[REVIEW]: Chitin Builder: a VMD tool for the generation of structures of chitin molecular crystals for atomistic simulations

editorialbot commented 1 year ago

Submitting author: !--author-handle-->@jfaraudo@majensen<!--end-editor-- Reviewers: @amoeba, @tonigi Archive: 10.5281/zenodo.3274725

Status

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Markdown: [![status](https://joss.theoj.org/papers/c409d05d1e558827d1dea6275faf8965/status.svg)](https://joss.theoj.org/papers/c409d05d1e558827d1dea6275faf8965)

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

@amoeba & @WangKehan573, 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 @majensen 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 @amoeba

📝 Checklist for @tonigi

jfaraudo commented 10 months ago

In our final check we have found a (really minor) typo in the paper, so we have corrected it. I think that now the work can be considered finished with all comments taken into account.

jfaraudo commented 10 months ago

@editorialbot generate pdf

editorialbot commented 10 months ago

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

amoeba commented 10 months ago

Thanks @jfaraudo. My review is now an accept @majensen.

Re: the updated archive, I think that's handled automatically when the submission is accepted and I pointed it out just to make sure the new 1.1 release is used everywhere.

jfaraudo commented 10 months ago

@editorialbot commands

editorialbot commented 10 months ago

Hello @jfaraudo, here are the things you can ask me to do:


# List all available commands
@editorialbot commands

# Get a list of all editors's GitHub handles
@editorialbot list editors

# Check the references of the paper for missing DOIs
@editorialbot check references

# Perform checks on the repository
@editorialbot check repository

# Adds a checklist for the reviewer using this command
@editorialbot generate my checklist

# Set a value for branch
@editorialbot set joss-paper as branch

# Generates the pdf paper
@editorialbot generate pdf

# Generates a LaTeX preprint file
@editorialbot generate preprint

# Get a link to the complete list of reviewers
@editorialbot list reviewers

jfaraudo commented 10 months ago

@editorialbot check repository

editorialbot commented 10 months ago

Software report:

github.com/AlDanial/cloc v 1.88  T=0.04 s (393.4 files/s, 55950.7 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
TeX                              1             50              0            690
Tcl/Tk                           2             76            125            659
Markdown                         9            113              0            209
Bourne Shell                     1              8             16             22
YAML                             1              1              4             18
-------------------------------------------------------------------------------
SUM:                            14            248            145           1598
-------------------------------------------------------------------------------

gitinspector failed to run statistical information for the repository

editorialbot commented 10 months ago

Wordcount for paper.md is 1069

jfaraudo commented 10 months ago

@majensen now that both reviewers finished their task, is that anything else that we have to do from our side? Or the work can be considered accepted?

majensen commented 10 months ago

@jfaraudo Thanks for all the work. I will do a quick editorial runthrough of the paper itself. That may generate a couple of fixes needed. Re archive, what JOSS requires is an open archive of your repository, in Zenodo or similar service. Have a look at this tutorial from another JOSS review.

majensen commented 10 months ago

Once you create your archive, please let me know the version and the DOI created, here in this thread. Thanks

jfaraudo commented 10 months ago

@majensen Zenodo DOI https://doi.org/10.5281/zenodo.10517626 Zenodo record https://zenodo.org/records/10517626 Archived version 1.1

majensen commented 10 months ago

Thanks @jfaraudo - the journal prefers that the title and authors on the archive match those on the paper, if you can update those items.

jfaraudo commented 10 months ago

OK @majensen The zenodo archive was generated automatically after creating the new software version (we had an automatic update of our GitHub repo in Zenodo) and it takes as title the GitHub repo name and as authos everyone that contributed in the repo (including referees like @amoeba that did a pull request on GitHub). We will try to correct this today. If a correction is not possible we will create manually another Zenodo archive for the JOSS publication.

jfaraudo commented 10 months ago

@majensen Corrected, now authors and title matches that of JOSS submission and files correspond to latest repository version . Same DOI: https://zenodo.org/doi/10.5281/zenodo.3274725

majensen commented 10 months ago

@editorialbot set v1.1 as version

editorialbot commented 10 months ago

Done! version is now v1.1

majensen commented 10 months ago

@editorialbot set 10.5281/zenodo.3274725 as archive

editorialbot commented 10 months ago

Done! archive is now 10.5281/zenodo.3274725

majensen commented 10 months ago

@editorialbot recommend-accept

editorialbot commented 10 months ago

Attempting dry run of processing paper acceptance...

