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myinit.org

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Packages

(setq package-archives
      '(("GNU ELPA"     . "https://elpa.gnu.org/packages/")
        ("MELPA Stable" . "https://stable.melpa.org/packages/")
        ("MELPA"        . "https://melpa.org/packages/"))
      package-archive-priorities
      '(("MELPA Stable" . 0)
        ("GNU ELPA"     . 5)
        ("MELPA"        . 10)))
(require 'package)
(package-initialize)

Use Package

(unless (package-installed-p 'use-package)
  (package-refresh-contents)
  (package-install 'use-package))

Interface Changes

(defun get-default-height ()
       (/ (- (display-pixel-height) 120)
          (frame-char-height)))

(add-to-list 'default-frame-alist '(width . 157))
(add-to-list 'default-frame-alist (cons 'height (get-default-height)))

(fset 'yes-or-no-p 'y-or-n-p)
(show-paren-mode 1)
(setq-default indent-tabs-mode nil)
(setq show-paren-delay 0)
;;(setq make-backup-files nil)

(setq completion-ignored-extensions '(".a" ".aux" ".bbl" ".blg" ".dvi" ".elc"
                    ".lof" ".log" ".lot" ".o" ".toc" "~"))
(defun ask-before-closing ()
  "Ask whether or not to close, and then close if y was pressed"
  (interactive)
  (if (y-or-n-p (format "Are you sure you want to exit Emacs? "))
      (if (< emacs-major-version 22)
          (save-buffers-kill-terminal)
        (save-buffers-kill-emacs))
    (message "Canceled exit")))

(when window-system
  (global-set-key (kbd "C-x C-c") 'ask-before-closing))
(setq auto-save-default nil)
(setq ring-bell-function 'ignore)
(winner-mode 1)
(windmove-default-keybindings)
(custom-set-variables
 '(show-paren-mode t)
 '(tool-bar-mode nil))

Magit

(use-package magit
  :ensure t
  :bind (("C-x g" . magit-status)))

Paths

(add-to-list 'load-path "~/.emacs.d/elpa")

(global-set-key [remap dabbrev-expand] 'hippie-expand)

(setq ring-bell-function 'ignore)
(winner-mode 1)
(windmove-default-keybindings)

Dired

(setq dired-listing-switches "-alh")

Yasnippet

(use-package yasnippet
  :ensure t
  :init
    (yas-global-mode 1))

Swiper

(use-package counsel
  :ensure t
  )

(use-package swiper
  :ensure t
  :config
  (progn
    (ivy-mode 1)
    (setq ivy-use-virtual-buffers t)
    (global-set-key "\C-s" 'swiper)
    (global-set-key (kbd "C-c C-r") 'ivy-resume)
    (global-set-key (kbd "<f6>") 'ivy-resume)
    (global-set-key (kbd "M-x") 'counsel-M-x)
    (global-set-key (kbd "C-x C-f") 'counsel-find-file)
    (global-set-key (kbd "<f1> f") 'counsel-describe-function)
    (global-set-key (kbd "<f1> v") 'counsel-describe-variable)
    (global-set-key (kbd "<f1> l") 'counsel-load-library)
    (global-set-key (kbd "<f2> i") 'counsel-info-lookup-symbol)
    (global-set-key (kbd "<f2> u") 'counsel-unicode-char)
    (global-set-key (kbd "C-c g") 'counsel-git)
    (global-set-key (kbd "C-c j") 'counsel-git-grep)
    (global-set-key (kbd "C-c k") 'counsel-ag)
    (global-set-key (kbd "C-x l") 'counsel-locate)
    (global-set-key (kbd "C-S-o") 'counsel-rhythmbox)
    (define-key read-expression-map (kbd "C-r") 'counsel-expression-history)
    ))

Paragraph Fill

	(defun refill-paragraphs-to-be-one-line ()
	  "fill individual paragraphs with large fill column"
	  (interactive)
	  (let ((fill-column 100000))
		(fill-individual-paragraphs (point-min) (point-max))))

