.spacemacs

;; This file is loaded by Spacemacs at startup.
;; It must be stored in your home directory.

(defun dotspacemacs/layers ()
  "Layer configuration:
This function should only modify configuration layer settings."
  (setq-default
   ;; Base distribution to use. This is a layer contained in the directory
   ;; `+distribution'. For now available distributions are `spacemacs-base'
   ;; or `spacemacs'. (default 'spacemacs)
   dotspacemacs-distribution 'spacemacs

   ;; Lazy installation of layers (i.e. layers are installed only when a file
   ;; with a supported type is opened). Possible values are `all', `unused'
   ;; and `nil'. `unused' will lazy install only unused layers (i.e. layers
   ;; not listed in variable `dotspacemacs-configuration-layers'), `all' will
   ;; lazy install any layer that support lazy installation even the layers
   ;; listed in `dotspacemacs-configuration-layers'. `nil' disable the lazy
   ;; installation feature and you have to explicitly list a layer in the
   ;; variable `dotspacemacs-configuration-layers' to install it.
   ;; (default 'unused)
   dotspacemacs-enable-lazy-installation 'unused

   ;; If non-nil then Spacemacs will ask for confirmation before installing
   ;; a layer lazily. (default t)
   dotspacemacs-ask-for-lazy-installation t

   ;; List of additional paths where to look for configuration layers.
   ;; Paths must have a trailing slash (i.e. "~/.mycontribs/")
   dotspacemacs-configuration-layer-path '()

