https://github.com/mooerslab/writinglogintypst
Template in typst for writing log for scientific journal article
https://github.com/mooerslab/writinglogintypst
template typst writing-log-for-journal-article writing-project-management
Last synced: 3 months ago
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Template in typst for writing log for scientific journal article
- Host: GitHub
- URL: https://github.com/mooerslab/writinglogintypst
- Owner: MooersLab
- Created: 2024-10-12T03:46:02.000Z (over 1 year ago)
- Default Branch: main
- Last Pushed: 2024-11-01T17:32:34.000Z (over 1 year ago)
- Last Synced: 2025-02-07T03:41:59.005Z (over 1 year ago)
- Topics: template, typst, writing-log-for-journal-article, writing-project-management
- Language: Typst
- Homepage:
- Size: 207 KB
- Stars: 1
- Watchers: 1
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
Awesome Lists containing this project
README
[](https://opensource.org/licenses/MIT)
# 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](https://mediasite.ouhsc.edu/Mediasite/Channel/python/browse/null/most-recent/null/0/null).
## 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](https://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 `.
```bash
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 "
return 2
elif [ $# -gt 1 ]; then
echo 1>&2 "$0: too many arguments"
echo "Usage1: typc "
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 "
```bash
function tmp {
echo "Preview typst file in browser via tinymist."
if [ $# -lt 1 ]; then
echo 1>&2 "$0: not enough arguments"
echo "Usage1: tmp "
return 2
elif [ $# -gt 1 ]; then
echo 1>&2 "$0: too many arguments"
echo "Usage1: typc "
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.
```bash
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)