[REVIEW]: smol: A Python package for cluster expansions and beyond #4504

editorialbot · 2022-06-25T16:55:12Z

Submitting author: @lbluque (Luis Barroso-Luque)
Repository: https://github.com/CederGroupHub/smol
Branch with paper.md (empty if default branch): paper
Version: v0.0.1
Editor: @jarvist
Reviewers: @TomTranter, @zhubonan
Archive: 10.5281/zenodo.7115050

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/e96a568ca53ee9d14548d7b8bed69b25"><img src="https://joss.theoj.org/papers/e96a568ca53ee9d14548d7b8bed69b25/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/e96a568ca53ee9d14548d7b8bed69b25/status.svg)](https://joss.theoj.org/papers/e96a568ca53ee9d14548d7b8bed69b25)

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

@kitmccoll & @TomTranter, 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 @jarvist 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 @TomTranter

📝 Checklist for @zhubonan

The text was updated successfully, but these errors were encountered:

editorialbot · 2022-06-25T16:55:13Z

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:

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

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editorialbot · 2022-06-25T16:55:24Z

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

OK DOIs

- 10.1002/adts.201900015 is OK
- 10.1103/PhysRevB.104.224203 is OK
- 10.1088/1361-648X/ab1bbc is OK
- 10.1557/jmr.2018.323 is OK
- 10.1038/s41578-019-0121-4 is OK
- 10.1063/1.4812323 is OK
- 10.1002/cpe.3505 is OK
- 10.1103/PhysRevB.46.12587 is OK
- 10.1038/s41563-020-00816-0 is OK
- 10.1016/j.commatsci.2017.07.030 is OK
- 10.1016/j.commatsci.2012.10.028 is OK
- 10.1016/0378-4371(84)90096-7 is OK
- 10.1016/S0364-5916(02)80006-2 is OK
- 10.1016/j.calphad.2008.12.005 is OK
- 10.1146/annurev-matsci-070317-124443 is OK
- 10.1007/s11669-015-0427-x is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot · 2022-06-25T16:56:12Z

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

arfon · 2022-06-25T16:56:30Z

@kitmccoll, @TomTranter –This is the review thread for the paper. All of our communications will happen here from now on.

Please read the "Reviewer instructions & questions" in the first comment above. Please create your checklist typing:

@editorialbot generate my checklist

As you go over the submission, please check any items that you feel have been satisfied. There are also links to the JOSS reviewer guidelines.

The JOSS review is different from most other journals. Our goal is to work with the authors to help them meet our criteria instead of merely passing judgment on the submission. As such, the reviewers are encouraged to submit issues and pull requests on the software repository. When doing so, please mention https://github.com/openjournals/joss-reviews/issues/4504 so that a link is created to this thread (and @jarvist can keep an eye on what is happening). Please also feel free to comment and ask questions on this thread. In my experience, it is better to post comments/questions/suggestions as you come across them instead of waiting until you've reviewed the entire package.

We aim for the review process to be completed within about 4-6 weeks but please make a start well ahead of this as JOSS reviews are by their nature iterative and any early feedback you may be able to provide to the author will be very helpful in meeting this schedule.

TomTranter · 2022-06-25T17:09:04Z

Review checklist for @TomTranter

Conflict of interest

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

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

General checks

Repository: Is the source code for this software available at the https://github.com/CederGroupHub/smol?
License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
Contribution and authorship: Has the submitting author (@lbluque) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines

Functionality

Installation: Does installation proceed as outlined in the documentation?
Functionality: Have the functional claims of the software been confirmed?
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

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

Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
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?
State of the field: Do the authors describe how this software compares to other commonly-used packages?
Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
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?

TomTranter · 2022-07-22T06:27:02Z

@arfon @jarvist I have completed my review

lbluque · 2022-07-22T17:13:05Z

@editorialbot generate pdf

editorialbot · 2022-07-22T17:14:30Z

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

lbluque · 2022-07-25T18:54:05Z

👋 @kitmccoll just want to check in on your timing on reviewing this. Thanks in advance

lbluque · 2022-08-01T20:38:05Z

wave @kitmccoll just want to check in on your timing on reviewing this. Thanks in advance

Hi @jarvist, it looks like @kitmccoll has not been very active on github. If you have another means to contact him, can you send him a ping regarding this review please? I worry this has slipped his mind by now.

lbluque · 2022-08-19T18:45:28Z

wave @kitmccoll just want to check in on your timing on reviewing this. Thanks in advance

Hi @jarvist, it looks like @kitmccoll has not been very active on github. If you have another means to contact him, can you send him a ping regarding this review please? I worry this has slipped his mind by now.

