Skip to content

Instantly share code, notes, and snippets.

Embed
What would you like to do?
Phd Workflow
\documentclass[a4paper]{article}
\input{./preamble.tex}
\input{./symbols.tex}
\input{./theorems.tex}
\input{./references.tex}
\usepackage{pgfmath}
\usepackage{pgfcalendar}
\let\d=\pgfcalendarshorthand
\newcommand\formatdate[2]{\pgfcalendar{cal}{#1}{#1}{#2}}
% \newcommand\firstdate{\year-\month-\day+-25}
\newcommand\firstdate{\year-\month-\day+-14}
% \newcommand\firstdate{\year-\month-\day+-50}
% \newcommand\firstdate{2021-11-20}
% \newcommand\firstdate{\year-\month-\day+-41}
\newcommand\lastdate{\year-\month-\day}
\newcommand\grayrule{{\color{gray} \noindent\makebox[\linewidth]{\rule{\paperwidth}{0.4pt}}}}
\begin{document}
\begin{center}
\huge{PhD Notes}\\[0.4em]
\Large{Gilles Castel}\\[0.2em]
\emph{
From \formatdate{\firstdate}{\d d- \d mt} to
\formatdate{\lastdate}{\d d- \d mt}
}
\end{center}
\tableofcontents
\bigskip
\pgfcalendar{cal}{\firstdate}{\lastdate}{%
\IfFileExists{./\d y0-\d m0-\d d0/note.tex}{
\ifdate{equals=\firstdate}{}{%
\bigskip
\ifdate{Monday}{\grayrule\\[-22pt]\grayrule}{\grayrule}
}%
\vspace*{1em}
\marginpar{\vspace*{1em}\textsf{ \d w., \d m. \d d- }}%
\addcontentsline{toc}{section}{\d wt, \d d0 \d m.}%
\def\formatteddate{\d{y}0-\d{m}0-\d{d}0}%
\input{./\formatteddate/note.tex}
\ifdate{equals=\lastdate}{}{\hfill \xournal}
}{}
}
\end{document}

Directory structure:

.
├── papers
│   ├── Title - Author.pdf
│   └── Title - Author.pdf
├── notes
│   ├── 2022-04-10
│   │   ├── note.tex
│   │   └── note.xoj
│   ├── 2022-04-11
│   │   ├── note.tex
│   │   └── note.xoj
│   ├── ...
│   ├── master.tex
│   ├── preamble.tex
│   ├── references.tex
│   ├── symbols.tex
│   └── theorems.tex
└── scripts
    ├── ...
    ├── shortcut.sh
    └── template.xoj

Sxhkd config:

# ~/.config/sxhkd/sxhkdrc 

alt + {a-z}
    bash ~/phd/scripts/shortcut.sh {a-z}

This way, any combination of Alt + $KEY calls scripts/shortcut.sh $KEY. This is a bash script with the following shortcuts:

  • Alt + F copies a reference to the currently opened pdf.
  • Alt + N opens the note of today.
  • Alt + O opens the compiled version of my notes.
  • Alt + P allows me to fuzzy search a paper.
  • Alt + R opens my file browser in my phd directory.
  • Alt + X opens today's handwritten notes and if not existing copies the template to today's directory and opens it .

You'll have to edit shortcut a bit to make this work on your system.