Ibuffer

	(global-set-key (kbd "C-x C-b") 'ibuffer)
	(setq ibuffer-saved-filter-groups
		  (quote (("default"
			   ("dired" (mode . dired-mode))
			   ("org" (name . "^.*org$"))
			   ("shell" (or (mode . eshell-mode) (mode . shell-mode)))
			   ("programming" (or
					   (mode . python-mode)
					   (mode . c++-mode)))
			   ("ein" (or 
					   (name . "^\\*ein: https:*")
					   (name . "^\\*ein:notebooklist*")
					   ))
			   ("htop" (name . "^htop*"))
			   ("jupyter" (name . "^jupyter*"))
			   ("emacs" (or
				 (name . "^\\*scratch\\*$")
				 (name . "^\\*Messages\\*$")))
			   ))))
	(add-hook 'ibuffer-mode-hook
		  (lambda ()
			(ibuffer-auto-mode 1)
			(ibuffer-switch-to-saved-filter-groups "default")))
	;; nearly all of this is the default layout
	(setq ibuffer-formats 
		  '((mark modified read-only " "
				  (name 65 65 :left :elide) ; change: 65s were originally 18s
				  " "
				  (size 9 -1 :right)
				  " "
				  (mode 16 16 :left :elide)
				  " " filename-and-process)
			(mark " "
				  (name 16 -1)
				  " " filename)))
	;; don't show these
						;(add-to-list 'ibuffer-never-show-predicates "zowie")
	;; Don't show filter groups if there are no buffers in that group
	(setq ibuffer-show-empty-filter-groups nil)

	;; Don't ask for confirmation to delete marked buffers
	(setq ibuffer-expert t)

Git-gutter

	(use-package git-gutter
	  :ensure t
	  :config
	  (progn
		(global-git-gutter-mode +1)
		(global-git-gutter-mode t)

		(global-set-key (kbd "C-x C-g") 'git-gutter)
		(global-set-key (kbd "C-x v =") 'git-gutter:popup-hunk)

		;; Jump to next/previous hunk
		(global-set-key (kbd "C-x p") 'git-gutter:previous-hunk)
		(global-set-key (kbd "C-x n") 'git-gutter:next-hunk)

		;; Stage current hunk
		(global-set-key (kbd "C-x v s") 'git-gutter:stage-hunk)

		;; Revert current hunk
		(global-set-key (kbd "C-x v r") 'git-gutter:revert-hunk)

		;; Mark current hunk
		(global-set-key (kbd "C-x v SPC") #'git-gutter:mark-hunk)	
	)
	)

Which-key

	(use-package which-key
	  :ensure t
	  :config 
	  (which-key-mode)
	  )

Swith-remote

(defun switch-remote ()
  "Ask whether or not to close, and then close if y was pressed"
  (interactive)
  (let* ((file (dired-copy-filename-as-kill)))
	    (find-file (concat "/ssh:[email protected]:" file))))


(global-set-key (kbd "C-c r") 'switch-remote)

Nsh

	;; Emacs, please load my new powerful nsh function
	(add-to-list 'load-path "~/.emacs.d/huntercode")
	(require 'nsh)

Zenburn

(use-package zenburn-theme
  :ensure t
  :config
  (load-theme 'zenburn t))


;; (use-package modus-operandi-theme
;;   :ensure t)

;; (use-package modus-vivendi-theme
;;   :ensure t)
;; ;;(load-theme 'modus-vivendi t)
;; (load-theme 'modus-operandi t)

Auctex

(use-package tex-mode
  :ensure auctex
)

Exec path from shell

(use-package exec-path-from-shell
  :ensure t
  :init 
  (when (memq window-system '(mac ns))
  (exec-path-from-shell-initialize)))

Unfill paragraph

   (defun unfill-paragraph (&optional region)
     "Takes a multi-line paragraph and makes it into a single line of text."
     (interactive (progn (barf-if-buffer-read-only) '(t)))
     (let ((fill-column (point-max))
	    ;; This would override `fill-column' if it's an integer.
	    (emacs-lisp-docstring-fill-column t))
	(fill-paragraph nil region)))
   (define-key global-map "\M-Q" 'unfill-paragraph)

Julia

(use-package julia-mode
  :ensure t
  )
  (add-to-list 'auto-mode-alist '("\\.julia$" . julia-mode))
  (add-to-list 'auto-mode-alist '("\\.jl$" . julia-mode))

Access init file

(defun access-init ()
    (interactive)
    (find-file "/Users/hunternisonoff/.emacs.d/myinit.org"))
  (global-set-key (kbd "C-c i") 'access-init)

Shell Name

(defun shell-name (nsh-name)
  (interactive "Mshell name: ")
  (shell (concat "shell-" nsh-name)))
(global-set-key (kbd "C-c t") 'shell-name)

Savio

(defun access-savio ()
  (interactive)
  (find-file "/ssh:[email protected]:~"))
(global-set-key (kbd "C-c s") 'access-savio)



(defun access-savio ()
  (interactive)
  (find-file "/ssh:[email protected]:~"))
(global-set-key (kbd "C-c s") 'access-savio)

