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pkg update and first config fix

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org-brain not working, add org-roam
This commit is contained in:
Daniel Weschke
2022-12-19 23:02:34 +01:00
parent 02b3e07185
commit 82f05baffe
885 changed files with 356098 additions and 36993 deletions
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148
lisp/ess/ess-tracebug.el
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@@ -39,16 +39,17 @@
;;; Code:
(eval-when-compile
(eval-and-compile
(when (< emacs-major-version 26)
(require 'cl))
(require 'cl-lib)
(require 'tramp)
(require 'subr-x))
(require 'subr-x)
(require 'ess-utils))
(require 'comint)
(require 'compile)
(require 'ring)
(require 'ess-utils)
(defvar text-scale-mode-amount)
(autoload 'text-scale-mode "face-remap" "[autoload]" nil)
@@ -91,6 +92,7 @@
(declare-function ess-r-package-source-dirs "ess-r-package")
(declare-function ess-roxy--region-p "ess-roxy")
;; Do not require tramp at runtime. It is expensive to load. Instead,
;; guard calls with (require 'tramp) and silence the byte compiler
;; here.
@@ -328,10 +330,12 @@ command conforms to VISIBLY."
(defun ess-tracebug-send-region (process start end &optional visibly message type)
"Send region to process adding source references as specified
by `ess-inject-source' variable."
(ess-eval-region--normalise-region start end)
;; Disable evaluation env if we're sending a roxy region. This is
;; not the ideal place to do this.
(let* ((ess-r-evaluation-env (unless (ess-roxy--region-p start end)
(let* ((se (ess-eval-region--normalise-region start end))
(start (car se))
(end (cdr se))
(ess-r-evaluation-env (unless (ess-roxy--region-p start end)
(ess-r-get-evaluation-env)))
(inject-p (cond ((eq type 'function)
ess-inject-source)
@@ -542,13 +546,13 @@ can use `ess--busy-slash', `ess--busy-B',`ess--busy-stars',
(defcustom inferior-ess-replace-long+ t
"Determines if ESS replaces long + sequences in output.
If 'strip, remove all such instances. Otherwise, if non-nil, '+
If \\='strip, remove all such instances. Otherwise, if non-nil, `+
+ + + ' containing 3 or more + is replaced by
`ess-long+replacement'.
This variable can be process-local but not buffer-local."
:group 'ess-tracebug
:type '(choice (const nil :tag "No replacement")
(const 'strip :tag "Replace all")
(const strip :tag "Replace all")
(const t :tag "Replace 3 or more +")))
(defvar ess-long+replacement ". + "
@@ -648,7 +652,7 @@ Pop up a compilation/grep/occur like buffer. Usual global key
bindings are available (\\[next-error] and \\[previous-error])
for `next-error' and `previous-error' respectively.
You can bind 'no-select' versions of this commands:
You can bind `no-select' versions of this commands:
\(define-key compilation-minor-mode-map [(?n)] #'next-error-no-select)
\(define-key compilation-minor-mode-map [(?p)] #'previous-error-no-select)"
(interactive)
@@ -722,7 +726,7 @@ This is the value of `next-error-function' in iESS buffers."
(at-error t)
(msg
(condition-case nil
(compilation-next-error n nil beg-pos)
(compilation-next-error n nil beg-pos)
(error
(when pbuff-p
(ess--tb-next-error-goto-process-marker))
@@ -775,12 +779,12 @@ This is the value of `next-error-function' in iESS buffers."
'(( "" "NONE" "NULL" )
( " r" "RECOVER" "utils::recover")
( " t" "TRACEBACK" "base::traceback"))
"Alist of 'on-error' actions.
"Alist of `on-error' actions.
Toggled with `ess-debug-toggle-error-action'. Each element must
have the form (DISP SYMB ACTION) where DISP is the string to be
displayed in the mode line when the action is in place. SYMB is
the symbolic name of an action. ACTION is the string giving the
actual expression to be assigned to 'error' user option. See R's
actual expression to be assigned to `error' user option. See R's
help ?options for more details."
:type '(alist :key-type string
:value-type (group string string))
@@ -830,7 +834,7 @@ In no-windowed Emacs an `overlay-arrow' is displayed at this position.")
(defcustom ess-debug-blink-interval .2
"Time in seconds to blink the background of the debug line.
Currently two events are defined 'ref-not-found' and 'same-ref'.
Currently two events are defined `ref-not-found' and `same-ref'.
Blinking colors for these events can be customized by
corresponding faces."
:group 'ess-debug
@@ -912,7 +916,7 @@ The SPEC should be one of the components of
(error "Unknown action"))))
(defun ess-debug-toggle-error-action ()
"Toggle the 'on-error' action.
"Toggle the `on-error' action.