@jarvist @kitmccoll just checking in on this again. It would be very much appreciated to get a response with an update.

jarvist · 2022-08-22T09:39:35Z

Hi @jarvist, it looks like @kitmccoll has not been very active on github. If you have another means to contact him, can you send him a ping regarding this review please? I worry this has slipped his mind by now.

I've emailed them using the original thread that I used to invite the review. It's a good point that they might not have noticed the prompts if they are not active GitHub users.

lbluque · 2022-08-22T19:56:39Z

Thanks a lot @jarvist! I hope we can get an answer relatively soon.

I would find it very helpful to have more transparent communication. It has been quite a frustrating experience to have month-long periods of silence without any statements on timing.

lbluque · 2022-09-05T23:27:59Z

Hi @jarvist checking in again...

Have you heard from @kitmccoll?

If you haven't heard anything, I'd appreciate it if we can find someone else to review.

From the pre-review it seemed MarDiehl was quite interested originally (hopefully that's still the case). #4356 (comment)

If not here's the list I had proposed with a few more potential options: #4356 (comment)

Thanks!

TomTranter · 2022-09-09T07:10:12Z

Hi @arfon, @jarvist, @lbluque I have been following the updates on this post (or lack thereof) and have to say I'm not very impressed by the quality of service being provided by JOSS here to a fellow researcher

lbluque · 2022-09-09T20:38:05Z

Hi @arfon, @jarvist, @lbluque I have been following the updates on this post (or lack thereof) and have to say I'm not very impressed by the quality of service being provided by JOSS here to a fellow researcher

Thanks for voicing your view on this @TomTranter. Indeed, as some of my previous comments on this and the pre-review issue suggest, my experience is consistent with your comment.

jarvist · 2022-09-12T12:41:37Z

Dear @lbluque and @TomTranter my apologies, I certainly could have been more communicative.
I have been attempting to contact Kit weekly, but with no response this side of summer.

I will extend the invitation to review.
But also, @kitmccoll, you are very welcome to contribute now if you've been away over summer.

jarvist · 2022-09-12T20:17:19Z

Some additional reviewers invited by email.

jarvist · 2022-09-13T11:43:54Z

@editorialbot add @zhubonan as reviewer

Thank you Bonan for agreeing to be an additional reviewer on an expedited timeframe of two weeks (27th September).

Bonan, there's some discussion on CederGroupHub/smol#227 from Tom and Luis which may help orientate you to the areas of discussion / focus.

editorialbot · 2022-09-13T11:43:58Z

@zhubonan added to the reviewers list!

jarvist · 2022-09-13T11:44:54Z

@editorialbot generate pdf

I believe you've made some edits since 25 Jun @lbluque ? This is a fresh PDF for you @zhubonan.

editorialbot · 2022-09-13T11:46:39Z

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

zhubonan · 2022-09-13T19:53:16Z

Review checklist for @zhubonan

Conflict of interest

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

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

General checks

Repository: Is the source code for this software available at the https://github.com/CederGroupHub/smol?
License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
Contribution and authorship: Has the submitting author (@lbluque) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
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.
Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
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

Installation: Does installation proceed as outlined in the documentation?
Functionality: Have the functional claims of the software been confirmed?
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

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

Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
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?
State of the field: Do the authors describe how this software compares to other commonly-used packages?
Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
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?

lbluque · 2022-09-14T19:56:12Z

Dear @lbluque and @TomTranter my apologies, I certainly could have been more communicative. I have been attempting to contact Kit weekly, but with no response this side of summer.

I will extend the invitation to review. But also, @kitmccoll, you are very welcome to contribute now if you've been away over summer.

Thank you @jarvist I can certainly understand getting a response from reviewers may be tricky or overly busy schedules can make them fall off the map entirely. As I stated before, it would have just been more helpful to get an update rather than getting no response month-long stretches of time.

