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26 changes: 20 additions & 6 deletions docs/editorial_bot.md
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Expand Up @@ -241,6 +241,17 @@ If everything looks good with the draft proofs from the `@editorialbot recommend

EditorialBot will accept the paper, assign it a DOI, deposit it and publish the paper.

### Updating an already accepted paper

If the draft has been updated after a paper has been published, JOSS editors-in-chief can update the published info and PDF with the following command:

```text
@editorialbot reaccept
```

EditorialBot will update the published paper and re-deposit it.


### Rejecting a paper

JOSS editors-in-chief can reject a submission with the following command:
Expand Down Expand Up @@ -304,12 +315,6 @@ JOSS editors-in-chief can withdraw a submission with the following command:
# Set a value for repository
@editorialbot set https://github.com/org/repo as repository
# Reject paper
@editorialbot reject
# Withdraw paper
@editorialbot withdraw
# Invite an editor to edit a submission (sending them an email)
@editorialbot invite @(.*) as editor
Expand All @@ -328,6 +333,15 @@ JOSS editors-in-chief can withdraw a submission with the following command:
# Accept and publish the paper
@editorialbot accept
# Update an accepted paper
@editorialbot reaccept
# Reject paper
@editorialbot reject
# Withdraw paper
@editorialbot withdraw
# Flag submission with questionable scope
@editorialbot query scope
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325 changes: 324 additions & 1 deletion docs/submitting.md
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Expand Up @@ -102,11 +102,334 @@ As this short list shows, JOSS papers are only expected to contain a limited set
.. important:: Your paper will be reviewed by two or more reviewers in a public GitHub issue. Take a look at the `review checklist <review_checklist.html>`_ and `review criteria <review_criteria.html>`_ to better understand how your submission will be reviewed.
```

## How should my paper be formatted?

Submitted articles must use Markdown and must provide a metadata section at the beginning of the article. Format metadata using YAML, a human-friendly data serialization language (The Official YAML Web Site, 2022). The information provided is included in the title and sidebar of the generated PDF.

### Article metadata

#### Names

Providing an author name is straight-forward: just set the `name` attribute. However, sometimes more control over the name is required.

##### Name parts

There are many ways to describe the parts of names; we support the following:

- given names,
- surname,
- dropping particle,
- non-dropping particle,
- and suffix.

We use a heuristic to parse names into these components. This parsing may produce the wrong result, in which case it is necessary to provide the relevant parts explicitly.

The respective field names are

- `given-names` (aliases: `given`, `first`, `firstname`)
- `surname` (aliases: `family`)
- `suffix`

The full display name will be constructed from these parts, unless the `name` attribute is given as well.

##### Particles

It's usually enough to place particles like "van", "von", "della", etc. at the end of the given name or at the beginning of the surname, depending on the details of how the name is used.

- `dropping-particle`
- `non-dropping-particle`

##### Literal names

The automatic construction of the full name from parts is geared towards common Western names. It may therefore be necessary sometimes to provide the display name explicitly. This is possible by setting the `literal` field, e.g., `literal: Tachibana Taki`. This feature should only be used as a last resort. <!-- e.g., `literal: 宮水 三葉`. -->

##### Example

```yaml
authors:
- name: John Doe
affiliation: '1'

- given-names: Ludwig
dropping-particle: van
surname: Beethoven
affiliation: '3'

# not recommended, but common aliases can be used for name parts.
- given: Louis
non-dropping-particle: de
family: Broglie
affiliation: '4'
```

The name parts can also be collected under the author's `name`:

