editorialbot commented 1 year ago

Submitting author: !--author-handle-->@stke9@zhubonan<!--end-editor-- Reviewers: @alexsquires, @ma-sadeghi Archive: 10.5281/zenodo.8177306

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Markdown: [![status](https://joss.theoj.org/papers/c2922e47173eafba702a8a755f97c3b4/status.svg)](https://joss.theoj.org/papers/c2922e47173eafba702a8a755f97c3b4)

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

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Checklists

📝 Checklist for @ma-sadeghi

📝 Checklist for @alexsquires

editorialbot commented 1 year ago

Hello humans, I'm @editorialbot, a robot that can help you with some common editorial tasks.

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editorialbot commented 1 year ago

Software report:

github.com/AlDanial/cloc v 1.88  T=0.09 s (377.4 files/s, 28324.1 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          10            239            304            988
Markdown                         8            177              0            372
TeX                              1             13              0            199
YAML                             6             18             35             81
make                             2             24              6             75
DOS Batch                        1              8              1             27
INI                              1              4              3             20
reStructuredText                 5              3             17              7
TOML                             1              0              0              6
-------------------------------------------------------------------------------
SUM:                            35            486            366           1775
-------------------------------------------------------------------------------

gitinspector failed to run statistical information for the repository

editorialbot commented 1 year ago

Wordcount for paper.md is 1173

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:

editorialbot commented 1 year ago

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

OK DOIs

- 10.1051/0004-6361/201629272 is OK
- 10.1051/0004-6361/201322068 is OK
- 10.1051/0004-6361/201629272 is OK
- 10.1016/j.softx.2021.100729 is OK
- 10.1016/j.softx.2016.09.002 is OK
- 10.1016/s1386-5056(98)00163-4 is OK
- 10.1111/gwat.12406 is OK
- 10.1149/2.0231803jes is OK
- 10.1002/aenm.202370009 is OK
- 10.1038/s41597-022-01744-1 is OK
- 10.1038/s41524-020-00386-4 is OK
- 10.1016/j.electacta.2017.07.152 is OK
- 10.1016/j.coche.2016.02.006 is OK

MISSING DOIs

- None

INVALID DOIs

- None

ma-sadeghi commented 1 year ago

Review checklist for @ma-sadeghi

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/tldr-group/taufactor?
[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 (@stke9) 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?

alexsquires commented 1 year ago

Review checklist for @alexsquires

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/tldr-group/taufactor?
[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 (@stke9) 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?

alexsquires commented 1 year ago

Hi @stke9 before raising any technical points as issues on the repo itself I just wanted to check an admin point.

I'm certain there is a straightforward explanation for this, I just want to do due diligence!

With regards to the point:

Contribution and authorship: Has the submitting author (@stke9) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

Could you clarify the contributions of the paper authors as going off the repo alone it is not clear.

alexsquires commented 1 year ago

I've been over the code, and my comments are included in:

I'm very happy to recommend taufactor 2 for publication if these can be addressed.

stke9 commented 1 year ago

Hi Alex, thanks so much for all your comments, was so useful to have some fresh eyes on the repo. WRT authorship, we have added the following:

'SK wrote the base, periodic and multiphase solvers with input from IS. IS wrote the electrode solver, metric calculations and documentation, and also performed speed tests for other software packages. The project was supervised by SC, and based on his original MATLAB tool. All authors contributed to the writing and editing of the manuscript.'

I moved lots of the code from a different repo i was working in to our groups gh, which is why i have v few contributions!

Let us know how the speed testing is coming along!

alexsquires commented 1 year ago

I suspected that or similar may have been the case, thanks for clarifying.

Aiming to complete the speed test by the end of tomorrow, and then I will have checked everything off.

alexsquires commented 1 year ago

Just a heads up as I said I would finish this today, I have been waiting for one of our institutions machine with lots of GPUs to come back online after some down time to run my tests. It's back and they are in the queue, hopefully they will run tonight, and then I can check this off!

stke9 commented 1 year ago

No worries, let us know if you come across any issues!

alexsquires commented 1 year ago

just this: https://github.com/tldr-group/taufactor/issues/74#issuecomment-1551112166

On Thu, 18 May 2023 at 10:49, stke9 @.***> wrote:

No worries, let us know if you come across any issues!

— Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/5358#issuecomment-1552811283, or unsubscribe https://github.com/notifications/unsubscribe-auth/AFMK74RRAK3FUDLLABQ5XA3XGXWEHANCNFSM6AAAAAAW3NPGDM . You are receiving this because you were mentioned.Message ID: @.***>

alexsquires commented 1 year ago

Hi @zhubonan,

I'm done! Looks good to me.

ma-sadeghi commented 1 year ago

Sorry for the wait, I'm about to finish my review, I'll update this thread.

zhubonan commented 1 year ago

@ma-sadeghi how is it going? BTW, If you have any update/concerns, please feel free to post them here.

zhubonan commented 1 year ago

@ma-sadeghi Just want to give a gentle reminder as the review is pending. I am looking forward to your comments. Would you be able to finish it in two weeks? If not, it would be great if you can let me know the time frame. Thanks a lot.

ma-sadeghi commented 1 year ago

@zhubonan I really apologize that I dropped the ball on this. I'm swamped at the moment, but that's no excuse.

Anyway, I will finish this in two weeks, I almost want to make a promise to do it sooner, but for the sake of not embarrassing myself again, let's aim for the two week window.

