[REVIEW]: SPyCi-PDB: A modular command-line interface for back-calculating experimental datatypes of protein structures

editorialbot commented 2 years ago

Submitting author: !--author-handle-->@menoliu@ppxasjsm<!--end-editor-- Reviewers: @dotsdl, @lohedges, @JenkeScheen, @sulstice Archive: 10.5281/zenodo.7887039

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menoliu commented 1 year ago

Thanks @ppxasjsm , I have incorporated your edits and have deposited v0.3.5 on Zenodo here: https://doi.org/10.5281/zenodo.7887039

ppxasjsm commented 1 year ago

@editorialbot set https://doi.org/10.5281/zenodo.7887039 as archive

editorialbot commented 1 year ago

Done! archive is now 10.5281/zenodo.7887039

ppxasjsm commented 1 year ago

@editorialbot generate pdf

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

- 10.1146/annurev.biophys.37.092707.153558 is OK
- 10.1080/152165401317291147 is OK
- 10.1136/mp.53.1.8 is OK
- 10.1016/j.sbi.2019.05.024 is OK
- 10.1038/s41586-021-03819-2 is OK
- 10.1126/science.abj8754 is OK
- 10.1016/j.sbi.2007.01.009 is OK
- 10.1093/bioinformatics/bts172 is OK
- 10.1002/(sici)1097-0134(20000501)39:2<112::aid-prot2>3.0.co;2-b is OK
- 10.1002/prot.1163 is OK
- 10.1021/acs.jpcb.0c02924 is OK
- 10.1021/acs.jpca.2c03726 is OK
- 10.1016/j.str.2018.10.016 is OK
- 10.1093/nar/28.1.235 is OK
- 10.1021/acs.jpclett.6b00885 is OK
- 10.1073/pnas.1800690115 is OK
- 10.1093/bioinformatics/bts701 is OK
- 10.1021/jacs.6b00351 is OK
- 10.48550/ARXIV.2206.12667 is OK
- 10.1038/s42004-020-0323-0 is OK
- 10.1007/978-1-0716-0270-6_15 is OK
- 10.1039/c9sc06561j is OK
- 10.1021/ja003724j is OK
- 10.1107/s1600576717007786 is OK
- 10.1016/j.bpj.2018.01.002 is OK
- 10.1021/ja0000908 is OK
- 10.1021/jacs.1c06264 is OK

MISSING DOIs

- None

INVALID DOIs

- None

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 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

- 10.1146/annurev.biophys.37.092707.153558 is OK
- 10.1080/152165401317291147 is OK
- 10.1136/mp.53.1.8 is OK
- 10.1016/j.sbi.2019.05.024 is OK
- 10.1038/s41586-021-03819-2 is OK
- 10.1126/science.abj8754 is OK
- 10.1016/j.sbi.2007.01.009 is OK
- 10.1093/bioinformatics/bts172 is OK
- 10.1002/(sici)1097-0134(20000501)39:2<112::aid-prot2>3.0.co;2-b is OK
- 10.1002/prot.1163 is OK
- 10.1021/acs.jpcb.0c02924 is OK
- 10.1021/acs.jpca.2c03726 is OK
- 10.1016/j.str.2018.10.016 is OK
- 10.1093/nar/28.1.235 is OK
- 10.1021/acs.jpclett.6b00885 is OK
- 10.1073/pnas.1800690115 is OK
- 10.1093/bioinformatics/bts701 is OK
- 10.1021/jacs.6b00351 is OK
- 10.48550/ARXIV.2206.12667 is OK
- 10.1038/s42004-020-0323-0 is OK
- 10.1007/978-1-0716-0270-6_15 is OK
- 10.1039/c9sc06561j is OK
- 10.1021/ja003724j is OK
- 10.1107/s1600576717007786 is OK
- 10.1016/j.bpj.2018.01.002 is OK
- 10.1021/ja0000908 is OK
- 10.1021/jacs.1c06264 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/4192, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

menoliu commented 1 year ago

Excellent! Thanks Toni. I'm just wondering before the EiC proceeds if we need to update the version number to v0.3.5 and the list of reviewers?

ppxasjsm commented 1 year ago

You mean on the paper?

ppxasjsm commented 1 year ago

Good point about the version. In terms of reviewers...I am not sure actually.

ppxasjsm commented 1 year ago

@editorialbot set v0.3.5 as version

editorialbot commented 1 year ago

Done! version is now v0.3.5

menoliu commented 1 year ago

Thanks! And yes on the paper for the list of reviewers, I thought it was just mirrored from the first bot comment in this issue? But it's no problem, I'm okay to wait for what the EiC says about that :)

Kevin-Mattheus-Moerman commented 1 year ago

@menoliu I've reviewed the paper, the archive, and the repository, and most seem in order. I only have the minor points below that require your attention:

[x] Please manually edit the ZENODO archive listed license to match your software license (it currently says Other (Open))
[x] I recommend write cartesian as Cartesian throughout.
[x] In your affiliations, please spell out USA as United States of America. Also zip codes are not a requirement so you may remove them if you wish.

