Fix conflicts between laptop and Desktop

.gitignore

@@ -6,3 +6,4 @@
 /var/
 tramp
 /elpy/
+/elpa/

elpa/archives/gnu/archive-contents.signed

@@ -1 +0,0 @@
-Good signature from 066DAFCB81E42C40 GNU ELPA Signing Agent (2019) <elpasign@elpa.gnu.org> (trust undefined) created at 2021-09-26T05:05:02-0400 using RSA

init.el

@@ -48,9 +48,9 @@
 
 ;; Ensure shell variables are loaded
 (use-package exec-path-from-shell :demand
-  :init
+	     :init
-  (exec-path-from-shell-initialize)
+	     (exec-path-from-shell-initialize)
-  )
+	     )
 
 ;; Profiling
 
@@ -60,60 +60,71 @@
 (use-package no-littering
 	     :demand t)
 
-;;;; Science Related
+;; Version control
-(use-package conda)
+(use-package magit)
-;;;; End Science Related
+
+;;;; Nix Related
+
+;; Nix direnv support
+(use-package direnv
+  :demand t
+  :config
+  (direnv-mode))
+
+(use-package nix-mode)
+
+;;;; End Nix Related
 
 ;;;; Web Related
 (use-package web-mode
-  :init
+	     :init
-  (add-to-list 'auto-mode-alist '("\\.phtml\\'" . web-mode))
+	     (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 '("\\.[agj]sp\\'" . web-mode))
-  (add-to-list 'auto-mode-alist '("\\.as[cp]x\\'" . 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 '("\\.erb\\'" . web-mode))
-  (add-to-list 'auto-mode-alist '("\\.mustache\\'" . 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 '("\\.djhtml\\'" . web-mode))
-  (add-to-list 'auto-mode-alist '("\\.html?\\'" . 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
+	     :bind
-  (("C-<tab>" . company-complete))
+	     (("C-<tab>" . company-complete))
-  :custom-face
+	     :custom-face
-  (company-preview ((t (:background "#000000" :foreground "#ffffff"))))
+	     (company-preview ((t (:background "#000000" :foreground "#ffffff"))))
-  (company-preview-common ((t (:inherit company-preview :foreground "#ff00cf"))))
+	     (company-preview-common ((t (:inherit company-preview :foreground "#ff00cf"))))
-  (company-preview-search ((t (:inherit company-preview :background "black"))))
+	     (company-preview-search ((t (:inherit company-preview :background "black"))))
-  (company-scrollbar-bg ((t (:background "grey35"))))
+	     (company-scrollbar-bg ((t (:background "grey35"))))
-  (company-scrollbar-fg ((t (:background "#a22390"))))
+	     (company-scrollbar-fg ((t (:background "#a22390"))))
-  (company-template-field ((t (:background "grey75" :foreground "black"))))
+	     (company-template-field ((t (:background "grey75" :foreground "black"))))
-  (company-tooltip ((t (:background "#353535" :foreground "white"))))
+	     (company-tooltip ((t (:background "#353535" :foreground "white"))))
-  (company-tooltip-common ((t (:foreground "magenta"))))
+	     (company-tooltip-common ((t (:foreground "magenta"))))
-  (company-tooltip-mouse ((t (:inherit company-tooltip-selection))))
+	     (company-tooltip-mouse ((t (:inherit company-tooltip-selection))))
-  (company-tooltip-search ((t (:inherit company-tooltip-selection))))
+	     (company-tooltip-search ((t (:inherit company-tooltip-selection))))
-  (company-tooltip-search-selection ((t (:inherit company-tooltip-selection))))
+	     (company-tooltip-search-selection ((t (:inherit company-tooltip-selection))))
-  (company-tooltip-selection ((t (:background "#4584a2" :foreground "white"))))
+	     (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
+	     :init
-  (setq lsp-keymap-prefix "C-c l")
+	     (setq lsp-keymap-prefix "C-c l")
-  :hook (
+	     :hook (
-         (dart-mode . lsp)
+		    (dart-mode . lsp)
-         (python-mode . lsp)
+		    (python-mode . lsp)
-	 (c-mode . lsp)
+		    (c-mode . lsp)
-	 (c++-mode . lsp)
+		    (c++-mode . lsp)
-	 (haskell-mode . lsp))
+		    (haskell-mode . lsp))
-         ;; which key support v v v
+             ;; which key support v v v
 
-  (lsp-mode . lsp-enable-which-key-integration)
+	     (lsp-mode . lsp-enable-which-key-integration)
-  :commands lsp)
+	     :commands lsp)
 
 ;; optionally
 (use-package lsp-ui :commands lsp-ui-mode)
@@ -128,74 +139,72 @@
 ;; (use-package dap-LANGUAGE) to load the dap adapter for your language
 ;; optional if you want which-key integration
 (use-package which-key
-    :config
+	     :config
-    (which-key-mode))
+	     (which-key-mode))
 ;; END LSP related
 
 ;; projectile
 (use-package projectile
-  :commands projectile-mode)
+	     :commands projectile-mode)
 (projectile-mode +1)
 ;; Recommended keymap prefix on macOS
 (define-key projectile-mode-map (kbd "s-p") 'projectile-command-map)
 ;; projectile
 
