editorialbot commented 1 year ago

Submitting author: !--author-handle-->@degiacom@richardjgowers<!--end-editor-- Reviewers: @rmeli, @JoaoRodrigues Archive: 10.5281/zenodo.8284102

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/781a409020f1c37417067aef6fbc3217"><img src="https://joss.theoj.org/papers/781a409020f1c37417067aef6fbc3217/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/781a409020f1c37417067aef6fbc3217/status.svg)](https://joss.theoj.org/papers/781a409020f1c37417067aef6fbc3217)

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

@rmeli & @JoaoRodrigues, 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 @richardjgowers 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 @RMeli

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=0.81 s (132.8 files/s, 58241.8 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
JavaScript                      13           4624           4624          16767
HTML                            33           1391              0          10823
Python                          32            884           1261           3539
CSS                              6            452             82           1791
TeX                              1              0              0            171
Markdown                         5             66              0            115
YAML                             5             14              4             86
reStructuredText                 9             62             61             65
DOS Batch                        1              8              1             26
make                             1              4              7              9
Bourne Shell                     1              1              0              2
-------------------------------------------------------------------------------
SUM:                           107           7506           6040          33394
-------------------------------------------------------------------------------

gitinspector failed to run statistical information for the repository

editorialbot commented 1 year ago

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

OK DOIs

- 10.1146/annurev-biochem-060614-034142 is OK
- 10.1038/s41586-021-03819-2 is OK
- 10.1126/science.abj8754 is OK
- 10.1016/j.str.2019.03.018 is OK
- 10.1103/PhysRevX.11.011052 is OK
- 10.48550/arXiv.1912.01703 is OK
- 10.1371/journal.pcbi.1005659 is OK
- 10.1110/ps.062416606 is OK
- 10.1093/bioinformatics/btx789 is OK
- 10.1063/5.0058639 is OK
- 10.1126/science.aaw1147 is OK
- 10.1063/1.5023804 is OK
- 10.1039/d0sc03635h is OK
- 10.1021/acs.jctc.2c00058 is OK
- 10.1021/acs.jctc.5b00255 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot commented 1 year ago

Wordcount for paper.md is 907

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:

RMeli commented 1 year ago

Review checklist for @RMeli

Conflict of interest

[x] I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

Code of Conduct

[x] I confirm that I read and will adhere to the JOSS code of conduct.

General checks

[x] Repository: Is the source code for this software available at the https://github.com/Degiacomi-Lab/molearn?
[x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
[x] Contribution and authorship: Has the submitting author (@degiacom) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
[x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
[x] Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
[x] Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
[x] Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

Functionality

[x] Installation: Does installation proceed as outlined in the documentation?
[x] Functionality: Have the functional claims of the software been confirmed?
[x] Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Documentation

[x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
[x] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
[x] Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
[x] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
[x] Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
[x] Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support

Software paper

[x] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
[x] A statement of need: Does the paper have a section titled 'Statement of need' that clearly states what problems the software is designed to solve, who the target audience is, and its relation to other work?
[x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
[x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
[x] References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

degiacom commented 1 year ago

@RMeli, thank you for your feedback! We have updated the paper according to your suggestions (see https://github.com/Degiacomi-Lab/molearn/issues/7#issuecomment-1585712845), and are looking into the installation issue on MacOS you reported.

degiacom 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:

degiacom commented 1 year ago

@Rmeli, the error you spotted in the molearn_notebook repo has been fixed (filenames of input data had been renamed, but one of the Jupyter notebooks had not been updated accordingly). See https://github.com/Degiacomi-Lab/molearn_notebook/issues/2#issuecomment-1590697392. Thank you for spotting this!

RMeli commented 1 year ago

Thanks @degiacom, sorry for the delayed reply! I opened other issues for a few additional small problems I found.

I started looking at the documentation checklist, and it seems that "Community guidelines" are now a requirement of JOSS. Would you mind adding a CONTRIBUTING.md file quickly outlining how to contribute to the software, how to report issues (a link to the issues page might be enough...), and how to seek support (although this is already stated in the README.md...)?

RMeli commented 1 year ago

Thanks @degiacom, sorry for the delayed reply! I opened other issues for a few additional small problems I found.

I started looking at the documentation checklist, and it seems that "Community guidelines" are now a requirement of JOSS. Would you mind adding a CONTRIBUTING.md file quickly outlining how to contribute to the software, how to report issues (a link to the issues page might be enough...), and how to seek support (although this is already stated in the README.md...)?

SCMusson commented 1 year ago

@RMeli I have added a CONTRIBUTING.md file. Hopefully it satisfies the requirements

RMeli commented 1 year ago

Thanks @SCMusson, LGTM!

degiacom commented 1 year ago

@RMeli, thank you for your feedback. Here is a summary of changes:

we fixed the problems with Jupyter notebooks.
now analysis features progress bars, to give the user some feedback during calculation of 2D landscapes
unittesting has been improved

Throughout, we have also applied minor feature updates and improved package management during installation. All of these changes will be part of a minor release when the reviewing process completes.

RMeli commented 1 year ago

Thanks for all the improvements @degiacom! I never realized how much progress bars could improve the UX. I think the only outstanding issue is the NGLview problem discussed in https://github.com/Degiacomi-Lab/molearn_notebook/issues/3, otherwise LGTM!

degiacom commented 1 year ago

Thank you @RMeli! We are still looking into the issue with NGLView in the notebooks. It appears it all boils down to identifying and pinning a combination of nglview, ipywidgets, and jupyter package versions working correctly with each other.