Thank you so much for your patience :)

ma-sadeghi commented 1 year ago

Thank you for your patience :) I've reviewed TauFactor and here's comments:

tldr-group/taufactor#77
tldr-group/taufactor#78
tldr-group/taufactor#79
tldr-group/taufactor#80
tldr-group/taufactor#81
tldr-group/taufactor#82

@stke9 TauFactor is a very useful piece of software. Thanks for making it available to the public!

zhubonan commented 1 year ago

@ma-sadeghi Thanks for doing the review.

stke9 commented 1 year ago

Thanks @ma-sadeghi really useful comments! Most issues resolved I think, just two to look (see your above list of issues). Cheers!

ma-sadeghi commented 1 year ago

@zhubonan All my comments have been addressed except tldr-group/taufactor#77 which is optional and I leave it to @stke9 to decide. Looks good to me! (and thank you all for your patience!)

zhubonan commented 1 year ago

Post-Review Checklist for Editor and Authors

Additional Author Tasks After Review is Complete

[x] Double check authors and affiliations (including ORCIDs)
[x] Make a release of the software with the latest changes from the review and post the version number here. This is the version that will be used in the JOSS paper.
[x] Archive the release on Zenodo/figshare/etc and post the DOI here.
[x] Make sure that the title and author list (including ORCIDs) in the archive match those in the JOSS paper.
[x] Make sure that the license listed for the archive is the same as the software license.

Editor Tasks Prior to Acceptance

[x] Read the text of the paper and offer comments/corrections (as either a list or a PR)
[x] Check the references in the paper for corrections (e.g. capitalization)
[x] Check that the archive title, author list, version tag, and the license are correct
[x] Set archive DOI with @editorialbot set <DOI here> as archive
[x] Set version with @editorialbot set <version here> as version
[x] Double check rendering of paper with @editorialbot generate pdf
[x] Specifically check the references with @editorialbot check references and ask author(s) to update as needed
[x] Recommend acceptance with @editorialbot recommend-accept

zhubonan 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:

zhubonan 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

- 10.1051/0004-6361/201629272 is OK
- 10.1051/0004-6361/201322068 is OK
- 10.1051/0004-6361/201629272 is OK
- 10.1016/j.softx.2021.100729 is OK
- 10.1016/j.softx.2016.09.002 is OK
- 10.1016/s1386-5056(98)00163-4 is OK
- 10.1111/gwat.12406 is OK
- 10.1149/2.0231803jes is OK
- 10.1002/aenm.202370009 is OK
- 10.1038/s41597-022-01744-1 is OK
- 10.1038/s41524-020-00386-4 is OK
- 10.1016/j.electacta.2017.07.152 is OK
- 10.1016/j.coche.2016.02.006 is OK

MISSING DOIs

- None

INVALID DOIs

- None

zhubonan commented 1 year ago

@stke9 I think this submission is almost ready to be accepted. Please make a release with the latest changes from the reviews included and archive this release on Zenodo (or other equivalent) and get back to me with the DOI as well as the new release version number here. Please also make sure the metadata in the archive matches with that in the paper (see "Additional Author Tasks After Review is Complete" above).

zhubonan commented 1 year ago

@editorialbot help

editorialbot commented 1 year ago

Hello @zhubonan, here are the things you can ask me to do:


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isaacsquires commented 1 year ago

Hi all, we have just released with the reviewer additions: v1.1.0

Here is the DOI for the Zenodo archive: 10.5281/zenodo.8177306

That should be everything, please let me know if you need anything else.

zhubonan commented 1 year ago

@editorialbot set 10.5281/zenodo.8177306 as archive

editorialbot commented 1 year ago

That doesn't look like a valid DOI value

zhubonan commented 1 year ago

@editorialbot set 10.5281/zenodo.8177306 as archive

editorialbot commented 1 year ago

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

@editorialbot commands

zhubonan commented 1 year ago

@editorialbot set 10.5281/zenodo.8177306 as archive

editorialbot commented 1 year ago

Done! archive is now 10.5281/zenodo.8177306

zhubonan commented 1 year ago

@editorialbot set v1.1.0 as version

editorialbot commented 1 year ago

Done! version is now v1.1.0

zhubonan commented 1 year ago

@isaacsquires Could you please make sure that the title of the archive matches with that of the paper? I think you should be able to edit the metadata without make a new release (hence no change in the DOI) for 10.5281/zenodo.8177306.

isaacsquires commented 1 year ago

@zhubonan sorry I missed that, just updated now. Let me know if anything else needs changing.

zhubonan commented 1 year ago

@editorialbot recommend-accept

editorialbot commented 1 year ago

Attempting dry run of processing paper acceptance...

editorialbot commented 1 year ago

Couldn't check the bibtex because branch name is incorrect: Joss-paper-revisions

editorialbot commented 1 year ago

:warning: Error preparing paper acceptance.

zhubonan commented 1 year ago

@editorialbot set main as branch

editorialbot commented 1 year ago

Done! branch is now main

zhubonan commented 1 year ago

@editorialbot recommend-accept

editorialbot commented 1 year ago

Attempting dry run of processing paper acceptance...

openjournals / joss-reviews

[REVIEW]: TauFactor 2: A GPU accelerated python tool for microstructural analysis #5358

Status

Reviewer instructions & questions

Checklists

Review checklist for @ma-sadeghi

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

Review checklist for @alexsquires

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