(defun access-savio-scratch ()
  (interactive)
  (find-file "/ssh:[email protected]:/global/scratch/hunter_nisonoff"))
(global-set-key (kbd "C-c w") 'access-savio-scratch)

Python Tab

(add-hook 'python-mode-hook
    (lambda ()
      (setq indent-tabs-mode 'nil)
      (setq tab-width 4)
      (setq python-indent-offset 4)))

HP Server

(defun hpserver ()
(interactive)
(find-file "/ssh:[email protected]:/home/hunter_nisonoff"))
(global-set-key (kbd "C-c h") 'hpserver)

Font Bigger

(set-face-attribute 'default nil :height 150)
;;(set-face-attribute 'default nil :height 150)

Ipython

 (when (executable-find "ipython")
   (setq python-shell-interpreter "ipython"))

 (require 'python)
 (setq python-shell-interpreter "ipython")
 ;;(setq python-shell-interpreter-args "--pylab")
 (setq python-shell-interpreter "ipython"
	  python-shell-interpreter-args "--simple-prompt -i")

ESS

(use-package ess
  :ensure t
  :config
  (require 'ess-r-mode)
  :bind 
  (:map ess-mode-map
        (";" . ess-insert-assign))
  (:map inferior-ess-mode-map
        (";" . ess-insert-assign)))

(defun then_R_operator ()
  "%>% operator or 'then' pipe operator"
  (interactive)
  (insert " %>%") ; note the space before the first %
  (reindent-then-newline-and-indent))
(global-set-key (kbd "C-\\") 'then_R_operator)

Emacs Ipython Notebook

(use-package ein
  :ensure t
)
(setq ein:output-area-inlined-images t)
;; (custom-set-variables
;;  '(ein:output-area-inlined-images t))

Eglot

(use-package eglot
  :ensure t
)

Command is meta

(setq mac-option-modifier 'meta)
(setq mac-command-modifier 'meta)

SCF Cluster

(defun scfcluster ()
  (interactive)
  (find-file "/ssh:[email protected]:")
)

LSP Mode

(use-package lsp-mode
  :ensure t
  :hook ((python-mode) . lsp-deferred) ; XYZ are to be replaced by python, c++, etc.
  :commands lsp)

(use-package lsp-ui
  :ensure t
  :commands lsp-ui-mode)

(use-package lsp-ui
  :commands lsp-ui-mode
  :ensure t
  :config
  (setq lsp-ui-doc-enable nil)
  (setq lsp-ui-doc-header t)
  (setq lsp-ui-doc-include-signature t)
  (setq lsp-ui-doc-border (face-foreground 'default))
  (setq lsp-ui-sideline-show-code-actions t)
  (setq lsp-ui-sideline-delay 0.05))

(use-package lsp-ivy
  :ensure t)

(use-package company
  :ensure t
  :after lsp-mode
  :hook (lsp-mode . company-mode)
  :bind (:map company-active-map
         ("<tab>" . company-complete-selection))
        (:map lsp-mode-map
         ("<tab>" . company-indent-or-complete-common))
  :custom
  (company-minimum-prefix-length 1)
  (company-idle-delay 0.0))

(use-package company-box
  :ensure t
  :hook (company-mode . company-box-mode))

Org Mode

(setq org-agenda-files '("~/.emacs.d/orgfiles/work.org"
                                "~/.emacs.d/orgfiles/private.org"))
(defun org-focus-private() "Set focus on private things."
       (interactive)
       (setq org-agenda-files '("~/.emacs.d/orgfiles/private.org")))
(defun org-focus-work() "Set focus on work things."
       (interactive)
       (setq org-agenda-files '("~/.emacs.d/orgfiles/work.org")))
(defun org-focus-all() "Set focus on all things."
       (interactive)
       (setq org-agenda-files '("~/.emacs.d/orgfiles/work.org"
                                "~/.emacs.d/orgfiles/private.org")))
(custom-set-variables
 '(org-capture-templates
      '(("b" "Add book to read" entry (file+headline "~/.emacs.d/orgfiles/private.org" "Books to read")
         (file "~/.emacs.d/orgfiles/tpl-book.txt")
         :empty-lines-after 2)
        ("p" "Add paper to read" entry (file+headline "~/.emacs.d/orgfiles/work.org" "Papers To Read")
         (file "~/.emacs.d/orgfiles/tpl-papers.txt"))
        ("i" "Add research idea" entry (file+headline "~/.emacs.d/orgfiles/work.org" "Research Ideas")
         (file "~/.emacs.d/orgfiles/tpl-idea.txt"))
        ("t" "Add todo" entry (file "~/.emacs.d/orgfiles/capture.org")
         (file "~/.emacs.d/orgfiles/tpl-task.txt"))
        ("c" "Add code" entry (file "~/.emacs.d/orgfiles/code.org")
         (file "~/.emacs.d/orgfiles/tpl-code.txt"))
        ))
 '(org-directory "~/.emacs.d/orgfiles/")
 '(org-outline-path-complete-in-steps nil)
 '(org-refile-allow-creating-parent-nodes t)
 '(org-refile-targets '((org-agenda-files :maxlevel . 2)))
 '(org-refile-use-outline-path 'file)
 )