While we chase that, @JoaoRodrigues, any chance you could provide us with your feedback too?

degiacom commented 1 year ago

@RMeli, we finally seem to have identified the problem with NGLview, see here!

JoaoRodrigues commented 1 year ago

Hi @degiacom, I've been tracking the thread quite carefully! I was on holidays at the beginning of the process and by the time I was about to make comments I thought it would be best to let @RMeli finish their incredibly in-depth and fantastic review before making mine. Just to avoid overlap/redundancy in comments/opinions.

RMeli commented 1 year ago

@degiacom thank you for tracking down the issue! I can confirm that the suggested fix works for me.

@JoaoRodrigues the floor is yours! ;)

degiacom commented 1 year ago

@Rmeli: I completely agree with @JoaoRodrigues, the time and effort you dedicated to this review is much appreciated!

degiacom 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:

degiacom commented 1 year ago

@JoaoRodrigues, following your comments on the paper, above you will find an updated version (turns out, the formatting here slightly differs from the preview service on Whedon, which slightly complicates getting all the text to fit nicely with page breaks).

JoaoRodrigues commented 1 year ago

No problem, if it's too complicated don't bother! Thanks for the changes, I'll continue the review today.

Message ID: @.***>

degiacom commented 1 year ago

Hi @JoaoRodrigues, was wondering could you confirm whether you are happy with the way we addressed the issues you raised in the molearn repo, on paper and code cleanliness? If so, happy to close the issues?

degiacom commented 1 year ago

@richardjgowers have not heard from the reviewer for a bit. I believe we have addressed their comments (for comfort, above I have just added breadcrumb trails to the two issues they had raised), would you be able to look into this?

richardjgowers commented 1 year ago

@JoaoRodrigues any updates on your review?

JoaoRodrigues commented 1 year ago

Hi Richard & Matteo,

Sorry for going MIA but I had some unexpected personal matters to attend to and I couldn't get back to the review.

I had planned going over the code in a little more detail but I was pretty happy with the paper and the code as it was. I would have only had minor suggestions to make.

I saw the authors addressed my minor comments on the manuscript and some others on the code/repo. I'm pretty happy with their work so feel free to go ahead and greenlight this for publication.

Thank you again for the invitation and apologies for the delays!

degiacom commented 1 year ago

Thank you for your feedback @JoaoRodrigues!

degiacom commented 1 year ago

@richardjgowers, was wondering if you had any chance to have a look at this?

richardjgowers commented 1 year ago

@degiacom ah sorry, I had been waiting for the other reviewer to fill out a checklist, but reading their comments and the issues we can proceed without this.

richardjgowers commented 1 year ago

@editorialbot check references

richardjgowers commented 1 year ago

@editorialbot generate pdf

editorialbot commented 1 year ago

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

OK DOIs

- 10.1146/annurev-biochem-060614-034142 is OK
- 10.1146/annurev-biochem-013118-111947 is OK
- 10.1038/s41586-021-03819-2 is OK
- 10.1126/science.abj8754 is OK
- 10.1016/j.str.2019.03.018 is OK
- 10.1103/PhysRevX.11.011052 is OK
- 10.48550/arXiv.1912.01703 is OK
- 10.1371/journal.pcbi.1005659 is OK
- 10.1110/ps.062416606 is OK
- 10.1093/bioinformatics/btx789 is OK
- 10.1063/5.0058639 is OK
- 10.1126/science.aaw1147 is OK
- 10.1063/1.5023804 is OK
- 10.1039/d0sc03635h is OK
- 10.1021/acs.jctc.2c00058 is OK
- 10.1021/acs.jctc.5b00255 is OK
- 10.1093/bioinformatics/btab785 is OK
- 10.1002/jcc.21787 is OK
- 10.1038/s41586-020-2649-2 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:

richardjgowers commented 1 year ago

@editorialbot recommend accept

editorialbot commented 1 year ago

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

@editorialbot commands

richardjgowers commented 1 year ago

@editorialbot recommend-accept

editorialbot commented 1 year ago

Paper is not ready for acceptance yet, the archive is missing

richardjgowers commented 1 year 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 PR)
[x] Check the references in the paper for corrections (e.g. capitalization)
[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
[ ] Recommend acceptance with @editorialbot recommend-accept

richardjgowers commented 1 year ago

@degiacom can you create a zenodo (or similar) archive and report this here?

SCMusson commented 1 year ago

@richardjgowers I have created release v2.0.3 and set up Zenodo to give: https://doi.org/10.5281/zenodo.8284102

degiacom commented 1 year ago

@richardjgowers Checked article and Zenodo metadata: title, authors, ORCID, and license are correct.

richardjgowers commented 1 year ago

@editorialbot set 10.5281/zenodo.8284102 as doi

editorialbot commented 1 year ago

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

@editorialbot commands

richardjgowers commented 1 year ago

@editorialbot set v2.0.3 as version

editorialbot commented 1 year ago

Done! version is now v2.0.3

richardjgowers commented 1 year ago

@editorialbot set 10.5281/zenodo.8284102 as archive

editorialbot commented 1 year ago

Done! archive is now 10.5281/zenodo.8284102

openjournals / joss-reviews

[REVIEW]: Molearn: a Python package streamlining the design of generative models of biomolecular dynamics #5523

Status

Reviewer instructions & questions

Checklists

Review checklist for @RMeli

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

Post-Review Checklist for Editor and Authors

Additional Author Tasks After Review is Complete

Editor Tasks Prior to Acceptance