[REVIEW]: doped: Python toolkit for robust and repeatable charged defect supercell calculations

editorialbot commented 4 months ago

Submitting author: !--author-handle-->@kavanase@rkurchin<!--end-editor-- Reviewers: @yuan-gist, @atimmins7 Archive: 10.5281/zenodo.10957359

Status

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HTML: <a href="https://joss.theoj.org/papers/503119907949941eb6f0fd1b5f71aff1"><img src="https://joss.theoj.org/papers/503119907949941eb6f0fd1b5f71aff1/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/503119907949941eb6f0fd1b5f71aff1/status.svg)](https://joss.theoj.org/papers/503119907949941eb6f0fd1b5f71aff1)

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

@yuan-gist & @atimmins7, 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 @rkurchin 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 @atimmins7

📝 Checklist for @yuan-gist

editorialbot commented 3 months ago

Attempting dry run of processing paper acceptance...

editorialbot commented 3 months ago

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

OK DOIs

- 10.1039/D3TA00532A is OK
- 10.1021/acsaem.2c03466 is OK
- 10.26434/chemrxiv-2024-hm6vh is OK
- 10.1038/s41467-022-32669-3 is OK
- 10.1021/acs.inorgchem.3c01510 is OK
- 10.1021/acs.jpclett.2c02436 is OK
- 10.1039/D2FD00043A is OK
- 10.1021/acsenergylett.1c00380 is OK
- 10.21105/joss.02102 is OK
- 10.1039/D1SC03775G is OK
- 10.1103/PRXEnergy.2.043002 is OK
- 10.1088/1361-648X/aa680e is OK
- 10.1021/acs.chemmater.3c03257 is OK
- 10.1021/acs.jpcc.3c05204 is OK
- 10.1038/s41524-023-00973-1 is OK
- 10.1039/D3CS00432E is OK
- 10.48550/arXiv.2401.12127 is OK
- 10.1016/j.matt.2021.06.003 is OK
- 10.21105/joss.04817 is OK
- 10.1088/2516-1075/ace014 is OK
- 10.1016/j.cpc.2018.01.011 is OK
- 10.1016/j.commatsci.2022.111434 is OK
- 10.1039/D3TA02429F is OK
- 10.1016/j.commatsci.2012.10.028 is OK
- 10.21105/joss.04962 is OK
- 10.48550/arXiv.1808.01590 is OK
- 10.1016/j.cpc.2021.108056 is OK
- 10.1103/PhysRevB.108.134102 is OK
- 10.1021/acs.chemmater.3c01628 is OK
- 10.1063/5.0170552 is OK
- 10.1021/acsenergylett.2c02306 is OK
- 10.1126/sciadv.adh8617 is OK
- 10.21105/joss.05974 is OK
- 10.1016/j.commatsci.2017.07.030 is OK
- 10.1038/s41597-020-00638-4 is OK
- 10.1016/j.cpc.2018.01.004 is OK
- 10.1103/PhysRevMaterials.5.123803 is OK
- 10.1088/1674-4926/43/4/042101 is OK
- 10.1103/PhysRevLett.102.016402 is OK
- 10.1103/PhysRevB.89.195205 is OK
- 10.1016/j.cpc.2021.107946 is OK
- 10.1016/j.commatsci.2016.12.040 is OK
- 10.21105/joss.05941 is OK
- 10.1088/0953-8984/16/27/010 is OK
- 10.1016/j.cplett.2017.01.001 is OK
- 10.1103/PhysRevB.54.11169 is OK
- 10.1088/0953-8984/21/39/395502 is OK
- 10.1524/zkri.220.5.567.65075 is OK
- 10.1016/j.cpc.2009.06.022 is OK
- 10.1063/5.0007045 is OK
- 10.48550/arXiv.2402.04434 is OK
- 10.1016/j.joule.2024.02.017 is OK
- 10.1038/s41524-023-01015-6 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot commented 3 months ago

:wave: @openjournals/bcm-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/5240, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

kavanase commented 3 months ago

Just to confirm, I have had a quick scan through the final proof and all looks good to me

kavanase commented 3 months ago

@editorialbot generate preprint

editorialbot commented 3 months ago

:page_facing_up: Preprint file created: Find it here in the Artifacts list :page_facing_up:

Kevin-Mattheus-Moerman commented 3 months ago

@kavanase as AEiC for JOSS I will now help to process this submission for acceptance in JOSS. I have checked this review, your repository, the archive link, and the paper. All seems in order, so I will now proceed to accept this work.

