[REVIEW]: DPFEHM: a differentiable subsurface physics simulator

[editorialbot]

Submitting author: !--author-handle-->@omalled<!--end-author-handle-- (Daniel O'Malley) Repository: https://github.com/OrchardLANL/DPFEHM.jl Branch with paper.md (empty if default branch): Version: v0.1.1 Editor: !--editor-->@jedbrown<!--end-editor-- Reviewers: @WilkAndy, @rtmills, @rezgarshakeri Archive: 10.5281/zenodo.8329952

Status

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HTML: <a href="https://joss.theoj.org/papers/8d7a69a54acce2406ed6f857501768c8"><img src="https://joss.theoj.org/papers/8d7a69a54acce2406ed6f857501768c8/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/8d7a69a54acce2406ed6f857501768c8/status.svg)](https://joss.theoj.org/papers/8d7a69a54acce2406ed6f857501768c8)

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

@WilkAndy & @rtmills & @rezgarshakeri, your review will be checklist based. Each of you will have a separate checklist that you should update when carrying out your review. First of all you need to run this command in a separate comment to create the checklist:

@editorialbot generate my checklist

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

✨ Please start on your review when you are able, and be sure to complete your review in the next six weeks, at the very latest ✨

Checklists

📝 Checklist for @WilkAndy

📝 Checklist for @rezgarshakeri

📝 Checklist for @rtmills

[omalled]

Here's the tagged version: https://github.com/OrchardLANL/DPFEHM.jl/tree/v0.1.1

I'll start working on archiving it.

[omalled]

I just archived the software on Zenodo: https://zenodo.org/record/8329952

The doi is 10.5281/zenodo.8329952

[omalled]

@jedbrown I think that checks all your boxes, right?

[arfon]

@jedbrown – friendly bump here.

[jedbrown]

@omalled Sorry about my delay. This looks good.

[jedbrown]

@editorialbot set v0.1.1 as version

[editorialbot]

Done! version is now v0.1.1

[jedbrown]

@editorialbot set 10.5281/zenodo.8329952 as archive

[editorialbot]

Done! archive is now 10.5281/zenodo.8329952

[jedbrown]

@editorialbot recommend-accept

[editorialbot]

Attempting dry run of processing paper acceptance...

[editorialbot]

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.3133/sir20105169 is OK
- 10.2172/1657092 is OK
- 10.1029/2021wr031188 is OK
- 10.3102/1076998615606113 is OK
- 10.1615/jmachlearnmodelcomput.2022042093 is OK
- 10.1038/s41598-022-22832-7 is OK
- 10.2172/1168703 is OK
- 10.2172/14903 is OK
- 10.5066/F7RF5S7G is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

:wave: @openjournals/pe-eics, this paper is ready to be accepted and published.

Check final proof :point_right::page_facing_up: Download article

If the paper PDF and the deposit XML files look good in https://github.com/openjournals/joss-papers/pull/4692, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

[kyleniemeyer]

@editorialbot accept

[editorialbot]

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

[editorialbot]

Ensure proper citation by uploading a plain text CITATION.cff file to the default branch of your repository.

If using GitHub, a Cite this repository menu will appear in the About section, containing both APA and BibTeX formats. When exported to Zotero using a browser plugin, Zotero will automatically create an entry using the information contained in the .cff file.

You can copy the contents for your CITATION.cff file here:

CITATION.cff

``` cff-version: "1.2.0" authors: - family-names: O'Malley given-names: Daniel orcid: "https://orcid.org/0000-0003-0432-3088" - family-names: Greer given-names: Sarah Y. orcid: "https://orcid.org/0000-0001-6463-0296" - family-names: Pachalieva given-names: Aleksandra orcid: "https://orcid.org/0000-0003-1246-0410" - family-names: Hao given-names: Wu orcid: "https://orcid.org/0000-0002-9402-7401" - family-names: Harp given-names: Dylan orcid: "https://orcid.org/0000-0001-9777-8000" - family-names: Vesselinov given-names: Velimir V. orcid: "https://orcid.org/0000-0002-6222-0530" contact: - family-names: O'Malley given-names: Daniel orcid: "https://orcid.org/0000-0003-0432-3088" doi: 10.5281/zenodo.8329952 message: If you use this software, please cite our article in the Journal of Open Source Software. preferred-citation: authors: - family-names: O'Malley given-names: Daniel orcid: "https://orcid.org/0000-0003-0432-3088" - family-names: Greer given-names: Sarah Y. orcid: "https://orcid.org/0000-0001-6463-0296" - family-names: Pachalieva given-names: Aleksandra orcid: "https://orcid.org/0000-0003-1246-0410" - family-names: Hao given-names: Wu orcid: "https://orcid.org/0000-0002-9402-7401" - family-names: Harp given-names: Dylan orcid: "https://orcid.org/0000-0001-9777-8000" - family-names: Vesselinov given-names: Velimir V. orcid: "https://orcid.org/0000-0002-6222-0530" date-published: 2023-10-18 doi: 10.21105/joss.04560 issn: 2475-9066 issue: 90 journal: Journal of Open Source Software publisher: name: Open Journals start: 4560 title: "DPFEHM: a differentiable subsurface physics simulator" type: article url: "https://joss.theoj.org/papers/10.21105/joss.04560" volume: 8 title: "DPFEHM: a differentiable subsurface physics simulator" ```

If the repository is not hosted on GitHub, a .cff file can still be uploaded to set your preferred citation. Users will be able to manually copy and paste the citation.

Find more information on .cff files here and here.

[editorialbot]

🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

[editorialbot]

🚨🚨🚨 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 :point_right: https://github.com/openjournals/joss-papers/pull/4702
1. Wait five minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.04560
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...

[kyleniemeyer]

Congratulations @omalled on your article's publication in JOSS! Please consider signing up to review in the future if you haven't already.

Many thanks to @WilkAndy, @rtmills, and @rezgarshakeri for reviewing this, and @jedbrown for editing.

[editorialbot]

:tada::tada::tada: Congratulations on your paper acceptance! :tada::tada::tada:

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.04560/status.svg)](https://doi.org/10.21105/joss.04560)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.04560">
  <img src="https://joss.theoj.org/papers/10.21105/joss.04560/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.04560/status.svg
   :target: https://doi.org/10.21105/joss.04560

This is how it will look in your documentation:

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