[ESS] how to organize init.el for both python and R/ESS? Your workflow?

[Paul Johnson]

I have to write python code now.

I put in a bunch of python bells and whistles and now ESS and R sessions
don't work the same.  I've got interference from flymake and something has
entirely broken the "_" to create <-.

I keep editing init.el to enable the ESS parts or comment them out and turn
on Python stuff, whole thing has become horribly confusing for me.

I need to understand how to write init.el as a sequence of files so that I
can load the ESS part when I need to write R, or the python part if I work
on that. Can you share your strategies for dealing with that?

my init.el now:

(require 'package)
(let* ((no-ssl (and (memq system-type '(windows-nt ms-dos))
                    (not (gnutls-available-p))))
       (proto (if no-ssl "http" "https")))
  (when no-ssl
    (warn "\
Your version of Emacs does not support SSL connections,
which is unsafe because it allows man-in-the-middle attacks.
There are two things you can do about this warning:
1. Install an Emacs version that does support SSL and be safe.
2. Remove this warning from your init file so you won't see it again."))
  ;; Comment/uncomment these two lines to enable/disable MELPA and MELPA
Stable as desired
  (add-to-list 'package-archives (cons "melpa" (concat proto "://
melpa.org/packages/")) t)
  ;;(add-to-list 'package-archives (cons "melpa-stable" (concat proto "://
stable.melpa.org/packages/")) t)
  (when (< emacs-major-version 24)
    ;; For important compatibility libraries like cl-lib
    (add-to-list 'package-archives (cons "gnu" (concat proto "://
elpa.gnu.org/packages/")))))
;; for stable packages, use this instead
;;add-to-list 'package-archives
;;             '("melpa-stable" . "https://stable.melpa.org/packages/") t)

(package-initialize)

;for the window-purpose package
(purpose-mode)
; C-c, D: `purpose-toggle-window-buffer-dedicated`

;; ; Python settings
;; ; see
http://emacs.stackexchange.com/questions/24453/weird-shell-output-when-using-ipython-5
;; ;; ;; Some python things I use, you may not need
(elpy-enable)
;; ;; recommended in elpy docs
(setq python-shell-interpreter "jupyter"
       python-shell-interpreter-args "console --simple-prompt"
       python-shell-prompt-detect-failure-warning nil)
(add-to-list 'python-shell-completion-native-disabled-interpreters
             "jupyter")
;; ;
https://stackoverflow.com/questions/25154809/how-can-i-stop-elpy-from-overriding-some-of-my-keybindings/25159354
;; ; https://emacs.stackexchange.com/questions/46247/cannot-bind-m-s-left
(eval-after-load "elpy"
  '(progn
     (define-key elpy-mode-map [(control return)] nil)
     (define-key elpy-mode-map [(shift return)]
'elpy-shell-send-statement-and-step)
     (define-key elpy-mode-map (kbd "\M-\t") nil)
     (define-key elpy-mode-map (kbd "s-<tab>") 'elpy-company-backend)
 )
)
(setq elpy-rpc-timeout 10)


;; Org-mode with R doesn't work without this
;; http://orgmode.org/worg/org-contrib/babel/how-to-use-Org-Babel-for-R.html
(custom-set-variables
 ;; custom-set-variables was added by Custom.
 ;; If you edit it by hand, you could mess it up, so be careful.
 ;; Your init file should contain only one such instance.
 ;; If there is more than one, they won't work right.
 '(ansi-color-names-vector
   ["#2e3436" "#a40000" "#4e9a06" "#c4a000" "#204a87" "#5c3566" "#729fcf"
"#eeeeec"])
 '(column-number-mode t)
 '(cua-auto-tabify-rectangles nil)
 '(cua-mode t nil (cua-base))
 '(custom-enabled-themes (quote (whiteboard)))
 '(inferior-R-args "--no-restore-history --no-save")
 '(package-selected-packages
   (quote
    (ivy window-purpose pyenv-mode py-autopep8 math-symbol-lists
material-theme ein ess-smart-underscore htmlize polymode
org-link-minor-mode markdown-mode julia-mode elpy dash)))
 '(show-paren-mode t))

(setq-default indent-tabs-mode nil)
(setq default-tab-width 4)


;; https://www.emacswiki.org/emacs/SmoothScrolling#toc1
;; scroll one line at a time (less "jumpy" than defaults)
    (setq mouse-wheel-scroll-amount '(1 ((shift) . 1))) ;; one line at a
time
    (setq mouse-wheel-progressive-speed nil) ;; don't accelerate scrolling
    (setq mouse-wheel-follow-mouse 't) ;; scroll window under mouse
    (setq scroll-step 1) ;; keyboard scroll one line at a time