   ;; List of configuration layers to load.
   dotspacemacs-configuration-layers
   '((mu4e :variables
           mu4e-installation-path "/usr/local/share/emacs/site-lisp/mu/mu4e"
           ;; This is set to 't' to avoid mail syncing issues when using mbsync
           send-mail-function 'smtpmail-send-it    ; should not be modified
           smtpmail-smtp-server "smtp.gmail.com" ; host running SMTP server
           smtpmail-smtp-service 587               ; SMTP service port number
           smtpmail-stream-type 'starttls          ; type of SMTP connections to use
           user-mail-address "cristian.groza.mcgill@gmail.com"
           mu4e-spacemacs-layout-name "@Mu4e"
           mu4e-spacemacs-layout-binding "m"
           mu4e-spacemacs-kill-layout-on-exit t
           org-mu4e-compose-org-mode t
           org-mu4e-convert-to-html t
           mu4e-change-filenames-when-moving t
           mu4e-update-interval (* 3 60)
           mu4e-headers-auto-update t                ; avoid to type `g' to update
           mu4e-view-show-images t                   ; show images in the view buffer
           mu4e-compose-signature-auto-include nil   ; I don't want a message signature
           mu4e-use-fancy-chars t                   ; allow fancy icons for mail threads
           mu4e-org-compose-support t
           org-mu4e-convert-to-html t
           mu4e-enable-mode-line t
           mu4e-enable-notifications t
           mu4e-enable-async-operations t
           mu4e-sent-messages-behavior 'delete
           mu4e-get-mail-command "mbsync -a"
           mu4e-maildir "~/email/mbsyncmail"
           mu4e-drafts-folder "/[Gmail]/Drafts"
           mu4e-sent-folder   "/[Gmail]/Sent Mail"
           mu4e-refile-folder "/[Gmail]/All Mail"
           mu4e-trash-folder  "/[Gmail]/Trash")
     javascript
     java
     (lsp :variables lsp-ui-doc-delay 0.5
          lsp-ui-doc-position 'bottom
          lsp-ui-doc-alignment 'window
          lsp-signature-auto-activate nil
          lsp-enable-symbol-highlighting nil
          lsp-rust-server "~/bin/rust-analyzer"
          lsp-idle-delay 1.0
          lsp-clients-clangd-executable "/usr/local/opt/llvm/bin/clangd"
          lsp-clang-executable "/usr/local/opt/llvm/bin/clangd"
          )
     rust
     common-lisp
     clojure
     (groovy :variables groovy-indent-offset 2)
     yaml
     themes-megapack
     html
     csv
     (python :variables live-py-version "python3"
             python-shell-interpreter "ipython"
             python-backend 'lsp
             python-lsp-server 'pylsp
             python-shell-interpreter-args "-i --simple-prompt")
     (c-c++ :variables c-c++-backend 'lsp-clangd)
     (bibtex :variables
             bibtex-completion-cite-prompt-for-optional-arguments nil
             bibtex-completion-bibliography '("/Users/cgroza/Library/CloudStorage/Dropbox/Bib/cgroza.bib"))
     (pandoc :variables org-pandoc-options-for-html5 '((standalone . t) (self-contained . t)))
     compleseus
     outshine
     (org :variables
          find-file-visit-truename t
          org-persp-startup-with-agenda "a"
          org-enable-reveal-js-support t
          org-enable-roam-support t
          org-enable-roam-protocol t
          org-directory "/Users/cgroza/Library/CloudStorage/Dropbox/Org"
          org-default-notes-file "/Users/cgroza/Library/CloudStorage/Dropbox/Org/notes.org"
          org-agenda-files '("/Users/cgroza/Library/CloudStorage/Dropbox/Org/school.org"
                             "/Users/cgroza/Library/CloudStorage/Dropbox/Org/notes.org"
                             "/Users/cgroza/Library/CloudStorage/Dropbox/Org/work.org"
                             "/Users/cgroza/Library/CloudStorage/Dropbox/Org/org-roam"
                             "/Users/cgroza/Library/CloudStorage/Dropbox/Org/personal.org")
          org-capture-templates ()
          org-agenda-span 'month
          org-ref-default-bibliography '("/Users/cgroza/Library/CloudStorage/Dropbox/Bib/cgroza.bib")
          org-roam-v2-ack t
          org-roam-directory "/Users/cgroza/Library/CloudStorage/Dropbox/Org/org-roam"
          org-todo-keywords '((sequence "TODO(t)" "|" "DONE(d!)" "CANCELED(c/!)"))
          org-confirm-babel-evaluate nil
          ;; inline image width
          org-image-actual-width 600
          org-export-with-drawers nil
          org-startup-indented nil
          ;; org src editing window position
          org-src-window-setup 'split-window-below
          ;; to support references in org-mode latex export
          org-babel-python-command "python3"
          org-babel-default-header-args '((:tangle . "yes")
                                          (:async . "yes")
                                          (:eval . "no-export")
                                          (:results . "replace")
                                          (:session . "none")
                                          (:hlines . "no")
                                          (:noweb . "no")
                                          (:cache . "no")
                                          (:exports . "results")
                                          ))
     (latex :variables TeX-view-program-selection '((output-pdf "PDF Tools"))
            TeX-view-program-list '(("PDF Tools" TeX-pdf-tools-sync-view))
            TeX-source-correlate-start-server t )
     pdf
     (auto-completion :variables auto-completion-return-key-behavior 'complete)
     better-defaults
     (treemacs :variables treemacs-use-follow-mode t treemacs-project-follow-cleanup t)
     emacs-lisp
     (git :variables magit-repository-directories '(("~/git" . 1))
          vc-follow-symlinks t)
     markdown
     (ess :variables ess-r-backed 'lsp ess-help-own-frame t ess-eval-visibly 'nowait)
     (shell :variables shell-default-height 30
            shell-default-position 'bottom
            shell-default-shell 'eshell)
     spell-checking
     syntax-checking
     version-control
     evil-snipe
     (languagetool :variables langtool-default-language "en-CA"
                   langtool-language-tool-jar "/usr/local/Cellar/languagetool/6.2/libexec/languagetool-commandline.jar"
                   ))
   ;; List of additional packages that will be installed without being
   ;; wrapped in a layer. If you need some configuration for these
   ;; packages, then consider creating a layer. You can also put the
   ;; configuration in `dotspacemacs/user-config'.
   dotspacemacs-additional-packages '(yasnippet-snippets yasnippet-snippets
                                                         dired-rsync
                                                         ob-async
                                                         mu4e-alert
                                                         (citar)
                                                         (citar-embark)
                                                         (evil-textobj-tree-sitter :location (recipe
                                                                                              :fetcher github
                                                                                              :repo "meain/evil-textobj-tree-sitter"))
                                                         tree-sitter-ess-r
                                                         (nextflow-mode :location (recipe :fetcher github :repo "jackkamm/nextflow-mode"))
                                                         exec-path-from-shell transpose-frame
                                                         (twauctex :location (recipe :fetcher github :repo "cgroza/twauctex" ))
                                                         ;; ;; polymode poly-R poly-noweb poly-markdown poly-org
                                                         )
   ;; A list of packages that cannot be updated.
   dotspacemacs-frozen-packages '()

   dotspacemacs-undo-system 'undo-fu

   ;; A list of packages that will not be installed and loaded.
   dotspacemacs-excluded-packages '(smartparens evil-escape)
   ;; Defines the behaviour of Spacemacs when installing packages.
   ;; Possible values are `used-only', `used-but-keep-unused' and `all'.
   ;; `used-only' installs only explicitly used packages and deletes any unused
   ;; packages as well as their unused dependencies. `used-but-keep-unused'
   ;; installs only the used packages but won't delete unused ones. `all'
   ;; installs *all* packages supported by Spacemacs and never uninstalls them.
   ;; (default is `used-only')
   dotspacemacs-install-packages 'used-only))