@ppxasjsm thanks for editing here. Minor side note, note sure if you've tried it yet but you can now call @editorialbot create post-review checklist before you recommend acceptance, it can help double-check some of the final bits and pieces, for instance it will list the thing about the license listed on the archive too. Thanks again

ppxasjsm commented 1 year ago

Oh thank you! I didn't know about the checklist, I'll use it next time!

menoliu commented 1 year ago

Thank you @Kevin-Mattheus-Moerman , I have completed all of the tasks

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:

menoliu commented 1 year ago

Just a small update, I was reading over the paper and have corrected co-ordinate to coordinate to maintain consistency. There were some GitHub actions issues too but I have since resolved them. I am happy with everything now!

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

@menoliu the paper change is fine. On the other changes, should we update the version tag here, e.g. to v0.3.9? And create a new ZENODO archive for it? Or should we proceed with the current ones?

menoliu commented 1 year ago

@Kevin-Mattheus-Moerman great! I think we should proceed with the current one (v0.3.5) as ReadTheDocs has issues building v0.3.9 (even though I have not changed any code/requirements from v0.3.5 only made edits to paper.md).

Edit: I should note that tox -e docs is not giving any issues (as per all my ci tests passing) so I will look into this another time with RtD.

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.

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CITATION.cff

``` cff-version: "1.2.0" authors: - family-names: Liu given-names: Zi Hao orcid: "https://orcid.org/0000-0002-8357-8507" - family-names: Zhang given-names: Oufan - family-names: Teixeira given-names: João M. C. orcid: "https://orcid.org/0000-0002-9113-0622" - family-names: Li given-names: Jie orcid: "https://orcid.org/0000-0002-4727-1786" - family-names: Head-Gordon given-names: Teresa orcid: "https://orcid.org/0000-0003-0025-8987" - family-names: Forman-Kay given-names: Julie D. orcid: "https://orcid.org/0000-0001-8265-972X" contact: - family-names: Liu given-names: Zi Hao orcid: "https://orcid.org/0000-0002-8357-8507" - family-names: Forman-Kay given-names: Julie D. orcid: "https://orcid.org/0000-0001-8265-972X" doi: 10.5281/zenodo.7887039 message: If you use this software, please cite our article in the Journal of Open Source Software. preferred-citation: authors: - family-names: Liu given-names: Zi Hao orcid: "https://orcid.org/0000-0002-8357-8507" - family-names: Zhang given-names: Oufan - family-names: Teixeira given-names: João M. C. orcid: "https://orcid.org/0000-0002-9113-0622" - family-names: Li given-names: Jie orcid: "https://orcid.org/0000-0002-4727-1786" - family-names: Head-Gordon given-names: Teresa orcid: "https://orcid.org/0000-0003-0025-8987" - family-names: Forman-Kay given-names: Julie D. orcid: "https://orcid.org/0000-0001-8265-972X" date-published: 2023-05-10 doi: 10.21105/joss.04861 issn: 2475-9066 issue: 85 journal: Journal of Open Source Software publisher: name: Open Journals start: 4861 title: "SPyCi-PDB: A modular command-line interface for back-calculating experimental datatypes of protein structures." type: article url: "https://joss.theoj.org/papers/10.21105/joss.04861" volume: 8 title: "SPyCi-PDB: A modular command-line interface for back-calculating experimental datatypes of protein structures." ```

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editorialbot commented 1 year ago

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

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/4217
Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.04861
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

lohedges commented 1 year ago

Many congratulations @menoliu!

Kevin-Mattheus-Moerman commented 1 year ago

Congratulations on this publication @menoliu !!

Thanks for editing @ppxasjsm, and a special thanks to the reviewers: @dotsdl, @lohedges, @JenkeScheen, @Sulstice !! :tada:

editorialbot commented 1 year ago

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

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