JOSS paper

[jagoosw]

To do:

• [x] Finish writing paper
• [x] Fix API documentation (some not being automatically imported for some reason)
• [x] Put package on Pkg
• [x] Make the OVS poster figures more size/shape appropriate
• [ ] Check I've not broken box models - examples double as tests
• [x] Fix figure

[jagoosw]

Docs now fixed and more complete #77

[jagoosw]

Now I've compiled the draft I do think I need to make the figure font sizes larger

[johnryantaylor]

It’s mostly the font sizes that are too small to easily read at 100% magnification.  However, the way that the sub panels are arrange might make it difficult to increase the font size.  It might be better to have all sub panels in a single column.  Another small comment is that the time for the Kelp Growth in Figure 1 might be confusing since the axis label starts at t=0, but the kelp don’t actually start growing until near the end of the second year.

On Mar 18, 2023 at 7:56 PM +0000, Jago Strong-Wright @.***>, wrote:

Now I've compiled the draft I do think I need to make the figure font sizes larger — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you are subscribed to this thread.Message ID: @.***>

[jagoosw]

@johnryantaylor For the column figure, do you think this is large enough font now? Or should I move the panels around?

https://github.com/OceanBioME/OceanBioME.jl/suites/11702149339/artifacts/608761660

[johnryantaylor]

The new Figure 1 looks great, thanks!  Fonts are still small in Figure 2 (but I think you haven’t updated that one). On Mar 21, 2023 at 11:23 AM +0000, Jago Strong-Wright @.***>, wrote:

For the column figure, do you think this is large enough font now? Or should I move the panels around? https://github.com/OceanBioME/OceanBioME.jl/suites/11702149339/artifacts/608761660 — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you commented.Message ID: @.***>

[jagoosw]

@johnryantaylor are you happy with how it is now? It does mean the colorbars are quite big but I don't think theres any other way to include them, and do think they need to be included.

https://github.com/OceanBioME/OceanBioME.jl/suites/11715754847/artifacts/609710562

[johnryantaylor]

Looks great, thanks! On Mar 21, 2023 at 8:15 PM +0000, Jago Strong-Wright @.***>, wrote:

@johnryantaylor are you happy with how it is now? It does mean the colorbars are quite big but I don't think theres any other way to include them, and do think they need to be included. https://github.com/OceanBioME/OceanBioME.jl/suites/11715754847/artifacts/609710562 — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you were mentioned.Message ID: @.***>

[jagoosw]

Made a mess trying to merge main

[codecov[bot]]

Codecov Report

All modified lines are covered by tests :white_check_mark:

Comparison is base (4cf6565) 65.78% compared to head (7e92e74) 65.78%.

Additional details and impacted files

```diff @@ Coverage Diff @@ ## main #76 +/- ## ======================================= Coverage 65.78% 65.78% ======================================= Files 27 27 Lines 1064 1064 ======================================= Hits 700 700 Misses 364 364 ```

:umbrella: View full report in Codecov by Sentry.
:loudspeaker: Have feedback on the report? Share it here.

[jagoosw]

Just realised the column figure is slightly wrong still

[jagoosw]

It's automatically adding an affiliation to "Collaborators", given that I think everyone else who has helped is affiliated with CliMA we could put that?

[johnryantaylor]

I noticed that too, but I don’t think that it matters right now - we can update as we add more names. On Jun 9, 2023 at 2:26 PM +0100, Jago Strong-Wright @.***>, wrote:

It's automatically adding an affiliation to "Collaborators", given that I think everyone else who has helped is affiliated with CliMA we could put that? — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you were mentioned.Message ID: @.***>

[jagoosw]

@johnryantaylor I've tried adding the suggestions from @glwagner. Not sure I've added them in the best place?

[glwagner]

I made a comment! Note, it's easier to comment on the markdown file if each sentence has it's own line.

[jagoosw]

I made a comment! Note, it's easier to comment on the markdown file if each sentence has it's own line.

Good to know, I'll add some line breaks to make it easier. Thanks!

[jagoosw]

Do we want British or American English? One of the spellings Grammarly caught was an American spelling but the rest are the British versions I think. The JOSS documentation doesn't seem to express a preference.

[jagoosw]

hi @jagoosw and @johnryantaylor, paper reads well! -- just a few minor comments. Nothing crucial, take them or leave them.

Thank you! These are very helpful

[navidcy]

Another remark is that sometimes we refer to packages using their .jl ending and sometimes not. Should we homogenize or is it clear you reckon?

[jagoosw]

Another remark is that sometimes we refer to packages using their .jl ending and sometimes not. Should we homogenize or is it clear you reckon?

This is a good point, I think it flows better to not have the .jl but other paper do consistently use the whole name in ` marks.

[jagoosw]

I've changed them now but it might look a bit funny so we might want to change them all back

[navidcy]

This looks pretty much ready!

We can include a Project.toml and Manifest.toml file in the paper directory so that the scripts that reproduce the figures are ensured to run. But we don't need to do this now in case we ask to revise the figures in the review process.

[jagoosw]

This looks pretty much ready!

We can include a Project.toml and Manifest.toml file in the paper directory so that the scripts that reproduce the figures are ensured to run. But we don't need to do this now in case we ask to revise the figures in the review process.

Great, thanks!

[jagoosw]

@johnryantaylor @syou83syou83 @glwagner should I submit this now if everyone's happy?

[simone-silvestri]

Hello @jagoosw, thanks for the addition. Good job with the paper; it reads very nicely. Also, good job with the package! I also have a couple of minor comments, take a look if you'd like.

[jagoosw]

Hi @simone-silvestri, thank you, these are very useful comments!

When we wrote about PISCES we were planning on implementing it, and I've done some of the work to do so in a branch that is very out of date now, so I will remove that from the list.

[jagoosw]

Hi all, I've attempted to make some of the changes suggested in the review for the paper here. Not sure it's all correct yet but hopefully should satisfy the queries. I'm also going to open a PR with the other docs changes.

[jagoosw]

I've tried to add a couple of sentences and a short code snippet about how easy it is to modify models, but I'm not sure if I've done it quite clumsily.

Francis has made a good point that this is an important feature that we should definitely note.

[jagoosw]

Okay, so I've tried rewriting the bit about adding models referencing the docs I've written #131. I'm not sure it's right still, thoughts would be appreciated.

[jagoosw]

I think this is now finalised if everyone is happy? @johnryantaylor

[navidcy]

I'm happy. Could you perhaps resolve the conflicts in simple_multi_G.jl?

[jagoosw]

I'm happy. Could you perhaps resolve the conflicts in simple_multi_G.jl?

done

[jagoosw]

I might have deleted a change you made to the sediment thing actually @navidcy ?

[jagoosw]

Once we're done we need to delete the draft workflow before merging too