Phd Workflow

master.tex

\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}

Phd workflow.md

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.

preamble.tex

\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}

references.tex

\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}}%

shortcut.sh

#!/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

symbols.tex

\newcommand{\C}{\mathbb C}
\newcommand{\R}{\mathbb R}
\newcommand{\Q}{\mathbb Q}
\newcommand{\Z}{\mathbb Z}
% ...

template.xoj

This is just an empty Xournal file I've saved.

theme-wide.rasi

/**
* 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;
}

theorems.tex

\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}

xournal-config

# 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

Thank you for sharing this and writing these article’s, have found them very helpful!

Rest in Peace.

Gilles Castel, † Deceased on July 18 2022. Link.

Gilles Castel had been an inspiration. I feel so sad because of this. He was so special for so many of us.
I will forever be indebted for all these things he created and shared.