pkg update and first config fix

org-brain not working, add org-roam

lisp/org/ob-comint.el

@@ -1,10 +1,10 @@
 ;;; ob-comint.el --- Babel Functions for Interaction with Comint Buffers -*- lexical-binding: t; -*-
 
-;; Copyright (C) 2009-2021 Free Software Foundation, Inc.
+;; Copyright (C) 2009-2022 Free Software Foundation, Inc.
 
 ;; Author: Eric Schulte
 ;; Keywords: literate programming, reproducible research, comint
-;; Homepage: https://orgmode.org
+;; URL: https://orgmode.org
 
 ;; This file is part of GNU Emacs.
 
@@ -30,6 +30,10 @@
 ;; org-babel at large.
 
 ;;; Code:
+
+(require 'org-macs)
+(org-assert-version)
+
 (require 'ob-core)
 (require 'org-compat)
 (require 'comint)
@@ -70,11 +74,26 @@ or user `keyboard-quit' during execution of body."
   (let ((buffer (nth 0 meta))
 	(eoe-indicator (nth 1 meta))
 	(remove-echo (nth 2 meta))
-	(full-body (nth 3 meta)))
+	(full-body (nth 3 meta))
+        (org-babel-comint-prompt-separator
+         "org-babel-comint-prompt-separator"))
     `(org-babel-comint-in-buffer ,buffer
        (let* ((string-buffer "")
 	      (comint-output-filter-functions
-	       (cons (lambda (text) (setq string-buffer (concat string-buffer text)))
+	       (cons (lambda (text)
+                       (setq string-buffer
+                             (concat
+                              string-buffer
+                              ;; Upon concatenation, the prompt may no
+                              ;; longer match `comint-prompt-regexp'.
+                              ;; In particular, when the regexp has ^
+                              ;; and the output does not contain
+                              ;; trailing newline.  Use more reliable
+                              ;; match to split the output later.
+                              (replace-regexp-in-string
+                               comint-prompt-regexp
+                               ,org-babel-comint-prompt-separator
+                               text))))
 		     comint-output-filter-functions))
 	      dangling-text)
 	 ;; got located, and save dangling text
@@ -105,7 +124,9 @@ or user `keyboard-quit' during execution of body."
 		      "\n" "[\r\n]+" (regexp-quote (or ,full-body "")))
 		     string-buffer))
 	   (setq string-buffer (substring string-buffer (match-end 0))))
-	 (split-string string-buffer comint-prompt-regexp)))))
+         (delete "" (split-string
+                     string-buffer
+                     ,org-babel-comint-prompt-separator))))))
 
 (defun org-babel-comint-input-command (buffer cmd)
   "Pass CMD to BUFFER.
@@ -124,9 +145,7 @@ statement (not large blocks of code)."
     (while (progn
              (goto-char comint-last-input-end)
              (not (and (re-search-forward comint-prompt-regexp nil t)
-                       (goto-char (match-beginning 0))
-                       (string= (face-name (face-at-point))
-                                "comint-highlight-prompt"))))
+                     (goto-char (match-beginning 0)))))
       (accept-process-output (get-buffer-process buffer)))))
 
 (defun org-babel-comint-eval-invisibly-and-wait-for-file
@@ -166,7 +185,7 @@ source block, and the name of the temp file.")
 (defvar-local org-babel-comint-async-chunk-callback nil
   "Callback function to clean Babel async output results before insertion.
 Its single argument is a string consisting of output from the
-comint process.  It should return a string that will be be passed
+comint process.  It should return a string that will be passed
 to `org-babel-insert-result'.")
 
 (defvar-local org-babel-comint-async-dangling nil