editorialbot commented 1 year ago

Submitting author: !--author-handle-->@matthewcarbone@ppxasjsm<!--end-editor-- Reviewers: @maurov, @larsenkg Archive: 10.5281/zenodo.8118592

Status

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Markdown: [![status](https://joss.theoj.org/papers/a9cabcd7f4b85a926a797997c6622b43/status.svg)](https://joss.theoj.org/papers/a9cabcd7f4b85a926a797997c6622b43)

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

@maurov, 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 @ppxasjsm 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 @maurov

📝 Checklist for @larsenkg

editorialbot commented 1 year ago

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

OK DOIs

- 10.1039/B926434E is OK
- 10.1103/PhysRevB.83.115106 is OK
- 10.1088/2516-1075/ab3123 is OK

MISSING DOIs

- 10.1016/j.commatsci.2011.02.023 may be a valid DOI for title: A high-throughput infrastructure for density functional theory calculations

INVALID DOIs

- None

ppxasjsm commented 1 year ago

Post-Review Checklist for Editor and Authors

Additional Author Tasks After Review is Complete

[x] Double check authors and affiliations (including ORCIDs)
[x] Make a release of the software with the latest changes from the review and post the version number here. This is the version that will be used in the JOSS paper.
[x] Archive the release on Zenodo/figshare/etc and post the DOI here.
[x] Make sure that the title and author list (including ORCIDs) in the archive match those in the JOSS paper.
[x] Make sure that the license listed for the archive is the same as the software license.

Editor Tasks Prior to Acceptance

[x] Read the text of the paper and offer comments/corrections (as either a list or a PR)
[x] Check the references in the paper for corrections (e.g. capitalization)
[x] Check that the archive title, author list, version tag, and the license are correct
[x] Set archive DOI with @editorialbot set <DOI here> as archive
[x] Set version with @editorialbot set <version here> as version
[x] Double check rendering of paper with @editorialbot generate pdf
[x] Specifically check the references with @editorialbot check references and ask author(s) to update as needed
[x] Recommend acceptance with @editorialbot recommend-accept

matthewcarbone commented 1 year ago

My TODO list:

[x] Double check authors and affiliations (including ORCIDs)
[x] Make a release of the software with the latest changes from the review and post the version number here. This is the version that will be used in the JOSS paper.
[x] Archive the release on Zenodo/figshare/etc and post the DOI here.
[x] Make sure that the title and author list (including ORCIDs) in the archive match those in the JOSS paper.
[x] Make sure that the license listed for the archive is the same as the software license.

@ppxasjsm All done!

ppxasjsm commented 1 year ago

@editorialbot set https://doi.org/10.5281/zenodo.8118592 as archive

editorialbot commented 1 year ago

Done! archive is now 10.5281/zenodo.8118592

ppxasjsm commented 1 year ago

@editorialbot set version as 0.1.3

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

ppxasjsm commented 1 year ago

@editorialbot generate pdf

ppxasjsm commented 1 year ago

@editorialbot set 0.1.3 as version

editorialbot commented 1 year ago

Done! version is now 0.1.3

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:

ppxasjsm commented 1 year ago

@editorialbot check references

editorialbot commented 1 year ago

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

OK DOIs

- 10.1039/B926434E is OK
- 10.1103/PhysRevB.83.115106 is OK
- 10.1088/2516-1075/ab3123 is OK

MISSING DOIs

- 10.1016/j.commatsci.2011.02.023 may be a valid DOI for title: A high-throughput infrastructure for density functional theory calculations

INVALID DOIs

- None

ppxasjsm commented 1 year ago

Hi @matthewcarbone, I have one last thing for you. Can you please add the DOI: https://doi.org/10.1016/j.commatsci.2011.02.023 to "A high-throughput infrastructure for density functional theory calculations" by Anhubhav et al. Thanks!

matthewcarbone commented 1 year ago

@ppxasjsm done!

matthewcarbone commented 1 year ago

@ppxasjsm anything else I need to do? Thanks!

ppxasjsm commented 1 year ago

All done! Thank you @matthewcarbone. I will now recommend accept.

ppxasjsm 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

- 10.1016/j.commatsci.2011.02.023 is OK
- 10.1039/B926434E is OK
- 10.1103/PhysRevB.83.115106 is OK
- 10.1088/2516-1075/ab3123 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot commented 1 year 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/4406, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

matthewcarbone commented 1 year ago

@ppxasjsm Awesome, thank you! I'm guessing you have to run the final command here, then we're done?

ppxasjsm commented 1 year ago

The Editor in Chief will now have a look at this and do the final bits.

Kevin-Mattheus-Moerman commented 1 year ago

@editorialbot set v0.1.3 as version

editorialbot commented 1 year ago

Done! version is now v0.1.3

Kevin-Mattheus-Moerman commented 1 year ago

@matthewcarbone I am the AEiC for this track and here to help with the final steps. I have reviewed the repository, the archive link, the paper, and this review thread. Most seems in order. Below are some points that do require your attention.

