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[REVIEW]: WRF-CMake: integrating CMake support into the Advanced Research WRF (ARW) modelling system #1468

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whedon opened this issue May 21, 2019 · 96 comments

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commented May 21, 2019

Submitting author: @letmaik (Maik Riechert)
Repository: https://github.com/WRF-CMake/WRF
Version: WRF-CMake-4.0.3
Editor: @arfon
Reviewer: @zbeekman, @andreas-h
Archive: 10.5281/zenodo.3403343

Status

status

Status badge code:

HTML: <a href="http://joss.theoj.org/papers/9a87d84b2ed00ed82a6e297a4c34b3cf"><img src="http://joss.theoj.org/papers/9a87d84b2ed00ed82a6e297a4c34b3cf/status.svg"></a>
Markdown: [![status](http://joss.theoj.org/papers/9a87d84b2ed00ed82a6e297a4c34b3cf/status.svg)](http://joss.theoj.org/papers/9a87d84b2ed00ed82a6e297a4c34b3cf)

Reviewers and authors:

Please avoid lengthy details of difficulties in the review thread. Instead, please create a new issue in the target repository and link to those issues (especially acceptance-blockers) by leaving comments in the review thread below. (For completists: if the target issue tracker is also on GitHub, linking the review thread in the issue or vice versa will create corresponding breadcrumb trails in the link target.)

Reviewer instructions & questions

@zbeekman & @andreas-h, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

  1. Make sure you're logged in to your GitHub account
  2. Be sure to accept the invite at this URL: https://github.com/openjournals/joss-reviews/invitations

The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @arfon know.

Please try and complete your review in the next two weeks

Review checklist for @zbeekman

Conflict of interest

Code of Conduct

General checks

  • Repository: Is the source code for this software available at the repository url?
  • License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
  • Version: WRF-CMake-4.0.3
  • Authorship: Has the submitting author (@letmaik) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

Functionality

  • Installation: Does installation proceed as outlined in the documentation?
  • Functionality: Have the functional claims of the software been confirmed?
  • Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Documentation

  • A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
  • Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
  • Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
  • Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
  • Automated tests: Are there automated tests or manual steps described so that the function of the software can be verified?
  • Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support

Software paper

  • Authors: Does the paper.md file include a list of authors with their affiliations?
  • A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
  • References: Do all archival references that should have a DOI list one (e.g., papers, datasets, software)?

Review checklist for @andreas-h

Conflict of interest

Code of Conduct

General checks

  • Repository: Is the source code for this software available at the repository url?
  • License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
  • Version: WRF-CMake-4.0.3
  • Authorship: Has the submitting author (@letmaik) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

Functionality

  • Installation: Does installation proceed as outlined in the documentation?
  • Functionality: Have the functional claims of the software been confirmed?
  • Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Documentation

  • A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
  • Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
  • Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
  • Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
  • Automated tests: Are there automated tests or manual steps described so that the function of the software can be verified?
  • Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support

Software paper

  • Authors: Does the paper.md file include a list of authors with their affiliations?
  • A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
  • References: Do all archival references that should have a DOI list one (e.g., papers, datasets, software)?
@whedon

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commented May 21, 2019

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @zbeekman, it looks like you're currently assigned as the reviewer for this paper 🎉.

⭐️ Important ⭐️

If you haven't already, you should seriously consider unsubscribing from GitHub notifications for this (https://github.com/openjournals/joss-reviews) repository. As a reviewer, you're probably currently watching this repository which means for GitHub's default behaviour you will receive notifications (emails) for all reviews 😿

To fix this do the following two things:

  1. Set yourself as 'Not watching' https://github.com/openjournals/joss-reviews:

watching

  1. You may also like to change your default settings for this watching repositories in your GitHub profile here: https://github.com/settings/notifications

notifications

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

@whedon commands
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commented May 21, 2019

Attempting PDF compilation. Reticulating splines etc...
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commented May 21, 2019

PDF failed to compile for issue #1468 with the following error:

Can't find any papers to compile :-(

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commented May 21, 2019

@zbeekman, @andreas-h - please carry out your review in this issue by updating the checklist above and giving feedback in this issue. The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html

Any questions/concerns please let me know.

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commented May 21, 2019

@whedon generate pdf from branch joss-paper

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commented May 21, 2019

Attempting PDF compilation from custom branch joss-paper. Reticulating splines etc...
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commented May 21, 2019

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commented May 21, 2019

@letmaik Is D. Meyer on GitHub? Trying to ensure no conflicts of interest but, it's hard to guarantee without being able to look up the other author. The institution/association ("Independent Scholar") is not helpful for this.

