[REVIEW]: FitSNAP: Atomistic machine learning with LAMMPS

[editorialbot]

Submitting author: !--author-handle-->@rohskopf<!--end-author-handle-- (Andrew Rohskopf) Repository: https://github.com/FitSNAP/FitSNAP Branch with paper.md (empty if default branch): Version: 3.0.1 Editor: !--editor-->@jmschrei<!--end-editor-- Reviewers: @tpurcell90, @bahung Archive: 10.5281/zenodo.7764752

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/daf91b67f1e71277e59f2ba6fc0b694f"><img src="https://joss.theoj.org/papers/daf91b67f1e71277e59f2ba6fc0b694f/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/daf91b67f1e71277e59f2ba6fc0b694f/status.svg)](https://joss.theoj.org/papers/daf91b67f1e71277e59f2ba6fc0b694f)

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

@tpurcell90 & @bahung, 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 @jmschrei 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 @tpurcell90

📝 Checklist for @bahung

[jmschrei]

Yes, a DOI is required. You can just download a zip file of the release (with the paper in it) and put it on Zenodo, though.

[rohskopf]

@editorialbot check references

[editorialbot]

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

OK DOIs

- 10.1016/j.cpc.2018.03.016 is OK
- 10.1021/acs.jctc.8b00770.s001 is OK
- 10.1103/physrevmaterials.6.013804 is OK
- 10.21203/rs.3.rs-244137/v1 is OK
- 10.1016/j.cpc.2016.05.010 is OK
- 10.26434/chemrxiv.12218294 is OK
- 10.1145/3458817.3487400 is OK
- 10.1038/s41524-021-00617-2 is OK
- 10.1088/1741-4326/abe7bd is OK
- 10.1021/acs.jpca.0c02450.s001 is OK
- 10.1021/acs.jpca.9b08723.s001 is OK
- 10.1016/j.cpc.2021.108171 is OK
- 10.2172/1763572 is OK
- 10.1103/physrevlett.104.136403 is OK
- 10.1063/1.4712397 is OK
- 10.1007/s10853-021-06865-3 is OK
- 10.1063/1.5017641 is OK
- 10.1016/j.jcp.2014.12.018 is OK
- 10.1103/physrevb.99.014104 is OK
- 10.1016/j.commatsci.2018.07.043 is OK

MISSING DOIs

- None

INVALID DOIs

- https://doi.org/10.1038/s41467-023-36329-y is INVALID because of 'https://doi.org/' prefix

[rohskopf]

@editorialbot check references

[editorialbot]

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

OK DOIs

- 10.1016/j.cpc.2018.03.016 is OK
- 10.1021/acs.jctc.8b00770.s001 is OK
- 10.1103/physrevmaterials.6.013804 is OK
- 10.21203/rs.3.rs-244137/v1 is OK
- 10.1038/s41467-023-36329-y is OK
- 10.1016/j.cpc.2016.05.010 is OK
- 10.26434/chemrxiv.12218294 is OK
- 10.1145/3458817.3487400 is OK
- 10.1038/s41524-021-00617-2 is OK
- 10.1088/1741-4326/abe7bd is OK
- 10.1021/acs.jpca.0c02450.s001 is OK
- 10.1021/acs.jpca.9b08723.s001 is OK
- 10.1016/j.cpc.2021.108171 is OK
- 10.2172/1763572 is OK
- 10.1103/physrevlett.104.136403 is OK
- 10.1063/1.4712397 is OK
- 10.1007/s10853-021-06865-3 is OK
- 10.1063/1.5017641 is OK
- 10.1016/j.jcp.2014.12.018 is OK
- 10.1103/physrevb.99.014104 is OK
- 10.1016/j.commatsci.2018.07.043 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[rohskopf]

@jmschrei here's the Zenodo info.

DOI: 10.5281/zenodo.7764752

Link: https://zenodo.org/record/7764752

Version number: 3.0.1

[rohskopf]

@editorialbot check references

[editorialbot]

