Update various configuration files

Signed-off-by: TuDatTr <tuan-dat.tran@tudattr.dev>

emacs/.doom.d/custom.el

@@ -3,6 +3,7 @@
  ;; 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.
+ '(org-cite-global-bibliography '("~/Documents/roam/bibliography.bib"))
  '(org-hugo-base-dir "~/Documents/hugo/")
  '(org-roam-capture-templates
    '(("d" "default" plain "* Description
@@ -66,7 +67,7 @@
 (file+head "%<%Y%m%d%H%M%S>-${slug}.org" "#+title: ${title}
 #+filetags: project")
 :unnarrowed t)
-("i" "ieee paper" plain "
+     ("i" "ieee paper" plain "
 #+title: %^{title}
 #+OPTIONS: toc:nil author:nil
 #+LaTeX_CLASS: paper
@@ -150,3 +151,9 @@
                ("\\paragraph{%s}" . "\\paragraph*{%s}")
                ("\\subparagraph{%s}" . "\\subparagraph*{%s}")))
 
+(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.
+ )

emacs/.doom.d/flycheck_config.el

@@ -0,0 +1,145 @@
+;;; $DOOMDIR/config.el -*- lexical-binding: t; -*-
+
+;; Place your private configuration here! Remember, you do not need to run 'doom
+;; sync' after modifying this file!
+
+
+;; Some functionality uses this to identify you, e.g. GPG configuration, email
+;; clients, file templates and snippets. It is optional.
+(setq user-full-name "Tuan-Dat Tran"
+      user-mail-address "tuan-dat.tran@tudattr.dev")
+
+;; Doom exposes five (optional) variables for controlling fonts in Doom:
+;;
+;; - `doom-font' -- the primary font to use
+;; - `doom-variable-pitch-font' -- a non-monospace font (where applicable)
+;; - `doom-big-font' -- used for `doom-big-font-mode'; use this for
+;;   presentations or streaming.
+;; - `doom-unicode-font' -- for unicode glyphs
+;; - `doom-serif-font' -- for the `fixed-pitch-serif' face
+;;
+;; See 'C-h v doom-font' for documentation and more examples of what they
+;; accept. For example:
+;;
+;;(setq doom-font (font-spec :family "Fira Code" :size 12 :weight 'semi-light)
+;;      doom-variable-pitch-font (font-spec :family "Fira Sans" :size 13))
+;;
+;; If you or Emacs can't find your font, use 'M-x describe-font' to look them
+;; up, `M-x eval-region' to execute elisp code, and 'M-x doom/reload-font' to
+;; refresh your font settings. If Emacs still can't find your font, it likely
+;; wasn't installed correctly. Font issues are rarely Doom issues!
+
+;; There are two ways to load a theme. Both assume the theme is installed and
+;; available. You can either set `doom-theme' or manually load a theme with the
+;; `load-theme' function. This is the default:
+(setq doom-theme 'doom-one)
+
+;; This determines the style of line numbers in effect. If set to `nil', line
+;; numbers are disabled. For relative line numbers, set this to `relative'.
+(setq display-line-numbers-type t)
+
+;; If you use `org' and don't want your org files in the default location below,
+;; change `org-directory'. It must be set before org loads!
+(setq org-directory "~/.emacs.d/org/")
+
+
+;; Whenever you reconfigure a package, make sure to wrap your config in an
+;; `after!' block, otherwise Doom's defaults may override your settings. E.g.
+;;
+;;   (after! PACKAGE
+;;     (setq x y))
+;;
+;; The exceptions to this rule:
+;;
+;;   - Setting file/directory variables (like `org-directory')
+;;   - Setting variables which explicitly tell you to set them before their
+;;     package is loaded (see 'C-h v VARIABLE' to look up their documentation).
+;;   - Setting doom variables (which start with 'doom-' or '+').
+;;
+;; Here are some additional functions/macros that will help you configure Doom.
+;;
+;; - `load!' for loading external *.el files relative to this one
+;; - `use-package!' for configuring packages
+;; - `after!' for running code after a package has loaded
