[REVIEW]: MolPainter: A Tool for Painting and Solvating Layered Molecular Systems

[editorialbot]

Submitting author: !--author-handle-->@gpantel<!--end-author-handle-- (George Pantelopulos) Repository: https://github.com/gpantel/MolPainter/ Branch with paper.md (empty if default branch): paper_joss Version: 1.1.5 Editor: !--editor-->@jgostick<!--end-editor-- Reviewers: @HubLot, @arkajitmandal Archive: https://doi.org/10.5281/zenodo.7846421

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/929842d02b46a27853520abd5b9c785c"><img src="https://joss.theoj.org/papers/929842d02b46a27853520abd5b9c785c/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/929842d02b46a27853520abd5b9c785c/status.svg)](https://joss.theoj.org/papers/929842d02b46a27853520abd5b9c785c)

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

@HubLot & @arkajitmandal, 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 @jgostick 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 @HubLot

📝 Checklist for @arkajitmandal

[jgostick]

@editorialbot check refereces

[editorialbot]

I'm sorry human, I don't understand that. You can see what commands I support by typing:

@editorialbot commands

[jgostick]

@editorialbot check references

[editorialbot]

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

OK DOIs

- 10.7554/eLife.19274 is OK
- 10.1002/jcc.21224 is OK
- 10.1002/jcc.20291 is OK
- 10.1002/jcc.20945 is OK
- 10.1021/acs.jcim.9b00269 is OK
- 10.1021/acs.jctc.5b00209 is OK
- 10.1093/bioinformatics/btv292 is OK
- 10.1021/acs.jctc.8b00765 is OK
- 10.1371/journal.pcbi.1003720 is OK
- 10.3390/membranes11050323 is OK
- 10.1016/S0006-3495(99)77369-8 is OK
- 10.1016/S0006-3495(02)75497-0 is OK
- 10.1002/jcc.24516 is OK
- 10.1063/1.4999709 is OK
- 10.1016/j.bpj.2018.10.011 is OK
- 10.1073/pnas.2212207119 is OK
- 10.1016/j.bpj.2022.07.031 is OK
- 10.1016/j.bpj.2020.01.044 is OK
- 10.1016/S0022-2275(20)31502-9 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[jgostick]

@editorialbot set https://doi.org/10.5281/zenodo.7846421 as archive

[editorialbot]

Done! Archive is now https://doi.org/10.5281/zenodo.7846421

[editorialbot]

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

[jgostick]

@editorialbot recommend-accept

[editorialbot]

Attempting dry run of processing paper acceptance...

[editorialbot]

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

OK DOIs

- 10.7554/eLife.19274 is OK
- 10.1002/jcc.21224 is OK
- 10.1002/jcc.20291 is OK
- 10.1002/jcc.20945 is OK
- 10.1021/acs.jcim.9b00269 is OK
- 10.1021/acs.jctc.5b00209 is OK
- 10.1093/bioinformatics/btv292 is OK
- 10.1021/acs.jctc.8b00765 is OK
- 10.1371/journal.pcbi.1003720 is OK
- 10.3390/membranes11050323 is OK
- 10.1016/S0006-3495(99)77369-8 is OK
- 10.1016/S0006-3495(02)75497-0 is OK
- 10.1002/jcc.24516 is OK
- 10.1063/1.4999709 is OK
- 10.1016/j.bpj.2018.10.011 is OK
- 10.1073/pnas.2212207119 is OK
- 10.1016/j.bpj.2022.07.031 is OK
- 10.1016/j.bpj.2020.01.044 is OK
- 10.1016/S0022-2275(20)31502-9 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

:warning: Error preparing paper acceptance. The generated XML metadata file is invalid.

Element isbn: [facet 'minLength'] The value has a length of '9'; this underruns the allowed minimum length of '10'.
Element isbn: [facet 'minLength'] The value has a length of '9'; this underruns the allowed minimum length of '10'.

[tarleb]

To explain the error: it seems that the isbn entry in Martinetz2009 contains the ISSN of the journal's web version instead of an ISBN. It's probably best to just remove the line.

Likewise, Wassenaar2015 also has an ISSN in the ISBN field. The respective line should be removed.

Additionally, please also remove line 149, which suffers from a similar problem but apparently didn't trigger the automatic check (yet?).

Please also note that references use both title case and sentence case, whereas JOSS uses APA style and hence title case for article titles. However, I'm not sure how strict the editors are with this. Best practice is generally to surround words with a second pair of braces only if the case of the characters must not be changed – wrapping the full title in two braces usually doesn't give the intended result.