\usepackage{cmbright}
% \usepackage{stix}
\usepackage[utf8]{inputenc}
\usepackage[T1]{fontenc}
\usepackage{textcomp}
\usepackage{amsmath, amssymb, amsthm}
\usepackage{mathtools}
\usepackage{tikz-cd}
% figure support
\usepackage{import}
\usepackage[shortlabels]{enumitem}
\usepackage{xifthen}
\pdfminorversion=7
\usepackage{pdfpages}
\usepackage{transparent}
\newcommand{\incfig}[1]{%
\def\svgwidth{\columnwidth}
\import{./figures/}{#1.pdf_tex}
}
\pdfsuppresswarningpagegroup=1
\usepackage{xcolor}
\usepackage{parskip}
\usepackage{soul}
\usepackage{hyperref}
\hypersetup{hidelinks}
\usepackage{fontawesome}
\usepackage{xifthen}% provides \isempty test
\newcommand\pdfref[3]{%
\href{phd://open-paper?id=#1&page=#2}{%
\textup{[\textbf{\ifthenelse{\isempty{#3}}{here}{#3}}]}}%
}
\newcommand\urlref[2]{%
\href{#1}{\raisebox{0.15ex}{\scriptsize \faLink}\:\textup{\textbf{#2}}}%
}
\newcommand\absolutefileref[2]{%
\href{run:#1}{\raisebox{0.15ex}{\scriptsize \faFile}\:\textup{\textbf{#2}}}%
}
% this will contain the current date in yyyy-mm-dd format
\def\formatteddate{}
\newcommand\fileref[2]{
\IfFileExists{./\formatteddate/#1}{
\absolutefileref{./\formatteddate/#1}{#2}
}{
\textcolor{gray}{\absolutefileref{./\formatteddate/#1}{#2}}
}
}
\newcommand{\xournal}{\fileref{note.xoj}{Handwritten notes}}%
#!/bin/bash
root="$(dirname "$(realpath "$0")")"
key="$1"
terminal="x-terminal-emulator -e zsh -i -c"
vim="nvim"
node="/usr/bin/node"
open_xournal () {
cd ~/phd/notes/$(date +"%F");
if [ -f "note.xoj" ]; then
xournal note.xoj;
else
cp ~/phd/scripts/template.xoj note.xoj;
xournal note.xoj;
fi
}
mkdir -p ~/phd/notes/$(date +"%F");
case $key in
p ) cd ~/phd/papers;
pdf_file="$(ls . | rofi -theme ~/.config/rofi/theme-wide.rasi -i -dmenu)";
[ -z "$pdf_file" ] && exit 0;
[ -f "$pdf_file" ] && zathura "$(realpath "$pdf_file")" || sensible-browser "https://google.com/search?q=$pdf_file" ;;
r ) $terminal "ranger ~/phd/notes/$(date +"%F")" ;;
n ) $terminal "cd ~/phd/notes/$(date +"%F"); $vim ~/phd/notes/$(date +"%F")/note.tex" ;;
o ) zathura ~/phd/notes/master.pdf ;;
x ) open_xournal ;;
f ) $node $root/copy-pdf-reference.js ;;
esac
\newcommand{\C}{\mathbb C}
\newcommand{\R}{\mathbb R}
\newcommand{\Q}{\mathbb Q}
\newcommand{\Z}{\mathbb Z}
% ...
This is just an empty Xournal file I've saved.
/**
* User: deadguy
* Copyright: deadguy
*/
configuration {
display-drun: "Open";
display-run: "Run";
display-window: "Window";
show-icons: true;
sidebar-mode: true;
}
* {
font: "Roboto 12";
background-color: #2E3440;
text-color: #E5E9F0;
selbg: #4C566A;
actbg: #242a36;
urgbg: #e53935;
winbg: #E5E9F0;
selected-normal-foreground: @winbg;
normal-foreground: @text-color;
selected-normal-background: @actbg;
normal-background: @background-color;
selected-urgent-foreground: @background-color;
urgent-foreground: @text-color;
selected-urgent-background: @urgbg;
urgent-background: @background-color;
selected-active-foreground: @winbg;
active-foreground: @text-color;
selected-active-background: @actbg;
active-background: @actbg;
line-margin: 2;
line-padding: 2;
separator-style: "none";
hide-scrollbar: "true";
margin: 0;
padding: 0;
}
window {
location: center;
anchor: center;
orientation: horizontal;
children: [mainbox];
width: 60%;
height: 30%;
}
mainbox {
spacing: 0.8em;
children: [ entry,listview ];
}
button { padding: 5px 2px; }
button selected {
background-color: @active-background;
text-color: @background-color;
}
inputbar {
padding: 5px;
spacing: 5px;
}
listview {
spacing: 0.5em;
dynamic: false;
cycle: true;
}
element {
padding: 10px 10px 10px 20px;
}
icon {
margin: 100px;
}
entry {
expand: false;
text-color: @normal-foreground;
vertical-align: 1;
padding: 20px 20px 10px 20px;
}
element normal.normal {
background-color: @normal-background;
text-color: @normal-foreground;
}
element normal.urgent {
background-color: @urgent-background;
text-color: @urgent-foreground;
}
element normal.active {
background-color: @active-background;
text-color: @active-foreground;
}
element selected.normal {
background-color: @selected-normal-background;
text-color: @selected-normal-foreground;
border: 0 5px solid 0 0;
border-color: @active-background;
}
element selected.urgent {
background-color: @selected-urgent-background;
text-color: @selected-urgent-foreground;
}
element selected.active {
background-color: @selected-active-background;