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

OK DOIs

- 10.1016/j.cpc.2018.03.016 is OK
- 10.1021/acs.jctc.8b00770.s001 is OK
- 10.1103/physrevmaterials.6.013804 is OK
- 10.21203/rs.3.rs-244137/v1 is OK
- 10.1038/s41467-023-36329-y is OK
- 10.1016/j.cpc.2016.05.010 is OK
- 10.26434/chemrxiv.12218294 is OK
- 10.1145/3458817.3487400 is OK
- 10.1038/s41524-021-00617-2 is OK
- 10.1088/1741-4326/abe7bd is OK
- 10.1021/acs.jpca.0c02450.s001 is OK
- 10.1021/acs.jpca.9b08723.s001 is OK
- 10.1016/j.cpc.2021.108171 is OK
- 10.2172/1763572 is OK
- 10.1103/physrevlett.104.136403 is OK
- 10.1063/1.4712397 is OK
- 10.1007/s10853-021-06865-3 is OK
- 10.1063/1.5017641 is OK
- 10.1016/j.jcp.2014.12.018 is OK
- 10.1103/physrevb.99.014104 is OK
- 10.1016/j.commatsci.2018.07.043 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[rohskopf]

@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:

[jmschrei]

@editorialbot set https://doi.org/10.5281/zenodo.7764752 as archive

[editorialbot]

Done! Archive is now https://doi.org/10.5281/zenodo.7764752

[jmschrei]

@editorialbot set 10.5281/zenodo.7764752 as archive

[editorialbot]

Done! Archive is now 10.5281/zenodo.7764752

[jmschrei]

@editorialbot set 3.0.1 as version

[editorialbot]

Done! version is now 3.0.1

[jmschrei]

@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

- 10.1016/j.cpc.2018.03.016 is OK
- 10.1021/acs.jctc.8b00770.s001 is OK
- 10.1103/physrevmaterials.6.013804 is OK
- 10.21203/rs.3.rs-244137/v1 is OK
- 10.1038/s41467-023-36329-y is OK
- 10.1016/j.cpc.2016.05.010 is OK
- 10.26434/chemrxiv.12218294 is OK
- 10.1145/3458817.3487400 is OK
- 10.1038/s41524-021-00617-2 is OK
- 10.1088/1741-4326/abe7bd is OK
- 10.1021/acs.jpca.0c02450.s001 is OK
- 10.1021/acs.jpca.9b08723.s001 is OK
- 10.1016/j.cpc.2021.108171 is OK
- 10.2172/1763572 is OK
- 10.1103/physrevlett.104.136403 is OK
- 10.1063/1.4712397 is OK
- 10.1007/s10853-021-06865-3 is OK
- 10.1063/1.5017641 is OK
- 10.1016/j.jcp.2014.12.018 is OK
- 10.1103/physrevb.99.014104 is OK
- 10.1016/j.commatsci.2018.07.043 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

The paper's PDF and metadata files generation produced some warnings that could prevent the final paper from being published. Please fix them before the end of the review process.

citation musaelian2022learning not found

[editorialbot]

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

IDREFS attribute rid references an unknown ID "ref-musaelian2022learning"

[rohskopf]

Sorry I'll fix this

[rohskopf]

Hi @jmschrei sorry about that, should be fixed now.

[rohskopf]

Hi @jmschrei , I fixed that reference. Anything else we need to do?

[jmschrei]

@editorialbot check references

[editorialbot]

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

OK DOIs

- 10.1016/j.cpc.2018.03.016 is OK
- 10.1021/acs.jctc.8b00770.s001 is OK
- 10.1103/physrevmaterials.6.013804 is OK
- 10.21203/rs.3.rs-244137/v1 is OK
- 10.1038/s41467-023-36329-y is OK
- 10.1016/j.cpc.2016.05.010 is OK
- 10.26434/chemrxiv.12218294 is OK
- 10.1145/3458817.3487400 is OK
- 10.1038/s41524-021-00617-2 is OK
- 10.1088/1741-4326/abe7bd is OK
- 10.1021/acs.jpca.0c02450.s001 is OK
- 10.1021/acs.jpca.9b08723.s001 is OK
- 10.1016/j.cpc.2021.108171 is OK
- 10.2172/1763572 is OK
- 10.1103/physrevlett.104.136403 is OK
- 10.1063/1.4712397 is OK
- 10.1007/s10853-021-06865-3 is OK
- 10.1063/1.5017641 is OK
- 10.1016/j.jcp.2014.12.018 is OK
- 10.1103/physrevb.99.014104 is OK
- 10.1016/j.commatsci.2018.07.043 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[jmschrei]

