diff --git a/template/docs/papers/joss/paper.md b/template/docs/papers/joss/paper.md new file mode 100644 index 00000000..e1811166 --- /dev/null +++ b/template/docs/papers/joss/paper.md @@ -0,0 +1,183 @@ +--- +title: >- + MyPackage: A Very Cool Python Application +authors: + - name: Jane Doe + affiliation: 1 + orcid: 0000-0000-0000-0001 + email: jane@doe.com + corresponding: true + - name: John L. Doe + orcid: 0000-0000-0000-0001 + affiliation: [ 1, 2 ] + equal-contrib: true + - name: John Smith + orcid: 0000-0000-0000-0001 + affiliation: [ 2, 3 ] + equal-contrib: true + - given-names: Ludwig + dropping-particle: van + surname: Beethoven + suffix: Jr + affiliation: 3 + email: email@example.com + orcid: 0000-0000-0000-0001 + corresponding: true + - given-names: Ludwig + non-dropping-particle: van + surname: Beethoven + suffix: Jr + affiliation: 3 + email: email1@example.com + orcid: 0000-0000-0000-0001 + - name: Ludwig Beethoven + given-names: Ludwig + non-dropping-particle: van + surname: Beethoven + suffix: Jr + affiliation: 3 + email: email2@example.com + orcid: 0000-0000-0000-0001 +affiliations: + - index: 1 + name: Independent Researcher, Country + - index: 2 + name: Institution Name, Country + - index: 3 + name: Lyman Spitzer, Jr. Fellow, Princeton University, United States + ror: 00hx57361 +tags: + - first keyword + - second keyword + - third keyword +software_repository_url: https://github.com/repodynamics/pypackit +archive_doi: 10.5281/zenodo.12345678 +date: 11 November 2024 +bibliography: ../paper.bib +--- + +# Summary + +Begin your paper with a summary of the high-level functionality +of your software for a non-specialist reader. +Avoid jargon in this section. + +JOSS welcomes submissions from broadly diverse research areas. +For this reason, we require that authors include in the paper some sentences +that explain the software functionality and domain of use to a non-specialist reader. +We also require that authors explain the research applications of the software. +The paper should be between 250-1000 words. +Authors submitting papers significantly longer than 1000 words +may be asked to reduce the length of their paper. + +JOSS papers are only expected to contain a limited set of metadata, +a Statement of need, Summary, Acknowledgements, and References sections. +Given this format, a “full length” paper is not permitted, +and software documentation such as API (Application Programming Interface) functionality +should not be in the paper and instead should be outlined in the software documentation. + +# Statement of Need + +A Statement of need section that clearly illustrates the research purpose +of the software and places it in the context of related work. + +# Other Sections + +Other than a **Summary** and a **Statement of Need** section, +your paper can also contain other main sections and sub-sections. + +## Citations + +Citations can be used like this [@michaud-agrawal2011mdanalysis] [@oliver_beckstein-proc-scipy-2016] [@alibay2023building], +or this [@pedregosa2011scikitlearn], or this @pedregosa2011scikitlearn. + +## Math Equations + +For inline math, use single dollars `$`; for example $f(x) = e^{\pi/x}$. + +For block math, use \LaTeX: + +\begin{equation} +\label{eq:fourier} +\hat f(\omega) = \int_{-\infty}^{\infty} f(x) e^{i\omega x} dx +\end{equation} + +Math blocks can be referenced like this \autoref{eq:fourier} or this \ref{eq:fourier}. + +## Markdown + +Links can be used like [this](https://example.com). + +For long dashes---like this one---use three hyphens. + +### Inline Markup + +Inline markup in Markdown should be semantic, not presentations. +It can be used to make *italic*, **bold**, ~~strikethrough~~, ~sub~script, ^super^script, +[underline]{.ul}, [Small Caps]{.sc}, and `inline code`. + +### Lists + +- apples +- citrus fruits + - lemons + - oranges + +### Ordered Lists + +0. If two systems are each in thermal equilibrium with a third, they are + also in thermal equilibrium with each other. +1. In a process without transfer of matter, the change in internal + energy, $\Delta U$, of a thermodynamic system is equal to the energy + gained as heat, $Q$, less the thermodynamic work, $W$, done by the + system on its surroundings. $$\Delta U = Q - W$$ + + +### Tables + +Read the [pandoc manual](https://pandoc.org/MANUAL.html#tables) for more details. + +Tables can be given captions like this: + +: This is the caption of the table; + it must start with a colon and be separated from the table by one empty line.\label{tab:example} + +| Header 1 | Header 2 | +|---------------|---------------| +| Row 1, Cell 1 | Row 1, Cell 2 | +| Row 2, Cell 1 | Row 2, Cell 2 | + +and referenced from text using \autoref{tab:example} or \ref{tab:example}. + +### Inline Images + +Inline images can be used like this ![](../full_light.png){height="9pt"} inside a paragraph. + +### Figures + +Figures can be included like this: + +![This is the caption of the figure.\label{fig:example}](../full_light.png){ width=50% } + +and referenced from text using \autoref{fig:example} or \ref{fig:example}. + +### Code Blocks + +Read the [pandoc manual](https://pandoc.org/MANUAL.html#verbatim-code-blocks) for more details. + +```{.python .numberLines} +def f(x): + return x +``` + + +### Footnotes + +Footnotes can be defined anywhere (see end of document) and referenced using [^first-footnote]. + + +# Acknowledgements + +# References + +[^first-footnote]: This is a footnote. \ No newline at end of file