text-color: @selected-active-foreground;
}
element alternate.normal {
background-color: @normal-background;
text-color: @normal-foreground;
}
element alternate.urgent {
background-color: @urgent-background;
text-color: @urgent-foreground;
}
element alternate.active {
background-color: @active-background;
text-color: @active-foreground;
}
\usepackage{mdframed}
\mdfsetup{
leftmargin=-1em,
rightmargin=-1em,
middlelinewidth=1.5pt,
middlelinecolor=white,
innertopmargin=1.5\topskip,
innerbottommargin=1\topskip,
skipabove=\baselineskip,
skipbelow=0,
nobreak=true
}
\newmdenv[
backgroundcolor = red!10
]{wrong}
\newmdenv[
backgroundcolor = green!10
]{correct}
\newmdtheoremenv[linewidth=0]{question}{Question}
\newmdtheoremenv[linewidth=0]{confusion}{Confusion}
\newmdtheoremenv[linewidth=0]{answer}{Answer}
\newmdtheoremenv[]{idea}{Idea}
\newmdtheoremenv[]{claim}{Claim}
\newmdtheoremenv[]{definition}{Definition}
\newmdtheoremenv[]{lemma}{Lemma}
\newmdtheoremenv[linewidth=0]{remark}{Remark}
\newmdtheoremenv[]{theorem}{Theorem}
\newmdtheoremenv[]{corollary}{Corollary}
\newmdtheoremenv[]{problem}{Problem}
\newmdtheoremenv[]{eg}{Example}
\newmdtheoremenv[linewidth=0]{todo}{TODO}
\newmdtheoremenv[backgroundcolor = blue!10, nobreak=false]{marco}{Marco}
\newmdtheoremenv[backgroundcolor=green!5]{mydefinition}{Definition}
\newmdtheoremenv[backgroundcolor=green!5]{mytheorem}{Theorem}
\newmdtheoremenv[backgroundcolor=green!5]{mylemma}{Lemma}
\renewmdenv[
bottomline=false,
topline=false,
rightline=false,
fontcolor=black!70
]{quote}
\newmdenv[fontcolor=black!10, linewidth=0]{ditch}
# Location: ~/.xournal/config.
# Xournal configuration file.
# This file is generated automatically upon saving preferences.
# Use caution when editing this file manually.
#
[general]
# the display resolution, in pixels per inch
display_dpi=96.00
# the initial zoom level, in percent
initial_zoom=176.14
# maximize the window at startup (true/false)
window_maximize=false
# start in full screen mode (true/false)
window_fullscreen=false
# the window width in pixels (when not maximized)
window_width=1411
# the window height in pixels
window_height=1000
# scrollbar step increment (in pixels)
scrollbar_speed=30
# the step increment in the zoom dialog box
zoom_dialog_increment=1
# the multiplicative factor for zoom in/out
zoom_step_factor=1.500
# continuous view (false = one page, true = continuous, horiz = horizontal)
view_continuous=true
# use XInput extensions (true/false)
use_xinput=true
# discard Core Pointer events in XInput mode (true/false)
discard_corepointer=false
# ignore events from other devices while drawing (true/false)
ignore_other_devices=true
# do not worry if device reports button isn't pressed while drawing (true/false)
ignore_btn_reported_up=true
# always map eraser tip to eraser (true/false)
use_erasertip=false
# always map touchscreen device to hand tool (true/false) (requires separate pen and touch devices)
touchscreen_as_hand_tool=false
# disable touchscreen device when pen is in proximity (true/false) (requires separate pen and touch devices)
pen_disables_touch=false
# name of touchscreen device for touchscreen_as_hand_tool
touchscreen_device_name=Touchscr
# buttons 2 and 3 switch mappings instead of drawing (useful for some tablets) (true/false)
buttons_switch_mappings=false
# automatically load filename.pdf.xoj instead of filename.pdf (true/false)
autoload_pdf_xoj=false
# enable periodic autosaves (true/false)
autosave_enabled=false
# delay for periodic autosaves (in seconds)
autosave_delay=5
# default path for open/save (leave blank for current directory)
default_path=/home/gilles/phd/logs/2022-04-10
# use pressure sensitivity to control pen stroke width (true/false)
pressure_sensitivity=false
# minimum width multiplier
width_minimum_multiplier=0.00
# maximum width multiplier
width_maximum_multiplier=1.25
# interface components from top to bottom
# valid values: drawarea menu main_toolbar pen_toolbar statusbar
interface_order=menu main_toolbar pen_toolbar drawarea statusbar
# interface components in fullscreen mode, from top to bottom
interface_fullscreen=main_toolbar pen_toolbar drawarea
# interface has left-handed scrollbar (true/false)
interface_lefthanded=false
# hide some unwanted menu or toolbar items (true/false)
shorten_menus=false
