[REVIEW]: AmpTorch: A Python package for scalable fingerprint-based neural network training on multi-element systems with integrated uncertainty quantification

editorialbot commented 1 year ago

Submitting author: !--author-handle-->@ajmedford@dhhagan<!--end-editor-- Reviewers: @ml-evs, @ianfhunter Archive: 10.5281/zenodo.8151492

Status

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Markdown: [![status](https://joss.theoj.org/papers/ba551fc487e19526830cab97097fd86d/status.svg)](https://joss.theoj.org/papers/ba551fc487e19526830cab97097fd86d)

Reviewers and authors:

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ajmedford commented 1 year ago

@dhhagan - @nicoleyghu has now fixed the minor typos, and I think this is ready to go. Let us know once its official!

dhhagan commented 1 year ago

@editorialbot generate pdf

editorialbot commented 1 year ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

dhhagan commented 1 year ago

@editorialbot remove @professoralkmin as reviewer

editorialbot commented 1 year ago

@professoralkmin removed from the reviewers list!

dhhagan commented 1 year ago

@ajmedford this looks great. Can you do the following?

Create a tagged release and archive it.
Report the final version number and DOI in this thread. Make sure the author list and title are identical to the paper here.

ajmedford commented 1 year ago

@mshuaibii @zulissi - can one of you take care of this? It seems that Nicole does not have the necessary permissions.

zulissi commented 1 year ago

I changed @nicoleyghu to maintainer on the repo; let me know if that's not sufficient!

ajmedford commented 1 year ago

@dhhagan - We have released and tagged the version and archived it. The release is here: https://github.com/ulissigroup/amptorch/releases/tag/v0.2.0-alpha, and the archived version is here: https://zenodo.org/record/8103323.

Let us know if you need anything else to get this finalized!

dhhagan commented 1 year ago

Hi @ajmedford - sorry for the delay! Can you update the title in Zenodo to match the paper title? Also, are you planning to update the release version to no longer indicate a pre-release? If so, now would be a good time to do that so that the paper and release in GitHub/zenodo all align?

ajmedford commented 1 year ago

@dhhagan Sure thing -- here is the updated Zenodo: https://zenodo.org/record/8151492

It has a new DOI (10.5281/zenodo.8151492), so maybe best to link to that one. Looking forward to having this out!

dhhagan commented 1 year ago

@editorialbot set v1.0 as version

editorialbot commented 1 year ago

Done! version is now v1.0

dhhagan commented 1 year ago

@editorialbot set https://zenodo.org/record/8151492 as doi

editorialbot commented 1 year ago

I'm sorry human, I don't understand that. You can see what commands I support by typing:

@editorialbot commands

dhhagan commented 1 year ago

@editorialbot set https://zenodo.org/record/8151492 as archive

editorialbot commented 1 year ago

That doesn't look like a valid DOI value

dhhagan commented 1 year ago

@editorialbot set 10.5281/zenodo.8151492 as archive

editorialbot commented 1 year ago

Done! archive is now 10.5281/zenodo.8151492

dhhagan commented 1 year ago

@editorialbot generate pdf

editorialbot commented 1 year ago

:warning: An error happened when generating the pdf.

dhhagan commented 1 year ago

@editorialbot generate pdf

dhhagan commented 1 year ago

⚠️ An error happened when generating the pdf.

Looks like there is an issue with one of the services used to build the pdf. Will try again and try again later today if needed.

editorialbot commented 1 year ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

dhhagan commented 1 year ago

@editorialbot recommend-accept

editorialbot commented 1 year ago

Attempting dry run of processing paper acceptance...

editorialbot commented 1 year ago

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

OK DOIs

- 10.1021/acs.jpclett.2c02100 is OK
- 10.1088/2632-2153/ACA7B1 is OK
- 10.1016/j.cpc.2016.05.010 is OK
- 10.48550/arxiv.1908.08381 is OK
- 10.1088/2632-2153/ac8fe0 is OK
- 10.1021/acs.jpcc.0c04225 is OK
- 10.1002/qua.24890 is OK
- 10.1088/1361-648X/AA680E is OK
- 10.1021/acscatal.0c04525 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot commented 1 year ago

