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[REVIEW]: MolPainter: A Tool for Painting and Solvating Layered Molecular Systems #5128

Closed editorialbot closed 1 year ago

editorialbot commented 1 year ago

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

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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

editorialbot commented 1 year ago

Hello humans, I'm @editorialbot, a robot that can help you with some common editorial tasks.

For a list of things I can do to help you, just type:

@editorialbot commands

For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:

@editorialbot generate pdf
editorialbot commented 1 year ago 
Software report:

github.com/AlDanial/cloc v 1.88  T=0.05 s (522.5 files/s, 101334.4 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          17            351            454           1994
JSON                             1              0              0           1194
TeX                              1              0              0            477
Markdown                         3            136              0            338
TOML                             2              6              0             34
Tcl/Tk                           1              1              0             34
YAML                             1              1              4             18
-------------------------------------------------------------------------------
SUM:                            26            495            458           4089
-------------------------------------------------------------------------------

gitinspector failed to run statistical information for the repository
editorialbot commented 1 year ago

Wordcount for paper.md is 2962

editorialbot commented 1 year ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.7554/eLife.19274 is OK
- 10.1021/cr0207123 is OK
- 10.1038/ncomms6229 is OK
- 10.1002/jcc.23702 is OK
- 10.1093/bioinformatics/btv292 is OK
- 10.1021/acs.jctc.5b00209 is OK
- 10.1002/jcc.20945 is OK
- 10.1002/jcc.24516 is OK
- 10.1039/c6cp08681k is OK
- 10.1021/acs.jctc.9b00453 is OK
- 10.3390/pharmaceutics12060533 is OK
- 10.1063/1.4999709 is OK
- 10.1016/j.bpj.2020.01.044 is OK
- 10.1126/science.1157834 is OK
- 10.1093/bioinformatics/btt680 is OK
- 10.1021/acs.jctc.8b00765 is OK
- 10.1371/journal.pcbi.1003720 is OK
- 10.1007/978-981-10-1128-3_5 is OK
- 10.1002/jcc.21224 is OK
- 10.1016/j.jmb.2021.166841 is OK
- 10.1016/j.bpj.2018.06.025 is OK
- 10.1002/jcc.20291 is OK
- 10.1016/j.bpj.2022.07.031 is OK
- 10.1021/acs.jpcb.0c07615 is OK
- 10.1002/pro.2385 is OK
- 10.1021/acs.chemrev.8b00451 is OK
- 10.1021/acs.jcim.9b00269 is OK
- 10.3390/membranes11050323 is OK
- 10.1073/pnas.2212207119 is OK
- 10.1016/S0006-3495(99)77369-8 is OK
- 10.1016/j.bpj.2018.10.011 is OK
- 10.1016/S0006-3495(02)75497-0 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:

jgostick commented 1 year ago

Hi @HubLot and @arkajitmandal. This review is now officially started. Reviewing for JOSS is pretty straight-forward....you just create a checklist for yourself using the command @editorialbot generate my checklist, then work your way through the items.

HubLot commented 1 year ago

Thanks @jgostick I'll start the review

HubLot commented 1 year ago

Review checklist for @HubLot

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

HubLot commented 1 year ago

Hi @jgostick and @gpantel, I have started my review and overall, I think it's a good software and clearly fulfils a need. The ability to create complex solvated lipid mixtures (or any layered molecular system) by painting is valuable.

However, at this stage, the submission does not fulfil JOSS Guidelines requirements:

I also have some minor issues which are suggestions:

gpantel commented 1 year ago

@HubLot Thank you for taking so much time to review our submission and making important suggestions I and @a-a-ron1 find helpful. We believe the suggested changes will make the program more accessible and easier to disseminate.

I'm preparing for a conference and hosting a visiting scientist this week so I'm not able to make all of these changes right away. May the JOSS Guidelines issues be prioritized for publication, and the remaining issues might be addressed in a follow-up update?

jgostick commented 1 year ago

@gpantel, you still have to wait for the other reviewers comments too, so perhaps let them add their input on top of the @HubLot's. Then you can address whatever makes sense of the course of the next 3-4 weeks.

gpantel commented 1 year ago

@jgostick Thank you for clarifying!

arkajitmandal commented 1 year ago

Review checklist for @arkajitmandal

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

arkajitmandal commented 1 year ago

Hi @jgostick and @gpantel, I have checked the software and used it following the documentation provided by the authors. The software overall is very well made and should be very useful in the field of computational chemistry/biophysics.

While this work is overall very nice, it does require a bit of clean up (addressing few issues) for it to be recommended for publication. I noticed many of them have been already been mentioned by the other reviewer (so I wont make a duplicate issue). The one additional issue, I think the authors should address is:

jgostick commented 1 year ago

Hey all, just checking to see how things are going? @gpantel, are you making progress addressing the questions asked by these reviewers?

gpantel commented 1 year ago

@jgostick Thank you for for checking in, and sorry for the slow response. We needed to a time to meet together to work on addressing the reviewer comments and conforming to the author guidelines. We have now addressed 6/6 issues raised in @HubLot's careful first review (and updated the tutorial README) and issue 1/1 raised in @arkajitmandal's second review.

