Joss-reviews: [PRE REVIEW]: Visually comparing climate model output with observations

[whedon]

Submitting author: @mvhulten (Marco van Hulten)
Repository: https://savannah.nongnu.org/projects/complot/
Version: 0.1
Editor: @lheagy
Reviewer: @AnsleyManke

Author instructions

Thanks for submitting your paper to JOSS @mvhulten. The JOSS editor (shown at the top of this issue) will work with you on this issue to find a reviewer for your submission before creating the main review issue.

@mvhulten if you have any suggestions for potential reviewers then please mention them here in this thread. In addition, this list of people have already agreed to review for JOSS and may be suitable for this submission.

Editor instructions

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@whedon commands

[whedon]

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For a list of things I can do to help you, just type:

@whedon commands

[kyleniemeyer]

@lheagy might this be a suitable submission for you to take on?

[lheagy]

@kyleniemeyer: I have never worked with Ferret, the language they are scripting in, however, I do think I can help find some suitable reviewers for this.

[kyleniemeyer]

@lheagy sounds good! I'll go ahead and give it to you then (though in the future feel free to assign yourself).

@whedon assign @lheagy as editor

[kyleniemeyer]

Hmm, not sure why that didn't work...

[kyleniemeyer]

@whedon assign @lheagy as editor

[whedon]

OK, the editor is @lheagy

[lheagy]

Thank you for your submission @mvhulten.

Before we start looking for reviewers, could you please include a paper.md in the repository? This should include an description of the software, provide some context and a statement of need (eg. http://joss.theoj.org/papers/b3adbbf7df62f4e427f19e99e70163f5).

Additionally, the site https://savannah.nongnu.org/projects/complot/ is a bit challenging to navigate. Would it be possible to also include links to the paper.md and source code in the description of the package?

Please let me know if you have any questions!

[mvhulten]

Thank you for accepting my paper for review!
I will respond more extensively later on, but I will quickly respond to @lheagy.

I tried to make a README.md that could be used as the paper. Maybe it is better to create a separate paper.md? Otherwise, I could symlink README.md to paper.md.

The repository is here: http://hg.savannah.nongnu.org/hgweb/complot/
Is it sufficient to add this to the paper.md? I was thinking about creating a decent website (served on the same location).

[lheagy]

Thanks @mvhulten, if you could please add a paper.md, that would make it more clear for both myself and the reviewers. Any references can be included as a bibtex file (paper.bib). For an example, see: https://github.com/arfon/fidgit/tree/master/paper

Upgrading the website would help elevate the usability of the project. Is this something you would like to do prior to engaging with reviewers? It would be a great opportunity to get feedback on a new website. This is not required, so please let me know what you would like to do!

[kyleniemeyer]

@mvhulten to add to what @lheagy said, JOSS requires an article, including references. Please see the author guidelines for a description of what is required in this.

The article does not serve the same purpose as a README, but should be a 250–1000 word high-level description of the software, including a statement of need and description of the software functionality. For example, see http://dx.doi.org/10.21105/joss.00301 and https://doi.org/10.21105/joss.00031 for good examples.

[mvhulten]

I am preparing the paper according to the guidelines.

I am not sure in what time frame I will have a proper website for ComPlot, so probably it is better to start the review without it (when I reply here with the info that I included a paper.md).

[mvhulten]

I have added a paper.md. As far as I am concerned, you may start with the review.

In the meanwhile I did think of several people who are qualified to do the review:

• Anne Mouchet
• Patrick Brockmann
• Ansley Manke

My colleagues at LSCE are heavy users of Ferret.
Ferret is developed at NOAA. Ansley is one of its main developers.

[lheagy]

Thanks @mvhulten. Of the reviewers that you have suggested, are they at arms length of the project, particularly those who are at the same institution as you? (eg. they are not currently contributors or currently providing you with feedback on ComPlot).

I do have a couple more requests prior to sending it for review:

• It is not necessarily obvious how to navigate from the main website to the location of the paper.md. Could you please add a link from the main page to where we can view the source code at: http://hg.savannah.nongnu.org/hgweb/complot/file/cbda29db682d. (At a minimum, instructions on how to navigate to the source-code should be stated in the main description of the package). Alternatively, if you would be open to putting the code up on github, it is widely used and the navigation is familiar for many.
  

