Add new snippets

config.org

@@ -4,34 +4,44 @@
 
 * Doom theme
 ** Use nerd-font in Emacs (for better support in vterm to liquidprompt)
-#+begin_src emacs-lisp :tangle yes
+#+begin_src emacs-lisp
-(setq doom-font (font-spec :family "Fira Code Nerd Font" :size 12)
+(setq doom-font (font-spec :family "FiraCode Nerd Font Mono" :size 12)
-      doom-big-font (font-spec :family "Fira Code Nerd Font" :size 24)
+      doom-big-font (font-spec :family "FiraCode Nerd Font Mono" :size 24)
-      doom-variable-pitch-font (font-spec :family "Fira Code Nerd Font" :size 12)
+      doom-variable-pitch-font (font-spec :family "FiraCode Nerd Font Mono" :size 12)
-      doom-unicode-font (font-spec :family "Fira Code Nerd Font")
+      doom-unicode-font (font-spec :family "FiraCode Nerd Font Mono")
-      doom-serif-font (font-spec :family "Fira Code Nerd Font" :size 12 :weight 'light))
+      doom-serif-font (font-spec :family "FiraCode Nerd Font Mono" :size 12 :weight 'light))
 #+end_src
+
 * UI
-#+begin_src emacs-lisp :tangle yes
+#+begin_src emacs-lisp
 (setq confirm-kill-emacs nil)
 #+end_src
 ** Expand initial Frame
 
-#+begin_src emacs-lisp :tangle yes
+#+begin_src emacs-lisp
 (add-hook 'window-setup-hook 'toggle-frame-maximized t)
 #+end_src
 
+
 * Edition modes
 
 ** Quarto
-#+begin_src emacs-lisp :tangle yes
+#+begin_src emacs-lisp
 (require 'quarto-mode)
 ;;(add-to-list 'auto-mode-alist '("\\.Rmd\\'" . poly-quarto-mode))
 #+end_src
 
 ** LaTeX
 
-#+begin_src emacs-lisp :tangle yes
+
+*** Enable LaTeX-mode by default
+
+#+begin_src emacs-lisp
+(setq TeX-default-mode #'LaTeX-mode ;; should already be the default mode
+      TeX-force-default-mode t)
+#+end_src
+
+#+begin_src emacs-lisp
 (setq TeX-quote-after-quote t)
 #+end_src
 
@@ -40,12 +50,12 @@
 I want my back quotes back.
 #+end_quote
 
-#+begin_src emacs-lisp :tangle yes
+#+begin_src emacs-lisp
 (setq cdlatex-math-symbol-prefix [f12])
 #+end_src
 
 Add custom LaTeX classes to ox-latex class.
-#+begin_src emacs-lisp :tangle yes
+#+begin_src emacs-lisp
 (defun custom-latex-classes ()
   (add-to-list 'org-latex-classes
                 '("scrartcl" "\\documentclass{scrartcl}"
@@ -90,12 +100,12 @@ Add custom LaTeX classes to ox-latex class.
   #'custom-latex-classes)
 #+end_src
 
-#+begin_src emacs-lisp :tangle yes
+#+begin_src emacs-lisp
 (setq org-latex-compiler "lualatex")
 #+end_src
 
 Use minted for code listings:
-#+begin_src emacs-lisp :tangle yes
+#+begin_src emacs-lisp
 (setq org-latex-listings 'minted
       org-latex-packages-alist '(("" "minted"))
       org-latex-pdf-process
@@ -103,18 +113,24 @@ Use minted for code listings:
         "lualatex -shell-escape -interaction nonstopmode -output-directory %o %f"))
 #+end_src
 Disable LateX preview in Org-mode by default
-#+begin_src emacs-lisp :tangle yes
+#+begin_src emacs-lisp :tangle no
 (setq org-startup-with-latex-preview nil)
 #+end_src
 
+#+begin_src emacs-lisp
+(setq org-highlight-latex-and-related '(native))
+#+end_src
+
 *** Add a hook so that the org file is tangled before the build
-#+begin_src emacs-lisp :tangle yes
+#+begin_src emacs-lisp
 (add-hook 'org-export-before-processing-hook #'org-babel-tangle)
 #+end_src
 
