Emacs for Data Science: a Newb-Friendly Setup

Update: Since the beginning of my experiment with Emacs, I have switched to Spacemacs. Spacemacs is a community-driven configuration for Emacs. It works well for most users right out of the box.

I recently took the plunge to using Emacs, coming from a Data Science background using RStudio for R and Spyder for Python.

While there are already a lot of people sharing their Emacs setting, I find most setups highly idiosyncratic, showing off the heavy customization that suits the author’s particular work style. That approach often confuses rather than helps newbies like me who are used to IDEs.

I recommend the following path to learning Emacs:

• First, Emacs’ built-in tutorial to get familiar with the terminology and the basics of moving around in Emacs
• Second, Mastering Emacs list of articles that lays out the best features Emacs has to offer
• Third, the tutorial that I mentions in each section of my init.el

So below is my Emacs configuration (init.el), built upon days of Googling. It strives to be:

• Minimal: No idiosyncratic choices. All decisions strives to mimic modern IDEs (RStudio, Spyder, TexStudio)
• Self-contained: Taking advantage of the use-package package, you can copy-paste my init.el into your setup. use-package will then download any missing packages by itself.
• Compartmentalized: Separate sections sets up separate tech stack, e.g. R, Python, Latex, Markdown. You can copy and paste only the parts you want and it will work. I highly recommend that you try one at a time.
• Documented: Links to blog posts and StackOverflow threads explain the why and the how behind each setting.

; See https://emacs.stackexchange.com/questions/5828/why-do-i-have-to-add-each-package-to-load-path-or-problem-with-require-packag
; Manually load package instead of waiting until after init.el is loaded
(package-initialize)
; Disable loading package again after init.el
(setq package-enable-at-startup nil)

; Enable "package", for installing packages
; Add some common package repositories
(require 'package)
(add-to-list 'package-archives '("melpa" . "http://melpa.org/packages/"))
(add-to-list 'package-archives '("marmalade" . "http://marmalade-repo.org/packages/"))
(add-to-list 'package-archives '("gnu" . "http://elpa.gnu.org/packages/"))
(add-to-list 'package-archives '("elpy" . "https://jorgenschaefer.github.io/packages/"))

; Use "package" to install "use-package", a better package management and config system
(unless (package-installed-p 'use-package)
  (package-refresh-contents)
  (package-install 'use-package))

(eval-when-compile
  (require 'use-package))

; Make OS shell path available in emacs exec path
(use-package exec-path-from-shell
  :ensure t
  :config (exec-path-from-shell-copy-env "PATH"))

; Create a 80-character line marker
; With a work-around so that fill-column-indicator works with company mode
; https://emacs.stackexchange.com/questions/147/how-can-i-get-a-ruler-at-column-80
(use-package fill-column-indicator
  :ensure t
  :config
  (setq fci-rule-column 80)
  (add-hook 'prog-mode-hook 'fci-mode))

(defvar-local company-fci-mode-on-p nil)

(defun company-turn-off-fci (&rest ignore)
  (when (boundp 'fci-mode)
    (setq company-fci-mode-on-p fci-mode)
    (when fci-mode (fci-mode -1))))

(defun company-maybe-turn-on-fci (&rest ignore)
  (when company-fci-mode-on-p (fci-mode 1)))

(add-hook 'company-completion-started-hook 'company-turn-off-fci)
(add-hook 'company-completion-finished-hook 'company-maybe-turn-on-fci)
(add-hook 'company-completion-cancelled-hook 'company-maybe-turn-on-fci)

; Set up auctex for Latex in Emacs
; Point auctex to my central .bib file
(use-package tex
  :ensure auctex
  :config
  (setq Tex-auto-save t)
  (setq Tex-parse-self t)
  (setq TeX-save-query nil)
  (add-hook 'LaTeX-mode-hook 'turn-on-reftex)
  (setq reftex-plug-into-AUCTeX t)
  (setq reftex-default-bibliography '("/home/anh/texmf/bibtex/bib/local/library.bib")))

