[REVIEW]: easyunfold: A Python package for unfolding electronic band structures

[editorialbot]

Submitting author: @zhubonan (Bonan Zhu)
Repository: https://github.com/SMTG-UCL/easyunfold
Branch with paper.md (empty if default branch): paper
Version: v0.3.5
Editor: @mbarzegary
Reviewers: @srmnitc, @awvwgk
Archive: 10.5281/zenodo.10510884

Status

Status badge code:

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Markdown: [![status](https://joss.theoj.org/papers/e874a8adc53c61f40573b2d707ebf1e4/status.svg)](https://joss.theoj.org/papers/e874a8adc53c61f40573b2d707ebf1e4)

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

@srmnitc & @awvwgk, 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 @mbarzegary 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 @srmnitc

📝 Checklist for @awvwgk

[editorialbot]

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]

Software report:

github.com/AlDanial/cloc v 1.88  T=2.47 s (24.3 files/s, 3369.3 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          18            896           1069           3247
Markdown                        14            376              0           1149
SVG                              3              3              3            818
TeX                              1             20              0            238
YAML                             6             39             11            234
Bourne Shell                     8             14             15             72
TOML                             1              5              0             30
DOS Batch                        1              8              1             26
make                             1              4              7              9
JSON                             6              0              0              8
reStructuredText                 1              2              3              3
-------------------------------------------------------------------------------
SUM:                            60           1367           1109           5834
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

[editorialbot]

Wordcount for paper.md is 1497

[editorialbot]

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

OK DOIs

- 10.1038/s41586-020-2649-2 is OK
- 10.1038/s41592-019-0686-2 is OK
- 10.1109/MCSE.2007.55 is OK
- 10.1103/PhysRevB.85.085201 is OK
- 10.1038/s41467-022-32669-3 is OK
- 10.1021/jacs.2c13336 is OK
- 10.1038/s41566-021-00950-4 is OK
- 10.1038/sdata.2016.18 is OK
- 10.1016/j.commatsci.2017.07.030 is OK
- 10.1002/adts.201900015 is OK
- 10.1021/acs.jpclett.2c02436 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

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

[mbarzegary]

@srmnitc and @awvwgk thanks for your help reviewing this work! This is where the review happens. I kindly ask you to now formally start the review. Follow the instructions above ☝️ to generate a check box list for yourself here to guide you through the process. Let me know if you have any questions.

[mbarzegary]

@zhubonan this is where the review takes place. Please keep an eye out for comments here from the reviewers, as well as any issues opened by them on your software repository. I recommend you aim to respond to these as soon as possible, and you can address them straight away as they come in if you like, to ensure we do not loose track of the reviewers.

[srmnitc]

Review checklist for @srmnitc

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/SMTG-UCL/easyunfold?
• 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 (@zhubonan) 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?

[awvwgk]

Review checklist for @awvwgk

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/SMTG-UCL/easyunfold?
• 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 (@zhubonan) 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?

[mbarzegary]

Hi @awvwgk and @srmnitc
how is your review going?

[srmnitc]

Hi @mbarzegary I have started the review, and opened two issues on the repo already. I will finish the reminder of my review this week.

[srmnitc]

@mbarzegary I have now finished my review. The package is in a really good state, with adequate documentation and example use cases to get a user started. It has already been used in a number of publications, and therefore definitely would make a good addition to JOSS. I only have three points that I need to check, for which I have opened issues in the repository: Automated tests, Community guidelines, and references. Addressing these issues would then complete the review. Thanks to the developers for this nice package!

[awvwgk]

I finished my review as well, easyunfold provides a comprehensive documentation with examples, tutorials, theory, and technical reference. The repository provides all the necessary parts to install the package and to follow the documentation. Besides the already raised issues, I opened a request to evaluate the need for tailored implementation of IO interfaces to Vasp and Castep, especially with a standard package like ASE which can handle and extract band structures already (see SMTG-Bham/easyunfold#41). Otherwise this package is good to publish in JOSS.