+
+
 *** Syntax highlighting in Org-mode
 
-#+begin_src emacs-lisp :tangle yes
+#+begin_src emacs-lisp
 ; (setq org-highlight-latex-and-related '(latex script entities))
 (setq org-highlight-latex-and-related '(native))
 ;; (add-hook 'org-mode-hook #'turn-on-org-cdlatex)
@@ -124,10 +140,11 @@ Disable LateX preview in Org-mode by default
 \(i \in \mathbf{N}\)
 
 *** Proper indentation in algorithmic
-#+begin_src emacs-lisp :tangle yes
+#+begin_src emacs-lisp
 (with-eval-after-load 'latex
     (add-to-list 'LaTeX-indent-environment-list '("algorithmic" current-indentation)))
 #+end_src
+
 ** Enable conda environment in a Org-mode
 
 #+begin_src emacs-lisp :tangle no
@@ -191,7 +208,7 @@ systemctl --user enable --now emacs
 
 * PlantUML
 
-#+begin_src emacs-lisp :tangle yes
+#+begin_src emacs-lisp
 (setq plantuml-default-exec-mode 'executable)
   ;; (setq plantuml-default-exec-mode 'jar)
   (setq plantuml-executable-path "/usr/bin/plantuml")
@@ -210,7 +227,7 @@ systemctl --user enable --now emacs
 
 * Org-ref-acronyms
 
-#+begin_src emacs-lisp :tangle yes
+#+begin_src emacs-lisp
 (after! org
   (require 'org-ref)
  (add-to-list 'org-latex-classes
@@ -236,7 +253,7 @@ systemctl --user enable --now emacs
 | org-ref-glossary-before-parsing | org-ref-acronyms-before-parsing | org-attach-expand-links |
 | org-ref-glossary-before-parsing | org-ref-acronyms-before-parsing | org-attach-expand-links |
 
-#+begin_src emacs-lisp :tangle yes
+#+begin_src emacs-lisp
 (after! org (org-add-link-type
  "latex" nil
  (lambda (path desc format)
@@ -246,3 +263,12 @@ systemctl --user enable --now emacs
     ((eq format 'latex)
      (format "\\%s{%s}" path desc))))))
 #+end_src
+
+
+#+begin_src emacs-lisp
+(global-set-key [(meta up)] 'transpose-line-up)
+(global-set-key [(meta down)] 'transpose-line-down)
+#+end_src
+
+#+RESULTS:
+: transpose-line-down

custom.el

@@ -0,0 +1,26 @@
+(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.
+ '(warning-suppress-log-types
+   '(((ox-latex))
+     ((ox-latex))
+     ((ox-latex))
+     ((ox-latex))
+     ((ox-latex))
+     (defvaralias)
+     (lexical-binding)))
+ '(warning-suppress-types
+   '(((ox-latex))
+     ((ox-latex))
+     ((ox-latex))
+     ((ox-latex))
+     (defvaralias)
+     (lexical-binding))))
+(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.
+ )

init.el

@@ -31,24 +31,24 @@
        ;;deft              ; notational velocity for Emacs
        doom              ; what makes DOOM look the way it does
        doom-dashboard    ; a nifty splash screen for Emacs
-       ;;doom-quit         ; DOOM quit-message prompts when you quit Emacs
+       doom-quit         ; DOOM quit-message prompts when you quit Emacs
        (emoji +unicode)  ; 🙂
        hl-todo           ; highlight TODO/FIXME/NOTE/DEPRECATED/HACK/REVIEW
        ;;hydra
        indent-guides     ; highlighted indent columns
-       ;;ligatures         ; ligatures and symbols to make your code pretty again
+       ligatures         ; ligatures and symbols to make your code pretty again
        ;;minimap           ; show a map of the code on the side
        modeline          ; snazzy, Atom-inspired modeline, plus API
        ;;nav-flash         ; blink cursor line after big motions
        ;;neotree           ; a project drawer, like NERDTree for vim
        ophints           ; highlight the region an operation acts on
        (popup +defaults)   ; tame sudden yet inevitable temporary windows
-       ;;tabs              ; a tab bar for Emacs
+       tabs              ; a tab bar for Emacs
        treemacs          ; a project drawer, like neotree but cooler
        unicode           ; extended unicode support for various languages
        (vc-gutter +pretty) ; vcs diff in the fringe
        vi-tilde-fringe   ; fringe tildes to mark beyond EOB
-       ;;window-select     ; visually switch windows
+       window-select     ; visually switch windows
        workspaces        ; tab emulation, persistence & separate workspaces
        ;;zen               ; distraction-free coding or writing
 