;; Section II. Keyboard and mouse customization
;; Mouse and cursor in the usual Mac/Windows way
(delete-selection-mode t)
;;
http://stackoverflow.com/questions/13036155/how-to-to-combine-emacs-primary-clipboard-copy-and-paste-behavior-on-ms-windows
(setq select-active-regions t)
;; Trying to make mouse middle-click only paste from primary
;; X11 selection, not clipboard and kill ring:
(global-set-key [mouse-2] 'mouse-yank-primary)
;; highlight does not alter Kill ring:
(setq mouse-drag-copy-region nil)
;; windows style binding C-x, C-v, C-c, C-z:
(cua-mode t)
;; Don't tabify after rectangle commands:
(setq cua-auto-tabify-rectangles nil)

;; Section III. Programming conveniences:
;; light-up matching parens:
(show-paren-mode t)
;; turn on syntax highlighting:
(global-font-lock-mode t)
;; Auto fill is TRUE in text modes:
(setq text-mode-hook (quote (turn-on-auto-fill text-mode-hook-identify)))


;; Section IV. ESS Emacs Statistics

(require 'ess-site)
;; soft require: no error if package not found
;;(require 'ess-smart-underscore nil 'noerror)

;;(require 'poly-R)
;;(require 'poly-markdown)

;;(add-to-list 'auto-mode-alist '("\\.Rmd" . poly-markdown+r-mode))
;; start R in current working directory, don't let R ask user:
(setq ess-ask-for-ess-directory nil)

;; Change shortcut "run this line" to use Shift-Return
;; Suggested by Vitalie Spinu 2013-09-30 to co-exist with Windows Emacs
(eval-after-load "ess"
 '(progn
   (define-key ess-mode-map [(control return)] nil)
   ;;(define-key ess-mode-map [(shift return)]
'ess-eval-region-or-line-and-step))
   (define-key ess-mode-map [(shift return)]
'ess-eval-region-or-line-visibly-and-step))
)
;; Help in frames? Consider
;; 1) create a new frame for each help instance
;; (setq ess-help-own-frame t)
;; or 2) If you want all help buffers to go into one frame do:
(setq ess-help-own-frame 'one)

;; I want the *R* process in its own frame
(setq inferior-ess-own-frame t)
(setq inferior-ess-same-window nil)

;; Problem in Windows about menus not displaying
;; https://stat.ethz.ch/pipermail/ess-help/2012-September/008207.html
;;(if (eq system-type 'windows-nt)
  (defun my-R-execute-options ()
(ess-command "options(menu.graphics = FALSE)\n"))
(add-hook 'ess-R-post-run-hook 'my-R-execute-options)
;;)

;; Put # flush left
;; See gmail thread in ESS group, this from Ista
(add-hook 'ess-mode-hook
 (lambda()
            ;; don't indent comments
            (setq ess-indent-with-fancy-comments nil)
            ;; turn on outline mode
            (setq-local outline-regexp "[# ]+")
            (outline-minor-mode t)))

;; Section V. Frames oriented Emacs
;; Discourage Emacs from horizontal splitting:
;; http://www.gnu.org/software/emacs/elisp/html_node/Choosing-Window.html
;;(setq split-window-preferred-function nil)

;; (setq pop-up-windows nil)

;; Make files opened from the menu bar appear in their own
;; frames. Adapted from Emacs menu-bar.el
(defun menu-find-existing ()
  "Edit the existing file FILENAME."
  (interactive)
  (let* ((mustmatch (not (and (fboundp 'x-uses-old-gtk-dialog)
                              (x-uses-old-gtk-dialog))))
         (filename (car (find-file-read-args "Find file: " mustmatch))))
    (if mustmatch
        (find-file-other-frame filename)
      (find-file filename))))
(define-key menu-bar-file-menu [new-file]
  '(menu-item "Open/Create" find-file-other-frame
 :enable (menu-bar-non-minibuffer-window-p)
 :help "Create a new file"))
(define-key menu-bar-file-menu [open-file]
  '(menu-item ,(purecopy "Open File...") menu-find-existing
              :enable (menu-bar-non-minibuffer-window-p)
              :help ,(purecopy "Read an existing file into an Emacs
buffer")))


;; Open directory list in new frame.
(define-key menu-bar-file-menu [dired]
  '(menu-item "Open Directory..." dired-other-frame
     :help "Read a directory; operate on its files (Dired)"
     :enable (not (window-minibuffer-p (frame-selected-window
menu-updating-frame)))))







;; Section VI: Miscellaneous convenience
;; Remove Emacs "splash screen" http://fuhm.livejournal.com/
(defadvice command-line-normalize-file-name
(before kill-stupid-startup-screen activate)
  (setq inhibit-startup-screen t))
(setq inhibit-splash-screen t)

;; Show file name in title bar
;; http://www.thetechrepo.com/main-articles/549
(setq frame-title-format "%b - Emacs")

;; Make Emacs scroll smoothly with down arrow key.
;; faq 5.45
http://www.gnu.org/s/emacs/emacs-faq.html#Modifying-pull_002ddown-menus
;;(setq scroll-conservatively most-positive-fixnum)