(defun dotspacemacs/init ()
  "Initialization:
This function is called at the very beginning of Spacemacs startup,
before layer configuration.
It should only modify the values of Spacemacs settings."
  ;; This setq-default sexp is an exhaustive list of all the supported
  ;; spacemacs settings.
  (setq-default
   ;; If non-nil then enable support for the portable dumper. You'll need to
   ;; compile Emacs 27 from source following the instructions in file
   ;; EXPERIMENTAL.org at to root of the git repository.
   ;;
   ;; WARNING: pdumper does not work with Native Compilation, so it's disabled
   ;; regardless of the following setting when native compilation is in effect.
   ;;
   ;; (default nil)
   dotspacemacs-enable-emacs-pdumper nil

   ;; Name of executable file pointing to emacs 27+. This executable must be
   ;; in your PATH.
   ;; (default "emacs")
   dotspacemacs-emacs-pdumper-executable-file "emacs"

   ;; Name of the Spacemacs dump file. This is the file will be created by the
   ;; portable dumper in the cache directory under dumps sub-directory.
   ;; To load it when starting Emacs add the parameter `--dump-file'
   ;; when invoking Emacs 27.1 executable on the command line, for instance:
   ;;   ./emacs --dump-file=$HOME/.emacs.d/.cache/dumps/spacemacs-27.1.pdmp
   ;; (default (format "spacemacs-%s.pdmp" emacs-version))
   dotspacemacs-emacs-dumper-dump-file (format "spacemacs-%s.pdmp" emacs-version)

   ;; If non-nil ELPA repositories are contacted via HTTPS whenever it's
   ;; possible. Set it to nil if you have no way to use HTTPS in your
   ;; environment, otherwise it is strongly recommended to let it set to t.
   ;; This variable has no effect if Emacs is launched with the parameter
   ;; `--insecure' which forces the value of this variable to nil.
   ;; (default t)
   dotspacemacs-elpa-https t

   ;; Maximum allowed time in seconds to contact an ELPA repository.
   dotspacemacs-elpa-timeout 5

   ;; Set `gc-cons-threshold' and `gc-cons-percentage' when startup finishes.
   ;; This is an advanced option and should not be changed unless you suspect
   ;; performance issues due to garbage collection operations.
   ;; (default '(100000000 0.1))
   dotspacemacs-gc-cons '(100000000 0.1)

   ;; Set `read-process-output-max' when startup finishes.
   ;; This defines how much data is read from a foreign process.
   ;; Setting this >= 1 MB should increase performance for lsp servers
   ;; in emacs 27.
   ;; (default (* 1024 1024))
   dotspacemacs-read-process-output-max (* 1024 1024)

   ;; If non-nil then Spacelpa repository is the primary source to install
   ;; a locked version of packages. If nil then Spacemacs will install the
   ;; latest version of packages from MELPA. Spacelpa is currently in
   ;; experimental state please use only for testing purposes.
   ;; (default nil)
   dotspacemacs-use-spacelpa nil

   ;; If non-nil then verify the signature for downloaded Spacelpa archives.
   ;; (default t)
   dotspacemacs-verify-spacelpa-archives t

   ;; If non-nil then spacemacs will check for updates at startup
   ;; when the current branch is not `develop'. Note that checking for
   ;; new versions works via git commands, thus it calls GitHub services
   ;; whenever you start Emacs. (default nil)
   dotspacemacs-check-for-update nil

   ;; If non-nil, a form that evaluates to a package directory. For example, to
   ;; use different package directories for different Emacs versions, set this
   ;; to `emacs-version'. (default 'emacs-version)
   dotspacemacs-elpa-subdirectory 'emacs-version

   ;; One of `vim', `emacs' or `hybrid'.
   ;; `hybrid' is like `vim' except that `insert state' is replaced by the
   ;; `hybrid state' with `emacs' key bindings. The value can also be a list
   ;; with `:variables' keyword (similar to layers). Check the editing styles
   ;; section of the documentation for details on available variables.
   ;; (default 'vim)
   dotspacemacs-editing-style 'vim

