[REVIEW]: Underworld2: Python Geodynamics Modelling for Desktop, HPC and Cloud

[whedon]

Submitting author: @jmansour (john mansour)
Repository: https://github.com/underworldcode/underworld2
Version: v2.9.2b
Editor: @leouieda
Reviewer: @gassmoeller, @gabersyd
Archive: 10.5281/zenodo.3687399

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/4e96f9dba4f8f129f64770e74abdec0e"><img src="https://joss.theoj.org/papers/4e96f9dba4f8f129f64770e74abdec0e/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/4e96f9dba4f8f129f64770e74abdec0e/status.svg)](https://joss.theoj.org/papers/4e96f9dba4f8f129f64770e74abdec0e)

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

@gassmoeller & @gabersyd, 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 @leouieda know.

✨ Please try and complete your review in the next two weeks ✨

Review checklist for @gassmoeller

Conflict of interest

• I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

Code of Conduct

• I confirm that I read and will adhere to the JOSS 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?
• Contribution and authorship: Has the submitting author (@jmansour) 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 functionality 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

• Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
• A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• State of the field: Do the authors describe how this software compares to other commonly-used packages?
• Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
• References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

Review checklist for @gabersyd

Conflict of interest

• I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

Code of Conduct

• I confirm that I read and will adhere to the JOSS 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?
• Contribution and authorship: Has the submitting author (@jmansour) 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 functionality 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

• Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
• A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• State of the field: Do the authors describe how this software compares to other commonly-used packages?
• Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
• References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

[whedon]

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @gassmoeller, @gabersyd it looks like you're currently assigned to review 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:

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

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

@whedon commands

For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

PDF failed to compile for issue #1797 with the following error:

Can't find any papers to compile :-(

[leouieda]

@whedon generate pdf from branch joss

[whedon]

Attempting PDF compilation from custom branch joss. Reticulating splines etc...

[whedon]

👉 Check article proof 📄 👈

[leouieda]

👋 @jmansour @gassmoeller @gabersyd this is the review thread for the paper. All of our communications will happen here from now on.

Both reviewers have checklists at the top of this thread with the JOSS requirements. As you go over the submission, please check any items that you feel have been satisfied. There are also links to the JOSS reviewer guidelines.

The JOSS review is different from most other journals. Our goal is to work with the authors to help them meet our criteria instead of merely passing judgment on the submission. As such, the reviewers are encouraged to submit issues and pull requests on the software repository. When doing so, please mention openjournals/joss-reviews#1797 so that a link is created to this thread (and I can keep an eye on what is happening). Please also feel free to comment and ask questions on this thread. In my experience, it is better to post comments/questions/suggestions as you come across them instead of waiting until you've reviewed the entire package.

We aim for reviews to be completed within about 4 weeks. Please let me know if any of you require some more time. We can also use Whedon (our bot) to set automatic reminders if you know you'll be away for a known period of time.

Please feel free to ping me here (@leouieda) or email me privately if you have any questions/concerns.

[gassmoeller]

@leouieda: I have a question about the following item on the reviewer checklist:

State of the field: Do the authors describe how this software compares to other commonly-used packages?

The authors do not explicitly describe this in the paper (although they do describe their main design principle of an easily usable library, which differs somewhat from many of the other software packages in our field), but I also have two problems with this item. First it is not mentioned on the https://joss.readthedocs.io/en/latest/submitting.html#submitting-a-paper-to-joss website, and neither on the https://joss.readthedocs.io/en/latest/review_criteria.html#review-criteria website. Thus, the authors were not asked to provide such a comparison. Second, this item can be a can of worms if you want to describe it thoroughly. I think this item should be revised somewhat to either only require a short / general comparison (including mentioning this expectation on the submission website), or it should be dropped from the review checklist. Do you think this is reasonable?

[jmansour]

@whedon generate pdf from branch joss

[whedon]

Attempting PDF compilation from custom branch joss
. Reticulating splines etc...

[whedon]

PDF failed to compile for issue #1797 with the following error:

error: pathspec 'joss
' did not match any file(s) known to git.
Can't find any papers to compile :-(

[jmansour]

@whedon generate pdf from branch joss

[whedon]

Attempting PDF compilation from custom branch joss. Reticulating splines etc...

[whedon]

👉 Check article proof 📄 👈

[leouieda]

I think this item should be revised somewhat to either only require a short / general comparison (including mentioning this expectation on the submission website), or it should be dropped from the review checklist. Do you think this is reasonable?

Hi @gassmoeller that is probably a new item on the checklist. I hadn't seen it before. I'll bring this up with the JOSS editors and see what we can do about it. I agree that we should be very explicit about what we want from that statement. I imagine the idea was to provide a general comparison statement, not a thorough performance/accuracy/features comparison. Thanks for pointing this out!