Kevin-Mattheus-Moerman commented 3 months ago

@editorialbot accept

editorialbot commented 3 months ago

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

editorialbot commented 3 months 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.

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

CITATION.cff

``` cff-version: "1.2.0" authors: - family-names: Kavanagh given-names: Seán R. orcid: "https://orcid.org/0000-0003-4577-9647" - family-names: Squires given-names: Alexander G. orcid: "https://orcid.org/0000-0001-6967-3690" - family-names: Nicolson given-names: Adair orcid: "https://orcid.org/0000-0002-8889-9369" - family-names: Mosquera-Lois given-names: Irea orcid: "https://orcid.org/0000-0001-7651-0814" - family-names: Ganose given-names: Alex M. orcid: "https://orcid.org/0000-0002-4486-3321" - family-names: Zhu given-names: Bonan orcid: "https://orcid.org/0000-0001-5601-6130" - family-names: Brlec given-names: Katarina orcid: "https://orcid.org/0000-0003-1485-1888" - family-names: Walsh given-names: Aron orcid: "https://orcid.org/0000-0001-5460-7033" - family-names: Scanlon given-names: David O. orcid: "https://orcid.org/0000-0001-9174-8601" contact: - family-names: Kavanagh given-names: Seán R. orcid: "https://orcid.org/0000-0003-4577-9647" doi: 10.5281/zenodo.10957359 message: If you use this software, please cite our article in the Journal of Open Source Software. preferred-citation: authors: - family-names: Kavanagh given-names: Seán R. orcid: "https://orcid.org/0000-0003-4577-9647" - family-names: Squires given-names: Alexander G. orcid: "https://orcid.org/0000-0001-6967-3690" - family-names: Nicolson given-names: Adair orcid: "https://orcid.org/0000-0002-8889-9369" - family-names: Mosquera-Lois given-names: Irea orcid: "https://orcid.org/0000-0001-7651-0814" - family-names: Ganose given-names: Alex M. orcid: "https://orcid.org/0000-0002-4486-3321" - family-names: Zhu given-names: Bonan orcid: "https://orcid.org/0000-0001-5601-6130" - family-names: Brlec given-names: Katarina orcid: "https://orcid.org/0000-0003-1485-1888" - family-names: Walsh given-names: Aron orcid: "https://orcid.org/0000-0001-5460-7033" - family-names: Scanlon given-names: David O. orcid: "https://orcid.org/0000-0001-9174-8601" date-published: 2024-04-15 doi: 10.21105/joss.06433 issn: 2475-9066 issue: 96 journal: Journal of Open Source Software publisher: name: Open Journals start: 6433 title: "doped: Python toolkit for robust and repeatable charged defect supercell calculations" type: article url: "https://joss.theoj.org/papers/10.21105/joss.06433" volume: 9 title: "doped: Python toolkit for robust and repeatable charged defect supercell calculations" ```

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 commented 3 months ago

🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

editorialbot commented 3 months 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/5244
Wait five minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.06433
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

kavanase commented 3 months ago

Thanks @rkurchin for handling our paper, @yuan-gist & @atimmins7 for the reviews and @Kevin-Mattheus-Moerman for the final processing!!

JOSS is a great journal

Kevin-Mattheus-Moerman commented 2 months ago

@kavanase congrats again on this publication!

Thanks for editing @rkurchin!

And a special thank you to the reviewers: @yuan-gist, @atimmins7 !

editorialbot commented 2 months ago

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

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