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

editorialbot commented 10 months ago

Submitting author: !--author-handle-->@zhubonan@mbarzegary<!--end-editor-- 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 commented 10 months 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 10 months ago

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 commented 10 months ago

Wordcount for paper.md is 1497

editorialbot commented 10 months ago

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 commented 10 months ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

mbarzegary commented 10 months ago

@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 commented 10 months ago

@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 commented 10 months ago

Review checklist for @srmnitc

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

awvwgk commented 10 months ago

Review checklist for @awvwgk

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

mbarzegary commented 10 months ago

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

srmnitc commented 10 months ago

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 commented 9 months ago

@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 commented 9 months ago

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 https://github.com/SMTG-Bham/easyunfold/issues/41). Otherwise this package is good to publish in JOSS.

mbarzegary commented 9 months ago

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 commented 9 months ago

@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 commented 9 months ago

@editorialbot generate pdf

editorialbot commented 9 months ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

zhubonan commented 9 months ago

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

srmnitc commented 9 months ago

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 commented 9 months ago

@editorialbot check references

editorialbot commented 9 months ago

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

MISSING DOIs

- None

INVALID DOIs

- https://doi.org/10.1016/0927-0256(96)00008-0 is INVALID because of 'https://doi.org/' prefix
- doi:10.1524/zkri.220.5.567.65075 is INVALID (failed connection)

mbarzegary commented 9 months ago

thank you @srmnitc and @awvwgk for finalizing your review.

@zhubonan can you please resolve the references problem? 👆

zhubonan commented 9 months ago

@editorialbot check references

editorialbot commented 9 months ago

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

zhubonan commented 9 months ago

@editorialbot generate pdf

editorialbot commented 9 months ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

zhubonan commented 9 months ago

@editorialbot generate pdf

editorialbot commented 9 months ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

mbarzegary commented 9 months ago

@zhubonan please merge my PR with some minor edits.

After that, could you:

[x] Make a tagged release of your software, and list the version tag of the archived version here.
[x] Archive the reviewed software in Zenodo or a similar service (e.g., figshare, an institutional repository)
[x] Check the archival deposit (e.g., in Zenodo) has the correct metadata. This includes the title (should match the paper title) and author list (make sure the list is correct and people who only made a small fix are not on it). You may also add the authors' ORCID.
[x] Please list the DOI of the archived version here.

I can then move forward with recommending acceptance of the submission.

zhubonan commented 9 months ago

[x] Make a tagged release of your software, and list the version tag of the archived version here.

Sure, I have made a release, the release version tag is v0.3.4 and the version number of the actual code is 0.3.4.

[x] Archive the reviewed software in Zenodo or a similar service (e.g., figshare, an institutional repository)

[x] Check the archival deposit (e.g., in Zenodo) has the correct metadata. This includes the title (should match the paper title) and author list (make sure the list is correct and people who only made a small fix are not on it). You may also add the authors' ORCID.

[x] Please list the DOI of the archived version here.

The archived DOI is 10.5281/zenodo.10396925

mbarzegary commented 8 months ago

@editorialbot generate pdf

editorialbot commented 8 months ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

mbarzegary commented 8 months ago

@editorialbot set 10.5281/zenodo.10396925 as archive

editorialbot commented 8 months ago

Done! archive is now 10.5281/zenodo.10396925

mbarzegary commented 8 months ago

@zhubonan I just noticed a minor spelling error in the title of the archive (electronic1 instead of electronic). Can you please fix it and make a new archive?

zhubonan commented 8 months ago

Sure, I have updated the title. The DOI remains the same.

mbarzegary commented 8 months ago

@editorialbot set v0.3.4 as version

editorialbot commented 8 months ago

Done! version is now v0.3.4

mbarzegary commented 8 months ago

@editorialbot check references

editorialbot commented 8 months ago

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

mbarzegary commented 8 months ago

@editorialbot recommend-accept

editorialbot commented 8 months ago

Attempting dry run of processing paper acceptance...

editorialbot commented 8 months ago

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 commented 8 months ago

: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/4870, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

Kevin-Mattheus-Moerman commented 8 months ago

@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.

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

[x] 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 commented 8 months ago

@editorialbot set 10.5281/zenodo.10396925 as archive

editorialbot commented 8 months ago

Done! archive is now 10.5281/zenodo.10396925

zhubonan commented 8 months ago

@editorialbot generate pdf

zhubonan commented 8 months ago

@editorialbot set v0.3.5 as version

editorialbot commented 8 months ago

Done! version is now v0.3.5

openjournals / joss-reviews