Written by SNTag
on March 26, 2024

Document Generator

Overview{#toc-overview}
- Setup/Install{#toc-setupinstall}
- Sites to go through for details:{#toc-sites-to-go-through-for-details}
- TO SOLVE FOR EASIER DOCUMENT MAKING{#toc-to-solve-for-easier-document-making}
- My Makefile General Guide{#toc-my-makefile-general-guide}
- To develop{#toc-to-develop}
- Autostart sh{#toc-autostart-sh}
PDF{#toc-pdf}
- Future developments{#toc-future-developments}
Presentations{#toc-presentations}
- Makefile (Mar 26th, 2024){#toc-makefile-mar-26th-2024}
- How To{#toc-how-to}

:title: Document Generator

Overview

This document is a summary of my document making process in markdown > latex > document. Setup on linux, pop~os~!

Requires:

latex
pandoc

Great pandoc guide Pandoc manual

Setup/Install

Texlive or Latex

To install, run `sudo apt install -y texlive texlive-full`

NOTE: texlive-full gets stuck at 'Pregenerating ConTeXt MarkIV format'. Solved by letting it run for a while, and then pressing "Enter" a whole lot, as mentioned by one user online.

Pandoc

Make sure to install at the same version as pandoc-crossref. See here for installation (run dpkg -i on downloads page dpkg release).

Extra note: handy to remove tags in url to find packages by version.

pandoc-crossref

Make sure to install at the same version as pandoc-crossref.

Place pandoc-crossref in `~/.local/bin/` & then restart. In `echo $PATH`, pandoc-crossref placed in ~/.local/bin will not show until restart.

Sites to go through for details:

https://alvinalexander.com/blog/post/latex/reference-figure-or-table-within-latex-document/ Nicely comprehensive: https://opensource.com/article/18/9/pandoc-research-paper https://boisgera.github.io/pandoc/markdown/ https://blog.cubieserver.de/2021/document-writing-with-markdown-and-latex/ https://allefeld.github.io/nerd-notes/Markdown/A%20writer's%20guide%20to%20Pandoc's%20Markdown.html Nice list of features: https://deatrich.github.io/doc-with-pandoc-markdown/current/doc-with-pandoc-markdown.html#fenced-code-blocks

TO SOLVE FOR EASIER DOCUMENT MAKING

[#B] alt txt font size

I suspect best option is not to use markdown approach but latex or html

[#B] MAKEFILE: Edits for handouts & regular slides?

https://gist.github.com/lmullen/c3d4c7883f081ed8692a#file-makefile

My Makefile General Guide

Start

Location for texlive documents is /usr/share/texlive when `sudo apt install texlive-full`

Declaring Documents to Use

File Types to Generate

Guide: -r input format. -s Produce output with an appropriate header and footer. -V specifics a theme already in the system. Needs –template for personal theme. -t output format. $(FILTERS) after –pdf-engine. –csl=$(CSL).csl –bibliography=$(BIB) -N –reference-doc Use with pptx templates [[[https://pandoc.org/MANUAL#option--toc\](https://pandoc.org/MANUAL#option--toc)[][–toc]] Table of Contents. Useless without the -s option

To Put Together The Finale Document

To develop

To put columns?

pandoc manual

[#C] spelling

yaml header: "spellchecker: hunspell" lua-filter=spellcheck

[#C] Figure out bib (NEEDS PANDOC-CROSSREF?)

[#A] PANDOC: crossref

https://emacs.stackexchange.com/questions/35775/how-to-kill-magit-diffs-buffers-on-quit

[#A] PDF: Figures prefix/reference using markdown syntax (NEEDS PANDOC-CROSSREF?)

Following seems specific to document making with markdown syntax. Needs pandoc-crossref? see stackoverflow response blog post focusing on markdown syntax in a paper

figPrefix:
 - "Figure"
 - "Figures"

tblPrefix:
 - "Table"
 - "Tables"

using md syntax, add `{#fig:scatter-matrix}` to end of figure. Ref using

[#C] PDF: Controlling image location

Autostart sh

This script is run on a terminal from the directory with the files. auto runs 'make' based on changes to the directory.

#!/bin/bash

# Automatically set WATCH_DIR to the directory where this script is located
SCRIPT_DIR="$(dirname "$(readlink -f "$0")")"
WATCH_DIR="${SCRIPT_DIR}" # Directory to watch for changes
MEXT="(md|yaml)" # Markdown file extension
SLEEPTIME=1 # Sleep time between checks in seconds

# Function to compile documents
compile_docs() {
    echo "Detected changes. Compiling documents..."
    make all
    echo "Compilation finished."
}

# Function to clean generated documents
clean_docs() {
    echo "Cleaning up generated documents..."
    make clean
    echo "Cleanup finished."
}

# Initial clean and compile
clean_docs
compile_docs

# Get the initial state of the directory
initial_state=$(ls -lR --time-style=full-iso $WATCH_DIR | grep -E "\.$MEXT")

echo "Watching for changes in $WATCH_DIR. Press [CTRL+C] to stop."

# Continuous loop to check for changes
while true; do
    sleep $SLEEPTIME
    current_state=$(ls -lR --time-style=full-iso $WATCH_DIR | grep -E "\.$MEXT")

    # Check if anything changed
    if [ "$initial_state" != "$current_state" ]; then
        compile_docs
        initial_state=$current_state
    fi
done

PDF

Future developments

Tuft handouts

Presentations

Makefile (Mar 26th, 2024)

This is the makefile used to generate the document.

