02 -05:00
ob-lob.el	Backport commit 6757f8e67 from Emacs	2024-07-14 12:20:46 -04:00
ob-lua.el	Backport commit a7dff8c53 from Emacs	2024-06-27 23:13:47 -04:00
ob-makefile.el	Merge branch 'bugfix'	2024-01-06 16:02:02 -05:00
ob-matlab.el	Backport commit 8e1c56ae4 from Emacs	2024-01-06 15:48:23 -05:00
ob-maxima.el	ob-*: Do not emit redundant messages about code block evaluation	2024-06-13 15:22:28 +02:00
ob-ocaml.el	Merge branch 'bugfix'	2024-01-06 16:02:02 -05:00
ob-octave.el	Merge branch 'bugfix'	2024-01-06 16:02:02 -05:00
ob-org.el	Clean up spacing to pass Emacs's pre-commit check	2024-05-27 21:18:59 -04:00
ob-perl.el	Backport commit 8e1c56ae4 from Emacs	2024-01-06 15:48:23 -05:00
ob-plantuml.el	Backport commit 6757f8e67 from Emacs	2024-07-14 12:20:46 -04:00
ob-processing.el	Merge branch 'bugfix'	2024-01-06 16:02:02 -05:00
ob-python.el	Add options to skip extra processing in org-babel-comint-with-output	2024-11-12 19:54:28 -08:00
ob-R.el	Add options to skip extra processing in org-babel-comint-with-output	2024-11-12 19:54:28 -08:00
ob-ref.el	Merge branch 'bugfix'	2024-01-06 16:02:02 -05:00
ob-ruby.el	Rename org-babel-comint-prompt-regexp-old' to ...-fallback'	2024-08-05 17:02:56 +02:00
ob-sass.el	Backport commit 8e1c56ae4 from Emacs	2024-01-06 15:48:23 -05:00
ob-scheme.el	Backport commit 6757f8e67 from Emacs	2024-07-14 12:20:46 -04:00
ob-screen.el	ob-*: Do not emit redundant messages about code block evaluation	2024-06-13 15:22:28 +02:00
ob-sed.el	ob-*: Do not emit redundant messages about code block evaluation	2024-06-13 15:22:28 +02:00
ob-shell.el	org-babel-sh-prompt: Fix Emacs 27 CI failures	2024-08-06 20:11:45 +02:00
ob-sql.el	Merge branch 'bugfix'	2024-07-25 13:22:41 +02:00
ob-sqlite.el	ob-sqlite: Add ability to open a database in readonly mode	2024-06-25 12:53:52 +02:00
ob-table.el	Merge branch 'bugfix'	2024-01-06 16:02:02 -05:00
ob-tangle.el	Backport commit 6757f8e67 from Emacs	2024-07-14 12:20:46 -04:00
ob.el	Backport commit 6757f8e67 from Emacs	2024-07-14 12:20:46 -04:00
oc-basic.el	Backport commit c0eefebab from Emacs	2024-06-27 22:47:14 -04:00
oc-biblatex.el	oc-biblatex: Allow native biblatex options in CITE_EXPORT	2024-04-26 15:23:29 +03:00
oc-bibtex.el	Merge branch 'bugfix'	2024-01-06 16:02:02 -05:00
oc-csl.el	oc-csl: New custom option `org-cite-csl-bibtex-titles-to-sentence-case'	2024-06-20 07:41:56 +02:00
oc-natbib.el	Merge branch 'bugfix'	2024-01-06 16:02:02 -05:00
oc.el	Merge branch 'bugfix'	2024-01-06 16:02:02 -05:00
ol-bbdb.el	Merge branch 'km/from-emacs-master'	2024-05-28 23:01:23 -04:00
ol-bibtex.el	Merge branch 'km/from-emacs-master'	2024-05-28 23:01:23 -04:00
ol-docview.el	Merge branch 'km/from-emacs-master'	2024-05-28 23:01:23 -04:00
ol-doi.el	Merge branch 'bugfix'	2024-01-06 16:02:02 -05:00
ol-eshell.el	org-id.el: Add search strings, inherit parent IDs	2024-02-24 15:56:44 +03:00
ol-eww.el	org-id.el: Add search strings, inherit parent IDs	2024-02-24 15:56:44 +03:00