In any case, thank you for taking the time to find someone else to review.

lbluque · 2022-09-14T19:57:49Z

@editorialbot generate pdf

I believe you've made some edits since 25 Jun @lbluque ? This is a fresh PDF for you @zhubonan.

The most recent changes I've made were 12 days ago.

editorialbot · 2022-09-28T09:27:39Z

Done! Archive is now 10.5281/zenodo.7115050

jarvist · 2022-09-28T09:27:58Z

@editorialbot check repository

jarvist · 2022-09-28T09:28:59Z

@editorialbot generate pdf

editorialbot · 2022-09-28T09:30:23Z

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

jarvist · 2022-09-28T09:31:42Z

OK, looks like just some of the auto checks are not working?

jarvist · 2022-09-28T09:33:54Z

@editorialbot recommend-accept

Everything is looking good manually for me. Thank you @TomTranter and @zhubonan for your reviews, @zhubonan for being so responsive and considerate of the time the paper has been in review, and @lbluque for your patience. 🎉

editorialbot · 2022-09-28T09:33:55Z

Attempting dry run of processing paper acceptance...

editorialbot · 2022-09-28T09:35:47Z

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

OK DOIs

- 10.1002/adts.201900015 is OK
- 10.1103/PhysRevB.104.224203 is OK
- 10.1088/1361-648X/ab1bbc is OK
- 10.1557/jmr.2018.323 is OK
- 10.1038/s41578-019-0121-4 is OK
- 10.1063/1.4812323 is OK
- 10.1002/cpe.3505 is OK
- 10.1103/PhysRevB.46.12587 is OK
- 10.1038/s41563-020-00816-0 is OK
- 10.1016/j.commatsci.2017.07.030 is OK
- 10.1016/j.commatsci.2012.10.028 is OK
- 10.1016/0378-4371(84)90096-7 is OK
- 10.1016/S0364-5916(02)80006-2 is OK
- 10.1016/j.calphad.2008.12.005 is OK
- 10.1146/annurev-matsci-070317-124443 is OK
- 10.1007/s11669-015-0427-x is OK
- 10.1038/s41524-022-00818-3 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot · 2022-09-28T09:36:13Z

👋 @openjournals/joss-eics, this paper is ready to be accepted and published.

Check final proof 👉📄 Download article

If the paper PDF and the deposit XML files look good in openjournals/joss-papers#3558, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

jarvist · 2022-09-28T09:37:38Z

Congratulations @lbluque ! This should be the end of my role as Editor. One of the Editor in Chief team should be along to do a final executive round of checks, and hopefully take the paper forwards to publication.

lbluque · 2022-09-28T17:34:30Z

Thank you @jarvist

Thanks a lot, @TomTranter for reviewing and for your helpful suggestions. Thanks, @zhubonan for the prompt review as well!

lbluque · 2022-09-28T17:58:29Z

Just made a (hopefully last) round of edits to the manuscript.

lbluque · 2022-09-28T17:58:41Z

@editorialbot generate pdf

editorialbot · 2022-09-28T18:00:11Z

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

arfon · 2022-09-29T16:06:01Z

@editorialbot recommend-accept

editorialbot · 2022-09-29T16:06:02Z

Attempting dry run of processing paper acceptance...

editorialbot · 2022-09-29T16:08:01Z

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

OK DOIs

- 10.1002/adts.201900015 is OK
- 10.1103/PhysRevB.104.224203 is OK
- 10.1088/1361-648X/ab1bbc is OK
- 10.1557/jmr.2018.323 is OK
- 10.1038/s41578-019-0121-4 is OK
- 10.1063/1.4812323 is OK
- 10.1002/cpe.3505 is OK
- 10.1103/PhysRevB.46.12587 is OK
- 10.1038/s41563-020-00816-0 is OK
- 10.1016/j.commatsci.2017.07.030 is OK
- 10.1016/j.commatsci.2012.10.028 is OK
- 10.1016/0378-4371(84)90096-7 is OK
- 10.1016/S0364-5916(02)80006-2 is OK
- 10.1016/j.calphad.2008.12.005 is OK
- 10.1146/annurev-matsci-070317-124443 is OK
- 10.1007/s11669-015-0427-x is OK
- 10.1038/s41524-022-00818-3 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot · 2022-09-29T16:08:23Z

👋 @openjournals/joss-eics, this paper is ready to be accepted and published.