   ;; If non-nil show the version string in the Spacemacs buffer. It will
   ;; appear as (spacemacs version)@(emacs version)
   ;; (default t)
   dotspacemacs-startup-buffer-show-version t

   ;; Specify the startup banner. Default value is `official', it displays
   ;; the official spacemacs logo. An integer value is the index of text
   ;; banner, `random' chooses a random text banner in `core/banners'
   ;; directory. A string value must be a path to an image format supported
   ;; by your Emacs build.
   ;; If the value is nil then no banner is displayed. (default 'official)
   dotspacemacs-startup-banner 'official

   ;; Scale factor controls the scaling (size) of the startup banner. Default
   ;; value is `auto' for scaling the logo automatically to fit all buffer
   ;; contents, to a maximum of the full image height and a minimum of 3 line
   ;; heights. If set to a number (int or float) it is used as a constant
   ;; scaling factor for the default logo size.
   dotspacemacs-startup-banner-scale 'auto

   ;; List of items to show in startup buffer or an association list of
   ;; the form `(list-type . list-size)`. If nil then it is disabled.
   ;; Possible values for list-type are:
   ;; `recents' `recents-by-project' `bookmarks' `projects' `agenda' `todos'.
   ;; List sizes may be nil, in which case
   ;; `spacemacs-buffer-startup-lists-length' takes effect.
   ;; The exceptional case is `recents-by-project', where list-type must be a
   ;; pair of numbers, e.g. `(recents-by-project . (7 .  5))', where the first
   ;; number is the project limit and the second the limit on the recent files
   ;; within a project.
   dotspacemacs-startup-lists '((recents . 5)
                                (projects . 7))

   ;; True if the home buffer should respond to resize events. (default t)
   dotspacemacs-startup-buffer-responsive t

   ;; Show numbers before the startup list lines. (default t)
   dotspacemacs-show-startup-list-numbers t

   ;; The minimum delay in seconds between number key presses. (default 0.4)
   dotspacemacs-startup-buffer-multi-digit-delay 0.4

   ;; If non-nil, show file icons for entries and headings on Spacemacs home buffer.
   ;; This has no effect in terminal or if "all-the-icons" package or the font
   ;; is not installed. (default nil)
   dotspacemacs-startup-buffer-show-icons nil

   ;; Default major mode for a new empty buffer. Possible values are mode
   ;; names such as `text-mode'; and `nil' to use Fundamental mode.
   ;; (default `text-mode')
   dotspacemacs-new-empty-buffer-major-mode 'text-mode

   ;; Default major mode of the scratch buffer (default `text-mode')
   dotspacemacs-scratch-mode 'text-mode

   ;; If non-nil, *scratch* buffer will be persistent. Things you write down in
   ;; *scratch* buffer will be saved and restored automatically.
   dotspacemacs-scratch-buffer-persistent nil

   ;; If non-nil, `kill-buffer' on *scratch* buffer
   ;; will bury it instead of killing.
   dotspacemacs-scratch-buffer-unkillable nil

   ;; Initial message in the scratch buffer, such as "Welcome to Spacemacs!"
   ;; (default nil)
   dotspacemacs-initial-scratch-message nil

   ;; List of themes, the first of the list is loaded when spacemacs starts.
   ;; Press `SPC T n' to cycle to the next theme in the list (works great
   ;; with 2 themes variants, one dark and one light)
   dotspacemacs-themes '(brin
                         monokai darkokai
                         solarized-light
                         solarized-dark
                         spacemacs-dark
                         spacemacs-light)
   ;; If non nil the cursor color matches the state color in GUI Emacs.
   dotspacemacs-colorize-cursor-according-to-state t
   ;; Default font, or prioritized list of fonts. `powerline-scale' allows to
   ;; quickly tweak the mode-line size to make separators look not too crappy.
   dotspacemacs-default-font '("Monaco"
                               :size 14
                               :weight normal
                               :width normal
                               :powerline-scale 0.8)
   ;; The leader key
   dotspacemacs-leader-key "SPC"

   ;; The key used for Emacs commands `M-x' (after pressing on the leader key).
   ;; (default "SPC")
   dotspacemacs-emacs-command-key "SPC"

   ;; The key used for Vim Ex commands (default ":")
   dotspacemacs-ex-command-key ":"