## Put this Makefile in your project directory---i.e., the directory
## containing the paper you are writing. Assuming you are using the
## rest of the toolchain here, you can use it to create .html, .tex,
## and .pdf output files (complete with bibliography, if present) from
## your markdown file.
## -    Change the paths at the top of the file as needed.
## -    Using `make` without arguments will generate html, tex, and pdf
##  output files from all of the files with the designated markdown
##  extension. The default is `.md` but you can change this.
## -    You can specify an output format with `make tex`, `make pdf`,
## -    `make html`, or `make docx`.
## -    Doing `make clean` will remove all the .tex, .html, .pdf, and .docx files
##  in your working directory. Make sure you do not have files in these
##  formats that you want to keep!

## IMPORTANT TODO
# [B] Two column slides, one with image? Adjusting width of columns
# [C] Figure out bib
# [D] What is 'submission'?

## Later things to learn
# What are slide levels, ex pandoc --slide-level 2
# Confirm what pandoc --toc does
# Possible to tell markdown to exclude titles?

OS := $(shell uname)

## Markdown extension (e.g. md, markdown, mdown).
MEXT = md

## All markdown files in the working directory
SRC = $(wildcard *.$(MEXT))

## Final doc
# This is a document that will be generated containing the sum.
FINAL_DOC := final_doc.md

## Location of Pandoc support files.
PREFIX = ${HOME}/.config/pandoc/

## Location of parent bibliography
#LIBRARY=library.bib # TODO Will this function with this line included, as well as the below bib mentions?

## Location of your working bibliography file
# Contains the citations
#BIB = bibexport.bib

## CSL stylesheet (located in the csl folder of the PREFIX directory).
#CSL = acrf  # For styling of Bibliography # TODO are there CSL stylesheets in texlive/pandoc?

## TEMPLATE
# Location for texlive documents is /usr/share/texlive when `sudo apt install texlive-full`
TEMPLATE    =   metropolis  # TODO where does it search for template? # NOTE Template document.

PDFS=$(SRC:.md=.pdf)
TEX=$(SRC:.md=.tex)
PPTX=$(SRC:.md=.pptx)

FILTERS = --filter pandoc-crossref # --filter pandoc-citeproc #--lua-filter=draftnotes # TODO any useful lua filters for presentations?

EXTENSIONS := simple_tables+table_captions+yaml_metadata_block+smart # TODO How are these extensions installed/added?

##############################
# DECLARING DOCUMENTS TO USE #
##############################

SUBMISSION  =   submit/GTK-AcRF-T1-2018.pdf  # TODO Where to save the file?

PDFENGINE=pdflatex

# NOTE When Available, add to line below:
# bibexport.bib $(TEMPLATE).latex $(CSL).csl
#final_presentation.pdf:    final_presentation.md presentation.md Makefile  # NOTE Files to generate .pdf # TODO Why is Makefile listed here?


all:    $(PDFS) $(TEX) $(PPTX)

pdf:    clean $(PDFS)
tex:    clean $(TEX)
pptx:   clean $(PPTX)

# GUIDE:
# See FINAL_DOC variable above
# NOTE Change this to arrange order of documents.
# Used to be grant.md.
$(FINAL_DOC):   00-metadata.yaml \
    01-presentation.md
    cat $^ >| $@

##########################
# FILE TYPES TO GENERATE #
##########################

# Guide:
# -r input format.
# -s enables titles?
# -V specifics a theme already in the system. Needs --template for personal theme.
# -t output format.
# $(FILTERS) after --pdf-engine.
# --csl=$(CSL).csl
# --bibliography=$(BIB)
# -N
# --reference-doc Use with pptx templates

%.pdf:  $(FINAL_DOC)
    pandoc -r markdown+$(EXTENSIONS) -t beamer \
    -s --pdf-engine=$(PDFENGINE) \
    $(FILTERS)  \
    -V theme:$(TEMPLATE) \
    -o $@ $<

%.tex:  $(FINAL_DOC)
    pandoc -r markdown+$(EXTENSIONS) \
    -s --pdf-engine=$(PDFENGINE) \
    $(FILTERS)  \
    -V theme:$(TEMPLATE) \
    -o $@ $<

# TODO Add  $(FILTERS)  \ to pptx?
%.pptx: $(FINAL_DOC)
    pandoc -r markdown+$(EXTENSIONS) -s -t pptx \
    -o $@ $<

clean:
    rm -f *.pdf *.tex *.pptx


#########################################
# # TO PUT TOGETHER THE FINALE DOCUMENT #
#########################################

# Guide:
# This segment will combine parts from multiple documents
# In this setup, it takes the $(GRANT_SHELL) page 1-8, places grant.pdf first 11 pages for 9-19, and back to $(GRANT_SHELL) for 20 onwards.
# TODO figure out this section

# $(SUBMISSION): final_presentation.pdf
#   pdfjam --a4paper $< \
#        --outfile $@

How To

Notes

stack overflow

Use either \note{}{=latex} or ::: note :::

Figures (LATEX)

Font size follows that in here

header-includes:
    - \usepackage[font={footnotesize},labelfont=bf]{caption}

\begin{figure}
    \includegraphics[width=0.5\textwidth,height=\textheight]{./images/EnvelopedmRNA.png}
    \caption{something here}
\end{figure}

Figures (MARKDOWN)

Haven't confirmed whether `#fig` works in this context

![alt_text](./image.pnd){ width=50% style="center" #fig:figurelabel }

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