@@ -56,7 +56,7 @@
        (evil +everywhere); come to the dark side, we have cookies
        file-templates    ; auto-snippets for empty files
        fold              ; (nigh) universal code folding
-       (format +onsave)  ; automated prettiness
+       format  ; automated prettiness
        ;;god               ; run Emacs commands without modifier keys
        ;;lispy             ; vim for lisp, for people who don't like vim
        ;;multiple-cursors  ; editing in many places at once
@@ -85,14 +85,14 @@
        ;;grammar           ; tasing grammar mistake every you make
 
        :tools
-       ;;ansible
+       ansible
        biblio            ; Writes a PhD for you (citation needed)
        ;;collab            ; buffers with friends
        ;;debugger          ; FIXME stepping through code, to help you add bugs
        ;;direnv
-       ;;docker
+       docker
        editorconfig      ; let someone else argue about tabs vs spaces
-       ;;ein               ; tame Jupyter notebooks with emacs
+       ein               ; tame Jupyter notebooks with emacs
        (eval +overlay)     ; run code, run (also, repls)
        ;;gist              ; interacting with github gists
        lookup              ; navigate your code and its documentation
@@ -107,7 +107,7 @@
        ;;terraform         ; infrastructure as code
        ;;tmux              ; an API for interacting with tmux
        tree-sitter       ; syntax and parsing, sitting in a tree...
-       ;;upload            ; map local to remote projects via ssh/ftp
+       upload            ; map local to remote projects via ssh/ftp
 
        :os
        ;;(:if IS-MAC macos)  ; improve compatibility with macOS
@@ -136,7 +136,7 @@
        ;;fsharp            ; ML stands for Microsoft's Language
        ;;fstar             ; (dependent) types and (monadic) effects and Z3
        ;;gdscript          ; the language you waited for
-       ;;(go +lsp)         ; the hipster dialect
+       (go +lsp)         ; the hipster dialect
        (graphql +lsp)    ; Give queries a REST
        (haskell +lsp)    ; a language that's lazier than I am
        ;;hy                ; readability of scheme w/ speed of python
@@ -154,7 +154,7 @@
        ;;nim               ; python + lisp at the speed of c
        ;;nix               ; I hereby declare "nix geht mehr!"
        (ocaml +lsp)             ; an objective camel
-       (org +roam2 +hugo +pandoc +brain)               ; organize your plain life in plain text
+       (org +hugo +pandoc +brain)               ; organize your plain life in plain text
        php               ; perl's insecure younger brother
        plantuml          ; diagrams for confusing people more
        ;;purescript        ; javascript, but functional
@@ -175,7 +175,7 @@
        ;;terra             ; Earth and Moon in alignment for performance.
        web               ; the tubes
        yaml              ; JSON, but readable
-       ;;zig               ; C, but simpler
+       zig               ; C, but simpler
 
        :email
        ;;(mu4e +org +gmail)

packages.el

@@ -63,6 +63,10 @@
 (package! ob-pasp
   :recipe (:host github :repo "samuelortion/ob-pasp"))
 
+(package! ob-hy
+  :recipe (:host github :repo "brantou/ob-hy"))
+(package! hy-mode)
+
 ;; (package! ox-hugo)
 
 (package! groovy-mode)
@@ -75,3 +79,5 @@
 ;;  (:host sourcehut :repo "meow_king/typst-ts-mode"))
 