Tramp

(setq explicit-shell-file-name "/bin/bash")

Anaconda

   (use-package anaconda-mode
     :ensure t
     :commands anaconda-mode
     :diminish anaconda-mode
     :init
     (progn
	(add-hook 'python-mode-hook 'anaconda-mode)
	(add-hook 'python-mode-hook 'eldoc-mode)))
(use-package conda
  :ensure t
  :init
  (progn
    (require 'conda)
    (if (cl-search "pascal" system-name)
        (custom-set-variables
         '(conda-anaconda-home (expand-file-name "/usr/workspace/nisonoff/anaconda3/"))
         '(conda-env-home-directory (expand-file-name "/usr/workspace/nisonoff/anaconda3/")))
      (if (cl-search "beef2" system-name)
          (custom-set-variables
           '(conda-anaconda-home (expand-file-name "/anaconda3/"))
           '(conda-env-home-directory (expand-file-name "/anaconda3/")))
        ;;; not pascal or beef2
        (custom-set-variables
         '(conda-anaconda-home (expand-file-name "~/anaconda3/"))
         '(conda-env-home-directory (expand-file-name "~/anaconda3/")))
          )
      )
    (conda-env-initialize-interactive-shells)
    (conda-env-autoactivate-mode t)
    (conda-env-initialize-eshell)
    ))
;;(setq conda-env-home-directory (expand-file-name "~/anaconda3/"))

Elisp

;;(require 'ielm)
;;(add-hook 'emacs-lisp-mode-hook 'ielm-auto-complete)

Ido Mode (Overriden by Swiper)

(ido-mode 1)
(setq ido-enable-flex-matching t)
(setq ido-everywhere t)
(defalias 'list-buffers 'ibuffer)

ShellCheck

(add-hook 'sh-mode-hook 'flycheck-mode)

PDF TOols

;; (if (cl-search "pascal" system-name)
;;     ()
;;   (if (cl-search "beef2" system-name)
;;       ()
;;     ;;; if not in pascal or beef
;;     (use-package pdf-tools
;;       :ensure t
;;       :pin manual ;; don't reinstall when package updates
;;       :mode  ("\\.pdf\\'" . pdf-view-mode)
;;       :config
;;       ;;(setq-default pdf-view-display-size 'fit-page)
;;       (setq pdf-annot-activate-created-annotations t)
;;       (pdf-tools-install :no-query)
;;       (setq pdf-view-use-scaling t
;;             pdf-view-use-imagemagick nil)
;;       (require 'pdf-occur))))

Copy Remote Emacs

(use-package clipetty
  :ensure t
  :hook (after-init . global-clipetty-mode))

Org Roam

(use-package org-roam
  :ensure t
  :init
  (setq org-roam-v2-ack t)
  :custom
  (org-roam-directory "/Users/hunternisonoff/Box Sync/PersonalProjects/orgroam")
  :bind (("C-c n l" . org-roam-buffer-toggle)
         ("C-c n f" . org-roam-noad-find)
         ("C-c n i" . org-roam-noad-insert))
  :config
  (org-roam-setup))

Elpy

;; (use-package elpy
;;   :ensure t
;;   :init
;;   (elpy-enable))

(setq python-shell-interpreter "ipython"
      python-shell-interpreter-args "-i --simple-prompt")

;; (when (load "flycheck" t t)
;;   (setq elpy-modules (delq 'elpy-module-flymake elpy-modules))
;;   (add-hook 'elpy-mode-hook 'flycheck-mode))

;; (add-hook 'elpy-mode-hook (lambda ()
;;                             (add-hook 'before-save-hook
;;                                       'elpy-format-code nil t)))

Yapfify

(use-package yapfify
  :ensure t
  )
(add-hook 'python-mode-hook 'yapf-mode)