   ;; The leader key accessible in `emacs state' and `insert state'
   ;; (default "M-m")
   dotspacemacs-emacs-leader-key "M-m"

   ;; Major mode leader key is a shortcut key which is the equivalent of
   ;; pressing `<leader> m`. Set it to `nil` to disable it. (default ",")
   dotspacemacs-major-mode-leader-key ","

   ;; Major mode leader key accessible in `emacs state' and `insert state'.
   ;; (default "C-M-m" for terminal mode, "<M-return>" for GUI mode).
   ;; Thus M-RET should work as leader key in both GUI and terminal modes.
   ;; C-M-m also should work in terminal mode, but not in GUI mode.
   dotspacemacs-major-mode-emacs-leader-key (if window-system "<M-return>" "C-M-m")

   ;; These variables control whether separate commands are bound in the GUI to
   ;; the key pairs `C-i', `TAB' and `C-m', `RET'.
   ;; Setting it to a non-nil value, allows for separate commands under `C-i'
   ;; and TAB or `C-m' and `RET'.
   ;; In the terminal, these pairs are generally indistinguishable, so this only
   ;; works in the GUI. (default nil)
   dotspacemacs-distinguish-gui-tab nil

   ;; Name of the default layout (default "Default")
   dotspacemacs-default-layout-name "Default"

   ;; If non-nil the default layout name is displayed in the mode-line.
   ;; (default nil)
   dotspacemacs-display-default-layout nil

   ;; If non-nil then the last auto saved layouts are resumed automatically upon
   ;; start. (default nil)
   dotspacemacs-auto-resume-layouts nil

   ;; If non-nil, auto-generate layout name when creating new layouts. Only has
   ;; effect when using the "jump to layout by number" commands. (default nil)
   dotspacemacs-auto-generate-layout-names nil

   ;; Size (in MB) above which spacemacs will prompt to open the large file
   ;; literally to avoid performance issues. Opening a file literally means that
   ;; no major mode or minor modes are active. (default is 1)
   dotspacemacs-large-file-size 1

   ;; Location where to auto-save files. Possible values are `original' to
   ;; auto-save the file in-place, `cache' to auto-save the file to another
   ;; file stored in the cache directory and `nil' to disable auto-saving.
   ;; (default 'cache)
   dotspacemacs-auto-save-file-location 'cache

   ;; Maximum number of rollback slots to keep in the cache. (default 5)
   dotspacemacs-max-rollback-slots 5

   ;; If non-nil, the paste transient-state is enabled. While enabled, after you
   ;; paste something, pressing `C-j' and `C-k' several times cycles through the
   ;; elements in the `kill-ring'. (default nil)
   dotspacemacs-enable-paste-transient-state nil

   ;; Which-key delay in seconds. The which-key buffer is the popup listing
   ;; the commands bound to the current keystroke sequence. (default 0.4)
   dotspacemacs-which-key-delay 0.4

   ;; Which-key frame position. Possible values are `right', `bottom' and
   ;; `right-then-bottom'. right-then-bottom tries to display the frame to the
   ;; right; if there is insufficient space it displays it at the bottom.
   ;; (default 'bottom)
   dotspacemacs-which-key-position 'bottom

   ;; Control where `switch-to-buffer' displays the buffer. If nil,
   ;; `switch-to-buffer' displays the buffer in the current window even if
   ;; another same-purpose window is available. If non-nil, `switch-to-buffer'
   ;; displays the buffer in a same-purpose window even if the buffer can be
   ;; displayed in the current window. (default nil)
   dotspacemacs-switch-to-buffer-prefers-purpose nil

   ;; If non-nil a progress bar is displayed when spacemacs is loading. This
   ;; may increase the boot time on some systems and emacs builds, set it to
   ;; nil to boost the loading time. (default t)
   dotspacemacs-loading-progress-bar t

   ;; If non-nil the frame is fullscreen when Emacs starts up. (default nil)
   ;; (Emacs 24.4+ only)
   dotspacemacs-fullscreen-at-startup nil

   ;; If non-nil `spacemacs/toggle-fullscreen' will not use native fullscreen.
   ;; Use to disable fullscreen animations in OSX. (default nil)
   dotspacemacs-fullscreen-use-non-native nil

   ;; If non-nil the frame is maximized when Emacs starts up.
   ;; Takes effect only if `dotspacemacs-fullscreen-at-startup' is nil.
   ;; (default t) (Emacs 24.4+ only)
   dotspacemacs-maximized-at-startup t

