[REVIEW]: spgrep: On-the-fly generator of space-group irreducible representations

editorialbot commented 1 year ago

Submitting author: !--author-handle-->@lan496@drvinceknight<!--end-editor-- Reviewers: @ml-evs, @mdavezac, @PKKeerati Archive: 10.5281/zenodo.7946899

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/9a9b64fd8961e7d09f21fc85a6a4fb4e"><img src="https://joss.theoj.org/papers/9a9b64fd8961e7d09f21fc85a6a4fb4e/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/9a9b64fd8961e7d09f21fc85a6a4fb4e/status.svg)](https://joss.theoj.org/papers/9a9b64fd8961e7d09f21fc85a6a4fb4e)

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

@ml-evs & @mdavezac & @PKKeerati, 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 @drvinceknight 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 @ml-evs

📝 Checklist for @PKKeerati

📝 Checklist for @mdavezac

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=0.15 s (459.2 files/s, 59095.6 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          26            691           1059           3555
Markdown                        31            320              0           1501
TeX                              2              0             37            478
Jupyter Notebook                 3              0            801            264
YAML                             5             30             15            216
TOML                             1              4              1             30
SVG                              1              0              0              4
reStructuredText                 1              0              0              2
-------------------------------------------------------------------------------
SUM:                            70           1045           1913           6050
-------------------------------------------------------------------------------

gitinspector failed to run statistical information for the repository

editorialbot commented 1 year ago

Wordcount for paper.md is 740

editorialbot commented 1 year ago

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

OK DOIs

- 10.1007/978-3-642-80021-4 is OK
- 10.1017/CBO9780511755736 is OK
- 10.1107/S0567739473001129 is OK
- 10.1038/s41586-020-2649-2 is OK
- 10.48550/ARXIV.1808.01590 is OK
- 10.48550/ARXIV.2211.15008 is OK
- 10.1142/0751 is OK
- 10.1107/97809553602060000114 is OK
- 10.1016/j.cpc.2021.108226 is OK
- 10.1016/j.cpc.2021.107948 is OK
- 10.1016/j.cpc.2020.107760 is OK
- 10.1016/j.cpc.2021.107993 is OK
- 10.1107/S0108767313007538 is OK
- 10.1107/S1600576717011712 is OK
- 10.1107/S0108767305040286 is OK
- 10.1103/PhysRevB.43.11010 is OK

MISSING DOIs

- None

INVALID DOIs

- doi:10.1524/zkri.2006.221.1.15 is INVALID (failed connection)

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:

ml-evs commented 1 year ago

Review checklist for @ml-evs

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/spglib/spgrep?
[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 (@lan496) 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?

PKKeerati commented 1 year ago

Review checklist for @PKKeerati

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/spglib/spgrep?
[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 (@lan496) 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?

mdavezac commented 1 year ago

Review checklist for @mdavezac

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/spglib/spgrep?
[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 (@lan496) 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?

mdavezac commented 1 year ago

spgrep gives users the ability to compute irreps from a minimal input set consistent with the inputs and outputs common in atomistic simulations. As such, it makes it easier to created simulation that mesh atomistic codes with group-theoretic methods. The paper is well written, the code is well tested and documented. I am happy to recommend it for publication in JOSS.

drvinceknight commented 1 year ago

Thank you @mdavezac and @PKKeerati.

@ml-evs I see that you haven't quite completed your check list, let me know if you no loner plan on doing that :)

ml-evs commented 1 year ago

@drvinceknight I have completed my review and I am happy to recommend spgrep for publication in JOSS, however I just have one minor outstanding issue with running one of the examples: https://github.com/spglib/spgrep/issues/77 I don't see this as blocking and it can be addressed in the final archival of the repository ready for publication.

The package is well-motivated, well-developed and well-documented, great job!

drvinceknight commented 1 year ago

@editorialbot generate pdf

drvinceknight 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

- 10.1007/978-3-642-80021-4 is OK
- 10.1017/CBO9780511755736 is OK
- 10.1107/S0567739473001129 is OK
- 10.1038/s41586-020-2649-2 is OK
- 10.48550/ARXIV.1808.01590 is OK
- 10.48550/ARXIV.2211.15008 is OK
- 10.1142/0751 is OK
- 10.1107/97809553602060000114 is OK
- 10.1016/j.cpc.2021.108226 is OK
- 10.1016/j.cpc.2021.107948 is OK
- 10.1016/j.cpc.2020.107760 is OK
- 10.1016/j.cpc.2021.107993 is OK
- 10.1107/S0108767313007538 is OK
- 10.1107/S1600576717011712 is OK
- 10.1107/S0108767305040286 is OK
- 10.1103/PhysRevB.43.11010 is OK

MISSING DOIs

- None

INVALID DOIs

- doi:10.1524/zkri.2006.221.1.15 is INVALID (failed connection)

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:

drvinceknight commented 1 year ago

doi:10.1524/zkri.2006.221.1.15 is INVALID (failed connection)

Could you take a look at that please?

lan496 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

- 10.1007/978-3-642-80021-4 is OK
- 10.1017/CBO9780511755736 is OK
- 10.1107/S0567739473001129 is OK
- 10.1038/s41586-020-2649-2 is OK
- 10.48550/ARXIV.1808.01590 is OK
- 10.48550/ARXIV.2211.15008 is OK
- 10.1142/0751 is OK
- 10.1107/97809553602060000114 is OK
- 10.1016/j.cpc.2021.108226 is OK
- 10.1016/j.cpc.2021.107948 is OK
- 10.1016/j.cpc.2020.107760 is OK
- 10.1016/j.cpc.2021.107993 is OK
- 10.1107/S0108767313007538 is OK
- 10.1107/S1600576717011712 is OK
- 10.1524/zkri.2006.221.1.15 is OK
- 10.1107/S0108767305040286 is OK
- 10.1103/PhysRevB.43.11010 is OK

MISSING DOIs

- None

INVALID DOIs

- None

lan496 commented 1 year ago

@drvinceknight I have fixed the bibtex entry.

drvinceknight 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:

drvinceknight commented 1 year ago

This all looks good @lan496!