; Set up elpy for Python in Emacs
(use-package elpy
  :ensure t
  :pin elpy
  :config
  (elpy-enable)
  ;; Enable elpy in a Python mode
  (add-hook 'python-mode-hook 'elpy-mode)
  (setq elpy-rpc-backend "jedi")
  ;; Open the Python shell in a buffer after sending code to it
  (add-hook 'inferior-python-mode-hook 'python-shell-switch-to-shell)
  ;; Use IPython as the default shell, with a workaround to accommodate IPython 5
  ;; https://emacs.stackexchange.com/questions/24453/weird-shell-output-when-using-ipython-5  (setq python-shell-interpreter "ipython")
  (setq python-shell-interpreter-args "--simple-prompt -i")
  ;; Enable pyvenv, which manages Python virtual environments
  (pyvenv-mode 1)
  ;; Tell Python debugger (pdb) to use the current virtual environment
  ;; https://emacs.stackexchange.com/questions/17808/enable-python-pdb-on-emacs-with-virtualenv
  (setq gud-pdb-command-name "python -m pdb "))

; Set up projectile, i.e. package management + helm, i.e. autocomplete
; Tutorial - recommended: https://tuhdo.github.io/helm-projectile.html
(use-package projectile
  :ensure t
  :config
  (projectile-global-mode)
  (setq projectile-completion-system 'helm)
  (setq projectile-switch-project-action 'helm-projectile))

(use-package helm-projectile
  :ensure t
  :config
  (helm-projectile-on))

(use-package helm-config
  :ensure helm
  :config
  (helm-mode 1)
  (global-set-key (kbd "M-x") 'helm-M-x)
  (global-set-key (kbd "C-x C-f") 'helm-find-files)) 

; Set up company, i.e. code autocomplete
(use-package company
  :ensure t
  :config
  ;; Enable company mode everywhere
  (add-hook 'after-init-hook 'global-company-mode)
  ;; Set up TAB to manually trigger autocomplete menu
  (define-key company-mode-map (kbd "TAB") 'company-complete)
  (define-key company-active-map (kbd "TAB") 'company-complete-common)
  ;; Set up M-h to see the documentation for items on the autocomplete menu
  (define-key company-active-map (kbd "M-h") 'company-show-doc-buffer))

; Set up company-jedi, i.e. tell elpy to use company autocomplete backend
(use-package company-jedi
  :ensure t
  :config
  (defun my/python-mode-hook ()
    (add-to-list 'company-backends 'company-jedi))
  (add-hook 'python-mode-hook 'my/python-mode-hook))

; Set up ESS, i.e. Statistics in Emacs, R, Stata, etc.
(use-package ess-site
  :ensure ess
  :config
  (ess-toggle-underscore nil) ; http://stackoverflow.com/questions/2531372/how-to-stop-emacs-from-replacing-underbar-with-in-ess-mode
  (setq ess-fancy-comments nil) ; http://stackoverflow.com/questions/780796/emacs-ess-mode-tabbing-for-comment-region
  ; Make ESS use RStudio's indenting style
  (add-hook 'ess-mode-hook (lambda() (ess-set-style 'RStudio)))
  ; Make ESS use more horizontal screen
  ; http://stackoverflow.com/questions/12520543/how-do-i-get-my-r-buffer-in-emacs-to-occupy-more-horizontal-space
  (add-hook 'ess-R-post-run-hook 'ess-execute-screen-options) 
  (define-key inferior-ess-mode-map "\C-cw" 'ess-execute-screen-options)
  ; Add path to Stata to Emacs' exec-path so that Stata can be found
  (setq exec-path (append exec-path '("/usr/local/stata14"))))

; Set up markdown in Emacs
; Tutorial: http://jblevins.org/projects/markdown-mode/
(use-package pandoc-mode
  :ensure t
  :config
  (add-hook 'markdown-mode-hook 'pandoc-mode))

(add-hook 'text-mode-hook (lambda() (flyspell-mode 1)))

(use-package markdown-mode
  :ensure t
  :commands (markdown-mode gfm-mode)
  :mode (("README\\.md\\'" . gfm-mode)
         ("\\.md\\'" . markdown-mode)
         ("\\.markdown\\'" . markdown-mode))
  :init (setq markdown-command "pandoc"))

; C-n add new lines at the end of buffer
(setq next-line-add-newlines t)
; open emacs full screen
(add-to-list 'default-frame-alist '(fullscreen . maximized))
; Make Emacs highlight paired parentheses
(show-paren-mode 1)










(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.

 ;;; auctex inverse search https://tex.stackexchange.com/questions/161797/how-to-configure-emacs-and-auctex-to-perform-forward-and-inverse-search
 '(TeX-source-correlate-method (quote synctex))
 '(TeX-source-correlate-mode t)
 '(TeX-source-correlate-start-server t)
 ;;; Tell Emacs to use stata-se instead of stata
 '(inferior-STA-program-name "stata-se"))
(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.
 )