   ;; If non-nil the frame is undecorated when Emacs starts up. Combine this
   ;; variable with `dotspacemacs-maximized-at-startup' to obtain fullscreen
   ;; without external boxes. Also disables the internal border. (default nil)
   dotspacemacs-undecorated-at-startup nil

   ;; A value from the range (0..100), in increasing opacity, which describes
   ;; the transparency level of a frame when it's active or selected.
   ;; Transparency can be toggled through `toggle-transparency'. (default 90)
   dotspacemacs-active-transparency 90

   ;; A value from the range (0..100), in increasing opacity, which describes
   ;; the transparency level of a frame when it's inactive or deselected.
   ;; Transparency can be toggled through `toggle-transparency'. (default 90)
   dotspacemacs-inactive-transparency 90

   ;; A value from the range (0..100), in increasing opacity, which describes the
   ;; transparency level of a frame background when it's active or selected. Transparency
   ;; can be toggled through `toggle-background-transparency'. (default 90)
   dotspacemacs-background-transparency 90

   ;; If non-nil show the titles of transient states. (default t)
   dotspacemacs-show-transient-state-title t

   ;; If non-nil show the color guide hint for transient state keys. (default t)
   dotspacemacs-show-transient-state-color-guide t

   ;; If non-nil unicode symbols are displayed in the mode line.
   ;; If you use Emacs as a daemon and wants unicode characters only in GUI set
   ;; the value to quoted `display-graphic-p'. (default t)
   dotspacemacs-mode-line-unicode-symbols t

   ;; If non-nil smooth scrolling (native-scrolling) is enabled. Smooth
   ;; scrolling overrides the default behavior of Emacs which recenters point
   ;; when it reaches the top or bottom of the screen. (default t)
   dotspacemacs-smooth-scrolling t

   ;; Show the scroll bar while scrolling. The auto hide time can be configured
   ;; by setting this variable to a number. (default t)
   dotspacemacs-scroll-bar-while-scrolling t

   ;; Control line numbers activation.
   ;; If set to `t', `relative' or `visual' then line numbers are enabled in all
   ;; `prog-mode' and `text-mode' derivatives. If set to `relative', line
   ;; numbers are relative. If set to `visual', line numbers are also relative,
   ;; but only visual lines are counted. For example, folded lines will not be
   ;; counted and wrapped lines are counted as multiple lines.
   ;; This variable can also be set to a property list for finer control:
   ;; '(:relative nil
   ;;   :visual nil
   ;;   :disabled-for-modes dired-mode
   ;;                       doc-view-mode
   ;;                       markdown-mode
   ;;                       org-mode
   ;;                       pdf-view-mode
   ;;                       text-mode
   ;;   :size-limit-kb 1000)
   ;; When used in a plist, `visual' takes precedence over `relative'.
   ;; (default nil)
   dotspacemacs-line-numbers nil

   ;; Code folding method. Possible values are `evil', `origami' and `vimish'.
   ;; (default 'evil)
   dotspacemacs-folding-method 'evil

   ;; If non-nil and `dotspacemacs-activate-smartparens-mode' is also non-nil,
   ;; `smartparens-strict-mode' will be enabled in programming modes.
   ;; (default nil)
   dotspacemacs-smartparens-strict-mode nil

   ;; If non-nil smartparens-mode will be enabled in programming modes.
   ;; (default t)
   dotspacemacs-activate-smartparens-mode t

   ;; If non-nil pressing the closing parenthesis `)' key in insert mode passes
   ;; over any automatically added closing parenthesis, bracket, quote, etc...
   ;; This can be temporary disabled by pressing `C-q' before `)'. (default nil)
   dotspacemacs-smart-closing-parenthesis nil

   ;; Select a scope to highlight delimiters. Possible values are `any',
   ;; `current', `all' or `nil'. Default is `all' (highlight any scope and
   ;; emphasis the current one). (default 'all)
   dotspacemacs-highlight-delimiters 'all

   ;; If non-nil, start an Emacs server if one is not already running.
   ;; (default nil)
   dotspacemacs-persistent-server t
   ;; List of search tool executable names. Spacemacs uses the first installed
   ;; tool of the list. Supported tools are `ag', `pt', `ack' and `grep'.
   ;; (default '("ag" "pt" "ack" "grep"))
   dotspacemacs-search-tools '("ag")
   ;; The default package repository used if no explicit repository has been
   ;; specified with an installed package.
   ;; Not used for now. (default nil)
   dotspacemacs-default-package-repository nil
   ;; Delete whitespace while saving buffer. Possible values are `all'
   ;; to aggressively delete empty line and long sequences of whitespace,
   ;; `trailing' to delete only the whitespace at end of lines, `changed'to
   ;; delete only whitespace for changed lines or `nil' to disable cleanup.
   ;; (default nil)
   dotspacemacs-whitespace-cleanup nil
   evil-want-Y-yank-to-eol nil
   ))