``` yaml
authors:
- name:
given-names: Kari
surname: Nordmann
```

<!-- - name: -->
<!-- literal: 立花 瀧 -->
<!-- given-names: 瀧 -->
<!-- surname: 立花 -->


### Internal references

The goal of Open Journals is to provide authors with a seamless and pleasant writing experience. Since Markdown has no default mechanism to handle document internal references, known as “cross-references”, Open Journals supports a limited set of LaTex commands. In brief, elements that were marked with `\label` and can be referenced with `\ref` and `\autoref`.

[Open Journals]: https://theoj.org

![View of coastal dunes in a nature reserve on Sylt, an island in
the North Sea. Sylt (Danish: *Slid*) is Germany's northernmost
island.](sylt.jpg){#sylt width="100%"}

#### Tables and figures

Tables and figures can be referenced if they are given a *label* in the caption. In pure Markdown, this can be done by adding an empty span `[]{label="floatlabel"}` to the caption. LaTeX syntax is supported as well: `\label{floatlabel}`.

Link to a float element, i.e., a table or figure, with `\ref{identifier}` or `\autoref{identifier}`, where `identifier` must be defined in the float's caption. The former command results in just the float's number, while the latter inserts the type and number of the referenced float. E.g., in this document `\autoref{proglangs}` yields "\autoref{proglangs}", while `\ref{proglangs}` gives "\ref{proglangs}".

: Comparison of programming languages used in the publishing tool. []{label="proglangs"}

| Language | Typing | Garbage Collected | Evaluation | Created |
|----------|:---------------:|:-----------------:|------------|---------|
| Haskell | static, strong | yes | non-strict | 1990 |
| Lua | dynamic, strong | yes | strict | 1993 |
| C | static, weak | no | strict | 1972 |

#### Equations

Cross-references to equations work similarly to those for floating elements. The difference is that, since captions are not supported for equations, the label must be included in the equation:

$$a^n + b^n = c^n \label{fermat}$$

Referencing, however, is identical, with `\autoref{eq:fermat}` resulting in "\autoref{eq:fermat}".

$$a^n + b^n = c^n \label{eq:fermat}$$

Authors who do not wish to include the label directly in the formula can use a Markdown span to add the label:

[$$a^n + b^n = c^n$$]{label="eq:fermat"}

### Behind the scenes

Readers may wonder about the reasons behind some of the choices made for paper writing. Most often, the decisions were driven by radical pragmatism. For example, Markdown is not only nearly ubiquitous in the realms of software, but it can also be converted into many different output formats. The archiving standard for scientific articles is JATS, and the most popular publishing format is PDF. Open Journals has built its pipeline based on [pandoc](https://pandoc.org), a universal document converter that can produce both of these publishing formats as well as many more.

A common method for PDF generation is to go via LaTeX. However, support for tagging -- a requirement for accessible PDFs -- is not readily available for LaTeX. The current method used ConTeXt, to produce tagged PDF/A-3.

### Markdown
Markdown is a lightweight markup language used frequently in software development and online environments. Based on email conventions, it was developed in 2004 by John Gruber and Aaron Swartz.

#### Inline markup

The markup in Markdown should be semantic, not presentations. The table below has some basic examples.

+---------------------+-------------------------+-----------------------+
| Markup | Markdown example | Rendered output |
+:====================+:=======================:+:=====================:+
| emphasis | `*this*` | *this* |
+---------------------+-------------------------+-----------------------+
| strong emphasis | `**that**` | **that** |
+---------------------+-------------------------+-----------------------+
| strikeout | `~~not this~~` | ~~not this~~ |
+---------------------+-------------------------+-----------------------+
| subscript | `H~2~O` | H~2~O |
+---------------------+-------------------------+-----------------------+
| superscript | `Ca^2+^` | Ca^2+^ |
+---------------------+-------------------------+-----------------------+
| underline | `[underline]{.ul}` | [underline]{.ul} |
+---------------------+-------------------------+-----------------------+
| small caps | `[Small Caps]{.sc}` | [Small Caps]{.sc} |
+---------------------+-------------------------+-----------------------+
| inline code | `` `return 23` `` | `return 23` |
+---------------------+-------------------------+-----------------------+

#### Links

Link syntax is `[link description](targetURL)`. E.g., this link to the [Journal of Open Source Software](https://joss.theoj.org/) is written as \
`[Journal of Open Source Software](https://joss.theoj.org/)`.

Open Journal publications are not limited by the constraints of print publications. We encourage authors to use hyperlinks for websites and other external resources. However, the standard scientific practice of citing the relevant publications should be followed regardless.

#### Grid Tables

Grid tables are made up of special characters which form the rows and columns, and also change table and style variables.

Complex information can be conveyed by using the following features not found in other table styles:

* spanning columns
* adding footers
* using intra-cellular body elements
* creating multi-row headers

Grid table syntax uses the characters "-", "=", "|", and "+" to represent the table outline:

* Hyphens (-) separate horizontal rows.
* Equals signs (=) produce a header when used to create the row under the header text.
* Equals signs (=) create a footer when used to enclose the last row of the table.
* Vertical bars (|) separate columns and also adjusts the depth of a row.
* Plus signs (+) indicates a juncture between horizontal and parallel lines.

Note: Inserting a colon (:) at the boundaries of the separator line after the header will change text alignment. If there is no header, insert colons into the top line.

Sample grid table:

+-------------------+------------+----------+----------+
| Header 1 | Header 2 | Header 3 | Header 4 |
| | | | |
+:=================:+:==========:+:========:+:========:+
| row 1, column 1 | column 2 | column 3 | column 4 |
+-------------------+------------+----------+----------+
| row 2 | cells span columns |
+-------------------+------------+---------------------+
| row 3 | cells | - body |
+-------------------+ span rows | - elements |
| row 4 | | - here |
+===================+============+=====================+
| Footer |
+===================+============+=====================+

#### Figures and Images

To create a figure, a captioned image must appear by itself in a paragraph. The Markdown syntax for a figure is a link, preceded by an exclamation point (!) and a description.
Example:
`![This description will be the figure caption](path/to/image.png)`

In order to create a figure rather than an image, there must be a description included and the figure syntax must be the only element in the paragraph, i.e., it must be surrounded by blank lines.

Images that are larger than the text area are scaled to fit the page. You can give images an explicit height and/or width, e.g. when adding an image as part of a paragraph. The Markdown `![Nyan cat](nyan-cat.png){height="9pt"}` includes the image saved as `nyan-cat.png` while scaling it to a height of 9 pt.

#### Citations

Bibliographic data should be collected in a file `paper.bib`; it should be formatted in the BibLaTeX format, although plain BibTeX is acceptable as well. All major citation managers offer to export these formats.

Cite a bibliography entry by referencing its identifier: `[@upper1974]`
will create the reference "(Upper 1974)". Omit the brackets when
referring to the author as part of a sentence: "For a case study on
writers block, see Upper (1974)." Please refer to the [pandoc
manual](https://pandoc.org/MANUAL#extension-citations) for additional
features, including page locators, prefixes, suffixes, and suppression
of author names in citations.

The full citation will display as

> Upper, D. 1974. "The Unsuccessful Self-Treatment of a Case of \"Writer's
> Block\"." *Journal of Applied Behavior Analysis* 7 (3): 497.
> <https://doi.org/10.1901/jaba.1974.7-497a>.
#### Mathematical Formulæ

Mark equations and other math content with dollar signs ($). Use a single dollar sign ($) for math that will appear directly within the text. Use two dollar signs ($$) when the formula is to be presented centered and on a separate line, in "display" style. The formula itself must be given using TeX syntax.

To give some examples: When discussing a variable *x* or a short formula like