• One comment regarding scope: the downloading instructions in the # Availability section are more suited for a README than the article. If you would still like to include a statement pointing readers to instructions for downloading the software, I would recommend putting it at the end of the article similar to what is done in: http://joss.theoj.org/papers/10.21105/joss.00031.

• I did not see the paper.bib in the repository. Could you please ensure it is included in the repository.

Thanks and please let me know if I can clarify any of these comments!

[mvhulten]

Thanks @lheagy.

LSCE is my previous institute. I did discuss with Patrick technical details, but not really about the package structure. The same is true for Ansley. Anne was just interested and did not provide any input to the package. Right now I am at the University of Bergen. In any case, they are neither contributors currently or in the past, nor are they currently providing me with feedback on ComPlot. Ansley and Patrick helped me, as many more people, with technical Ferret issues.

Savannah was a conscious choice. Moreover, it might be a good idea to try to keep JOSS independent of the hosting service (and version control system). I am hoping this will work out.

I added the link to the source code on the project page.

I moved the availability section, and added paper.bib to the repository (thanks for noticing!).

[lheagy]

Thanks @mvhulten! I will start reaching out to reviewers

[lheagy]

@whedon commands

[whedon]

Here are some things you can ask me to do:

# List all of Whedon's capabilities
@whedon commands

# Assign a GitHub user as the reviewer of this submission
@whedon assign @username as reviewer

# List the GitHub usernames of the JOSS editors
@whedon list editors

# List of JOSS reviewers together with programming language preferences and domain expertise
@whedon list reviewers

# Change editorial assignment
@whedon assign @username as editor

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@whedon set 10.0000/zenodo.00000 as archive

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:construction: Important :construction:

This is all quite new. Please make sure you check the top of the issue after running a @whedon command (you might also need to refresh the page to see the issue update).

[lheagy]

@whedon list reviewers

[whedon]

Here's the current list of JOSS reviewers: https://github.com/openjournals/joss/blob/master/docs/reviewers.csv

[lheagy]

@mvhulten: sorry for the delayed update. Here is a quick overview on where we are at with reviewers.

I have heard back from Ansley and she is willing to review. I sent a follow up email asking her to sign up for github so we can get the ball rolling and got a vacation responder from her, so I will follow up again first thing next week.

Anne has declined to review and I am still waiting to hear back from Patrick. Feel free to also reach out to Patrick to ask if he is willing to review. I sent one follow up email to him and will also try again next week. If we don't hear back from him, we can start asking reviewers from the JOSS list.

[mvhulten]

Thank you @lheagy for the status update.

I approached two people for review, but received no positive response so far. Specifically, I asked Patrick Brockmann who is positive about the idea of reviewing this but is on holidays until the end of the month, and Alessandro Tagliabue from who I got an auto-reply with the same information.

It would be fine with me to go ahead with the JOSS list.

[lheagy]

@jsta, @pboesu have either of you worked with Ferret? Would you be willing to review this submission?

[lheagy]

Thanks @AnsleyManke for volunteering to review. Ideally, we will find at least one more reviewer to help out as well.

[lheagy]

@whedon assign @AnsleyManke as reviewer

[whedon]

OK, the reviewer is @AnsleyManke

[lheagy]

@whedon start review

[whedon]

You didn't say the magic word! Try this:

@whedon start review magic-word=bananas

[lheagy]

@whedon start review magic-word=bananas

[whedon]

OK, I've started the review over in https://github.com/openjournals/joss-reviews/issues/368. Feel free to close this issue now!

[pboesu]

@lheagy While I have a background in biological oceanography, I unfortunately I don't have any experience with Ferret and only limited experience with python, so I'd be hesitant to review this contribution, unless you think a review of a "naive user" would be of use.

[lheagy]

Thanks @pboesu, no problem. @AnsleyManke is a involved with the Ferret project and has agreed to review, so I think we are in good shape.