:warning: Error preparing paper acceptance.

ajmedford commented 1 year ago

@dhhagan - not sure what's causing this error. Let us know if any action is needed from our side.

dhhagan commented 1 year ago

@editorialbot recommend-accept

editorialbot commented 1 year ago

Attempting dry run of processing paper acceptance...

editorialbot commented 1 year ago

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

OK DOIs

- 10.1021/acs.jpclett.2c02100 is OK
- 10.1088/2632-2153/ACA7B1 is OK
- 10.1016/j.cpc.2016.05.010 is OK
- 10.48550/arxiv.1908.08381 is OK
- 10.1088/2632-2153/ac8fe0 is OK
- 10.1021/acs.jpcc.0c04225 is OK
- 10.1002/qua.24890 is OK
- 10.1088/1361-648X/AA680E is OK
- 10.1021/acscatal.0c04525 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot commented 1 year ago

:wave: @openjournals/dsais-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/4428, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

ajmedford commented 1 year ago

Looks good to me!

gkthiruvathukal commented 1 year ago

Everything looks to be in good shape here. I'm proceeding with final acceptance.

gkthiruvathukal commented 1 year ago

@editorialbot accept

editorialbot commented 1 year ago

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

editorialbot commented 1 year ago

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.

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CITATION.cff

``` cff-version: "1.2.0" authors: - family-names: Shuaibi given-names: Muhammed - family-names: Hu given-names: Yuge orcid: "https://orcid.org/0000-0003-3648-7749" - family-names: Lei given-names: Xiangyun - family-names: Comer given-names: Benjamin M. - family-names: Adams given-names: Matt - family-names: Paras given-names: Jacob - family-names: Chen given-names: Rui Qi - family-names: Musa given-names: Eric - family-names: Musielewicz given-names: Joseph - family-names: Peterson given-names: Andrew A. orcid: "https://orcid.org/0000-0003-2855-9482" - family-names: Medford given-names: Andrew J. orcid: "https://orcid.org/0000-0001-8311-9581" - family-names: Ulissi given-names: Zachary orcid: "https://orcid.org/0000-0002-9401-4918" contact: - family-names: Ulissi given-names: Zachary orcid: "https://orcid.org/0000-0002-9401-4918" doi: 10.5281/zenodo.8151492 message: If you use this software, please cite our article in the Journal of Open Source Software. preferred-citation: authors: - family-names: Shuaibi given-names: Muhammed - family-names: Hu given-names: Yuge orcid: "https://orcid.org/0000-0003-3648-7749" - family-names: Lei given-names: Xiangyun - family-names: Comer given-names: Benjamin M. - family-names: Adams given-names: Matt - family-names: Paras given-names: Jacob - family-names: Chen given-names: Rui Qi - family-names: Musa given-names: Eric - family-names: Musielewicz given-names: Joseph - family-names: Peterson given-names: Andrew A. orcid: "https://orcid.org/0000-0003-2855-9482" - family-names: Medford given-names: Andrew J. orcid: "https://orcid.org/0000-0001-8311-9581" - family-names: Ulissi given-names: Zachary orcid: "https://orcid.org/0000-0002-9401-4918" date-published: 2023-07-26 doi: 10.21105/joss.05035 issn: 2475-9066 issue: 87 journal: Journal of Open Source Software publisher: name: Open Journals start: 5035 title: "AmpTorch: A Python package for scalable fingerprint-based neural network training on multi-element systems with integrated uncertainty quantification" type: article url: "https://joss.theoj.org/papers/10.21105/joss.05035" volume: 8 title: "AmpTorch: A Python package for scalable fingerprint-based neural network training on multi-element systems with integrated uncertainty quantification" ```

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.

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editorialbot commented 1 year ago

🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

editorialbot commented 1 year ago

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

Here's what you must now do:

Check final PDF and Crossref metadata that was deposited :point_right: https://github.com/openjournals/joss-papers/pull/4435
Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.05035
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

editorialbot commented 1 year ago

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

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   :target: https://doi.org/10.21105/joss.05035

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