+;; - `add-load-path!' for adding directories to the `load-path', relative to
+;;   this file. Emacs searches the `load-path' when you load packages with
+;;   `require' or `use-package'.
+;; - `map!' for binding new keys
+;;
+;; To get information about any of these functions/macros, move the cursor over
+;; the highlighted symbol at press 'K' (non-evil users must press 'C-c c k').
+;; This will open documentation for it, including demos of how they are used.
+;; Alternatively, use `C-h o' to look up a symbol (functions, variables, faces,
+;; etc).
+;;
+;; You can also try 'gd' (or 'C-c c d') to jump to their definition and see how
+;; they are implemented.
+
+; Rust
+(use-package rustic
+  :bind (:map rustic-mode-map
+              ("M-j" . lsp-ui-imenu)
+              ("M-?" . lsp-find-references)
+              ("C-c C-c l" . flycheck-list-errors)
+              ("C-c C-c a" . lsp-execute-code-action)
+              ("C-c C-c r" . lsp-rename)
+              ("C-c C-c q" . lsp-workspace-restart)
+              ("C-c C-c Q" . lsp-workspace-shutdown)
+              ("C-c C-c s" . lsp-rust-analyzer-status))
+  :config
+  (setq rustic-format-on-save t)
+  (add-hook 'rustic-mode-hook 'rk/rustic-mode-hook))
+
+(defun rk/rustic-mode-hook ()
+  ;; so that run C-c C-c C-r works without having to confirm, but don't try to
+  ;; save rust buffers that are not file visiting. Once
+  ;; https://github.com/brotzeit/rustic/issues/253 has been resolved this should
+  ;; no longer be necessary.
+  (when buffer-file-name
+    (setq-local buffer-save-without-query t))
+  (add-hook 'before-save-hook 'lsp-format-buffer nil t))
+
+(use-package lsp-mode
+  :commands lsp
+  :custom
+  ;; what to use when checking on-save. "check" is default, I prefer clippy
+  (lsp-rust-analyzer-cargo-watch-command "clippy")
+  (lsp-eldoc-render-all t)
+  (lsp-idle-delay 0.6)
+  ;; enable / disable the hints as you prefer:
+  (lsp-rust-analyzer-server-display-inlay-hints t)
+  (lsp-rust-analyzer-display-lifetime-elision-hints-enable "skip_trivial")
+  (lsp-rust-analyzer-display-chaining-hints t)
+  (lsp-rust-analyzer-display-lifetime-elision-hints-use-parameter-names nil)
+  (lsp-rust-analyzer-display-closure-return-type-hints t)
+  (lsp-rust-analyzer-display-parameter-hints nil)
+  (lsp-rust-analyzer-display-reborrow-hints nil)
+  :config
+  (add-hook 'lsp-mode-hook 'lsp-ui-mode))
+
+(use-package lsp-ui
+  :commands lsp-ui-mode
+  :custom
+  (lsp-ui-peek-always-show t)
+  (lsp-ui-sideline-show-hover t)
+  (lsp-ui-doc-enable nil))
+
+; Latex
+(setq +latex-viewers '(zathura))
+
+; Roam
+(setq org-roam-directory "~/Documents/roam/")
+(use-package! websocket
+    :after org-roam)
+
+(use-package! org-roam-ui
+    :after org-roam ;; or :after org
+;;         normally we'd recommend hooking orui after org-roam, but since org-roam does not have
+;;         a hookable mode anymore, you're advised to pick something yourself
+;;         if you don't care about startup time, use
+;;  :hook (after-init . org-roam-ui-mode)
+    :config
+    (setq org-roam-ui-sync-theme t
+          org-roam-ui-follow t
+          org-roam-ui-update-on-save t
+          org-roam-ui-open-on-start t))

emacs/.doom.d/init.el

@@ -172,8 +172,7 @@
        ;;php               ; perl's insecure younger brother
        ;;plantuml          ; diagrams for confusing people more
        ;;purescript        ; javascript, but functional
-       (python
-         +lsp)             ; beautiful is better than ugly
+       python             ; beautiful is better than ugly
        ;;qt                ; the 'cutest' gui framework ever
        ;;racket            ; a DSL for DSLs
        ;;raku              ; the artist formerly known as perl6