 (package! org-ref)
+
+(package! cobol-mode)

snippets/latex-mode/begin

@@ -0,0 +1,8 @@
+# -*- mode: snippet -*-
+# name: begin
+# key: \begin
+# condition: t
+# --
+\begin{$1}
+$2
+\end{$1}

snippets/latex-mode/columns

@@ -0,0 +1,13 @@
+# -*- mode: snippet -*-
+# name: columns
+# key: columns
+# condition: t
+# --
+\begin{columns}
+\begin{column}{0.5\textwidth}
+$1
+\end{column}
+\begin{column}{0.5\textwidth}
+$2
+\end{column}
+\end{columns}

snippets/latex-mode/figure

@@ -0,0 +1,10 @@
+# -*- mode: snippet -*-
+# name: figure
+# key: figure
+# condition: t
+# --
+\begin{figure}[H]
+\centering
+\includegraphics[width=\columnwidth]{$1}
+\caption{\label{fig:$2}$3}
+\end{figure}

snippets/latex-mode/ispellfrench

@@ -0,0 +1,8 @@
+# -*- mode: snippet -*-
+# name: ispellfrench
+# key: ispellfrench
+# condition: t
+# --
+% Local Variables:
+%  ispell-local-dictionary: "fr"
+% End:

snippets/latex-mode/proof

@@ -0,0 +1,8 @@
+# -*- mode: snippet -*-
+# name: proof
+# key: proof
+# condition: t
+# --
+\begin{proof}
+
+\end{proof}

snippets/lisp-mode/readfile

@@ -0,0 +1,10 @@
+# -*- mode: snippet -*-
+# name: readfile
+# key: readfile
+# condition: t
+# --
+(with-open-file (in "$1")
+  (do ((line (read-line in nil)
+             (read-line in nil)))
+      ((null line))
+    $2))

snippets/org-mode/R

@@ -0,0 +1,8 @@
+# -*- mode: snippet -*-
+# name: R
+# key: R
+# condition: t
+# --
+#+begin_src R :session *R*
+$0
+#+end_src

snippets/org-mode/align*

@@ -0,0 +1,7 @@
+# -*- mode: snippet -*-
+# name: align
+# key: align
+# --
+\begin{align*}
+    $1
+\end{align*}

snippets/org-mode/begin

@@ -0,0 +1,8 @@
+# -*- mode: snippet -*-
+# name: begin
+# key: \begin
+# condition: t
+# --
+\begin{$1}
+$2
+\end{$1}

snippets/org-mode/cm

@@ -0,0 +1,12 @@
+# -*- mode: snippet -*-
+# name: cm
+# key: cm
+# condition: t
+# --
+#+title: $1
+#+author: Samuel Ortion
+#+date: 2024
+#+LATEX_CLASS: scrartcl
+#+LATEX_HEADER: \usepackage{mus}
+
+* $2

snippets/org-mode/definition

@@ -0,0 +1,7 @@
+# -*- mode: snippet -*-
+# name: definition
+# key: definition
+# --
+\begin{definition}[$1]
+
+\end{definition}

snippets/org-mode/figure

@@ -0,0 +1,10 @@
+# -*- mode: snippet -*-
+# name: figure
+# key: figure
+# condition: t
+# --
+\begin{figure}[H]
+\centering
+\includegraphics[width=\columnwidth]{$1}
+\caption{\label{fig:$2}$3}
+\end{figure}

snippets/org-mode/frame

@@ -0,0 +1,7 @@
+# -*- mode: snippet -*-
+# name: frame
+# key: frame
+# --
+\begin{frame}{$1}
+
+\end{frame}

snippets/org-mode/header

@@ -0,0 +1,12 @@
+# -*- mode: snippet -*-
+# name: header
+# key: header
+# condition: t
+# --
+#+PROPERTY: HEADER-ARGS+ :eval no-export
+#+title: $1
+#+author: Samuel Ortion
+#+date: $2
+#+latex_class: scrartcl
+#+latex_header: \usepackage{mus}
+#+bibliography: ../references.bib