-; Python
+;; Python
 (use-package pyvenv
-  :init
+	     :init
-  (setenv "WORKON_HOME" "~/.pyenv/versions")
+	     (setenv "WORKON_HOME" "~/.pyenv/versions")
-  :hook (
+	     :hook (
-	 (python-mode . pyvenv-mode)
+		    (python-mode . pyvenv-mode)
-	 )
+		    )
-  )
+	     )
 
-; C related
+;; C related
 (use-package company-ctags)
 (use-package company-c-headers)
 
-; Haskell
+;; Haskell
 (use-package company-ghci)
 ;;;; End Company Related
 
 ;;;; Haskell Related
 (use-package haskell-mode
-  :config
+	     :config
-  (setq haskell-mode-hook '(flyspell-prog-mode interactive-haskell-mode))
+	     (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
+;; -- TODO
-  :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
+	     :commands rainbow-delimiters-mode
-  :hook (
+	     :hook (
-	 (emacs-lisp-mode . rainbow-delimiters-mode)
+		    (emacs-lisp-mode . rainbow-delimiters-mode)
-	 (geiser-mode . rainbow-delimiters-mode)
+		    (geiser-mode . rainbow-delimiters-mode)
-	 )
+		    )
-  :custom-face
+	     :custom-face
-  (rainbow-delimiters-depth-1-face ((t (:foreground "#69f"))) )
+	     (rainbow-delimiters-depth-1-face ((t (:foreground "#69f"))) )
-  (rainbow-delimiters-depth-2-face ((t (:foreground "#39b"))) )
+	     (rainbow-delimiters-depth-2-face ((t (:foreground "#39b"))) )
-  (rainbow-delimiters-depth-3-face ((t (:foreground "#278"))) )
+	     (rainbow-delimiters-depth-3-face ((t (:foreground "#278"))) )
-  (rainbow-delimiters-depth-4-face ((t (:foreground "#281"))) )
+	     (rainbow-delimiters-depth-4-face ((t (:foreground "#281"))) )
-  (rainbow-delimiters-depth-5-face ((t (:foreground "#047"))) )
+	     (rainbow-delimiters-depth-5-face ((t (:foreground "#047"))) )
-  (rainbow-delimiters-depth-6-face ((t (:foreground "#138"))) )
+	     (rainbow-delimiters-depth-6-face ((t (:foreground "#138"))) )
-  (rainbow-delimiters-depth-7-face ((t (:foreground "#708"))) )
+	     (rainbow-delimiters-depth-7-face ((t (:foreground "#708"))) )
-  (rainbow-delimiters-depth-8-face ((t (:foreground "#920"))) )
+	     (rainbow-delimiters-depth-8-face ((t (:foreground "#920"))) )
-  )
+	     )
 (use-package paredit
-  :hook (
+	     :hook (
-	 (emacs-lisp-mode . paredit-mode)
+		    (emacs-lisp-mode . paredit-mode)
-	 (geiser-mode . paredit-mode)
+		    (geiser-mode . paredit-mode)
-	 )
+		    )
-  )
+	     )
 ;;; End Lisp / Parentheses Related
 
 ;;;; Racket Related
@@ -203,76 +212,98 @@
 ;;;; End Racket Related
 
 ;;;; Org Related
-;; (use-package org)
-(use-package org-contrib)
-(use-package org
-  :config
-  (require 'doi-utils)
-  (require 'org-ref)
 
-  (require 'org-tempo)
+;; Completion engine
-  (tempo-define-template
+(use-package ivy-bibtex)
-   "Lab Template" '("#+TITLE: PHY324: LAB TITLE"n
+;; Interactive menus
-		    "#+AUTHOR: ***REMOVED*** | ***REMOVED***"n
+(use-package helm-bibtex)
-		    "#+DATE: \\today"n
+;; PDF preview etc.
-		    "#+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)
+;; References etc.
+(use-package org-ref)
 
-; better TEX
+(use-package org
+	     :straight (:type built-in)
+	     :config
+	     (require 'doi-utils)
+	     (require 'org-ref)
+	     (require 'org-ref-ivy)
+	     (require 'org-ref-helm)
+	     (require 'org-tempo)
+
+	     (setq org-src-fontify-natively t
+		   org-confirm-babel-evaluate nil
+		   org-src-preserve-indentation t)
+	     
+	     (setq bibtex-completion-bibliography
+		   (list (expand-file-name "~/Documents/Bibliography/references.bib")))
+
+	     (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/")
+
+	     (setq org-ref-insert-link-function 'org-ref-insert-link-hydra/body
+		   org-ref-insert-cite-function 'org-ref-cite-insert-helm
+		   org-ref-insert-label-function 'org-ref-insert-label-link
+		   org-ref-insert-ref-function 'org-ref-insert-ref-link
+		   org-ref-cite-onclick-function (lambda (_) (org-ref-citation-hydra/body)))
+
+	     (define-key org-mode-map (kbd "C-c ]") 'org-ref-insert-link)
+	     (define-key org-mode-map (kbd "s-[") 'org-ref-insert-link-hydra/body)
+	     
+	     (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")))
+	     )
+(use-package ox-pandoc
+	     :after org)
+;; better TEX
 (use-package auctex
-  :after org)
+	     :after org)
 
-; Plotting support
+;; Plotting support
 (use-package gnuplot)
 
 ;;Org Auto Wrap Config