# interface items to hide (customize at your own risk!)
# see source file xo-interface.c for a list of item names
shorten_menu_items=optionsProgressiveBG optionsLeftHanded optionsButtonSwitchMapping
# highlighter opacity (0 to 1, default 0.5)
# warning: opacity level is not saved in xoj files!
highlighter_opacity=0.50
# auto-save preferences on exit (true/false)
autosave_prefs=true
# force PDF rendering through cairo (slower but nicer) (true/false)
poppler_force_cairo=false
# prefer xournal's own PDF code for exporting PDFs (true/false)
exportpdf_prefer_legacy=false
# fix origin of strokes (devices with unreliable button press coordinates, e.g. Lenovo's AES pens) (true/false)
fix_stroke_origin=false
# when attempting to open a non-existent file, treat it as a new file (true/false)
autocreate_new_xoj=false
# export successive layers on separate pages in PDFs (true/false)
exportpdf_layers=false
[paper]
# the default page width, in points (1/72 in)
width=612.00
# the default page height, in points (1/72 in)
height=792.00
# the default paper color
color=white
# the default paper style (plain, lined, ruled, or graph)
style=lined
# apply paper style changes to all pages (true/false)
apply_all=false
# preferred unit (cm, in, px, pt)
default_unit=cm
# include paper ruling when printing or exporting to PDF (true/false)
print_ruling=true
# when creating a new page, duplicate a PDF or image background instead of using default paper (true/false)
new_page_duplicates_bg=false
# just-in-time update of page backgrounds (true/false)
progressive_bg=true
# bitmap resolution of PS/PDF backgrounds rendered using ghostscript (dpi)
gs_bitmap_dpi=144
# bitmap resolution of PDF backgrounds when printing with libgnomeprint (dpi)
pdftoppm_printing_dpi=150
[tools]
# selected tool at startup (pen, eraser, highlighter, selectregion, selectrect, vertspace, hand, image)
startup_tool=pen
# Use the pencil from cursor theme instead of a color dot (true/false)
pen_cursor=false
# default pen color
pen_color=black
# default pen thickness (fine = 1, medium = 2, thick = 3)
pen_thickness=2
# default pen is in ruler mode (true/false)
pen_ruler=false
# default pen is in shape recognizer mode (true/false)
pen_recognizer=false
# default eraser thickness (fine = 1, medium = 2, thick = 3)
eraser_thickness=2
# default eraser mode (standard = 0, whiteout = 1, strokes = 2)
eraser_mode=2
# default highlighter color
highlighter_color=yellow
# default highlighter thickness (fine = 1, medium = 2, thick = 3)
highlighter_thickness=2
# default highlighter is in ruler mode (true/false)
highlighter_ruler=false
# default highlighter is in shape recognizer mode (true/false)
highlighter_recognizer=false
# button 2 tool (pen, eraser, highlighter, text, selectregion, selectrect, vertspace, hand, image)
btn2_tool=hand
# button 2 brush linked to primary brush (true/false) (overrides all other settings)
btn2_linked=true
# button 2 brush color (for pen or highlighter only)
btn2_color=white
# button 2 brush thickness (pen, eraser, or highlighter only)
btn2_thickness=0
# button 2 ruler mode (true/false) (for pen or highlighter only)
btn2_ruler=false
# button 2 shape recognizer mode (true/false) (pen or highlighter only)
btn2_recognizer=false
# button 2 eraser mode (eraser only)
btn2_erasermode=2
# button 3 tool (pen, eraser, highlighter, text, selectregion, selectrect, vertspace, hand, image)
btn3_tool=eraser
# button 3 brush linked to primary brush (true/false) (overrides all other settings)
btn3_linked=true
# button 3 brush color (for pen or highlighter only)
btn3_color=white
# button 3 brush thickness (pen, eraser, or highlighter only)
btn3_thickness=2
# button 3 ruler mode (true/false) (for pen or highlighter only)
btn3_ruler=false
# button 3 shape recognizer mode (true/false) (pen or highlighter only)
btn3_recognizer=false
# button 3 eraser mode (eraser only)
btn3_erasermode=2
# thickness of the various pens (in points, 1 pt = 1/72 in)
pen_thicknesses=0.42;0.85;1.41;2.26;5.67
# thickness of the various erasers (in points, 1 pt = 1/72 in)
eraser_thicknesses=2.83;8.50;19.84
# thickness of the various highlighters (in points, 1 pt = 1/72 in)
highlighter_thicknesses=2.83;8.50;19.84
# name of the default font
default_font=Sans
# default font size
default_font_size=12.0
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment