editorialbot commented 3 months ago

Submitting author: !--author-handle-->@lxvm@rkurchin<!--end-editor-- Reviewers: @mamunm, @Luthaf Archive: 10.5281/zenodo.13915617

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/3be47b03e504321874adc46dbcb05e6c"><img src="https://joss.theoj.org/papers/3be47b03e504321874adc46dbcb05e6c/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/3be47b03e504321874adc46dbcb05e6c/status.svg)](https://joss.theoj.org/papers/3be47b03e504321874adc46dbcb05e6c)

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

@mamunm & @Luthaf, 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 @rkurchin 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 @mamunm

📝 Checklist for @Luthaf

editorialbot commented 3 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 3 months ago

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

OK DOIs

- 10.1063/1.5144261 is OK
- 10.1016/j.cpc.2020.107778 is OK
- 10.21468/SciPostPhys.10.5.117 is OK
- 10.1016/j.cpc.2016.03.014 is OK
- 10.1137/141000671 is OK
- 10.1103/RevModPhys.68.13 is OK
- 10.1088/2399-6528/ab2937 is OK
- 10.4208/cicp.OA-2021-0094 is OK
- 10.21468/SciPostPhys.15.2.062 is OK
- 10.3389/fchem.2019.00106 is OK
- 10.1016/j.cpc.2007.11.016 is OK
- 10.1038/s41524-021-00498-5 is OK
- 10.1038/s41524-020-0312-y is OK

MISSING DOIs

- No DOI given, and none found for title: High-order and adaptive optical conductivity calcu...
- No DOI given, and none found for title: AutoBZCore.Jl: Wannier Interpolation and Intergrat...
- No DOI given, and none found for title: FourierSeriesEvaluators.Jl: Fourier Series Evaluat...
- No DOI given, and none found for title: HChebInterp.Jl: Multi-dimensional h-Adaptive Cheby...
- No DOI given, and none found for title: NonlinearSolve. jl: High-Performance and Robust So...

INVALID DOIs

- None

editorialbot commented 3 months ago

Software report:

github.com/AlDanial/cloc v 1.90  T=0.06 s (1197.1 files/s, 133502.2 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Julia                           53            765           1119           3705
TOML                             4            288              1           1324
Markdown                        14            139              0            866
TeX                              1             17              0            222
YAML                             5              9              9            123
-------------------------------------------------------------------------------
SUM:                            77           1218           1129           6240
-------------------------------------------------------------------------------

Commit count by author:

   476  lxvm
    14  Lorenzo Van Munoz
     7  Lorenzo X. Van Muñoz
     4  phibeck
     1  Jason Kaye
     1  Sophie Beck
     1  jasonkaye

editorialbot commented 3 months ago

Paper file info:

📄 Wordcount for paper.md is 868

✅ The paper includes a Statement of need section

editorialbot commented 3 months ago

License info:

✅ License found: MIT License (Valid open source OSI approved license)

editorialbot commented 3 months ago

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

rkurchin commented 3 months ago

@lxvm note that NonlinearSolve.jl does have a CITATION.cff file that includes a DOI, so be sure to update that.

rkurchin commented 3 months ago

@mamunm, let me know if you have any questions about getting your review started!

mamunm commented 3 months ago

Review checklist for @mamunm

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/lxvm/AutoBZ.jl?
[x] License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
[x] Contribution and authorship: Has the submitting author (@lxvm) 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?

rkurchin commented 2 months ago

Hi @Luthaf, just sending a friendly reminder to get started on this review when possible. Hope you had a great vacation!

Luthaf commented 2 months ago

Review checklist for @Luthaf

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/lxvm/AutoBZ.jl?
[x] License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
[x] Contribution and authorship: Has the submitting author (@lxvm) 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?

rkurchin commented 2 months ago

Hi reviewers @mamunm and @Luthaf, just checking in on progress here!

Luthaf commented 2 months ago

@lxvm regarding

Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?

It would be nice to mention that the code is made for materials science/electronic structure/crystals a bit earlier in the summary. The current version feels like it addresses an audience of people already familiar with Brillouin Zone and material science. This is partially done at the end of the summary but I think it would help to move it closer to the beginning.

rkurchin commented 1 month ago

Pinging again here, @mamunm and @Luthaf, if there are other issues preventing you from completing your checklists, please do make sure that @lxvm knows about them so they can be addressed!

