spacemacs

;; -*- mode: emacs-lisp; lexical-binding: t -*-
;; 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
   '(helm
     ranger
     treemacs
     fasd
     auto-completion
     yaml
     better-defaults
     (spell-checking :variables spell-checking-enable-by-default nil)
     syntax-checking
     (org :variables
          org-startup-indented t
          org-startup-numerated nil
          org-startup-with-inline-images t
          org-image-actual-width '(600)
          org-goto-auto-isearch nil
          org-pretty-entities nil
          org-hide-emphasis-markers t
          org-enable-appear-support t
          org-ellipsis "⤵"
          org-list-demote-modify-bullet '(("-" . "*") ("*" . "+") ("+" . "-"))
          org-superstar-item-bullet-alist
          '((?- . ?-)
            (?* . ?*)
            (?+ . ?+))
          org-src-tab-acts-natively nil
          org-enable-github-support t
          org-enable-jira-support t
          org-enable-hugo-support t
          org-enable-bootstrap-support t
          org-pomodoro-clock-break t
          org-user-mail-address "srnesdoly@gmail.com"
          org-agenda-files (list "~/Dropbox/org/agendas/"))
     latex
     bibtex
     ;; <<Coding Tools>>
     julia
     python
     java
     (ess :variables ess-indent-with-fancy-comments nil) ;; R
     octave ;; MATLAB syntax highlighting
     rust
     emacs-lisp
     vimscript
     haskell
     sql
     php
     javascript
     html
     csv
     markdown
     multiple-cursors
     ;; lsp
     version-control
     git
     shell-scripts
     windows-scripts
     (shell :variables
            shell-default-height 50
            shell-default-position 'bottom
            shell-default-shell 'multi-term
            multi-term-program-switches "--login")
     )


   ;; List of additional packages that will be installed without being wrapped
   ;; in a layer (generally the packages are installed only and should still be
   ;; loaded using load/require/use-package in the user-config section below in
   ;; this file). If you need some configuration for these packages, then
   ;; consider creating a layer. You can also put the configuration in
   ;; `dotspacemacs/user-config'. To use a local version of a package, use the
   ;; `:location' property: '(your-package :location "~/path/to/your-package/")
   ;; Also include the dependencies as they will not be resolved automatically.
   dotspacemacs-additional-packages
   '(yasnippet-snippets
     exec-path-from-shell)

   ;; A list of packages that cannot be updated.
   dotspacemacs-frozen-packages '()

   ;; A list of packages that will not be installed and loaded.
   dotspacemacs-excluded-packages '()

   ;; 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.
   ;; (default 5)
   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 t

   ;; 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 '(spacemacs-dark
                         spacemacs-light)

   ;; Set the theme for the Spaceline. Supported themes are `spacemacs',
   ;; `all-the-icons', `custom', `doom', `vim-powerline' and `vanilla'. The
   ;; first three are spaceline themes. `doom' is the doom-emacs mode-line.
   ;; `vanilla' is default Emacs mode-line. `custom' is a user defined themes,
   ;; refer to the DOCUMENTATION.org for more info on how to create your own
   ;; spaceline theme. Value can be a symbol or list with additional properties.
   ;; (default '(spacemacs :separator wave :separator-scale 1.5))
   dotspacemacs-mode-line-theme '(spacemacs :separator wave :separator-scale 1.5)

   ;; If non-nil the cursor color matches the state color in GUI Emacs.
   ;; (default t)
   dotspacemacs-colorize-cursor-according-to-state t

   ;; Default font or prioritized list of fonts. The `:size' can be specified as
   ;; a non-negative integer (pixel size), or a floating-point (point size).
   ;; Point size is recommended, because it's device independent. (default 10.0)
   dotspacemacs-default-font '(("Fira Code"
                                :size 13.0
                                :weight normal
                                :width normal)
                               ("Source Code Pro"
                                :size 14.0
                                :weight normal
                                :width normal))

   ;; The leader key (default "SPC")
   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 nil) (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-enable-server nil

   ;; Set the emacs server socket location.
   ;; If nil, uses whatever the Emacs default is, otherwise a directory path
   ;; like \"~/.emacs.d/server\". It has no effect if
   ;; `dotspacemacs-enable-server' is nil.
   ;; (default nil)
   dotspacemacs-server-socket-dir nil

