;; -*- lexical-binding: t -*-

;; Bootstrap straight.el for package management
(defvar bootstrap-version)
(let ((bootstrap-file
       (expand-file-name "straight/repos/straight.el/bootstrap.el" user-emacs-directory))
      (bootstrap-version 5))
  (unless (file-exists-p bootstrap-file)
    (with-current-buffer
        (url-retrieve-synchronously
         "https://raw.githubusercontent.com/raxod502/straight.el/develop/install.el"
         'silent 'inhibit-cookies)
      (goto-char (point-max))
      (eval-print-last-sexp)))
  (load bootstrap-file nil 'nomessage))
;; Disable package.el from loading at startup
(setq package-enable-at-startup nil)

;; Ensure custom writes to specific file
(setq custom-file (expand-file-name "custom.el" user-emacs-directory))
(load custom-file 'noerror 'nomessage)

;; Change the location of file backups/locks into the emacs.d/backups/
(setq backup-directory-alist
      `(("." . ,(concat user-emacs-directory "backups"))))

;;;; VISUAL

;; Disable Scroll bar, menubar
(menu-bar-mode -1)
(tool-bar-mode -1)
(scroll-bar-mode -1)

;; Set location of custom theme dir
(setq custom-theme-directory (concat user-emacs-directory "themes"))
(load-theme 'UniverseHighContrast)

;;;; END VISUAL

;;;; PACKAGE INSTALL AND CONFIG

;; Set the packagemanager of use-package
(setq straight-use-package-by-default t)
;; Default to lazy loading
(setq use-package-always-defer t)
;; Ensure use-package.el is installed
(straight-use-package 'use-package)

;; Ensure shell variables are loaded
(use-package exec-path-from-shell :demand
  :init
  (exec-path-from-shell-initialize)
  )

;; Profiling

(use-package esup)

;; Prevents emacs and packages from messily writing to dirs
(use-package no-littering
	     :demand t)

;;;; Science Related
(use-package conda)
;;;; End Science Related

;;;; Web Related
(use-package web-mode
  :init
  (add-to-list 'auto-mode-alist '("\\.phtml\\'" . web-mode))
  (add-to-list 'auto-mode-alist '("\\.[agj]sp\\'" . web-mode))
  (add-to-list 'auto-mode-alist '("\\.as[cp]x\\'" . web-mode))
  (add-to-list 'auto-mode-alist '("\\.erb\\'" . web-mode))
  (add-to-list 'auto-mode-alist '("\\.mustache\\'" . web-mode))
  (add-to-list 'auto-mode-alist '("\\.djhtml\\'" . web-mode))
  (add-to-list 'auto-mode-alist '("\\.html?\\'" . web-mode))
  )

(use-package php-mode)
;;;; End Web related

;;;; Company Related
(use-package company :demand t
  :bind
  (("C-<tab>" . company-complete))
  :custom-face
  (company-preview ((t (:background "#000000" :foreground "#ffffff"))))
  (company-preview-common ((t (:inherit company-preview :foreground "#ff00cf"))))
  (company-preview-search ((t (:inherit company-preview :background "black"))))
  (company-scrollbar-bg ((t (:background "grey35"))))
  (company-scrollbar-fg ((t (:background "#a22390"))))
  (company-template-field ((t (:background "grey75" :foreground "black"))))
  (company-tooltip ((t (:background "#353535" :foreground "white"))))
  (company-tooltip-common ((t (:foreground "magenta"))))
  (company-tooltip-mouse ((t (:inherit company-tooltip-selection))))
  (company-tooltip-search ((t (:inherit company-tooltip-selection))))
  (company-tooltip-search-selection ((t (:inherit company-tooltip-selection))))
  (company-tooltip-selection ((t (:background "#4584a2" :foreground "white"))))
  )
(add-hook 'after-init-hook 'global-company-mode)

;; LSP related
(use-package lsp-haskell)
(use-package lsp-mode
  :init
  (setq lsp-keymap-prefix "C-c l")
  :hook (
         (dart-mode . lsp)
         (python-mode . lsp)
	 (c-mode . lsp)
	 (c++-mode . lsp)
	 (haskell-mode . lsp))
         ;; which key support v v v

  (lsp-mode . lsp-enable-which-key-integration)
  :commands lsp)

;; optionally
(use-package lsp-ui :commands lsp-ui-mode)
;; if you are helm user
(use-package helm-lsp :commands helm-lsp-workspace-symbol)
;; if you are ivy user
(use-package lsp-ivy :commands lsp-ivy-workspace-symbol)
(use-package lsp-treemacs :commands lsp-treemacs-errors-list)

;; optionally if you want to use debugger
(use-package dap-mode)
;; (use-package dap-LANGUAGE) to load the dap adapter for your language
;; optional if you want which-key integration
(use-package which-key
    :config
    (which-key-mode))
;; END LSP related

;; projectile
(use-package projectile
  :commands projectile-mode)
(projectile-mode +1)
;; Recommended keymap prefix on macOS
(define-key projectile-mode-map (kbd "s-p") 'projectile-command-map)
;; projectile

; Python
(use-package pyvenv
  :init
  (setenv "WORKON_HOME" "~/.pyenv/versions")
  :hook (
	 (python-mode . pyvenv-mode)
	 )
  )

; C related
(use-package company-ctags)
(use-package company-c-headers)

