editorialbot commented 9 months ago

Submitting author: !--author-handle-->@JaGeo@RMeli<!--end-editor-- Reviewers: @berquist, @srmnitc Archive: 10.5281/zenodo.10713348

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/4e8524125e36486c65a4b435bbfe2df2"><img src="https://joss.theoj.org/papers/4e8524125e36486c65a4b435bbfe2df2/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/4e8524125e36486c65a4b435bbfe2df2/status.svg)](https://joss.theoj.org/papers/4e8524125e36486c65a4b435bbfe2df2)

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

@berquist & @srmnitc, 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 @RMeli 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 @berquist

📝 Checklist for @srmnitc

editorialbot commented 8 months ago

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

RMeli commented 8 months ago

Check the archive deposit has the correct metadata (title and author list), and request the author edit it if it doesn’t match the paper.

This is only a preference, but the set of authors in Zenodo can be a superset of the authors in the paper.

Please go ahead and make a new release. Just make sure that all the authors of the paper appear on the Zenodo archive (with the correct affiliation/ORCID if possible).

JaGeo commented 8 months ago

Will do.

JaGeo commented 8 months ago

The release is done including the title change and including all relevant authors with correct affiliations and ORCID: https://pypi.org/project/lobsterpy/ (new release is on pypi) https://zenodo.org/records/10713348

RMeli commented 8 months ago

@editorialbot check references

editorialbot commented 8 months ago

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

OK DOIs

- 10.1021/jp202489s is OK
- 10.1002/jcc.23424 is OK
- 10.1002/jcc.24300 is OK
- 10.21105/joss.00717 is OK
- 10.1016/j.commatsci.2012.10.028 is OK
- 10.1021/j100135a014 is OK
- 10.1515/9783111167213 is OK
- 10.1021/acsomega.3c00395 is OK
- 10.1038/s41597-023-02477-5 is OK
- 10.1021/jacs.2c11908 is OK
- 10.1021/acs.chemmater.1c03349 is OK
- 10.1002/anie.198708461 is OK
- 10.1016/j.apsusc.2022.156064 is OK
- 10.1021/ja00349a027 is OK
- 10.1021/acs.jpcc.1c00718 is OK
- 10.1002/cplu.202200123 is OK
- 10.1002/adfm.202314565 is OK
- 10.1063/1.4812323 is OK

MISSING DOIs

- None

INVALID DOIs

- None

RMeli commented 8 months ago

@editorialbot set https://doi.org/10.5281/zenodo.10713348 as archive

editorialbot commented 8 months ago

Done! archive is now 10.5281/zenodo.10713348

RMeli commented 8 months ago

@editorialbot set v0.3.8 as version

editorialbot commented 8 months ago

Done! version is now v0.3.8

RMeli commented 8 months ago

@editorialbot recommend-accept

editorialbot commented 8 months ago

Attempting dry run of processing paper acceptance...

editorialbot commented 8 months ago

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

OK DOIs

- 10.1021/jp202489s is OK
- 10.1002/jcc.23424 is OK
- 10.1002/jcc.24300 is OK
- 10.21105/joss.00717 is OK
- 10.1016/j.commatsci.2012.10.028 is OK
- 10.1021/j100135a014 is OK
- 10.1515/9783111167213 is OK
- 10.1021/acsomega.3c00395 is OK
- 10.1038/s41597-023-02477-5 is OK
- 10.1021/jacs.2c11908 is OK
- 10.1021/acs.chemmater.1c03349 is OK
- 10.1002/anie.198708461 is OK
- 10.1016/j.apsusc.2022.156064 is OK
- 10.1021/ja00349a027 is OK
- 10.1021/acs.jpcc.1c00718 is OK
- 10.1002/cplu.202200123 is OK
- 10.1002/adfm.202314565 is OK
- 10.1063/1.4812323 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot commented 8 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/5055, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

JaGeo commented 8 months ago

@RMeli Thank you so much! And thanks also for the great review experience! 😀

RMeli commented 8 months ago

Thank you @JaGeo for engaging so well with this review. I was happy to recommend publication, according to the reviewers suggestions. Now the EiC will do the final checks.

Thank you again to @srmnitc and @berquist for the in depth and constructive review!

Kevin-Mattheus-Moerman commented 8 months ago

@RMeli thanks for editing this one. It looks like perhaps @editorialbot create post-review checklist was not used yet. I'll call it now and take it from here. I recommend using it in the future to prevent overlooking some of the last steps. In this case for instance the license on the archive link doesn't match up yet. No worries though we'll sort this out now. Thanks again.