Could you make a tagged release and archive, and report the version number and archive DOI here.

lan496 commented 1 year ago

Thank you for your reply! I have finished:

tagged release: v0.3.4 https://github.com/spglib/spgrep/releases/tag/v0.3.4
archive (zenodo): https://zenodo.org/record/7946899
doi: 10.5281/zenodo.7946899

drvinceknight commented 1 year ago

Thanks @ian496 could you edit the Zenodo archive so that the title matches the paper title : spgrep: On-the-fly generator of space-group irreducible representations

lan496 commented 1 year ago

Sure. I've updated the title. https://zenodo.org/record/7946899

drvinceknight commented 1 year ago

@editorialbot set 10.5281/zenodo.7946899 as archive

editorialbot commented 1 year ago

Done! archive is now 10.5281/zenodo.7946899

drvinceknight commented 1 year ago

@editorialbot set v0.3.4 as version

editorialbot commented 1 year ago

Done! version is now v0.3.4

drvinceknight commented 1 year ago

@editorialbot recommend-accept

editorialbot commented 1 year ago

Attempting dry run of processing paper acceptance...

editorialbot commented 1 year ago

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

OK DOIs

- 10.1007/978-3-642-80021-4 is OK
- 10.1017/CBO9780511755736 is OK
- 10.1107/S0567739473001129 is OK
- 10.1038/s41586-020-2649-2 is OK
- 10.48550/ARXIV.1808.01590 is OK
- 10.48550/ARXIV.2211.15008 is OK
- 10.1142/0751 is OK
- 10.1107/97809553602060000114 is OK
- 10.1016/j.cpc.2021.108226 is OK
- 10.1016/j.cpc.2021.107948 is OK
- 10.1016/j.cpc.2020.107760 is OK
- 10.1016/j.cpc.2021.107993 is OK
- 10.1107/S0108767313007538 is OK
- 10.1107/S1600576717011712 is OK
- 10.1524/zkri.2006.221.1.15 is OK
- 10.1107/S0108767305040286 is OK
- 10.1103/PhysRevB.43.11010 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot commented 1 year ago

:wave: @openjournals/csism-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/4254, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

danielskatz commented 1 year ago

@lan496 - I'm the track editor who will handle the final processing for this submission. I have proofread it, and suggest one minor changes in https://github.com/spglib/spgrep/pull/86 Please merge this (unless you disagree with it), then we can proceed with acceptance and publication.

lan496 commented 1 year ago

@danielskatz Thank you for your proofreading. I have merged the minor change.

danielskatz commented 1 year ago

@editorialbot accept

editorialbot commented 1 year ago

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

editorialbot commented 1 year ago

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: Shinohara given-names: Kohei orcid: "https://orcid.org/0000-0002-5907-2549" - family-names: Togo given-names: Atsushi orcid: "https://orcid.org/0000-0001-8393-9766" - family-names: Tanaka given-names: Isao orcid: "https://orcid.org/0000-0002-4616-118X" contact: - family-names: Shinohara given-names: Kohei orcid: "https://orcid.org/0000-0002-5907-2549" doi: 10.5281/zenodo.7946899 message: If you use this software, please cite our article in the Journal of Open Source Software. preferred-citation: authors: - family-names: Shinohara given-names: Kohei orcid: "https://orcid.org/0000-0002-5907-2549" - family-names: Togo given-names: Atsushi orcid: "https://orcid.org/0000-0001-8393-9766" - family-names: Tanaka given-names: Isao orcid: "https://orcid.org/0000-0002-4616-118X" date-published: 2023-05-23 doi: 10.21105/joss.05269 issn: 2475-9066 issue: 85 journal: Journal of Open Source Software publisher: name: Open Journals start: 5269 title: "spgrep: On-the-fly generator of space-group irreducible representations" type: article url: "https://joss.theoj.org/papers/10.21105/joss.05269" volume: 8 title: "spgrep: On-the-fly generator of space-group irreducible representations" ```

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 commented 1 year ago

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

editorialbot commented 1 year ago

🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

editorialbot commented 1 year ago

🚨🚨🚨 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 :point_right: https://github.com/openjournals/joss-papers/pull/4256
Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.05269
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

danielskatz commented 1 year ago

Congratulations to @lan496 (Kohei Shinohara) and co-authors!!

And thanks to @ml-evs, @mdavezac, and @PKKeerati for reviewing, and to @drvinceknight for editing! We couldn't do this without your voluntary effort

editorialbot commented 1 year ago

: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.05269/status.svg)](https://doi.org/10.21105/joss.05269)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.05269">
  <img src="https://joss.theoj.org/papers/10.21105/joss.05269/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.05269/status.svg
   :target: https://doi.org/10.21105/joss.05269

This is how it will look in your documentation:

We need your help!

The Journal of Open Source Software is a community-run journal and relies upon volunteer effort. If you'd like to support us please consider doing either one (or both) of the the following:

Volunteering to review for us sometime in the future. You can add your name to the reviewer list here: https://reviewers.joss.theoj.org/join
Making a small donation to support our running costs here: https://numfocus.org/donate-to-joss

openjournals / joss-reviews