[x] Please add contributing guidelines. It is recommended to have a dedicated CONTRIBUTING.md file, and to refer to it in the README.md as well. The file content can be quite basic/simple if you like. There are many sites offering examples/templates for this (just saw this site too which might help: https://contributing.md/example/). Let me know if you have questions.

Some references need formatting/updating. Our system did not detect these (@openjournals/dev @xuanxu why not actually?) but there seem to be many DOIs that are missing, below are some examples, but please check all your references and add DOIs where possible.

[x] Effects of electron-phonon coupling on absorption spectrum: K edge of hexagonal boron nitride: https://doi.org/10.1103/PhysRevB.98.235205
[x] Advanced calculations of X-ray spectroscopies with FEFF10 and Corvus : https://doi.org/10.1107/S1600577521008614
[x] Projector augmented wave calculation of x-ray absorption spectra at the L2,3 edges : https://doi.org/10.1103/PhysRevB.87.205105
[x] First-principles calculations of x-ray absorption in a scheme based on ultrasoft pseudopotentials : https://doi.org/10.1103/PhysRevB.80.075102
[x] Multi-code Benchmark on Simulated Ti K-edge X-ray Absorption Spectra of Ti-O Compounds : https://doi.org/10.48550/arXiv.2303.17089
[x] Advances in the OCEAN-3 spectroscopy package : https://doi.org/10.1039/D2CP01030E

[x] This reference seems to be incomplete in terms of the title and the DOI:

Jain, A., Ong, S. P., Hautier, G., Chen, W., Richards, W. D., Dacek, S., Cholia, S., Gunter,
D., Skinner, D., Ceder, G., & Persson, K. a. (2013). APL Materials, 1(1), 011002.

https://doi.org/10.1063/1.4812323

When you've completed the above you can update the draft and check the references again using @editorialbot check references.

matthewcarbone commented 1 year ago

Making a TODO list for myself. Stay tuned. Thanks!

[x] Please add contributing guidelines. It is recommended to have a dedicated CONTRIBUTING.md file, and to refer to it in the README.md as well. The file content can be quite basic/simple if you like. There are many sites offering examples/templates for this (just saw this site too which might help: https://contributing.md/example/). Let me know if you have questions.

[x] Effects of electron-phonon coupling on absorption spectrum: K edge of hexagonal boron nitride: https://doi.org/10.1103/PhysRevB.98.235205

[x] Advanced calculations of X-ray spectroscopies with FEFF10 and Corvus : https://doi.org/10.1107/S1600577521008614

[x] Projector augmented wave calculation of x-ray absorption spectra at the L2,3 edges : https://doi.org/10.1103/PhysRevB.87.205105

[x] First-principles calculations of x-ray absorption in a scheme based on ultrasoft pseudopotentials : https://doi.org/10.1103/PhysRevB.80.075102

[x] Multi-code Benchmark on Simulated Ti K-edge X-ray Absorption Spectra of Ti-O Compounds : https://doi.org/10.48550/arXiv.2303.17089

[x] Advances in the OCEAN-3 spectroscopy package : https://doi.org/10.1039/D2CP01030E

[x] This reference seems to be incomplete in terms of the title and the DOI: Jain, A., Ong, S. P., Hautier, G., Chen, W., Richards, W. D., Dacek, S., Cholia, S., Gunter, D., Skinner, D., Ceder, G., & Persson, K. a. (2013). APL Materials, 1(1), 011002.

matthewcarbone commented 1 year ago

@Kevin-Mattheus-Moerman we do already have a CONTRIBUTING.md file in the root directory of the project. Note that the joss-manuscript branch is completely standalone and that the main project is on master. Are the current contributing guidelines sufficient? There is also a link to this in the README as well as summary instructions.

matthewcarbone 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:

matthewcarbone commented 1 year ago

@editorialbot check references

editorialbot commented 1 year ago

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

OK DOIs

- 10.1063/1.4812323 is OK
- 10.1016/j.commatsci.2011.02.023 is OK
- 10.1039/B926434E is OK
- 10.1103/PhysRevB.80.075102 is OK
- 10.1103/PhysRevB.87.205105 is OK
- 10.1103/PhysRevB.83.115106 is OK
- 10.1039/D2CP01030E is OK
- 10.1103/PhysRevB.98.235205 is OK
- 10.1088/2516-1075/ab3123 is OK
- 10.48550/arXiv.2303.17089 is OK
- 10.1107/S1600577521008614 is OK

MISSING DOIs

- None

INVALID DOIs

- None

Kevin-Mattheus-Moerman commented 1 year ago

@matthewcarbone On the community guidelines, apologies, I seem to have missed it. Thanks, what you have there is simple/concise, but sufficient. Thanks also for implementing those DOI changes, note this one still seems missing from the paper:

[x] First-principles calculations of x-ray absorption in a scheme based on ultrasoft pseudopotentials : https://doi.org/10.1103/PhysRevB.80.075102

matthewcarbone commented 1 year ago

@Kevin-Mattheus-Moerman No problem. Note, I think we might be looking at different drafts. This is what I'm seeing after downloading from this post by the bot:

DOI looks correct.