[gpantel]

@tarleb Thank you very much for the detailed explanation. I changed the BIB file. I removed the isbn entries, removed the second brackets on the titles, and changed all titles to title-case. The titles were generated in sentence-case in the resulting PDF.

[jgostick]

@editorialbot recommend-accept

[editorialbot]

Attempting dry run of processing paper acceptance...

[editorialbot]

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

OK DOIs

- 10.7554/eLife.19274 is OK
- 10.1002/jcc.21224 is OK
- 10.1002/jcc.20291 is OK
- 10.1002/jcc.20945 is OK
- 10.1021/acs.jcim.9b00269 is OK
- 10.1021/acs.jctc.5b00209 is OK
- 10.1093/bioinformatics/btv292 is OK
- 10.1021/acs.jctc.8b00765 is OK
- 10.1371/journal.pcbi.1003720 is OK
- 10.3390/membranes11050323 is OK
- 10.1016/S0006-3495(99)77369-8 is OK
- 10.1016/S0006-3495(02)75497-0 is OK
- 10.1002/jcc.24516 is OK
- 10.1063/1.4999709 is OK
- 10.1016/j.bpj.2018.10.011 is OK
- 10.1073/pnas.2212207119 is OK
- 10.1016/j.bpj.2022.07.031 is OK
- 10.1016/j.bpj.2020.01.044 is OK
- 10.1016/S0022-2275(20)31502-9 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

:wave: @openjournals/pe-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/4148, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

[kyleniemeyer]

Hi @gpantel, I'm doing some final checks before publishing your submission.

In the paper, could you go through and make sure that citations appear before punctuation in sentences, and also have a space between them and any preceding words? It looks like they were inserted like footnotes, but these are in-text citations.

[jgostick]

Hi @kyleniemeyer, I'm really sorry that I always seem to miss something in the final stages of submission.

[kyleniemeyer]

@jgostick no worries! This is what the final EIC checks are for!

[gpantel]

@kyleniemeyer @jgostick Thank you! All citations now always appear before punctuation and always preceded by a single space.

[kyleniemeyer]

@editorialbot generate pdf

[editorialbot]

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

[kyleniemeyer]

@editorialbot accept

[editorialbot]

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

[editorialbot]

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: Pantelopulos given-names: George A. orcid: "https://orcid.org/0000-0002-4373-1677" - family-names: Liberatore given-names: Aaron contact: - family-names: Pantelopulos given-names: George A. orcid: "https://orcid.org/0000-0002-4373-1677" doi: "https://doi.org/10.5281/zenodo.7846421" message: If you use this software, please cite our article in the Journal of Open Source Software. preferred-citation: authors: - family-names: Pantelopulos given-names: George A. orcid: "https://orcid.org/0000-0002-4373-1677" - family-names: Liberatore given-names: Aaron date-published: 2023-04-21 doi: 10.21105/joss.05128 issn: 2475-9066 issue: 84 journal: Journal of Open Source Software publisher: name: Open Journals start: 5128 title: "MolPainter: A Tool for Painting and Solvating Layered Molecular Systems" type: article url: "https://joss.theoj.org/papers/10.21105/joss.05128" volume: 8 title: "MolPainter: A Tool for Painting and Solvating Layered Molecular Systems" ```

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]

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

[editorialbot]

🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

[editorialbot]

🚨🚨🚨 THIS IS NOT A DRILL, YOU HAVE JUST ACCEPTED A PAPER INTO JOSS! 🚨🚨🚨

Here's what you must now do:

0. Check final PDF and Crossref metadata that was deposited :point_right: https://github.com/openjournals/joss-papers/pull/4165
1. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.05128
2. If everything looks good, then close this review issue.
3. Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

[kyleniemeyer]

Congratulations @gpantel on your article's publication in JOSS!

Many thanks to @HubLot and @arkajitmandal for reviewing this submission, and @jgostick for editing.

[editorialbot]

: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.05128/status.svg)](https://doi.org/10.21105/joss.05128)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.05128">
  <img src="https://joss.theoj.org/papers/10.21105/joss.05128/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.05128/status.svg
   :target: https://doi.org/10.21105/joss.05128

This is how it will look in your documentation:

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[gpantel]

Thank you all very much! Thanks to the unique publication requirements and critical efforts of the reviewers and editor, this was a pleasantly enjoyable, helpful, and educational peer-review experience that significantly improved our program, its documentation, and its visibility.