```eval_rst
.. math::
\sin \frac{\pi}{2}
```

we would write $x$ and

$\sin \frac{\pi}{2}$

respectively. However, for more complex formulæ, display style is more appropriate. Writing

$$\int_{-\infty}^{+\infty} e^{-x^2} \, dx = \sqrt{\pi}$$

will give us

$$\int_{-\infty}^{+\infty} e^{-x^2} \, dx = \sqrt{\pi}$$

#### Footnotes

Syntax for footnotes centers around the "caret" character `^`. The symbol is also used as a delimiter for superscript text and thereby mirrors the superscript numbers used to mark a footnote in the final text.

``` markdown
Articles are published under a Creative Commons license[^1].
Software should use an OSI-approved license.

[^1]: An open license that allows reuse.
```

The above example results in the following output:

> ```eval_rst
>
> Articles are published under a Creative Commons license [#f1]_. Software should use an OSI-approved license.
>
> .. rubric:: Footnotes
>
> .. [#f1] An open license that allows reuse.
>
> ```
Note: numbers do not have to be sequential, they will be reordered automatically in the publishing step. In fact, the identifier of a note can be any sequence of characters, like `[^marker]`, but may not contain whitespace characters.


#### Blocks

The larger components of a document are called "blocks".

##### Headings

Headings are added with `#` followed by a space, where each additional `#` demotes the heading to a level lower in the hierarchy:

```markdown
# Section

## Subsection

### Subsubsection
```

Please start headings on the first level. The maximum supported level is 5, but paper authors are encouraged to limit themselves to headings of the first two or three levels.

###### Deeper nesting

Fourth- and fifth-level subsections – like this one and the following heading – are supported by the system; however, their use is discouraged. Use lists instead of forth- and fifth-level headings.


#### Lists

Bullet lists and numbered lists, a.k.a. enumerations, offer an additional method to present sequential and hierarchical information.

``` markdown
- apples
- citrus fruits
- lemons
- oranges
```

- apples
- citrus fruits
- lemons
- oranges

Enumerations start with the number of the first item. Using the the first two [laws of thermodynamics](https://en.wikipedia.org/wiki/Laws_of_thermodynamics) as example,

``` markdown
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. $$\Delta U = Q - W$$
```

Rendered:

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. $$\Delta U = Q - W$$

## Example paper and bibliography

This example `paper.md` is adapted from _Gala: A Python package for galactic dynamics_ by Adrian M. Price-Whelan [http://doi.org/10.21105/joss.00388](http://doi.org/10.21105/joss.00388).

For a complete description of available options to describe author names [see here](https://github.com/openjournals/inara/blob/main/docs/names.md/).
For a complete description of available options to describe author names [see here](#names).

```
---
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