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commented May 21, 2019

Howdy @zbeekman. There shouldn't be any with me.

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commented May 21, 2019

Yup, did some git archeology and figured that was probably you. Thanks!

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commented May 21, 2019

@arfon @letmaik the version is listed simply as 4 but in the repository I see:

  1. Git tag v4.0
  2. pre-release with assets, notes & tag WRF-CMake-4.0](https://github.com/WRF-CMake/WRF/releases/tag/WRF-CMake-4.0)
  3. pre-release with assets, notes & tag WRF-CMake-4.0.3
  4. Numerous other tags with v4.x.y in them.
  • @letmaik: Which one of these should we be reviewing to correspond to the paper?
  • @arfon:
    • Do we need this issue to be more precise about the version under review?
    • Is it OK to be reviewing something tagged as a pre-release?
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commented May 21, 2019

Do we need this issue to be more precise about the version under review?

It's important that the authors specify which version they're expecting you to review.

Is it OK to be reviewing something tagged as a pre-release?

Yes, as long as the authors are happy to tag a new release at the end of the review based on the pre-release content (this often happens for JOSS reviews).

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commented May 21, 2019

I'm working under the assumption that pre-release with assets, notes & tag WRF-CMake-4.0.3 is the version that the authors want reviewed and that will form the basis of the new release.

@letmaik (and/or @dmey): please confirm.

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commented May 22, 2019

Clarification regarding the pre-release marker: This only refers to the pre-built binaries under assets which we'd like to declare as "experimental" (meaning use at your own risk, despite our testing efforts), the software itself is not pre-release. Please let us know if you have an idea to make this more clear.

Please review the WRF-CMake-4.0.3 tag. The main difference to the default branch wrf-cmake is that we recently added a new CI setup (based on Azure Pipelines) which also produced the plots in the paper; the software is unchanged. See e.g. https://dev.azure.com/WRF-CMake/WRF/_build/results?buildId=254. If you click on Artifacts -> wats_plots, you can find the paper plots at:
A.0 -> d02/T0/OSALL/ext_boxplot.png
A.60 -> d02/T6/OSALL/ext_boxplot.png
B.0 -> d02/T0/OSALL/nrmse.png
B.60 -> d02/T6/OSALL/nrmse.png

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commented May 22, 2019

Should the version be updated at the top of this issue, @arfon?

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commented May 22, 2019

Should the version be updated at the top of this issue, @arfon?

We can do that yes. Can you confirm the version should be WRF-CMake-4.0.3 @letmaik?

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commented May 22, 2019

@arfon Yes, it's WRF-CMake-4.0.3. How is the process if we need to make changes, e.g. to the docs? Do we have to release a new version which this paper is then ultimately based on? The paper itself is also in a branch currently and not part of 4.0.3.

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commented May 23, 2019

@whedon set WRF-CMake-4.0.3 as version

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commented May 23, 2019

OK. WRF-CMake-4.0.3 is the version.

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commented May 23, 2019

@arfon Yes, it's WRF-CMake-4.0.3. How is the process if we need to make changes, e.g. to the docs? Do we have to release a new version which this paper is then ultimately based on? The paper itself is also in a branch currently and not part of 4.0.3.

We ask that authors make a new release that includes the changes made during the review, that way we can be sure the archived version reflects the work of our reviewers too. The paper doesn't need to be part of the final version.

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commented May 26, 2019

@arfon Makes sense. Our project strictly follows the WRF version numbers to avoid confusion. The next version therefore would be WRF-CMake 4.1. For the purpose of reviewing, there is no difference between WRF-CMake 4.0.3 and 4.1 (except the addition of continuous integration via Azure Pipelines). We re-ran the scripts that produce the paper plots and the conclusions are unchanged. We will update the plots as there are minor changes but this doesn't affect the review. To clarify, all feedback from the JOSS review is incorporated into the wrf-cmake (our "master") branch from which we will then cut the 4.1 release that the paper is linked to. Does that all make sense?

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commented May 26, 2019

Does that all make sense?

👍 sounds good to me.

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commented Jun 12, 2019

👋 @andreas-h - please try and complete your review soon.

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commented Jun 21, 2019

@arfon I noticed that @andreas-h is yet to complete the checklist -- would you know his status?