ol-gnus.el	Merge branch 'km/from-emacs-master'	2024-05-28 23:01:23 -04:00
ol-info.el	Merge branch 'km/from-emacs-master'	2024-05-28 23:01:23 -04:00
ol-irc.el	org-id.el: Add search strings, inherit parent IDs	2024-02-24 15:56:44 +03:00
ol-man.el	Merge branch 'km/from-emacs-master'	2024-05-28 23:01:23 -04:00
ol-mhe.el	Merge branch 'km/from-emacs-master'	2024-05-28 23:01:23 -04:00
ol-rmail.el	Merge branch 'km/from-emacs-master'	2024-05-28 23:01:23 -04:00
ol-w3m.el	Backport commit 0f3be9596 from Emacs	2024-05-28 22:58:43 -04:00
ol.el	Replace use of if-let and when-let, obsolete in Emacs 31.0.50	2024-10-27 10:34:05 +08:00
org-agenda.el	org-agenda-write: Remove redundant `set-buffer'	2024-07-28 20:49:25 +02:00
org-archive.el	Merge branch 'km/from-emacs-master'	2024-05-28 23:01:23 -04:00
org-attach-git.el	Backport commit 8e1c56ae4 from Emacs	2024-01-06 15:48:23 -05:00
org-attach.el	Replace use of if-let and when-let, obsolete in Emacs 31.0.50	2024-10-27 10:34:05 +08:00
org-capture.el	org-capture-templates: Allow headline/olp target to be function or symbol	2024-06-18 14:33:55 +02:00
org-clock.el	Replace use of if-let and when-let, obsolete in Emacs 31.0.50	2024-10-27 10:34:05 +08:00
org-colview.el	org-colview: Fix ignoring org-agenda-columns-add-appointments-to-effort-sum	2024-10-12 09:31:44 +02:00
org-compat.el	Replace use of if-let and when-let, obsolete in Emacs 31.0.50	2024-10-27 10:34:05 +08:00
org-crypt.el	Never pass error message verbatim as the first argument for message'/error'	2024-02-25 13:15:04 +03:00
org-ctags.el	org-ctags: Don't assume ctags-program-name is bound	2024-05-28 23:23:39 -04:00
org-cycle.el	Backport commit 77d0eed74 from Emacs	2024-06-09 20:50:50 -04:00
org-datetree.el	Merge branch 'km/from-emacs-master'	2024-05-28 23:01:23 -04:00
org-duration.el	Merge branch 'km/from-emacs-master'	2024-05-28 23:01:23 -04:00
org-element-ast.el	Replace use of if-let and when-let, obsolete in Emacs 31.0.50	2024-10-27 10:34:05 +08:00
org-element.el	Replace use of if-let and when-let, obsolete in Emacs 31.0.50	2024-10-27 10:34:05 +08:00
org-entities.el	Merge branch 'km/from-emacs-master'	2024-05-28 23:01:23 -04:00
org-faces.el	Backport commit 6757f8e67 from Emacs	2024-07-14 12:20:46 -04:00
org-feed.el	Merge branch 'km/from-emacs-master'	2024-05-28 23:01:23 -04:00
org-fold-core.el	Backport commit a6cab228d from Emacs	2024-07-20 15:24:27 -04:00
org-fold.el	Backport commit 6757f8e67 from Emacs	2024-07-14 12:20:46 -04:00
org-footnote.el	org-footnote-new: Do not throw an error at bol for inline/anonymous footnotes	2024-10-13 11:03:32 +02:00
org-goto.el	Replace use of if-let and when-let, obsolete in Emacs 31.0.50	2024-10-27 10:34:05 +08:00
org-habit.el	Backport commit 6757f8e67 from Emacs	2024-07-14 12:20:46 -04:00
org-id.el	org-id: Guard against unwarranted major-mode change when querying id	2024-09-22 12:41:54 +02:00
