Writing log template in Typst for journal article

A nice introduction to Typst in October 2024 by Dr. Chase Brown of the University of Central Florida is found here.

Purpose

Support the preparation of a scientific journal article for submission by providing space for thinking and planning the manuscript rather than doing this in the margins of the manuscript document.

What is typst?

A type-setting program built on top of the programming language Rust. It compiles small documents almost instantly, so it can be used interactively. The typst.app is analogous to Overleaf in the LaTeX world.

Features

• table of contents
• Project initiation metadata
• Project management metadata
• Daily log
• To dos
• Future off-shoots
• Protocols
• List of typst links
• index
• bibliography
• single- and double-spacing
• running title in header
• 1/N page numbering
• BibLaTeX

Sample of first page

Contents

• typst source file template
• biblatex file
• sample PDF
• wordcount.csv

Requirements

• typst version 0.11.0 or more recent
• in-dexter v0.6.0 to generate an index (optional).
• cheq v0.2.0 to generate checklists (optional)

How to install packages locally

Git clone the package in {data-dir}/typst/packages/{namespace}/{name}/{version} to make it available on your system.

Here, {data-dir} is one of the following:

Linux: $XDG_DATA_HOME or ~/.local/share on Linux MacOS: ~/Library/Application Support on macOS Windows: %APPDATA% on Windows

Packages in the data directory have precedence over ones in the cache directory. A good namespace for system-local packages is local: Import the package in your typst file with #import "@local/mypkg:1.0.0": *.

Bash or zsh function to compile to PDF and open in Preview.app on Mac (optional)

Typst compiles the *.typfile so quickly that you might as well pop open the PDF: typc <filename prefix>.

function typc {
echo "Compile typst file to PDF and display PDF file."
if [ $# -lt 1 ]; then
  echo 1>&2 "$0: not enough arguments"
  echo "Usage1: typc <filename prefix>"
  return 2
elif [ $# -gt 1 ]; then
  echo 1>&2 "$0: too many arguments"
  echo "Usage1: typc  <typst filename prefix>"
  return 2
fi
typst compile $1.typ && pre $1.pdf
}

Bash or zsh function to preview typst file with tinymist (optional)

Yes, I hate typing: `tmp "

function tmp {
echo "Preview typst file in browser via tinymist."
if [ $# -lt 1 ]; then
  echo 1>&2 "$0: not enough arguments"
  echo "Usage1: tmp <filename prefix>"
  return 2
elif [ $# -gt 1 ]; then
  echo 1>&2 "$0: too many arguments"
  echo "Usage1: typc  <filename prefix>"
  return 2
fi
tinymist preview $1.typ
}

Optional bash functions to ease copying the template to a new project

Store in .bashrc or .zshrc. Edit file paths to suit. Two functions are provided, so you do not have to remember the order of the component names in the function name.

function typlog {
echo "Copy template writing log in typst with project number in title."
if [ $# -lt 1 ]; then
  echo 1>&2 "$0: not enough arguments"
  echo "Usage1: typlog projectID"
  return 2
elif [ $# -gt 1 ]; then
  echo 1>&2 "$0: too many arguments"
  echo "Usage1: typlog projectID"
  return 2
fi
projectID="$1"
echo "Write writing log to log$1.typ file."
cp  ~/6112MooersLabGitHubLabRepos/writingLogInTypst/logTemplate.org log$1.typ
cp  ~/6112MooersLabGitHubLabRepos/writingLogTemplateInTypst/wordcount.csv .
cp  ~/6112MooersLabGitHubLabRepos/writingLogTemplateInTypst/template.bib $1.bib
}

function logtyp {
echo "Copy template writing log in typst with project number in title."
if [ $# -lt 1 ]; then
  echo 1>&2 "$0: not enough arguments"
  echo "Usage1: logtyp projectID"
  return 2
elif [ $# -gt 1 ]; then
  echo 1>&2 "$0: too many arguments"
  echo "Usage1: logtyp projectID"
  return 2
fi
projectID="$1"
echo "Write writing log to log$1.typ file."
cp  ~/6112MooersLabGitHubLabRepos/writingLogInTypst/logTemplate.org log$1.typ
cp  ~/6112MooersLabGitHubLabRepos/writingLogTemplateInTypst/wordcount.csv .
cp  ~/6112MooersLabGitHubLabRepos/writingLogTemplateInTypst/template.bib $1.bib
}

Update history

Version	Changes	Date
Version 0.1	Initiate project. Added badges, funding, and update table.	2024 October 11
Version 0.2	Added two bash convience functions to README.md.	2024 October 19

Sources of funding

• NIH: R01 CA242845
• NIH: R01 AI088011
• NIH: P30 CA225520 (PI: R. Mannel)
• NIH: P20 GM103640 and P30 GM145423 (PI: A. West)