(defun dotspacemacs/user-init ()
  "Initialization function for user code.
It is called immediately after `dotspacemacs/init', before layer configuration
executes.
 This function is mostly useful for variables that need to be set
before packages are loaded. If you are unsure, you should try in setting them in
`dotspacemacs/user-config' first."
  (setq latex-build-command "LatexMk")
  (add-to-list 'load-path "/usr/local/share/emacs/site-lisp/mu/mu4e")
  )

(defun dotspacemacs/user-config ()
  "Configuration function for user code.
This function is called at the very end of Spacemacs initialization after
layers configuration.
This is the place where most of your configurations should be done. Unless it is
explicitly specified that a variable should be set before a package is loaded,
you should place your code here."
  ;; import PATH from a running shell instance
  (when (memq window-system '(mac ns x))
    (exec-path-from-shell-initialize))

  (setq warning-minimum-level :error)

  ;; layouts

  ;; custom key bindings
  ;; (define-key evil-normal-state-map (kbd "SPC '") 'my-shell)
  ;; (global-set-key (kbd "<f5>") 'yas-expand)

  (use-package tree-sitter-ess-r :ensure t)
  (use-package evil-textobj-tree-sitter :ensure t)

  (setq tree-sitter-langs--queries-dir "~/git/evil-textobj-tree-sitter/queries")
  (define-key evil-outer-text-objects-map "f" (evil-textobj-tree-sitter-get-textobj "function.outer"))
  (define-key evil-outer-text-objects-map "c" (evil-textobj-tree-sitter-get-textobj "call.outer"))

  (define-key evil-inner-text-objects-map "f" (evil-textobj-tree-sitter-get-textobj "function.inner"))
  (define-key evil-inner-text-objects-map "c" (evil-textobj-tree-sitter-get-textobj "call.inner"))

  (define-key vertico-map (kbd "C-.") (lambda ()
                                        (interactive)
                                        (embark-select)
                                        (vertico-next)))

  ;; asynchronous execution of code blocks
  ;; org babel languages
  (org-babel-do-load-languages 'org-babel-load-languages
                               '((shell . t)
                                 (R . t)
                                 (python . t)
                                 (emacs-lisp . t)))

  (global-set-key [f5] 'avy-pop-mark)

  (spacemacs/set-leader-keys-for-major-mode 'python-mode
    "s l" 'python-shell-send-line
    "s L" 'python-shell-send-line-switch)

  (spacemacs/set-leader-keys "gfm" 'magit-file-dispatch
    "ow" 'writeroom-mode
    "ot" 'transpose-frame
    "oT" 'treemacs
    "ob" 'citar-insert-citation
    "-" 'imenu-list-minor-mode
    "ol" 'my-cleanup-latex
    )

  ;; org roam
  (spacemacs/declare-prefix
    "or"  "org-roam"
    "ord" "org-roam-dailies"
    "ort" "org-roam-tags")

  (spacemacs/set-leader-keys
    "ordy" 'org-roam-dailies-goto-yesterday
    "ordt" 'org-roam-dailies-goto-today
    "ordT" 'org-roam-dailies-goto-tomorrow
    "ordd" 'org-roam-dailies-goto-date
    "orc" 'org-roam-capture
    "orf" 'org-roam-node-find
    "org" 'org-roam-graph
    "ori" 'org-roam-node-insert
    "orl" 'org-roam-buffer-toggle
    "orta" 'org-roam-tag-add
    "ortr" 'org-roam-tag-remove
    "ora" 'org-roam-alias-add
    "orF" 'compleseus-search-org-roam
    )

  ;; user defined variables
  (setq projectile-switch-project-action 'projectile-dired
        read-process-output-max (* 1024 1024)
        c-default-style "gnu"
        evil-want-Y-yank-to-eol nil
        compilation-scroll-output t
        ;; file associations
        auto-mode-alist
        (append '(("\\.nf$" . nextflow-mode)) auto-mode-alist)
        winum-scope 'frame-local)

  ;; to use pdfview with auctex
  (with-eval-after-load 'reftex
    (add-to-list 'reftex-default-bibliography "~/Dropbox/Bib/cgroza.bib"))