snippets/org-mode/image-ggplot

@@ -0,0 +1,17 @@
+# -*- mode: snippet -*-
+# name: r image-ggplot
+# key: r-imgg
+# --
+#+begin_src R :session *R* :results output graphics file :file notebooks/plots/${1:file}.png
+library(ggplot2)
+library(scales)
+data <- $2
+theme_set(theme_gray(base_size = 6))
+gg <- ggplot(data, aes())
+gg <- gg + <type of plot>
+gg <- gg + scale_x_discrete("X title")
+gg <- gg + scale_y_continuous("Y title")
+gg <- gg + ggtitle("")
+gg <- gg + theme(plot.title = element_text(hjust = 0.5))
+gg
+#+end_src

snippets/org-mode/image-python

@@ -0,0 +1,14 @@
+# -*- mode: snippet -*-
+# name: image-python
+# key: image-python
+# condition: t
+# --
+#+begin_src python :session *Python* :results graphics file output :file "./plots/`(format-time-string "%Y%m%d")`_$1" :exports results
+fig, ax = plt.subplots()
+
+data = $2
+
+ax.plot(data, '.b')
+
+fig
+#+end_src

snippets/org-mode/ispellfrench

@@ -0,0 +1,8 @@
+# -*- mode: snippet -*-
+# name: ispellfrench
+# key: ispellfrench
+# condition: t
+# --
+# Local Variables:
+#  ispell-local-dictionary: "fr"
+# End:

snippets/org-mode/proof

@@ -0,0 +1,8 @@
+# -*- mode: snippet -*-
+# name: proof
+# key: proof
+# condition: t
+# --
+\begin{proof}
+
+\end{proof}

snippets/org-mode/pseudocode

@@ -0,0 +1,13 @@
+# -*- mode: snippet -*-
+# name: pseudocode
+# key: pseudocode
+# --
+\begin{algorithm}[H]
+    \caption{$1}
+    \begin{algorithmic}[1]
+        \Function{$2}{}
+            $3
+            \State \Return $4
+        \EndFunction
+    \end{algorithmic}
+\end{algorithm}

snippets/org-mode/pyhead-lamme

@@ -0,0 +1,20 @@
+# -*- mode: snippet -*-
+# name: pyhead-lamme
+# key: pyhead
+# condition: t
+# --
+#+begin_src emacs-lisp :exports none
+(pyvenv-activate "../.venv/lamme2025")
+#+end_src
+
+#+RESULTS:
+
+#+begin_src python :session *Python* :results silent
+import matplotlib.pyplot as plt
+import pandas as pd
+import numpy as np
+#+end_src
+
+#+begin_src python :session *Python* :results silent
+plt.style.use("lamme2025")
+#+end_src

snippets/org-mode/python

@@ -0,0 +1,8 @@
+# -*- mode: snippet -*-
+# name: python
+# key: python
+# condition: t
+# --
+#+begin_src python :session *Python*
+$0
+#+end_src

snippets/org-mode/tabulate

@@ -0,0 +1,9 @@
+# -*- mode: snippet -*-
+# name: tabulate
+# key: tabulate
+# condition: t
+# --
+tabulate(
+    df,
+    headers=df.columns,
+    tablefmt="orgtbl")

snippets/org-mode/taocp

@@ -0,0 +1,10 @@
+# -*- mode: snippet -*-
+# name: myexercise
+# key: myexercise
+# --
+\begin{myexercise}{$1}{$2}
+    $4
+    \begin{myanswer}
+    $5
+    \end{myanswer}
+\end{myexercise}

snippets/org-mode/tikzfig

@@ -0,0 +1,15 @@
+# -*- mode: snippet -*-
+# name: tikzfig
+# key: tikzfig
+# --
+\documentclass[tikz]{standalone}
+
+\usepackage{tikz}
+
+\begin{document}
+
+\begin{tikzpicture}
+$0
+\end{tikzpicture}
+
+\end{document}

snippets/snakemake-mode/rule

@@ -0,0 +1,20 @@
+# -*- mode: snippet -*-
+# name: Snakemake complete rule
+# key: rule
+# condition: t
+# --
+
+rule $1:
+     input:
+        $2
+     output:
+         $3
+     params:
+         $4
+     log:
+         stdout="logs/$5.stdout",
+         stderr="logs/$6.stderr"
+     shell:
+         """
+         $7 > "{log.stdout}" 2> "{log.stderr}"
+         """