TITLE: My workflow, tmux, vim, etc.
DATE: 2017-11-01
AUTHOR: John L. Godlee
====================================================================


I thought I should do the sort of post that everyone seems to do 
and show off my workflow, with all the horrendously try-hard 
command line utilities, and DIY config files. You can find my 
dotfiles here.

  [here]: https://github.com/johngodlee/dotfiles

I spend most of my time working on my macbook pro, within an iTerm2 
window running tmux.

I have a bash script that builds a tmux session and fills it with 
useful programs. I have vim in one window, then a whole load of 
small empty shell panes in the next window, and finally cmus in the 
last window for playing music:

    #!/bin/sh

    # Create new session
    tmux -2 new -s 'dash'

    # Start vim
    tmux send-keys "vim" Enter

    # New window, split into 4
    tmux new-window -n 'bash'
    tmux split-window -v
    tmux split-window -h
    tmux select-pane -t 1
    tmux split-window -h

    # Split pane 1 vertically
    tmux select-pane -t 1
    tmux split-window -v

    # Split pane 5 horizontally
    tmux select-pane -t 5
    tmux split-window -h

    # Resize panes
    tmux resize-pane -D 8

    # New window, start cmus
    tmux new-window -n 'cmus'
    tmux send-keys "cmus" Enter

    # Detach and reattach to make it work properly
    tmux detach
    tmux a -t dash
    tmux select-window -t 1

I dabbled in using tmux-resurrect and tmux-continuum to save my 
tmux sessions when I rebooted, but I found that these plugins 
weren't always reliable. Besides, I don't usually reboot my laptop 
unless I've first saved all my files.

I used to have a lot more things running in tmux. I used alpine to 
manage email from my gmail account, and I used the calendar.vim 
plugin with a custom .vimrc to link to my google calendar, but when 
I started back working full time I found that it actually saved me 
a bit of time to just use the default macOS Calendar and Mail apps.

Note-taking

I use vim to take all my notes. I use markdown to format all my 
notes. I have a note for each day, or at least each workday. The 
basic format of my daily note is:

    # Item 1
    * Thing to do one
    * Thing to do two
        * detail 1
        * detail 2

    <hr>    

    # Item 2
    * Thing to do one

    ==================DONE===================
    * Thing to do, done

    ==================DONE===================

At the end of the day, I copy that day's note into a new note with 
tomorrow's date. So in the end I have a folder of notes with names 
like this:

    Daily_2017_10_26.md
    Daily_2017_10_27.md
    Daily_2017_10_28.md

I also have this neat way of roughly tracking how productive I've 
been. I can count the number of lines within the 
==================DONE=================== tags. Then I can turn 
that into a csv, then import that into R and plot a graph of how 
much I've done over time. It's not that useful, but was a fun 
project to put together, and a way to learn about grep.

The bash script:

    #!/bin/bash

    # Create csv file of completed items from daily notes by 
counting lines between #DONE# marks
    touch ~/Desktop/word_count.txt

    # Using a for loop and multiple sed arguments to amend the file 
(takes longer)
    for f in ./*; do { printf '%s ' "$f"; sed -n '/DONE/,/DONE/p' 
"$f" | wc -l; } >> ~/Desktop/word_count.txt; done

    # Make multiple whitespace into 1 whitespace, to csv
    awk '{$1=$1}1' ~/Desktop/word_count.txt > 
~/Desktop/word_count.csv

    # Replace "md " with "md,"
    perl -pi -w -e  's/md\s/md,/g;' ~/Desktop/word_count.csv

    # Add column names
    echo -e "date,count\n$(cat ~/Desktop/word_count.csv)" > 
~/Desktop/word_count.csv

    # delete txt file
    rm ~/Desktop/word_count.txt

    # Run R script
    Rscript ~/Google_Drive/Code/R/done_count.R

The R script:

    # Personal productivity by #DONE# items in Daily notes

    # Packages ----
    library(ggplot2)
    library(dplyr)

    # Load data ----
    prod <- read.csv("~/Desktop/word_count.csv")

    # Clean up ----
    prod$date <- prod$date %>%
        gsub("./Daily_", "", .) %>%  # Remove leading filename 
section
        gsub(".md", "", .) %>%  # Remove trailing filename section
        as.Date(., format = "%Y_%m_%d")  # Transform to Date class

    # ggplot line graph ----
    done_count <- ggplot(prod, aes(x = date, y = count)) +
        geom_line() +
        scale_x_date(date_labels = "%b", date_breaks = "1 month")

    ggsave(filename = "ggplot_done_count.png",
                 plot = done_count,
                 width = 20, height = 20, units = "cm")

Edit 2017_12_08

I've been thinking more about the note-taking philosophy and have 
noticed a few trends in my own note-taking that make it easier for 
me to read things back at a later date. This has mostly come about 
because I am now starting to re-read my notes on academic papers as 
I start to write my confirmation report.

-   Keep notes short - It's much easier to read notes back when 
they are only on short lines. Only one sentence per line
-   Nested bullet points - In line with trying to keep notes short, 
it follows that nested bullet points are a great way to give some 
sense of inherent structure to your note taking, and make it easier 
to memorise things like lists of species. Nested notes also do a 
good job at maintaining a logical flow to discussions, by allowing 
you to put a retort to a particular piece of evidence as a nested 
bullet under the main bullet point.
-   Use keywords and repeat yourself - I find it much easier to 
search through long sets of notes if I have keywords to search for. 
In this sense, it follows that each bullet point should be its own 
self-encapsulated bundle of information, which relies little on 
other bullet points to give it context, this makes it much easier 
to scan through bullet points for the useful information.
-   Use Markdown - This isn't entirely necessary, but I've found it 
to be a great way of quickly applying formatting to my notes, as 
opposed to what I used to do with Microsoft Word and WYSIWYG 
formatting.

Screens and deskspace

I do nearly all of my work at my desk in the University. I have a 
widescreen monitor with a trailing HDMI cable that I can plug into 
my laptop, then to the right I have a HP all-in-one running Windows 
that is hooked up to the University network, just in case I need to 
use some piece of Windows software. For example, when I'm testing 
workshops for undergraduate students.

  ![Desk](https://johngodlee.xyz/img_full/terminal/desk.jpg)