Luthaf commented 1 month ago

My only remaining concern is about the summary as explained above, I'll tick as soon as I see new proofs!

rkurchin commented 1 month ago

@mamunm, I see that you've completed your checklist. Can you confirm that you're happy for this software to be published in its current state?

@lxvm, any thoughts on the suggestions @Luthaf has made regarding the summary?

mamunm commented 1 month ago

@rkurchin I confirm that I am happy for this software to be published in its current state.

lxvm commented 1 month ago

@Luthaf Thank you for your feedback on the summary and I have made a few modifications in order to emphasize the applications to electronic structure of crystals in the first few sentences. Please see the latest proofs for these changes.

Luthaf commented 1 month ago

@editorialbot generate pdf

editorialbot commented 1 month ago

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

Luthaf commented 1 month ago

Thanks @lxvm, this looks good to me!

rkurchin commented 1 month ago

@editorialbot check references

editorialbot commented 1 month ago

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

✅ OK DOIs

- 10.1063/1.5144261 is OK
- 10.1016/j.cpc.2020.107778 is OK
- 10.21468/SciPostPhys.10.5.117 is OK
- 10.1016/j.cpc.2016.03.014 is OK
- 10.1137/141000671 is OK
- 10.1103/RevModPhys.68.13 is OK
- 10.1088/2399-6528/ab2937 is OK
- 10.4208/cicp.OA-2021-0094 is OK
- 10.21468/SciPostPhys.15.2.062 is OK
- 10.3389/fchem.2019.00106 is OK
- 10.1016/j.cpc.2007.11.016 is OK
- 10.1038/s41524-021-00498-5 is OK
- 10.1038/s41524-020-0312-y is OK
- 10.5281/zenodo.10397607 is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: High-order and adaptive optical conductivity calcu...
- No DOI given, and none found for title: AutoBZCore.Jl: Wannier Interpolation and Intergrat...
- No DOI given, and none found for title: FourierSeriesEvaluators.Jl: Fourier Series Evaluat...
- No DOI given, and none found for title: HChebInterp.Jl: Multi-dimensional h-Adaptive Cheby...

❌ MISSING DOIs

- None

❌ INVALID DOIs

- None

rkurchin commented 1 month ago

Post-Review Checklist for Editor and Authors

Additional Author Tasks After Review is Complete

Double check authors and affiliations (including ORCIDs)
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.
Archive the release on Zenodo/figshare/etc and post the DOI here.
Make sure that the title and author list (including ORCIDs) in the archive match those in the JOSS paper.
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 pull request)
[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

rkurchin commented 1 month ago

@lxvm congrats on finishing review, we're almost done! I'll send some editorial comments shortly, and in the meantime you can start working on the other author tasks above, and send me the relevant info (version tag and DOI) once you have them. Almost there!

rkurchin commented 1 month ago

Editorial remarks:

I would move Julia citation to be after the word "Julia" rather than after "package"
18: need a hyphen in "low-temperature" and again on lines 20-21, 36-37, and 42 (compound adjectives)
19: need space before citation and comma after
23: hyphenate "ground-state"
53 "Ref. (parenthetical citation)" looks awkward, maybe just change to "algorithm of Hart et al. (cite)" instead?
55: change "which" to "that", also missing space before citation
figure 1 caption: chemical formula should have subscript 3

Citations:

make sure things are consistently sentence case (some are Title Case)
add DOI for https://arxiv.org/abs/2406.15466

lxvm commented 1 month ago

Thank you @rkurchin for your comments. I have made edits to include all of your suggestions and the last question I have is regarding capitalization following a colon. For example, in the title I have written "AutoBZ.jl: automatic, adaptive ..." whereas in one of the references I wrote "wannier90: A tool ..." in the style of the original publication title. It seems I should capitalize after the colon as follows: "AutoBZ.jl: Automatic, adaptive ...". Would you agree?