;; adjust the size of the frames, uncomment this, adjust values
;;(setq default-frame-alist '((width . 90) (height . 65)))


;; Remember password when connected to remote sites via Tramp
;;
http://stackoverflow.com/questions/840279/passwords-in-emacs-tramp-mode-editing
;; Emacs "tramp" service (ssh connection) constantly
;; asks for the log in password without this
(setq password-cache-expiry nil)


;; Emacs shells work better
;; http://snarfed.org/why_i_run_shells_inside_emacs
(setq ansi-color-for-comint-mode 'filter)
(setq comint-prompt-read-only t)
(setq comint-scroll-to-bottom-on-input t)
(setq comint-scroll-to-bottom-on-output t)
(setq comint-move-point-for-output t)




;; A stata stanza from Brendan Halpin

;; Stata equivalent of ess-eval-region

(defun delimit-do (start end toggle &optional clear message)
  "Send the current region to the inferior ESS process, Stata do-editor
style.
Creates a temporary file, \"do\"-es it, deletes it.
With prefix argument toggle the meaning of `ess-eval-visibly-p';
this does not apply when using the S-plus GUI, see
`ess-eval-region-ddeclient'."
  (interactive "r\nP")
  (ess-force-buffer-current "Process to use: ")
  (message "Starting evaluation...")
  (setq message (or message "Eval region"))

  (save-excursion
    ;; don't send new lines (avoid screwing the debugger)
    (goto-char start)
    (skip-chars-forward "\n\t ")
    (setq start (point))

    (unless mark-active
      (ess-blink-region start end))

    ;; don't send new lines at the end (avoid screwing the debugger)
    (goto-char end)
    (skip-chars-backward "\n\t ")
    (setq end (point)))

  (let* (delimit
         (commands (buffer-substring-no-properties start end))
         (delimit-do-file (make-temp-file "delimit-do" nil ".do"))
         (proc (get-process ess-local-process-name))
         (visibly (if toggle (not ess-eval-visibly-p) ess-eval-visibly-p))
         (dev-p (process-get proc 'developer))
         (tb-p  (process-get proc 'tracebug)))
    ;; Go to the start of the section and look back for #delimit
    ;; if found set delimit unless the delimiter is not ";"
    (save-excursion
      (goto-char start)
      (setq delimit (re-search-backward "^#delimit +\\(.+\\)$" nil t))
      (if delimit
          (if (not (string-match ";" (match-string 1))) (setq delimit
nil))))

    (with-temp-buffer
      (if clear (insert "clear\n"))
      (if delimit (insert "#delimit ;\n"
                          commands
                          "\n#delimit cr\n")
        (insert commands "\n"))
      (write-file delimit-do-file nil)
      (kill-buffer (current-buffer)))

    (process-send-string
     (get-ess-process ess-current-process-name)
     (format "do %s\nrm %s\n" delimit-do-file delimit-do-file))
    )
  (if (and (fboundp 'deactivate-mark) ess-eval-deactivate-mark)
      (deactivate-mark))
  ;; return value
  (list start end))



; 20161115: Things I was using in Emacs25 to do
; org-mode documents
;http://vislab-ccom.unh.edu/~schwehr/rt/9-bash-scripting.html
;(require 'org-install)
(org-babel-do-load-languages
   'org-babel-load-languages
   '(
     (shell . t) ;; emacs-26.1
     (R . t)
     ;;(sh . t) ;; pre-emacs 26.1
    )
)

;;
https://www.reddit.com/r/emacs/comments/tbj09/using_shift_selection_in_orgmode_buffers_without/
;
;; (defadvice org-call-for-shift-select (before
org-call-for-shift-select-cua activate)
;;   (if (and cua-mode
;;            org-support-shift-select
;;            (not (use-region-p)))
;;      (cua-set-mark)))
;; (require 'ox-md nil t)


; See: http://mescal.imag.fr/membres/arnaud.legrand/misc/init.php

;(setq org-hide-leading-stars t)
;(setq org-alphabetical-lists t)
;(setq org-src-fontify-natively t)  ;; you want this to activate coloring
in blocks
;(setq org-src-tab-acts-natively t) ;; you want this to have completion in
blocks
;(setq org-hide-emphasis-markers t) ;; to hide the *,=, or / markers
;(setq org-pretty-entities t)       ;; to have \alpha, \to and others
display as utf8 http://orgmode.org/manual/Special-symbols.html
;



;   (require 'yasnippet)
;   (yas-global-mode 1)


(load "auctex.el" nil t t)
(load "preview-latex.el" nil t t)
(custom-set-faces
 ;; custom-set-faces was added by Custom.
 ;; If you edit it by hand, you could mess it up, so be careful.
 ;; Your init file should contain only one such instance.
 ;; If there is more than one, they won't work right.
 )







-- 
Paul E. Johnson   http://pj.freefaculty.org
Director, Center for Research Methods and Data Analysis http://crmda.ku.edu

To write to me directly, please address me at pauljohn at ku.edu.

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