loiseaujc / Template-Scientific-Paper

Simple template for writing a scientific paper

Simple template for writing a scientific article with $\LaTeX$

This is a template repository for writing scientific papers, most notably with $\LaTeX$. The structure of the repository is shown below.

.
├── data
├── manuscript
│   ├── archives
│   ├── cover letter
│   └── main
├── notebooks
├── papers
├── plots
├── scripts
├── src
└── test

Each of these folders serve the following purposes:

• data: This folder contains all the (pre-processed) data needed for generating the different figures.
• manuscript: This folder contains all the files related to the manuscript.
  • archives: This folder contains the archived versions of the manuscript as well as the communications with the journal to which it has been submitted.
  • cover letter: This folder contains the cover letter send to the editor of the journal.
  • main: This folder contains the current version of the manuscript.
• notebooks: This folder contains all the illustratory notebooks provided as supplementary material (if any).
• papers: This folder contains (whenever possible) the pdf of the different articles cited in the manuscript.
• plots: This folder contains all of the plots included in the manuscript as well as those possibly generated for seminars and presentations.
• scripts: This folder contains all the scripts (e.g. Python, R, or Julia) needed to regenerate the figures.
• src: This folder includes all of the source code (Julia, Python, Fortran, etc) needed to re-run the computations.
• test: This folder contains all the tests (if any) used to validate the different implementations.

This template repository also sets up some GitHub Actions to automatically compile the pdf associated with manuscript/main/Main.tex. Note that this Action is only executed when changes to any files in manuscript/main are being pushed. Modifications of any other file in the repository will not trigger it. The resulting pdf can be found from the Actions tab on github.com by clicking on the Summary associated with the last Action executed. A similar GitHub Action is set up to automatically compiled the cover letter if any changes to manuscript/cover_letter are being pushed.

Good practices in $\LaTeX$

The folder manuscript/main contains the template of a paper written using $\LaTeX$. It includes the files:

• preamble.tex: Import of various $\LaTeX$ packages,
• macros.tex: Definition of various math-related macros and (re)definition of commands.

Note that it only is a starting point. Feel free to modify it to your convenience by adding or removing any packages or macros you want. Numerous resources for good $\LaTeX$ practices can be found online. You will find below a non-exhaustive list:

• latex-advice by Diomidis Spinellis

Here are also a few useful resources about how to make nice figures using matplotlib:

• tikzplotlib: A nice Python utility to translate matplotlib figure into tikz code that can easily be incorporated into a $\LaTeX$ document.
• HowToMakeAPlot: Slides and code by Ciaran O'Hare focused around specific examples to improve plots using matplotlib.
• SciencePlots: A Python package providing different matplotlib styles to format figures for scientific papers.
• Scientific Visualization: Python + Matplotlib: An open source by Nicolas Rougier which I highly recommend!

Reproducible research

Miscellaneous