; Haskell
(use-package company-ghci)
;;;; End Company Related

;;;; Haskell Related
(use-package haskell-mode
  :config
  (setq haskell-mode-hook '(flyspell-prog-mode interactive-haskell-mode))
  )
(use-package lsp-haskell)

(use-package ghci-completion)
;;;; End Haskell Related

;;;; NEURON Related
(use-package nrnhoc
  :straight (:package nrnhoc :type git :host github :repo "***REMOVED***csterratt/neuron-emacs"))

;;;; END NEURON Related

;;; Lisp / Parentheses Related
(use-package rainbow-delimiters
  :commands rainbow-delimiters-mode
  :hook (
	 (emacs-lisp-mode . rainbow-delimiters-mode)
	 (geiser-mode . rainbow-delimiters-mode)
	 )
  :custom-face
  (rainbow-delimiters-depth-1-face ((t (:foreground "#69f"))) )
  (rainbow-delimiters-depth-2-face ((t (:foreground "#39b"))) )
  (rainbow-delimiters-depth-3-face ((t (:foreground "#278"))) )
  (rainbow-delimiters-depth-4-face ((t (:foreground "#281"))) )
  (rainbow-delimiters-depth-5-face ((t (:foreground "#047"))) )
  (rainbow-delimiters-depth-6-face ((t (:foreground "#138"))) )
  (rainbow-delimiters-depth-7-face ((t (:foreground "#708"))) )
  (rainbow-delimiters-depth-8-face ((t (:foreground "#920"))) )
  )
(use-package paredit
  :hook (
	 (emacs-lisp-mode . paredit-mode)
	 (geiser-mode . paredit-mode)
	 )
  )
;;; End Lisp / Parentheses Related

;;;; Racket Related
(use-package geiser-racket)
;;;; End Racket Related

;;;; Org Related
;; (use-package org)
(use-package org-contrib)
(use-package org
  :config
  (require 'org-ref)
  (require 'org-tempo)
  (tempo-define-template
   "Lab Template" '("#+TITLE: PHY324: LAB TITLE"n
		    "#+AUTHOR: ***REMOVED*** | ***REMOVED***"n
		    "#+DATE: \\today"n
		    "#+LATEX_HEADER: \\usepackage{natbib}"n
		    "#+LATEX_HEADER: \\usepackage{float}"n
		    "#+LATEX_CLASS: labtemplate"n
		    "#+OPTIONS: toc:nil"n
		    ""n
		    "* Abstract:"n
		    "* Introduction:"n > p
		    "* Methods:"n
		    "* Results:"n
		    "* Discussion:"n
		    "bibliographystyle:ieeetr"n
		    "bibliography:~/Documents/Bibliography/references.bib" >)
   "<LAB" "Insert Lab Template With Headings")
  (tempo-define-template "Fig. Caption"
			 '("" (P "Image: " image t)
			   (P "Caption: " caption t)
			   (P "Figure Name: " name t)
			   "#+CAPTION: " (s caption) > n >
			   "#+NAME: fig:" (s name) > n >
			   "#+ATTR_LaTeX: :placement [H]" > n >
			   "[[" (s image) "]]" > n > p >)
			 "<fig" "Inserts Figure with Caption")
  (with-eval-after-load 'ox-latex
  (add-to-list 'org-latex-packages-alist '("" "minted"))
  (setq org-latex-listings 'minted) 
  
  (add-to-list 'org-latex-classes
	       '("labtemplate" "\\documentclass{labtemplate}"
		 ("\\section{%s}" . "\\section*{%s}")
		 ("\\subsection{%s}" . "\\subsection*{%s}")
		 ("\\subsubsection{%s}" . "\\subsubsection*{%s}")
		 ("\\paragraph{%s}" . "\\paragraph*{%s}")
		 ("\\subparagraph{%s}" . "\\subparagraph*{%s}"))
	       )

  (setq org-latex-pdf-process
	'("%latex -shell-escape -interaction nonstopmode -output-directory %o %f" "%latex -shell-escape -interaction nonstopmode -output-directory %o %f" "bibtex %b" "%latex -shell-escape -interaction nonstopmode -output-directory %o %f" "%latex -shell-escape -interaction nonstopmode -output-directory %o %f")))

  )
; References etc.
(use-package org-ref
  :config
  (setq reftex-default-bibliography '("~/Documents/Bibliography/references.bib"))
  ;; see org-ref for use of these variables
  (setq org-ref-bibliography-notes "~/Documents/Bibliography/notes.org"
	org-ref-default-bibliography '("~/Documents/Bibliography/references.bib")
	org-ref-pdf-directory "~/Documents/Bibliography/bibtex-pdfs/")
  )
(use-package ox-pandoc
  :after org)
; PDF preview etc.
(use-package pdf-tools)

; better TEX
(use-package auctex
  :after org)

; Plotting support
(use-package gnuplot)

;;Org Auto Wrap Config
(add-hook 'org-mode-hook 'auto-fill-mode)
(set-fill-column 100)
;;;; End Org Related

;; ghci-completion company-ghci
;; exec-path-from-shell nix-haskell-mode haskell-mode
;; pyvenv rainbow-mode company-ctags company-jedi
;; company-anaconda anaconda-mode matlab-mode markdown-mode company-irony-c-headers company-irony irony rust-mode company-c-headers cdlatex auctex use-package smog conda gnuplot php-mode web-mode org-ref pdf-tools chess

;;; Flutter Related
(use-package dart-mode)
(use-package lsp-dart)
;;; End Flutter Related

;;;
(use-package gnu-apl-mode)

;;;; END PACKAGES