   ;; If non-nil, advise quit functions to keep server open when quitting.
   ;; (default nil)
   dotspacemacs-persistent-server nil

   ;; List of search tool executable names. Spacemacs uses the first installed
   ;; tool of the list. Supported tools are `rg', `ag', `pt', `ack' and `grep'.
   ;; (default '("rg" "ag" "pt" "ack" "grep"))
   dotspacemacs-search-tools '("rg" "ag" "pt" "ack" "grep")

   ;; Format specification for setting the frame title.
   ;; %a - the `abbreviated-file-name', or `buffer-name'
   ;; %t - `projectile-project-name'
   ;; %I - `invocation-name'
   ;; %S - `system-name'
   ;; %U - contents of $USER
   ;; %b - buffer name
   ;; %f - visited file name
   ;; %F - frame name
   ;; %s - process status
   ;; %p - percent of buffer above top of window, or Top, Bot or All
   ;; %P - percent of buffer above bottom of window, perhaps plus Top, or Bot or All
   ;; %m - mode name
   ;; %n - Narrow if appropriate
   ;; %z - mnemonics of buffer, terminal, and keyboard coding systems
   ;; %Z - like %z, but including the end-of-line format
   ;; If nil then Spacemacs uses default `frame-title-format' to avoid
   ;; performance issues, instead of calculating the frame title by
   ;; `spacemacs/title-prepare' all the time.
   ;; (default "%I@%S")
   dotspacemacs-frame-title-format "%I@%U"

   ;; Format specification for setting the icon title format
   ;; (default nil - same as frame-title-format)
   dotspacemacs-icon-title-format nil

   ;; Color highlight trailing whitespace in all prog-mode and text-mode derived
   ;; modes such as c++-mode, python-mode, emacs-lisp, html-mode, rst-mode etc.
   ;; (default t)
   dotspacemacs-show-trailing-whitespace t

   ;; 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

   ;; If non-nil activate `clean-aindent-mode' which tries to correct
   ;; virtual indentation of simple modes. This can interfere with mode specific
   ;; indent handling like has been reported for `go-mode'.
   ;; If it does deactivate it here.
   ;; (default t)
   dotspacemacs-use-clean-aindent-mode t

   ;; Accept SPC as y for prompts if non-nil. (default nil)
   dotspacemacs-use-SPC-as-y nil

   ;; If non-nil shift your number row to match the entered keyboard layout
   ;; (only in insert state). Currently supported keyboard layouts are:
   ;; `qwerty-us', `qwertz-de' and `querty-ca-fr'.
   ;; New layouts can be added in `spacemacs-editing' layer.
   ;; (default nil)
   dotspacemacs-swap-number-row nil

   ;; Either nil or a number of seconds. If non-nil zone out after the specified
   ;; number of seconds. (default nil)
   dotspacemacs-zone-out-when-idle nil

   ;; Run `spacemacs/prettify-org-buffer' when
   ;; visiting README.org files of Spacemacs.
   ;; (default nil)
   dotspacemacs-pretty-docs nil

   ;; If nil the home buffer shows the full path of agenda items
   ;; and todos. If non-nil only the file name is shown.
   dotspacemacs-home-shorten-agenda-source nil

   ;; If non-nil then byte-compile some of Spacemacs files.
   dotspacemacs-byte-compile nil))

(defun dotspacemacs/user-env ()
  "Environment variables setup.
This function defines the environment variables for your Emacs session. By
default it calls `spacemacs/load-spacemacs-env' which loads the environment
variables declared in `~/.spacemacs.env' or `~/.spacemacs.d/.spacemacs.env'.
See the header of this file for more information."
  (spacemacs/load-spacemacs-env)
)

(defun dotspacemacs/user-init ()
  "Initialization for user code:
This function is called immediately after `dotspacemacs/init', before layer
configuration.
It is mostly for variables that should be set before packages are loaded.
If you are unsure, try setting them in `dotspacemacs/user-config' first."
)


(defun dotspacemacs/user-load ()
  "Library to load while dumping.
This function is called only while dumping Spacemacs configuration. You can
`require' or `load' the libraries of your choice that will be included in the
dump."
)


(defun dotspacemacs/user-config ()
  "Configuration for user code:
This function is called at the very end of Spacemacs startup, after layer
configuration.
Put your configuration code here, except for variables that should be set
before packages are loaded."