HubLot commented 1 year ago

great @gpantel! I'll look into it.

HubLot 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:

HubLot commented 1 year ago

Hi,

My review is finished. The authors addressed the issued I opened. The paper has been lightened, community guidelines added and the documentation has been improved. Tests have been added although there are minimalist. Authors said they will add more for the next version. Overall, I can recommend this software for publication.

jgostick commented 1 year ago

Wow, thanks @HubLot for such as thorough review and your time!

arkajitmandal commented 1 year ago

Hi ! I have checked the modified draft, it looks good! I recommend the work for publication.

jgostick commented 1 year ago

Great @arkajitmandal, I have checked your last boxes on your behalf so I don't get confused. Thanks to you also for your time.

jgostick commented 1 year ago

Post-Review Checklist for Editor and Authors

Additional Author Tasks After Review is Complete

Editor Tasks Prior to Acceptance

jgostick commented 1 year ago

Hi @gpantel, well done on addressing all the reviewer comments and suggestions. Now we can proceed to the next steps. You'll notice that I generated another checklist for you and I. Can you start working your parts?

gpantel commented 1 year ago

Hi all. Thank you again for your time and effort in reviewing and handling this submission. (1) Author names were double-checked.

(2) Release 1.1.3 incorporates the changes made to address the reviews, and (3) has been deposited on Zenodo at https://doi.org/10.5281/zenodo.7787544 (4) with the same author list, ORCIDs, and (5) license.

I do have an outstanding question regarding how the author names are appearing in the citations of the built PDF: https://github.com/gpantel/MolPainter/issues/23#issue-1648702347

gpantel commented 1 year ago

@jgostick Sorry to poke you -- were notified of my previous message?

jgostick 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:

tarleb commented 1 year ago

The problem with author names is due to disambiguation: one bib entry uses Georg A. with a dot, while the others use Georg A without a dot. Disambiguation happens on the raw names so the algorithm detects them as different and adds the first name in an attempt to make the names distinct. This might be a bug in jgm/citeproc, but I'm not sure.

Either way, removing the dot after Georg A. in Pantel2017 fixes the issue.

jgostick 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:

jgostick commented 1 year ago

Hi @gpantel, now that we have solved the bibtex issues, let's move on the process. I have created a checkliss above with some tasks for you. Start tackling those when you have a chance.

jgostick commented 1 year ago

Ooops, I see that you have put the doi and other info in the text.

jgostick commented 1 year ago

@editorialbot set https://doi.org/10.5281/zenodo.7787544 as archive

editorialbot commented 1 year ago

Done! Archive is now https://doi.org/10.5281/zenodo.7787544

jgostick commented 1 year ago

@editorialbot set 1.1.3 as version

editorialbot commented 1 year ago

Done! version is now 1.1.3

jgostick commented 1 year ago

Hi @gpantel, it seems that the spelling of your name on zenodo is not the same as in the paper. The zenodo one looks like a typo (Geirge instead George?)

jgostick 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

- 10.7554/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

MISSING DOIs

- 10.1016/s0022-2275(20)31502-9 may be a valid DOI for title: Phase behavior of lipid mixtures based on human ceramides: coexistence of crystalline and liquid phases

INVALID DOIs

- https://doi.org/10.1016/j.bpj.2020.01.044 is INVALID because of 'https://doi.org/' prefix
jgostick commented 1 year ago

@gpantel can you also deal with the DOI issues that editorialbot found?

gpantel commented 1 year ago

@jgostick Ok I've corrected the DOI entry for MacDermaid2022 ( https://doi.org/10.1016/j.bpj.2020.01.044 -> 10.1016/j.bpj.2020.01.044). The entry "10.1016/s0022-2275(20)31502-9" is correct. My name is corrected in the Zenodo entry now (thanks for checking!).

Also, not important to this process, but we added the more complete test for MolPainter @HubLot requested in v1.1.4 and a bug fix and documentation improvement involving MolSolvator in v1.1.5, part of the latest tag and v1.1.5 on pypi.

jgostick commented 1 year ago

@editorialbot set 1.1.5 as version

editorialbot commented 1 year ago

Done! version is now 1.1.5

jgostick 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

- 10.7554/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

MISSING DOIs

- 10.1016/s0022-2275(20)31502-9 may be a valid DOI for title: Phase behavior of lipid mixtures based on human ceramides: coexistence of crystalline and liquid phases

INVALID DOIs

- None
jgostick commented 1 year ago

Hi @gpantel, can you also add the suggested DOI for the Bouwstra paper? I checked and it seems to be correct.

Also, I need to check with the team about which version of the code should be archived on zenodo because you have 1.1.3 over there, and 1.1.5 is your latest version. I think there is a way to have zenodo create a new doi for each release. That is what happens for my repos (https://zenodo.org/record/7016049).

gpantel commented 1 year ago

Hi @jgostick,

Thanks again, the entry for Bouwstra is fixed now.

I manually updated the zenodo to the current version v1.1.5 https://doi.org/10.5281/zenodo.7846421

Next time we work on an update as a candidate for tagging we'll discuss automating zenodo and pypi updates.

jgostick commented 1 year ago

@editorialbot generate pdf