The action list is in `ess-debug-error-action-alist'."
(interactive)
(ess-force-buffer-current)
@@ -947,7 +951,8 @@ The action list is in `ess-debug-error-action-alist'."
(move-marker ess--dbg-current-debug-position (point-at-bol)))
(defun ess--dbg-deactivate-overlays ()
"Deletes markers and overlays. Overlay arrow remains to indicate the last debug position."
"Delete debugger markers and overlays.
Overlay arrow remains to indicate the last debug position."
(delete-overlay ess--dbg-current-debug-overlay)
(set-marker ess--dbg-current-debug-position nil))
@@ -1531,7 +1536,7 @@ the output into *ess.dbg* buffer."
:keymap ess-debug-minor-mode-map)
(defun ess--dbg-goto-last-ref-and-mark (dbuff &optional other-window)
"Open the most recent debug reference, and set all the necessary marks and overlays.
"Open the most recent debug reference and set the necessary marks and overlays.
It's called from `inferior-ess-tracebug-output-filter'. DBUFF
must be the *ess.dbg* buffer associated with the process. If
OTHER-WINDOW is non nil, attempt to open the location in a
@@ -1630,59 +1635,65 @@ nil, or TB-INDEX is not found return nil."
(org-babel-tangle-jump-to-org))
(list (point-marker) (copy-marker (point-at-eol))))))))))
(defvar ess-r-package-library-paths)
(defun ess--dbg-find-buffer (filename)
"Find a buffer for file FILENAME.
If FILENAME is not found at all, ask the user where to find it if
`ess--dbg-ask-for-file' is non-nil. Search the directories in
`ess-tracebug-search-path'."
`ess-tracebug-search-path' and `ess-r-package-library-paths'."
(let ((dirs (append
(ess-r-package-source-dirs)
(cl-loop for d in ess-tracebug-search-path
ess-r-package-library-paths
(cl-loop for d in (append ess-tracebug-search-path)
append (ess-r-package--all-source-dirs d))))
(filematch (format "%s\\'" filename))
buffer name)
(setq dirs (cons default-directory dirs)) ;; TODO: should be R working dir
;; 1. search already open buffers for match (associated file might not even exist yet)
(cl-dolist (bf (buffer-list))
(with-current-buffer bf
(when (and buffer-file-name
(string-match (format "%s\\'" filename) buffer-file-name))
(setq buffer bf)
(cl-return))))
;; 2. The file name is absolute. Use its explicit directory as
(setq dirs (delq nil (cons (with-ess-process-buffer t default-directory) dirs)))
;; 1. The file name is absolute. Use its explicit directory as
;; the first in the search path, and strip it from FILENAME.
(when (and (null buffer)
(file-name-absolute-p filename))
(setq filename (abbreviate-file-name (expand-file-name filename))
dirs (cons (file-name-directory filename) dirs)
filename (file-name-nondirectory filename)))
;; 3. Now search the path.
(while (and (null buffer) dirs)
(let ((thisdir (pop dirs)))
(setq name (expand-file-name filename thisdir)
buffer (and (file-exists-p name)
(find-file-noselect name)))))
;; 4. Ask for file if not found (tothink: maybe remove this part?)
(if (and (null buffer)
ess-debug-ask-for-file)
(save-excursion ;This save-excursion is probably not right.
(let* ((pop-up-windows t)
(name (read-file-name
(format "Find next line in (default %s): " filename)
nil filename t nil))
(origname name))
(cond
((not (file-exists-p name))
(message "Cannot find file `%s'" name)
(ding) (sit-for 2))
((and (file-directory-p name)
(not (file-exists-p
(setq name (expand-file-name filename name)))))
(message "No `%s' in directory %s" filename origname)
(ding) (sit-for 2))
(t
(setq buffer (find-file-noselect name)))))))
;; nil if not found
buffer))
(or
;; 2. Search the path.
(while (and (null buffer) dirs)
(let ((thisdir (pop dirs)))
(setq name (expand-file-name filename thisdir)
buffer (and (file-exists-p name)
(find-file-noselect name)))))
buffer
;; 3. search already open buffers for match (associated file might not even exist yet)
(cl-dolist (bf (buffer-list))
(with-current-buffer bf
(when (and buffer-file-name
(string-match filematch buffer-file-name))
(setq buffer bf)
(cl-return))))
buffer
;; 4. Ask for file if not found (tothink: maybe remove this part?)
(when ess-debug-ask-for-file
(save-excursion ;This save-excursion is probably not right.
