Create paper.md

template/docs/papers/joss/paper.md

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+---
+title: >-
+    MyPackage: A Very Cool Python Application
+authors:
+  - name: Jane Doe
+    affiliation: 1
+    orcid: 0000-0000-0000-0001
+    email: [email protected]
+    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 protected]
+    orcid: 0000-0000-0000-0001
+    corresponding: true
+  - given-names: Ludwig
+    non-dropping-particle: van
+    surname: Beethoven
+    suffix: Jr
+    affiliation: 3
+    email: [email protected]
+    orcid: 0000-0000-0000-0001
+  - name: Ludwig Beethoven
+    given-names: Ludwig
+    non-dropping-particle: van
+    surname: Beethoven
+    suffix: Jr
+    affiliation: 3
+    email: [email protected]
+    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.