[mbarzegary]

Thank you @srmnitc and @awvwgk for the review.

@zhubonan please can you provide an update on the above, in terms of responding to the issues raised? It would be good to respond to issues raised in a timely manor, to avoid delays and to avoid loosing track of reviewers.

[zhubonan]

@mbarzegary Sure, sorry for the delay and @srmnitc and @awvwgk thanks for review this package.
I will address the issues in the next few days.

[zhubonan]

@editorialbot generate pdf

[editorialbot]

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

[zhubonan]

I have addressed the issues from @srmnitc @awvwgk , please let me know if there are further comments. Thanks a lot 😄

[srmnitc]

I have addressed the issues from @srmnitc @awvwgk , please let me know if there are further comments. Thanks a lot 😄

Thanks! I closed the issues now. Some of the newly added citations do not seem to resolve properly. Other than that, I have no further comments, once again, thanks for the nice work!

[mbarzegary]

@editorialbot check references

[editorialbot]

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

OK DOIs

- 10.1038/s41586-020-2649-2 is OK
- 10.1038/s41592-019-0686-2 is OK
- 10.1109/MCSE.2007.55 is OK
- 10.1103/PhysRevB.85.085201 is OK
- 10.1038/s41467-022-32669-3 is OK
- 10.1021/jacs.2c13336 is OK
- 10.1038/s41566-021-00950-4 is OK
- 10.1038/sdata.2016.18 is OK
- 10.1016/j.commatsci.2017.07.030 is OK
- 10.1002/adts.201900015 is OK
- 10.1021/acs.jpclett.2c02436 is OK
- 10.1021/acs.jpcc.3c05204 is OK
- 10.21105/joss.00717 is OK
- 10.1088/2515-7655/aba081 is OK
- 10.1103/PhysRevB.54.11169 is OK
- 10.1016/0927-0256(96)00008-0 is OK
- 10.1524/zkri.220.5.567.65075 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

👋 @openjournals/bcm-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#4870, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

[Kevin-Mattheus-Moerman]

@zhubonan as AEiC I will now help to process this work for acceptance in JOSS. I have checked your repository, this review, the archive link, and the paper. Most seems in order. However, I do have the below points that require your attention.

• Please modify the Zenodo listed version tag to read: v0.3.4, i.e. include the v.
• You use analyse and colour, Brittish English, but also serialization, American English, consider using one consistently.
• This reference

Huber, S. P., Zoupanos, S., Uhrin, M., Talirz, L., Kahle, L., Häuselmann, R., Gresch, D., Müller,
T., Yakutovich, A. V., Andersen, C. W., Ramirez, F. F., Adorf, C. S., Gargiulo, F., Kumbhar,
S., Passaro, E., Johnston, C., Merkys, A., Cepellotti, A., Mounet, N., … Pizzi, G. (2020).
AiiDA 1.0, a scalable computational infrastructure for automated reproducible workflows
and data provenance. arXiv:2003.12476 [Cond-Mat]. http://arxiv.org/abs/2003.12476

Has now been published as a paper. Please use this reference rather than the preprint: https://doi.org/10.1038/s41597-020-00638-4 (unless the pre-print version is intended to be cited e.g. if it is different).

[zhubonan]

@editorialbot set 10.5281/zenodo.10396925 as archive

[editorialbot]

Done! archive is now 10.5281/zenodo.10396925

[zhubonan]

@editorialbot generate pdf

[zhubonan]

@editorialbot set v0.3.5 as version

[editorialbot]

Done! version is now v0.3.5

[zhubonan]

@editorialbot check references

[editorialbot]