(let* ((pop-up-windows t)
(name (read-file-name
(format "Find next line in (default %s): " filename)
nil filename t nil))
(origname name))
(cond
((not (file-exists-p name))
(message "Cannot find file `%s'" name)
(ding) (sit-for 2))
((and (file-directory-p name)
(not (file-exists-p
(setq name (expand-file-name filename name)))))
(message "No `%s' in directory %s" filename origname)
(ding) (sit-for 2))
(t
(setq buffer (find-file-noselect name)))))))
buffer)))
(defun ess--dbg-get-next-ref (n &optional pt BOUND REG nF nL nC)
"Move point to the next reference in the *ess.dbg* buffer.
@@ -1694,9 +1705,9 @@ to move forwards (or backwards, if negative). Optional arg PT,
if non-nil, specifies the value of point to start looking for the
next message, default to (point). BOUND is the limiting position
of the search. REG is the regular expression to search with. nF
- sub-expression of REG giving the 'file'; defaults to 1. nL -
giving the 'line'; defaults to 2. nC - sub-expr giving the
'column'; defaults to 3."
- sub-expression of REG giving the `file'; defaults to 1. nL -
giving the `line'; defaults to 2. nC - sub-expr giving the
`column'; defaults to 3."
(unless ess--dbg-buf-p
(error "Not in *ess.dbg* buffer"))
(setq nF (or nF 1)
@@ -1765,7 +1776,7 @@ If supplied, EV must be a proper key event or a string representing the digit."
(defun ess-debug-command-next ()
"Step next in debug mode.
Equivalent to 'n' at the R prompt."
Equivalent to `n' at the R prompt."
(interactive)
(ess-force-buffer-current)
(unless (ess--dbg-is-active-p)
@@ -1879,7 +1890,7 @@ ARGS are ignored to allow using this function in process hooks."
(((class color) (background dark) (min-colors 88)) (:foreground "deep sky blue"))
(((background light) (min-colors 8)) (:foreground "blue"))
(((background dark) (min-colors 8)) (:foreground "cyan")))
"Face used to highlight 'browser' breakpoints."
"Face used to highlight `browser' breakpoints."
:group 'ess-debug)
(defface ess-bp-fringe-recover-face
@@ -1887,7 +1898,7 @@ ARGS are ignored to allow using this function in process hooks."
(((class color) (background dark) (min-colors 88)) (:foreground "magenta"))
(((background light) (min-colors 8)) (:foreground "magenta"))
(((background dark) (min-colors 8)) (:foreground "magenta")))
"Face used to highlight 'recover' breakpoints fringe."
"Face used to highlight `recover' breakpoints fringe."
:group 'ess-debug)
(defun ess--bp-pipe-block-p ()
@@ -1898,9 +1909,18 @@ ARGS are ignored to allow using this function in process hooks."
(end-of-line)
(looking-back "%>%[ \t]*" (point-at-bol)))))
(defun ess--bp-pipe-native-block-p ()
(save-excursion
(let ((inhibit-point-motion-hooks t)
(inhibit-field-text-motion t))
(forward-line -1)
(end-of-line)
(looking-back "|>[ \t]*" (point-at-bol)))))
(defvar ess--bp-identifier 1)
(defcustom ess-bp-type-spec-alist
'((pipe ".ess_pipe_browser() %%>%%" "B %>%\n" filled-square ess-bp-fringe-browser-face ess--bp-pipe-block-p)
(pipe-native ".ess_pipe_browser() |>" "B |>\n" filled-square ess-bp-fringe-browser-face ess--bp-pipe-native-block-p)
(browser "browser(expr=is.null(.ESSBP.[[%s]]));" "B>\n" filled-square ess-bp-fringe-browser-face)
(recover "recover()" "R>\n" filled-square ess-bp-fringe-recover-face))
"List of lists of breakpoint types.
@@ -2465,8 +2485,10 @@ string giving the actual R expression."
wal)))
(defun ess-watch--parse-assoc (al)
"Return a string of the form 'assign(\".ess_watch_expressions\", list(a = parse(expr_a), b= parse(expr_b)), envir = .GlobalEnv)'
ready to be send to R process. AL is an association list as return by `ess-watch--make-alist'"
"Return a string command ready to be passed to R process.
The command is of the form `assign(\".ess_watch_expressions\",
list(a = parse(expr_a), b= parse(expr_b)), envir = .GlobalEnv)'.
AL is an association list as return by `ess-watch--make-alist'"
(concat ".ess_watch_assign_expressions(list("
(mapconcat (lambda (el)
(if (> (length (cadr el) ) 0)
@@ -2572,7 +2594,7 @@ Optional N if supplied gives the number of backward steps."
(ess-watch-refresh-buffer-visibly (current-buffer))))
(defun ess-watch-add ()
"Ask for new R expression and name and append it to the end of the list of watch expressions."
"Ask for new R expression and append to the current list of watch expressions."
(interactive)
(let (nr expr name)
(goto-char (point-max))