  ;; Set $PATH and `exec-path' correctly for windowed Emacs on macOS.
  (when (memq window-system '(mac ns))
    (exec-path-from-shell-initialize))

  (setq-default tab-width 4)

  ;; Define column beyond which text is automatically wrapped. Some modes
  ;; override this value based on convention (e.g. Python is 79).
  (setq-default fill-column 80)

  ;; Automatically break lines
  (add-hook 'prog-mode-hook 'auto-fill-mode)
  (add-hook 'text-mode-hook 'auto-fill-mode)

  ;; Activate column indicator for programming & text modes, but not org-mode
  (add-hook 'prog-mode-hook 'spacemacs/toggle-fill-column-indicator-on)
  (add-hook 'text-mode-hook 'spacemacs/toggle-fill-column-indicator-on)
  (add-hook 'org-mode-hook 'spacemacs/toggle-fill-column-indicator-off)

  ;; Set width of first column in helm-mini to the longest buffer name found
  (setq helm-buffer-max-length nil)

  ;; Show whitespace in makefiles
  (add-hook 'makefile-mode-hook 'whitespace-mode)

  ;; Configure build process for exporting org files to PDF via `pdflatex'.
  ;; Supports BibTeX citations, nomenclature (`nomencl'), and syntax
  ;; highlighting.
  ;;
  ;; WARNING: using `-shell-escape' permits the LaTeX processor (here,
  ;; `pdflatex') to run arbitrary commands on your machine; only use this on
  ;; input from trusted sources.
  (setq org-latex-pdf-process
        '("pdflatex -shell-escape -interaction nonstopmode -output-directory %o %f"
          "bibtex %b"
          "makeindex %b.nlo -s nomencl.ist -o %b.nls"
          "pdflatex -shell-escape -interaction nonstopmode -output-directory %o %f"
          "pdflatex -shell-escape -interaction nonstopmode -output-directory %o %f"))

  ;; Syntax highlighting with LaTeX package `minted', which uses the Python
  ;; package `Pygments', installable via `pip'. See variable
  ;; `LaTeX-minted-pygmentize-program', which should point to the `pygmentize'
  ;; executable (/opt/homebrew/bin/pygmentize).
  (setq org-latex-listings 'minted
        org-latex-packages-alist '(("" "minted")))

  ;; Bibtex defaults
  (setq org-ref-default-bibliography '("~/bibliography/Mendeley/library.bib")
        org-ref-pdf-directory "~/bibliography/bibtex-pdfs/"
        org-ref-bibliography-notes "~/bibliography/notes.org")
  (setq bibtex-completion-bibliography "~/bibliography/Mendeley/library.bib"
        bibtex-completion-library-path "~/bibliography/bibtex-pdfs")

  ;; (add-to-list 'load-path "~/.emacs.d/elpa/26.3/develop/org-plus-contrib-20200727/ob-julia.el")
  ;; (org-babel-do-load-languages
  ;;   'org-babel-load-languages
  ;;   '((julia . t)
  ;;     (python . t)
  ;;     (R . t)
  ;;     (java . t)))
  ;; (matlab . t)
  ;; (haskell . t)
  ;; (sql . t)
  ;; (sh . t)
  ;; (latex . t)
  ;; (awk . t)
  ;; (sed . t)))

  ;; Open pdf with system pdf viewer (works on mac)
  ;; (setq bibtex-completion-pdf-open-function
  ;;       (lambda (fpath)
  ;;         (start-process "open" "*open*" "open" fpath)))

  ;; Set NeoTree theme
  (setq neo-theme 'nerd)

  ;; Set aspell as the external spell-checking program
  (setq ispell-program-name "/opt/homebrew/bin/aspell")

  ;; Run flyspell with aspell (instead of ispell)
  (setq ispell-list-command "list")

  ;; kill buffers that were opened while browsing directories with ranger
  (setq ranger-cleanup-eagerly t)

  ;; Magit: set explicit path to the arm64 version of git
  (setq magit-git-executable "/opt/homebrew/bin/git")

  ;; Max length for the summary line of git commits (creates a visual reminder)
  (setq git-commit-summary-max-length 50)
)