Kevin-Mattheus-Moerman 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:

Kevin-Mattheus-Moerman commented 1 year ago

@matthewcarbone currently your paper.bib file says: Screenshot from 2023-07-28 09-45-30

Hence the above updated paper draft still lacks the DOI:

Screenshot from 2023-07-28 09-45-01

Perhaps you were working in a different branch? Can you update your bib file and the paper in the joss-manuscript branch?

matthewcarbone commented 1 year ago

@Kevin-Mattheus-Moerman ah that's a different reference. Ok all is fixed now.

matthewcarbone 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:

Kevin-Mattheus-Moerman commented 1 year ago

@matthewcarbone I think all looks good now. So we can proceed.

Kevin-Mattheus-Moerman commented 1 year ago

@larsenkg thanks for your review here. Since the community guidelines are there (see CONTRIBUTING.md on repo), and the references have been fixed. We will proceed now with acceptance, but for completeness it would be great if you could tick those last boxes :point_up: .

Kevin-Mattheus-Moerman commented 1 year ago

@editorialbot recommend accept

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

Kevin-Mattheus-Moerman 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.

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

CITATION.cff

``` cff-version: "1.2.0" authors: - family-names: Carbone given-names: Matthew R. orcid: "https://orcid.org/0000-0002-5181-9513" - family-names: Meng given-names: Fanchen orcid: "https://orcid.org/0000-0001-9869-9005" - family-names: Vorwerk given-names: Christian orcid: "https://orcid.org/0000-0002-2516-9553" - family-names: Maurer given-names: Benedikt orcid: "https://orcid.org/0000-0001-9152-7390" - family-names: Peschel given-names: Fabian orcid: "https://orcid.org/0000-0003-0619-6713" - family-names: Qu given-names: Xiaohui orcid: "https://orcid.org/0000-0001-5651-8405" - family-names: Stavitski given-names: Eli orcid: "https://orcid.org/0000-0002-3337-2930" - family-names: Draxl given-names: Claudia orcid: "https://orcid.org/0000-0003-3523-6657" - family-names: Vinson given-names: John orcid: "https://orcid.org/0000-0002-7619-7060" - family-names: Lu given-names: Deyu orcid: "https://orcid.org/0000-0003-4351-6085" contact: - family-names: Carbone given-names: Matthew R. orcid: "https://orcid.org/0000-0002-5181-9513" - family-names: Meng given-names: Fanchen orcid: "https://orcid.org/0000-0001-9869-9005" doi: 10.5281/zenodo.8118592 message: If you use this software, please cite our article in the Journal of Open Source Software. preferred-citation: authors: - family-names: Carbone given-names: Matthew R. orcid: "https://orcid.org/0000-0002-5181-9513" - family-names: Meng given-names: Fanchen orcid: "https://orcid.org/0000-0001-9869-9005" - family-names: Vorwerk given-names: Christian orcid: "https://orcid.org/0000-0002-2516-9553" - family-names: Maurer given-names: Benedikt orcid: "https://orcid.org/0000-0001-9152-7390" - family-names: Peschel given-names: Fabian orcid: "https://orcid.org/0000-0003-0619-6713" - family-names: Qu given-names: Xiaohui orcid: "https://orcid.org/0000-0001-5651-8405" - family-names: Stavitski given-names: Eli orcid: "https://orcid.org/0000-0002-3337-2930" - family-names: Draxl given-names: Claudia orcid: "https://orcid.org/0000-0003-3523-6657" - family-names: Vinson given-names: John orcid: "https://orcid.org/0000-0002-7619-7060" - family-names: Lu given-names: Deyu orcid: "https://orcid.org/0000-0003-4351-6085" date-published: 2023-07-29 doi: 10.21105/joss.05182 issn: 2475-9066 issue: 87 journal: Journal of Open Source Software publisher: name: Open Journals start: 5182 title: "Lightshow: a Python package for generating computational x-ray absorption spectroscopy input files" type: article url: "https://joss.theoj.org/papers/10.21105/joss.05182" volume: 8 title: "Lightshow: a Python package for generating computational x-ray absorption spectroscopy input files" ```

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 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/4436
Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.05182
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

Kevin-Mattheus-Moerman commented 1 year ago

@matthewcarbone congratulations on this JOSS publication!

@ppxasjsm thanks for editing!

And a special thanks to the reviewers: @maurov, @larsenkg

openjournals / joss-reviews

[REVIEW]: Lightshow: a Python package for generating computational x-ray absorption spectroscopy input files #5182

Status

Reviewer instructions & questions

Checklists

Post-Review Checklist for Editor and Authors

Additional Author Tasks After Review is Complete

Editor Tasks Prior to Acceptance