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commented Jun 21, 2019

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commented Sep 2, 2019

@letmaik - looks like the paper figure placement issue is resolved now. Could you remove the TODO statement from the paper?

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commented Sep 2, 2019

@letmaik - could you also merge this PR: WRF-CMake/wrf#39

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commented Sep 2, 2019

@letmaik - after making the two changes above, could you make a new release of this software that includes the changes that have resulted from this review. Then, please make an archive of the software in Zenodo/figshare/other service and update this thread with the DOI of the archive? For the Zenodo/figshare archive, please make sure that:

  • The title of the archive is the same as the JOSS paper title
  • That the authors of the archive are the same as the JOSS paper authors

I can then move forward with accepting the submission.

@letmaik letmaik referenced this issue Sep 2, 2019
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commented Sep 3, 2019

@whedon generate pdf

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commented Sep 3, 2019

Attempting PDF compilation. Reticulating splines etc...
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commented Sep 3, 2019

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commented Sep 3, 2019

@zbeekman @andreas-h We'd like to add you two to the acknowledgments list. Are you ok with that?

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commented Sep 3, 2019

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commented Sep 4, 2019

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commented Sep 7, 2019

@arfon As Zenodo requires the software's list of authors to be included when depositing the software on their website, we were wondering what the best way is to clearly show that our work is merely an extension (build-system enhancement) of the great work carried out by Skamarock et al., (2018; and previous papers).

Have you had a similar case before or have any idea how to best show this on Zenodo? On GitHub this is perhaps easier to see given that the project is already marked as a fork of WRF and includes a statement under the how to cite section in the README that links to the WRF model publication.

@zbeekman and @andreas-h if you also have any tips which you think could make this clearer, or think we should add anything else in the README etc, please let us know!

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commented Sep 8, 2019

@arfon As Zenodo requires the software's list of authors to be included when depositing the software on their website, we were wondering what the best way is to clearly show that our work is merely an extension (build-system enhancement) of the great work carried out by Skamarock et al., (2018; and previous papers).

Hrm, good question. I this situation I think it's probably best to just include the authors that have extended the package in this fork.

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commented Sep 9, 2019

@arfon OK, thanks. I have added the following in the description on Zenodo to hopefully make it clear:

As WRF-CMake is an extension of the original WRF model and software, we ask to please cite both model (i.e. Skamarock et al., (2018)), and software with version. For more information on how to do this correctly, please see the How to cite section on the project's GitHub page.

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commented Sep 9, 2019

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commented Sep 9, 2019

@whedon accept

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commented Sep 9, 2019

No archive DOI set. Exiting...

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commented Sep 9, 2019

@whedon set 10.5281/zenodo.3403343 as archive

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commented Sep 9, 2019

OK. 10.5281/zenodo.3403343 is the archive.

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commented Sep 9, 2019

@whedon accept

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commented Sep 9, 2019

Attempting dry run of processing paper acceptance...
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commented Sep 9, 2019

Check final proof 👉 openjournals/joss-papers#958

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#958, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true
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commented Sep 9, 2019

Looks good!

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commented Sep 9, 2019

@whedon accept deposit=true

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commented Sep 9, 2019

Doing it live! Attempting automated processing of paper acceptance...

@whedon whedon added the accepted label Sep 9, 2019

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commented Sep 9, 2019

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

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commented Sep 9, 2019

🚨🚨🚨 THIS IS NOT A DRILL, YOU HAVE JUST ACCEPTED A PAPER INTO JOSS! 🚨🚨🚨

Here's what you must now do:

  1. Check final PDF and Crossref metadata that was deposited 👉 openjournals/joss-papers#959
  2. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.01468
  3. If everything looks good, then close this review issue.
  4. Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? notify your editorial technical team...

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commented Sep 9, 2019

@zbeekman, @andreas-h - many thanks for your reviews here

@letmaik - your paper is now accepted into JOSS ⚡️🚀💥

@arfon arfon closed this Sep 9, 2019

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commented Sep 9, 2019

🎉🎉🎉 Congratulations on your paper acceptance! 🎉🎉🎉

If you would like to include a link to your paper from your README use the following code snippets:

Markdown:
[![DOI](https://joss.theoj.org/papers/10.21105/joss.01468/status.svg)](https://doi.org/10.21105/joss.01468)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.01468">
  <img src="https://joss.theoj.org/papers/10.21105/joss.01468/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.01468/status.svg
   :target: https://doi.org/10.21105/joss.01468

This is how it will look in your documentation:

DOI

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