Check final proof 👉📄 Download article

If the paper PDF and the deposit XML files look good in openjournals/joss-papers#3564, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

lbluque · 2022-09-29T17:24:05Z

Thanks @arfon ! The proof looks good on my end.

arfon · 2022-09-29T19:21:50Z

@editorialbot accept

editorialbot · 2022-09-29T19:21:51Z

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

editorialbot · 2022-09-29T19:24:45Z

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

editorialbot · 2022-09-29T19:24:46Z

🚨🚨🚨 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 👉 Creating pull request for 10.21105.joss.04504 joss-papers#3567
Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.04504
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

arfon · 2022-09-29T19:33:18Z

@TomTranter, @zhubonan – many thanks for your reviews here and to @jarvist for editing this submission! JOSS relies upon the volunteer effort of people like you and we simply wouldn't be able to do this without you ✨

@lbluque – your paper is now accepted and published in JOSS ⚡🚀💥

editorialbot · 2022-09-29T19:33:19Z

🎉🎉🎉 Congratulations on your paper acceptance! 🎉🎉🎉

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TomTranter · 2022-10-11T07:33:56Z

Congratulations and happy to be part of the process. Nice work on the code

…

On Thu, 29 Sep 2022 at 18:24, Luis Barroso-Luque ***@***.***> wrote: Thanks @arfon <https://github.com/arfon> ! The proof looks good on my end. — Reply to this email directly, view it on GitHub <#4504 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABV5YRK7JXUQNUEIDDFFXETWAXGEDANCNFSM5Z2RMBHQ> . You are receiving this because you were mentioned.Message ID: ***@***.***>

editorialbot added the review label Jun 25, 2022

editorialbot assigned jarvist Jun 25, 2022

editorialbot mentioned this issue Jun 25, 2022

[PRE REVIEW]: smol: A Python package for cluster expansions and beyond #4356

Closed

TomTranter mentioned this issue Jul 14, 2022

JOSS review CederGroupHub/smol#227

Closed

editorialbot added the Track: 2 (BCM) Biomedical Engineering, Biosciences, Chemistry, and Materials label Sep 10, 2022

editorialbot added the recommend-accept Papers recommended for acceptance in JOSS. label Sep 28, 2022

editorialbot added accepted published Papers published in JOSS labels Sep 29, 2022

arfon closed this as completed Sep 29, 2022

[REVIEW]: smol: A Python package for cluster expansions and beyond #4504

[REVIEW]: smol: A Python package for cluster expansions and beyond #4504

Comments

editorialbot commented Jun 25, 2022 • edited by arfon Loading

Status

Reviewer instructions & questions

Checklists

editorialbot commented Jun 25, 2022

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editorialbot commented Jun 25, 2022

arfon commented Jun 25, 2022 • edited Loading

TomTranter commented Jun 25, 2022 • edited Loading

Review checklist for @TomTranter

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

TomTranter commented Jul 22, 2022

lbluque commented Jul 22, 2022

editorialbot commented Jul 22, 2022

lbluque commented Jul 25, 2022

lbluque commented Aug 1, 2022

lbluque commented Aug 19, 2022

jarvist commented Aug 22, 2022

lbluque commented Aug 22, 2022

lbluque commented Sep 5, 2022

TomTranter commented Sep 9, 2022

lbluque commented Sep 9, 2022

jarvist commented Sep 12, 2022

jarvist commented Sep 12, 2022

jarvist commented Sep 13, 2022

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jarvist commented Sep 13, 2022

editorialbot commented Sep 13, 2022

zhubonan commented Sep 13, 2022 • edited Loading

Review checklist for @zhubonan

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

lbluque commented Sep 14, 2022

lbluque commented Sep 14, 2022

editorialbot commented Sep 28, 2022

jarvist commented Sep 28, 2022

jarvist commented Sep 28, 2022

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jarvist commented Sep 28, 2022

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jarvist commented Sep 28, 2022

lbluque commented Sep 28, 2022

lbluque commented Sep 28, 2022

lbluque commented Sep 28, 2022

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arfon commented Sep 29, 2022

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lbluque commented Sep 29, 2022

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TomTranter commented Oct 11, 2022 via email

editorialbot commented Jun 25, 2022 •

edited by arfon

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edited

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zhubonan commented Sep 13, 2022 •

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