  (use-package embark-consult
    :ensure t ; only need to install it, embark loads it after consult if found
    :hook
    (embark-collect-mode . consult-preview-at-point-mode))

  (use-package citar
    :custom
    (citar-bibliography '("/Users/cgroza/Library/CloudStorage/Dropbox/Bib/cgroza.bib"))
    (bibtex-completion-cite-prompt-for-optional-arguments nil)
    :hook
    (LaTeX-mode . citar-capf-setup)
    (org-mode . citar-capf-setup))

  (use-package citar-embark
    :after citar embark
    :no-require
    :config (citar-embark-mode))

  ;; (use-package poly-org
  ;;   :ensure t)
  ;; Hooks
  ;; auto hide compilation buffer when successful
  (add-hook 'compilation-finish-functions
            (lambda (buf str)
              (if (null (string-match ".*exited abnormally.*" str))
                  ;;no errors, make the compilation window go away in a few seconds
                  (progn
                    (run-at-time
                     "1 sec" nil 'delete-windows-on
                     (get-buffer-create "*compilation*"))
                    (message "No Compilation Errors!")))))

  ;; (remove-hook 'org-mode-hook 'poly-org-mode)
  ;; to have the buffer refresh after compilation
  (add-hook 'TeX-after-compilation-finished-functions
            #'TeX-revert-document-buffer)
  ;; hooks
  (add-hook 'TeX-mode-hook 'orgtbl-mode)
  (add-hook 'org-capture-after-finalize-hook 'org-roam-db-sync)
  (remove-hook 'eshell-mode-hook #'company-mode)
  ;; interferes with twauctex
  (remove-hook 'LaTeX-mode-hook #'latex/auto-fill-mode)
  ;; disable highlighting current line
  (global-hl-line-mode -1)
  (global-visual-fill-column-mode -1)
  (global-eldoc-mode -1)
  (twauctex-global-mode)
  (yas-global-mode t)
  (global-tree-sitter-mode)
  (spacemacs/toggle-maximize-frame-on)
  (server-start)
  )

(defvar my-latex-cleanup-referenced-files
  "\\\\\\(includegraphics\\|addbibresource\\|include\\)\\(\\[.*\\]\\)?{\\(.*\\)}"
  )

;; Custom functions
(defun my-cleanup-latex ()
  """
Copies the TeX file to a new directory.
Walks all includegraphics, include, addbibresource states and copies referenced files to the root of the new directories.
Edits the referenced file paths in the copied TeX files to point to the new paths in the new root directory.
Assumes that all referenced file paths are relative to the directory of the TeX file, and are not absolute.
  """
  (interactive)
  (if TeX-mode-p
      (if buffer-file-name
          (let* ((clean-directory (read-directory-name "Export directory"))
                 (new-latex-file (concat clean-directory (file-name-nondirectory buffer-file-name)))
                 (original-directory (file-name-directory buffer-file-name)))
            (message "%s %s %s" clean-directory original-directory new-latex-file)
            (make-directory clean-directory t)
            (save-buffer)
            (copy-file buffer-file-name new-latex-file)
            (save-excursion
              (switch-to-buffer (find-file new-latex-file))
              (beginning-of-buffer)
              (while (re-search-forward my-latex-cleanup-referenced-files nil t)
                (let* ((referenced-file (concat original-directory (string-trim (match-string 3)) ))
                       (referenced-name (file-name-nondirectory referenced-file))
                       (destination-file (concat clean-directory referenced-name)))
                  (message "Copying %s to %s" referenced-file destination-file)
                  (copy-file referenced-file destination-file)
                  (replace-match (format "\\\\\\1\\2{%s}" referenced-name))
                  )
                )
              (save-buffer)
              (kill-current-buffer)
              )
            )
        (message "Not visiting a file."))
    (message "Not a TeX file!"))
  )

;; (defun my-shell ()
;;   (interactive)
;;   (eshell (generate-new-buffer-name "shell"))
;;   )

(defun compleseus-search-org-roam ()
  "Search in current directory with `ag'."
  (interactive)
  (spacemacs/compleseus-search t org-roam-directory))

(defun python-shell-send-line ()
  (interactive)
  (python-shell-send-string (thing-at-point 'line t)))

(defun python-shell-send-line-switch ()
  (interactive)
  (python-shell-send-string (thing-at-point 'line t))
  (python-shell-switch-to-shell)
  )