org-indent.el	Backport commit fb11294d4 from Emacs	2024-06-27 23:13:49 -04:00
org-inlinetask.el	Backport commit 6757f8e67 from Emacs	2024-07-14 12:20:46 -04:00
org-keys.el	Add repeat-mode keymap for navigation commands	2024-10-12 19:39:56 +02:00
org-lint.el	Replace use of if-let and when-let, obsolete in Emacs 31.0.50	2024-10-27 10:34:05 +08:00
org-list.el	org-list-struct-apply-struct: Fix item contents breaking out of the item	2024-07-10 15:39:26 +02:00
org-macro.el	Merge branch 'km/from-emacs-master'	2024-05-28 23:01:23 -04:00
org-macs.el	Merge branch 'bugfix'	2024-11-01 17:14:48 -07:00
org-mobile.el	Backport commit 6757f8e67 from Emacs	2024-07-14 12:20:46 -04:00
org-mouse.el	org-mouse-context-menu: Fix `grep' command to handle filenames starting with '-'	2024-11-09 15:33:38 +01:00
org-num.el	org-num-skip-tags: Avoid using function that is not pre-loaded in autoloads	2024-06-14 14:25:03 +02:00
org-pcomplete.el	Backport commit 77d0eed74 from Emacs	2024-06-09 20:50:50 -04:00
org-persist.el	Replace use of if-let and when-let, obsolete in Emacs 31.0.50	2024-10-27 10:34:05 +08:00
org-plot.el	org-plot/gnuplot-to-data: Do not assume that `orgtbl-to-generic' preserves buffer	2024-07-24 12:32:32 +02:00
org-protocol.el	Merge branch 'km/from-emacs-master'	2024-05-28 23:01:23 -04:00
org-refile.el	org-refile: calculate file part of the outline path once per file	2024-10-15 20:48:10 +02:00
org-src.el	Merge branch 'bugfix'	2024-07-25 13:22:41 +02:00
org-table.el	Replace use of if-let and when-let, obsolete in Emacs 31.0.50	2024-10-27 10:34:05 +08:00
org-tempo.el	Merge branch 'km/from-emacs-master'	2024-05-28 23:01:23 -04:00
org-timer.el	Merge branch 'km/from-emacs-master'	2024-05-28 23:01:23 -04:00
org.el	Merge branch 'bugfix'	2024-11-09 15:01:40 +01:00
ox-ascii.el	Merge branch 'km/from-emacs-master'	2024-05-28 23:01:23 -04:00
ox-beamer.el	Replace use of if-let and when-let, obsolete in Emacs 31.0.50	2024-10-24 17:04:40 +08:00
ox-html.el	Replace use of if-let and when-let, obsolete in Emacs 31.0.50	2024-10-27 10:34:05 +08:00
ox-icalendar.el	ox-icalendar: Fix export of diary-style timestamps	2024-09-22 12:22:33 +02:00
ox-koma-letter.el	Merge branch 'km/from-emacs-master'	2024-05-28 23:01:23 -04:00
ox-latex.el	Replace use of if-let and when-let, obsolete in Emacs 31.0.50	2024-10-27 10:34:05 +08:00
ox-man.el	Merge branch 'km/from-emacs-master'	2024-05-28 23:01:23 -04:00
ox-md.el	Merge branch 'km/from-emacs-master'	2024-05-28 23:01:23 -04:00
ox-odt.el	Merge branch 'km/from-emacs-master'	2024-05-28 23:01:23 -04:00
ox-org.el	Merge branch 'km/from-emacs-master'	2024-05-28 23:01:23 -04:00
ox-publish.el	lisp/ox-publish.el: Use publish time in publish cache	2024-08-15 20:24:42 +02:00
ox-texinfo.el	ox-texinfo: Fix definitions containing Org markup	2024-10-26 10:36:59 +02:00
ox.el	Replace use of if-let and when-let, obsolete in Emacs 31.0.50	2024-10-27 10:34:05 +08:00