@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

- 10.1016/j.cpc.2018.03.016 is OK
- 10.1021/acs.jctc.8b00770.s001 is OK
- 10.1103/physrevmaterials.6.013804 is OK
- 10.21203/rs.3.rs-244137/v1 is OK
- 10.1038/s41467-023-36329-y is OK
- 10.1016/j.cpc.2016.05.010 is OK
- 10.26434/chemrxiv.12218294 is OK
- 10.1145/3458817.3487400 is OK
- 10.1038/s41524-021-00617-2 is OK
- 10.1088/1741-4326/abe7bd is OK
- 10.1021/acs.jpca.0c02450.s001 is OK
- 10.1021/acs.jpca.9b08723.s001 is OK
- 10.1016/j.cpc.2021.108171 is OK
- 10.2172/1763572 is OK
- 10.1103/physrevlett.104.136403 is OK
- 10.1063/1.4712397 is OK
- 10.1007/s10853-021-06865-3 is OK
- 10.1063/1.5017641 is OK
- 10.1016/j.jcp.2014.12.018 is OK
- 10.1103/physrevb.99.014104 is OK
- 10.1016/j.commatsci.2018.07.043 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

:warning: Error preparing paper acceptance.

[rohskopf]

@jmschrei do you know if this is a problem with the paper? Here's the error message from Actions:

[editorialbot]

: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/4080, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

[rohskopf]

Hi @jmschrei, the final proof looks good on our end.

[rohskopf]

@editorialbot accept

[editorialbot]

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

[rohskopf]

@editorialbot sorry, didn't know 😃

[editorialbot]

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

@editorialbot commands

[jmschrei]

@rohskopf sorry for the confusion -- the next step is for one of our EiC's to take a look and make sure everything is good from an administrative point of view, and then they will accept it.

[arfon]

@editorialbot recommend-accept

[editorialbot]

Attempting dry run of processing paper acceptance...

[arfon]

(debugging the earlier @editorialbot issues)

[editorialbot]

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

OK DOIs

- 10.1016/j.cpc.2018.03.016 is OK
- 10.1021/acs.jctc.8b00770.s001 is OK
- 10.1103/physrevmaterials.6.013804 is OK
- 10.21203/rs.3.rs-244137/v1 is OK
- 10.1038/s41467-023-36329-y is OK
- 10.1016/j.cpc.2016.05.010 is OK
- 10.26434/chemrxiv.12218294 is OK
- 10.1145/3458817.3487400 is OK
- 10.1038/s41524-021-00617-2 is OK
- 10.1088/1741-4326/abe7bd is OK
- 10.1021/acs.jpca.0c02450.s001 is OK
- 10.1021/acs.jpca.9b08723.s001 is OK
- 10.1016/j.cpc.2021.108171 is OK
- 10.2172/1763572 is OK
- 10.1103/physrevlett.104.136403 is OK
- 10.1063/1.4712397 is OK
- 10.1007/s10853-021-06865-3 is OK
- 10.1063/1.5017641 is OK
- 10.1016/j.jcp.2014.12.018 is OK
- 10.1103/physrevb.99.014104 is OK
- 10.1016/j.commatsci.2018.07.043 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

: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/4087, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

[rohskopf]

Hi @arfon and @jmschrei, the proof looks good to us. Anything we need to do?

[Kevin-Mattheus-Moerman]

Post-Review Checklist for Editor and Authors

Additional Author Tasks After Review is Complete

• [x] Double check authors and affiliations (including ORCIDs)
• [x] 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.
• [x] Archive the release on Zenodo/figshare/etc and post the DOI here.
• [x] Make sure that the title and author list (including ORCIDs) in the archive match those in the JOSS paper.
• [x] 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
• [x] Recommend acceptance with @editorialbot recommend-accept

[Kevin-Mattheus-Moerman]

@jmschrei thanks for your help here as editor. I recommend you use this new functionality: @editorialbot create post-review checklist in the future when you are close to ready to recommend acceptance. It will help avoid forgetting minor things e.g. the boxes I left unticked. I think one thing we may need to spell out more clearly is that we also require them to create a tagged release on their repository. I ask for this below too.

[Kevin-Mattheus-Moerman]

@rohskopf I am the AEiC on this track and here to help process the final steps. For the moment can you check the following:

• [x] Only the first author shows with an ORCID id. Can you check if you can add more/all? Note we also recommend that you add the ORCID information on the ZENODO archive.
• [x] Please update the license listed on the ZENODO archive to match you software's open source license.
• [x] Your repository does not currently seem to list a release with the version tag 3.0.1. Can you please create one.

See also checkboxes above :point_up:

[rohskopf]

@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:

[rohskopf]

Thanks @Kevin-Mattheus-Moerman.

✓ Added ORCIDs to the paper and ZENODO (one author does not have an ORCID). ✓ Updated the ZENODO license. ✓ Created a release with proper version tag 3.0.1