[leouieda]

On that note, @gassmoeller @gabersyd what is the status of the review? Any updates?

[gassmoeller]

I am satisfied with the current state of the software and paper, and think this is an important contribution. The authors have responded productively and fixed the small comments and objections I had. I am only waiting for underworldcode/underworld2#428 to be fixed (one of the authors is currently not on the paper, because he has no ORCID so far), and afterwards this is ready from my side. I particularly liked the easy distribution and online tutorials. Nice work!

[gabersyd]

@leouieda, I need one more week to give a complete feedback. Gabriele Morra <http://scholar.google.com/citations?sortby=pubdate&hl=en&user=DDuTppAAAAAJ&view_op=list_works> , Department of Physics <http://physics.louisiana.edu>, School of Geosciences <http://geos.louisiana.edu>, University of Louisiana at Lafayette <http://www.louisiana.edu>

…

On Wed, Oct 30, 2019 at 1:45 PM Rene Gassmoeller ***@***.***> wrote: I am satisfied with the current state of the software and paper, and think this is an important contribution. The authors have responded productively and fixed the small comments and objections I had. I am only waiting for underworldcode/underworld2#428 <underworldcode/underworld2#428> to be fixed (one of the authors is currently not on the paper, because he has no ORCID so far), and afterwards this is ready from my side. I particularly liked the easy distribution and online tutorials. Nice work! — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#1797?email_source=notifications&email_token=AEZDHHYDDKSZJA6MVJIEAZLQRHI3VA5CNFSM4I7I24FKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOECVLOFI#issuecomment-548058901>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AEZDHH2EKPPAKTLDU565ANDQRHI3VANCNFSM4I7I24FA> .

[jmansour]

Thanks @gassmoeller & @gabersyd

[jmansour]

Hi @leouieda

Are the ORCID identifiers strictly necessary for submission? One of our authors is somewhat privacy concerned and would rather not sign up for an ORCID.

[leouieda]

@jmansour ORCIDs are encouraged but not strictly required if an author feels strongly about not providing one (our own example paper has an authors without an ORCID).

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

Check final proof 👉 openjournals/joss-papers#1341

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#1341, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

[jmansour]

Hi @leouieda

Am I able to update the title of an existing Zenodo archive? In any case, I've created a new release (v2.9.2) with the updated title. Here's the corresponding Zenodo reference:
https://zenodo.org/record/3687399

[leouieda]

@jmansour thanks for the update. You should be able to edit the title but I can update the version and archive here instead.

[leouieda]

@whedon set v2.9.2b as version

[whedon]

OK. v2.9.2b is the version.

[leouieda]

@whedon set 10.5281/zenodo.3687399 as archive

[whedon]

OK. 10.5281/zenodo.3687399 is the archive.

[leouieda]

@whedon accept

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

👋 @openjournals/joss-eics, this paper is ready to be accepted and published

. Check final proof 👉 openjournals/joss-papers#1350

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#1350, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

[leouieda]

👋 Hi @@openjournals/joss-eics just making sure this didn't get lost in the current updates to Whedon.

[Kevin-Mattheus-Moerman]

@leouieda Thanks. I'm on it.

[Kevin-Mattheus-Moerman]

I read the paper and think it looks good.

[Kevin-Mattheus-Moerman]

@whedon accept deposit=true

[whedon]

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

[whedon]

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

[whedon]

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

Here's what you must now do:

0. Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.21105.joss.01797 joss-papers#1354
1. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.01797
2. If everything looks good, then close this review issue.
3. Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? notify your editorial technical team...

[whedon]

🎉🎉🎉 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.01797/status.svg)](https://doi.org/10.21105/joss.01797)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.01797">
  <img src="https://joss.theoj.org/papers/10.21105/joss.01797/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.01797/status.svg
   :target: https://doi.org/10.21105/joss.01797

This is how it will look in your documentation:

We need your help!

Journal of Open Source Software is a community-run journal and relies upon volunteer effort. If you'd like to support us please consider doing either one (or both) of the the following:

• Volunteering to review for us sometime in the future. You can add your name to the reviewer list here: https://joss.theoj.org/reviewer-signup.html
• Making a small donation to support our running costs here: https://numfocus.org/donate-to-joss

[leouieda]

Thanks @Kevin-Mattheus-Moerman, didn't mean to pressure.

@jmansour congratulations on your publication and I hope the JOSS submission/review process was enjoyable 🎉 🎊

@gassmoeller @gabersyd thank you very for your reviews and feedback 🥇

[jmansour]

Excellent result!

I'd also like to thank @gassmoeller & @gabersyd for the time they put in reviewing this and the valuable feedback they provided. 🙏🙏

And thanks to @leouieda & @Kevin-Mattheus-Moerman and the rest of the JOSS crew. The review process was straightforward and even fun. 🙂