Update: I forgot to create a Zenodo archive as requested in the author tasks above and will complete that soon

Edit: I read that the sentence case convention is to capitalize the first word after a colon if the colon is followed by a complete sentence. I have updated the proof accordingly.

lxvm commented 1 month ago

@rkurchin I finished the author checklist, including releasing AutoBZ.jl v0.5.6 with the paper and all code and documentation changes made during the review as well as making a Zenodo archive with DOI 10.5281/zenodo.13915617. Thank you for your support throughout the review!

rkurchin commented 1 month ago

@editorialbot set 0.5.6 as version

editorialbot commented 1 month ago

Done! version is now 0.5.6

rkurchin commented 1 month ago

@lxvm last thing: please change the title of the archive to match the title of the paper. Thanks!

lxvm commented 1 month ago

@rkurchin done!

rkurchin commented 1 month ago

@editorialbot set 10.5281/zenodo.13915617 as archive

editorialbot commented 1 month ago

Done! archive is now 10.5281/zenodo.13915617

rkurchin commented 1 month ago

@editorialbot recommend-accept

editorialbot commented 1 month ago

Attempting dry run of processing paper acceptance...

editorialbot commented 1 month ago

:warning: Error preparing paper acceptance.

lxvm commented 1 month ago

@rkurchin The failure could be due to the fact I merged the joss branch to the main branch and made the tags and release on main. Do you think there is a way to fix this?

rkurchin commented 1 month ago

@editorialbot set main as branch

editorialbot commented 1 month ago

Done! branch is now main

rkurchin commented 1 month ago

@editorialbot recommend-accept

editorialbot commented 1 month ago

Attempting dry run of processing paper acceptance...

editorialbot commented 1 month ago

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

✅ OK DOIs

- 10.1063/1.5144261 is OK
- 10.1016/j.cpc.2020.107778 is OK
- 10.21468/SciPostPhys.10.5.117 is OK
- 10.48550/arXiv.2406.15466 is OK
- 10.1016/j.cpc.2016.03.014 is OK
- 10.1137/141000671 is OK
- 10.1103/RevModPhys.68.13 is OK
- 10.1088/2399-6528/ab2937 is OK
- 10.4208/cicp.OA-2021-0094 is OK
- 10.21468/SciPostPhys.15.2.062 is OK
- 10.3389/fchem.2019.00106 is OK
- 10.1016/j.cpc.2007.11.016 is OK
- 10.1038/s41524-021-00498-5 is OK
- 10.1038/s41524-020-0312-y is OK
- 10.5281/zenodo.10397607 is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: AutoBZCore.jl: Wannier interpolation and integrati...
- No DOI given, and none found for title: FourierSeriesEvaluators.jl: Fourier series evaluat...
- No DOI given, and none found for title: HChebInterp.jl: Multi-dimensional h-adaptive Cheby...

❌ MISSING DOIs

- None

❌ INVALID DOIs

- None

editorialbot commented 1 month 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/5999, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

rkurchin commented 4 weeks ago

@openjournals/bcm-eics just pinging on this, thanks!

Kevin-Mattheus-Moerman commented 3 weeks ago

@editorialbot set v0.5.6 as version

editorialbot commented 3 weeks ago

Done! version is now v0.5.6

Kevin-Mattheus-Moerman commented 3 weeks ago

@lxvm as AEiC for JOSS I will now help to process this submission for acceptance in JOSS. I will now process some final checks:

Checks on repository

[x] Project has OSI approved license
[x] Project features contributing guidelines

Checks on review issue

[x] Review completed
[x] Software license tag listed here matches a tagged release

Checks on archive

[x] Archive listed title and authors matches paper
[x] Archive listed license matches software license
[x] Archive listed version tag matches tagged release (and includes a potential v).

Checks on paper

[x] Checked paper formatting
[x] Check affiliations to make sure country acronyms are not used
[x] Checked reference rendering
[x] Checked if pre-print citations can be updated by published versions
[x] Checked for typos

Kevin-Mattheus-Moerman commented 3 weeks ago

@editorialbot accept

editorialbot commented 3 weeks ago

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

openjournals / joss-reviews

[REVIEW]: AutoBZ.jl: automatic, adaptive Brillouin zone integration of response functions using Wannier interpolation #7080

Status

Reviewer instructions & questions

Checklists

Review checklist for @mamunm

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

Review checklist for @Luthaf

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

Post-Review Checklist for Editor and Authors

Additional Author Tasks After Review is Complete

Editor Tasks Prior to Acceptance

Checks on repository

Checks on review issue

Checks on archive

Checks on paper