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

OK DOIs

- 10.1038/s41586-020-2649-2 is OK
- 10.1038/s41592-019-0686-2 is OK
- 10.1109/MCSE.2007.55 is OK
- 10.1103/PhysRevB.85.085201 is OK
- 10.1038/s41467-022-32669-3 is OK
- 10.1021/jacs.2c13336 is OK
- 10.1038/s41566-021-00950-4 is OK
- 10.1038/s41597-020-00638-4 is OK
- 10.1038/sdata.2016.18 is OK
- 10.1016/j.commatsci.2017.07.030 is OK
- 10.1002/adts.201900015 is OK
- 10.1021/acs.jpclett.2c02436 is OK
- 10.1021/acs.jpcc.3c05204 is OK
- 10.21105/joss.00717 is OK
- 10.1088/2515-7655/aba081 is OK
- 10.1103/PhysRevB.54.11169 is OK
- 10.1016/0927-0256(96)00008-0 is OK
- 10.1524/zkri.220.5.567.65075 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

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

[Kevin-Mattheus-Moerman]

@zhubonan as an author (who happens to also be an editor) please refrain from using the editor commands here.

[Kevin-Mattheus-Moerman]

@editorialbot set 10.5281/zenodo.10510884 as archive

[editorialbot]

Done! archive is now 10.5281/zenodo.10510884

[Kevin-Mattheus-Moerman]

@zhubonan please edit the archive listed license to match your software license.

Note also that I updated the archive link here to use the one that relates to the new version v0.3.5.

[zhubonan]

@zhubonan as an author (who happens to also be an editor) please refrain from using the editor commands here.

Err sorry...

please edit the archive listed license to match your software license.

Sure, I have just updated the archive's licence to MIT to match the code.

[Kevin-Mattheus-Moerman]

@openjournals/dev can we make it that an author cannot run the editor command for the issue they are listed as author for (such that the commands do not work even if the submitting author happens to be a JOSS editor?)?

[Kevin-Mattheus-Moerman]

@zhubonan thanks for making those changes. I think all looks good now, so we can proceed.

[Kevin-Mattheus-Moerman]

@editorialbot accept

[editorialbot]

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

[editorialbot]

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: Zhu
  given-names: Bonan
  orcid: "https://orcid.org/0000-0001-5601-6130"
- family-names: Kavanagh
  given-names: Seán R.
  orcid: "https://orcid.org/0000-0003-4577-9647"
- family-names: Scanlon
  given-names: David
  orcid: "https://orcid.org/0000-0001-9174-8601"
doi: 10.5281/zenodo.10510884
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Zhu
    given-names: Bonan
    orcid: "https://orcid.org/0000-0001-5601-6130"
  - family-names: Kavanagh
    given-names: Seán R.
    orcid: "https://orcid.org/0000-0003-4577-9647"
  - family-names: Scanlon
    given-names: David
    orcid: "https://orcid.org/0000-0001-9174-8601"
  date-published: 2024-01-15
  doi: 10.21105/joss.05974
  issn: 2475-9066
  issue: 93
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 5974
  title: "easyunfold: A Python package for unfolding electronic band
    structures"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.05974"
  volume: 9
title: "easyunfold: A Python package for unfolding electronic band
  structures"

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]

🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

[editorialbot]

🚨🚨🚨 THIS IS NOT A DRILL, YOU HAVE JUST ACCEPTED A PAPER INTO JOSS! 🚨🚨🚨

Here's what you must now do:

0. Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.21105.joss.05974 joss-papers#4910
1. Wait five minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.05974
2. If everything looks good, then close this review issue.
3. Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

[Kevin-Mattheus-Moerman]

@zhubonan congratulations on this JOSS paper!!!

Thanks for editing @mbarzegary !!

And a special thanks to the reviewers: @srmnitc, @awvwgk !!

[editorialbot]

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

If you would like to include a link to your paper from your README use the following code snippets:

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HTML:
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  <img src="https://joss.theoj.org/papers/10.21105/joss.05974/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.05974/status.svg
   :target: https://doi.org/10.21105/joss.05974

This is how it will look in your documentation:

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[arfon]

@openjournals/dev can we make it that an author cannot run the editor command for the issue they are listed as author for (such that the commands do not work even if the submitting author happens to be a JOSS editor?)?

I understand the request, but I think this is best handled with training/guidelines rather than code.