editorialbot commented 10 months ago

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

OK DOIs

- 10.1021/ma0477246 is OK
- 10.1351/pac-rep-10-01-01 is OK
- 10.1021/bm201512t is OK
- 10.1016/j.cpc.2013.03.010 is OK
- 10.1021/ma0203849 is OK
- 10.1016/j.carbpol.2017.06.099 is OK
- 10.1115/1.4038883 is OK
- 10.1021/acs.biomac.5b01653 is OK
- 10.1021/bm801251e is OK
- 10.1007/s10570-016-0968-0 is OK
- 10.1016/0166-218x(88)90012-1 is OK
- 10.1038/nature23268 is OK
- 10.1103/physrevlett.120.068001 is OK
- 10.1371/journal.pone.0039376 is OK
- 10.1021/ma102240r is OK
- 10.1021/ma0477246 is OK
- 10.1016/S1381-5148(00)00038-9 is OK
- 10.1002/cben.201400025 is OK
- 10.1021/acssuschemeng.8b06372 is OK
- 10.1002/jcc.22959 is OK
- 10.1021/ct8002964 is OK
- 10.1021/ct200328p is OK
- 10.1081/MC-120006451 is OK
- 10.1351/pac-rep-10-01-01 is OK
- 10.1021/bm201512t is OK
- 10.1016/j.cpc.2013.03.010 is OK
- 10.1021/ma0203849 is OK
- 10.1016/j.carbpol.2017.06.099 is OK
- 10.1021/ct700301q is OK
- 10.1002/jcc.20291 is OK
- 10.1007/s12668-013-0097-2 is OK
- 10.1115/1.4038883 is OK
- 10.1021/acs.jpcb.6b05999 is OK
- 10.1007/s10853-015-9271-y is OK
- 10.1016/J.CIS.2019.02.003 is OK
- 10.1021/acs.biomac.5b01653 is OK
- 10.1016/J.CARBPOL.2017.08.076 is OK
- 10.1002/pola.20176 is OK
- 10.1021/bm801251e is OK
- 10.1007/s10570-016-0968-0 is OK
- 10.1002/jcc.20289 is OK
- 10.1016/0166-218x(88)90012-1 is OK
- 10.1039/C6GC00628K is OK
- 10.1039/C6RA00107F is OK
- 10.1038/nature23268 is OK
- 10.1103/physrevlett.120.068001 is OK
- 10.1016/0263-7855(96)00018-5 is OK
- 10.1371/journal.pone.0039376 is OK
- 10.1021/ma102240r is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot commented 10 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/4958, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

jfaraudo commented 10 months ago

@editorialbot accept

editorialbot commented 10 months ago

I'm sorry @jfaraudo, I'm afraid I can't do that. That's something only eics are allowed to do.

jfaraudo commented 10 months ago

Everything (pdf file, etc) looks good to me.

Kevin-Mattheus-Moerman commented 10 months ago

@jfaraudo As AEiC I will now help to process final steps towards acceptance in JOSS. I have just checked your repository, this review, the archive link, and the paper. All seems in order, so I will now proceed to accept this work.

Kevin-Mattheus-Moerman commented 10 months ago

@editorialbot accept

editorialbot commented 10 months ago

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

editorialbot commented 10 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: Malaspina given-names: David orcid: "https://orcid.org/0000-0002-5420-9534" - family-names: Faraudo given-names: Jordi orcid: "https://orcid.org/0000-0002-6315-4993" contact: - family-names: Faraudo given-names: Jordi orcid: "https://orcid.org/0000-0002-6315-4993" doi: 10.5281/zenodo.3274725 message: If you use this software, please cite our article in the Journal of Open Source Software. preferred-citation: authors: - family-names: Malaspina given-names: David orcid: "https://orcid.org/0000-0002-5420-9534" - family-names: Faraudo given-names: Jordi orcid: "https://orcid.org/0000-0002-6315-4993" date-published: 2024-01-29 doi: 10.21105/joss.05771 issn: 2475-9066 issue: 93 journal: Journal of Open Source Software publisher: name: Open Journals start: 5771 title: "Chitin Builder: a VMD tool for the generation of structures of chitin molecular crystals for atomistic simulations" type: article url: "https://joss.theoj.org/papers/10.21105/joss.05771" volume: 9 title: "Chitin Builder: a VMD tool for the generation of structures of chitin molecular crystals for atomistic simulations" ```

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 10 months ago

🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

editorialbot commented 10 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/4963
Wait five minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.05771
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 10 months ago

@jfaraudo congratulations on this JOSS publication ! Thanks for editing @majensen

And a special thank you to the reviewers: @amoeba, @tonigi !!

editorialbot commented 10 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:
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HTML:
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  <img src="https://joss.theoj.org/papers/10.21105/joss.05771/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.05771/status.svg
   :target: https://doi.org/10.21105/joss.05771

This is how it will look in your documentation:

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majensen commented 10 months ago

Really great to finally get this out - thanks to all for thier perseverance!

jfaraudo commented 10 months ago

Thanks to all @majensen @tonigi @amoeba

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