;; Do not write anything past this comment. This is where Emacs will
;; auto-generate custom variable definitions.
(defun dotspacemacs/emacs-custom-settings ()
  "Emacs custom settings.
This is an auto-generated function, do not modify its content directly, use
Emacs customize menu instead.
This function is called at the very end of Spacemacs initialization."
(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.
 '(helm-external-programs-associations (quote (("org" . "open"))))
 '(org-agenda-files
   (quote
    ("~/bbme/thesis/host-factors/host-factors.org" "~/bbme/docs/meetings/191118-kamen/191118-kamen.org" "~/org/example.org")))
 '(package-selected-packages
   (quote
    (java-snippets lsp-ui lsp-treemacs lsp-python-ms lsp-java helm-lsp company-lsp gnu-elpa-keyring-update flycheck-package flycheck-julia yatemplate ox-twbs yaml-mode lsp-julia lsp-mode julia-repl phpunit phpcbf php-extras php-auto-yasnippets drupal-mode company-php ac-php-core xcscope php-mode tern livid-mode skewer-mode js2-refactor multiple-cursors js2-mode js-doc import-js grizzl helm-gtags ggtags counsel-gtags add-node-modules-path yasnippet-snippets org-ref lv all-the-icons-dired pubmed xterm-color shell-pop multi-term transient eshell-z eshell-prompt-extras esh-help poly-R easy-hugo polymode toml-mode racer flycheck-rust cargo rust-mode cdlatex org-mime pdf-tools key-chord ivy tablist helm-bibtex parsebib biblio biblio-core fasd tldr auctex-latexmk company-auctex auctex ess-smart-equals ess-R-data-view ctable ess julia-mode vimrc-mode dactyl-mode csv-mode typo insert-shebang fish-mode company-shell company-emacs-eclim eclim web-mode tagedit slim-mode scss-mode sass-mode pug-mode less-css-mode helm-css-scss haml-mode emmet-mode company-web web-completion-data ranger yapfify pyvenv pytest pyenv-mode py-isort pip-requirements live-py-mode hy-mode dash-functional helm-pydoc cython-mode company-anaconda anaconda-mode pythonic stickyfunc-enhance srefactor unfill smeargle orgit org-projectile org-category-capture org-present org-pomodoro alert log4e gntp org-download mwim mmm-mode markdown-toc markdown-mode magit-gitflow htmlize helm-gitignore helm-company helm-c-yasnippet gnuplot gitignore-mode gitconfig-mode gitattributes-mode git-timemachine git-messenger git-link git-gutter-fringe+ git-gutter-fringe fringe-helper git-gutter+ git-gutter gh-md fuzzy flyspell-correct-helm flyspell-correct flycheck-pos-tip pos-tip flycheck evil-magit magit magit-popup git-commit ghub let-alist with-editor diff-hl company-statistics company auto-yasnippet yasnippet auto-dictionary ac-ispell auto-complete ws-butler winum which-key volatile-highlights vi-tilde-fringe uuidgen use-package toc-org spaceline powerline restart-emacs request rainbow-delimiters popwin persp-mode pcre2el paradox spinner org-plus-contrib org-bullets open-junk-file neotree move-text macrostep lorem-ipsum linum-relative link-hint info+ indent-guide hydra hungry-delete hl-todo highlight-parentheses highlight-numbers parent-mode highlight-indentation hide-comnt help-fns+ helm-themes helm-swoop helm-projectile helm-mode-manager helm-make projectile pkg-info epl helm-flx helm-descbinds helm-ag google-translate golden-ratio flx-ido flx fill-column-indicator fancy-battery eyebrowse expand-region exec-path-from-shell evil-visualstar evil-visual-mark-mode evil-unimpaired evil-tutor evil-surround evil-search-highlight-persist evil-numbers evil-nerd-commenter evil-mc evil-matchit evil-lisp-state smartparens evil-indent-plus evil-iedit-state iedit evil-exchange evil-escape evil-ediff evil-args evil-anzu anzu evil goto-chg undo-tree eval-sexp-fu highlight elisp-slime-nav dumb-jump f dash s diminish define-word column-enforce-mode clean-aindent-mode bind-map bind-key auto-highlight-symbol auto-compile packed aggressive-indent adaptive-wrap ace-window ace-link ace-jump-helm-line helm avy helm-core popup async)))
 '(paradox-github-token t))
(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.
 ;;
 ;; To customize, see 'M-x customize-face':
 ;;   https://orgmode.org/worg/org-tutorials/org-appearance.html
 '(org-document-title ((t (:inherit bold :foreground "#bc6ec5" :underline nil :height 1.0)))))
)