Changes for JOSS reviewing process

[michael-petersen]

There are several adjustments and improvements to make as part of the JOSS review process; this branch will handle them in one place.

[michael-petersen]

First, a quality-of-life improvement with adding an issue template.

[michael-petersen]

Some draft paper updates to resolve #97.

Anything else we should add, @The9Cat?

[The9Cat]

That seems good to me. I suppose we could add the original S-L description in the 1999 paper, but the recent other paper(s) are more complete and refer to the 1999 paper, and that paper doesn't describe EXP per se.

[michael-petersen]

To keep notes in the same place: #95 is being addressed in the relevant repositories, see links in that issue.

[michael-petersen]

Following up on openjournals/joss-reviews#7302 (comment):

We've updated and run through the tutorials using the latest main branch of EXP (which is also the Docker image), and think we've caught all the bugs now!

[michael-petersen]

Note that this link won't work until merge.

[michael-petersen]

Addressing openjournals/joss-reviews#7302 (comment):

We've added a CITATIONS.bib; this will also update upon JOSS acceptance to include the citation!

[michael-petersen]

I believe the last un-addressed comment is openjournals/joss-reviews#7302 (comment):

1. Do we want to update some images to .svg?
2. I'm imagining the inputs/outputs graphic would be command-line screenshots (or equivalently put into markdown)? Or is there an obvious flowchart idea I'm missing?

[The9Cat]

As I understand it, the idea is to improve the tutorial walk through showing both code input & output. It's a good idea but one that would take a bit of time. My take on the comment is the suggestion to save screenshots from the browser running Jupyter to svg. There is a Firefox extension for that, I believe. Random bitmapped graphics won't be improved by svg.

[michael-petersen]

Many of the pyEXP-examples entries have their own notebooks that have input/output stored -- do you think this is enough? Or is the relevant thing to consider what the EXP-examples needs for input/output examples?

[michael-petersen]

@The9Cat has helpfully set up a notebook renderer in EXP-code/EXP-docs#33. This means that for readthedocs, notebooks that are generated as part of the tutorials in pyEXP-examples. Check it out by clicking any of the links in the Jupyter branch of readthedocs!

We'll merge this in to EXP-docs once everyone is happy.

This addresses openjournals/joss-reviews#7302 (comment).

[The9Cat]

The last commit included a few additional wording fixes, added a note about the data to run the examples, and added navigation stubs to the imported ipynb files back to the Github pyEXP-examples repo. Looks fine to me now.

[michael-petersen]

@The9Cat, we've received word this satisfies the reviewers -- can you take a quick look and approve+merge when ready?

[The9Cat]

Sure, I'll take a quick look now. I've already reviewed this casually and didn't find any issues.