Kevin-Mattheus-Moerman commented 8 months ago

Post-Review Checklist for Editor and Authors

Additional Author Tasks After Review is Complete

Double check authors and affiliations (including ORCIDs)
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.
Archive the release on Zenodo/figshare/etc and post the DOI here.
Make sure that the title and author list (including ORCIDs) in the archive match those in the JOSS paper.
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 pull request)
[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

Kevin-Mattheus-Moerman commented 8 months ago

@JaGeo As AEiC on this track I will now help process the final steps to help with acceptance in JOSS. I have just checked the paper, this review, your repository, and the archive link. Most seems in order. I'd only ask you to please ensure that the license listed on the archive link matches your software license. Can you edit this please?

JaGeo commented 8 months ago

@Kevin-Mattheus-Moerman Thank you. I have edited the repo metadata and changed the license to the 'BSD 3-Clause "New" or "Revised" License"

(see https://doi.org/10.5281/zenodo.10713348)

Kevin-Mattheus-Moerman commented 8 months ago

@editorialbot accept

editorialbot commented 8 months ago

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

editorialbot commented 8 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: Naik given-names: Aakash Ashok orcid: "https://orcid.org/0000-0002-6071-6786" - family-names: Ueltzen given-names: Katharina orcid: "https://orcid.org/0009-0003-2967-1182" - family-names: Ertural given-names: Christina orcid: "https://orcid.org/0000-0002-7696-5824" - family-names: Jackson given-names: Adam J. orcid: "https://orcid.org/0000-0001-5272-6530" - family-names: George given-names: Janine orcid: "https://orcid.org/0000-0001-8907-0336" doi: 10.5281/zenodo.10713348 message: If you use this software, please cite our article in the Journal of Open Source Software. preferred-citation: authors: - family-names: Naik given-names: Aakash Ashok orcid: "https://orcid.org/0000-0002-6071-6786" - family-names: Ueltzen given-names: Katharina orcid: "https://orcid.org/0009-0003-2967-1182" - family-names: Ertural given-names: Christina orcid: "https://orcid.org/0000-0002-7696-5824" - family-names: Jackson given-names: Adam J. orcid: "https://orcid.org/0000-0001-5272-6530" - family-names: George given-names: Janine orcid: "https://orcid.org/0000-0001-8907-0336" date-published: 2024-02-27 doi: 10.21105/joss.06286 issn: 2475-9066 issue: 94 journal: Journal of Open Source Software publisher: name: Open Journals start: 6286 title: "LobsterPy: A package to automatically analyze LOBSTER runs" type: article url: "https://joss.theoj.org/papers/10.21105/joss.06286" volume: 9 title: "LobsterPy: A package to automatically analyze LOBSTER runs" ```

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 8 months ago

🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

editorialbot commented 8 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/5060
Wait five minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.06286
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

JaGeo commented 8 months ago

Thank you very much, @Kevin-Mattheus-Moerman .

And, of course, thank you so mich, @srmnitc and @berquist for your reviews, as well!

RMeli commented 8 months ago

Congratulations @JaGeo!

@Kevin-Mattheus-Moerman this was my very fist time editing, thank you for double checking everything carefully and suggesting the "Post-Review Checklist" (I used the one on the Editorial Guide, but clearly slipped on the last point).

RMeli commented 8 months ago

@Kevin-Mattheus-Moerman can I close the issue once the paper is accepted? (I expected the bot to close it automatically, but I just noticed that it's still open.)

Kevin-Mattheus-Moerman commented 8 months ago

I'll do that shortly after some thanks/congratulations messages. Thanks

Kevin-Mattheus-Moerman commented 8 months ago

@JaGeo congratulations on this JOSS publication!!!

@RMeli Thanks for editing!

And a special thank you to the reviewers: @berquist, @srmnitc !!

editorialbot commented 8 months ago

: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.06286/status.svg)](https://doi.org/10.21105/joss.06286)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.06286">
  <img src="https://joss.theoj.org/papers/10.21105/joss.06286/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.06286/status.svg
   :target: https://doi.org/10.21105/joss.06286

This is how it will look in your documentation:

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openjournals / joss-reviews

[REVIEW]: LobsterPy: A package to automatically analyze LOBSTER runs #6286

Status

Reviewer instructions & questions

Checklists

Post-Review Checklist for Editor and Authors

Additional Author Tasks After Review is Complete

Editor Tasks Prior to Acceptance