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

editorialbot · 2023-04-12T09:35:05Z

Submitting author: @stke9 (Steven Kench)
Repository: https://github.com/tldr-group/taufactor
Branch with paper.md (empty if default branch): main
Version: v1.1.0
Editor: @zhubonan
Reviewers: @alexsquires, @ma-sadeghi
Archive: 10.5281/zenodo.8177306

Status

Status badge code:

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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

@alexsquires & @ma-sadeghi, your review will be checklist based. Each of you will have a separate checklist that you should update when carrying out your review.
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Checklists

📝 Checklist for @ma-sadeghi

📝 Checklist for @alexsquires

The text was updated successfully, but these errors were encountered:

editorialbot · 2023-04-12T09:35:07Z

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

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editorialbot · 2023-04-12T09:35:10Z

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 · 2023-04-12T09:35:11Z

Wordcount for paper.md is 1173

editorialbot · 2023-04-12T09:36:36Z

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

editorialbot · 2023-04-12T09:37:10Z

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 · 2023-04-12T20:14:17Z

Review checklist for @ma-sadeghi

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

alexsquires · 2023-04-13T05:36:12Z

Review checklist for @alexsquires

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

alexsquires · 2023-04-19T16:30:36Z

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 · 2023-05-04T09:33:35Z

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 · 2023-05-15T10:10:02Z

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 · 2023-05-15T10:22:45Z

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 · 2023-05-16T15:51:25Z

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 · 2023-05-18T09:49:44Z

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

alexsquires · 2023-05-18T09:51:03Z

just this: tldr-group/taufactor#74 (comment)

…

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 <#5358 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AFMK74RRAK3FUDLLABQ5XA3XGXWEHANCNFSM6AAAAAAW3NPGDM> . You are receiving this because you were mentioned.Message ID: ***@***.***>

alexsquires · 2023-05-23T12:19:58Z

Hi @zhubonan,

I'm done! Looks good to me.

ma-sadeghi · 2023-05-23T19:04:05Z

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

zhubonan · 2023-06-06T15:46:53Z

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

zhubonan · 2023-06-20T14:03:21Z

@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 · 2023-06-21T15:32:10Z

@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 · 2023-06-28T16:59:53Z

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

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

zhubonan · 2023-06-28T21:37:34Z

@ma-sadeghi Thanks for doing the review.

stke9 · 2023-06-29T20:21:14Z

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

editorialbot · 2023-08-03T09:02:41Z

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

editorialbot · 2023-08-03T09:04:59Z

⚠️ Error preparing paper acceptance. The generated XML metadata file is invalid.

No declaration for attribute displaystyle of element mfrac
No declaration for attribute displaystyle of element mfrac
No declaration for attribute displaystyle of element mfrac

Kevin-Mattheus-Moerman · 2023-08-03T09:06:20Z

@openjournals/dev can you help here ☝️

xuanxu · 2023-08-03T09:38:19Z

The errors come from the math equations code using displaymode with \dfrac. It looks like that function is not fully supported by our compilation tool. This PR modifies the code for the equations, and running recommend-accept after is merged should work (or at least don't display those same errors).

isaacsquires · 2023-08-03T16:27:23Z

Have merged the PR!

zhubonan · 2023-08-04T00:13:58Z

@editorialbot recommend-accept

editorialbot · 2023-08-04T00:14:00Z

Attempting dry run of processing paper acceptance...

editorialbot · 2023-08-04T00:14:09Z

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

editorialbot · 2023-08-04T00:15:38Z

👋 @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#4453, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

stke9 · 2023-08-04T07:18:35Z

All looks good to us!

Kevin-Mattheus-Moerman · 2023-08-08T11:01:07Z

@stke9 I have checked the paper, this review, your repository, and the archive, and all seems in order. However I did find a minor typo in the paper which you can fix:

Fix calaculated -> calculated

Next I noticed you say Materials characterisation..., the plural "materials", may be intentional, but check if this should be Material characterisation.... Feel free to ignore if this was intentional.

isaacsquires · 2023-08-09T10:11:41Z

The 'calaculated' typo has been fixed by the latest PR. The plural in materials is intentional, 'materials science' and 'materials characterisation' is our preferred syntax.

zhubonan · 2023-08-09T11:43:26Z

@editorialbot generate pdf

editorialbot · 2023-08-09T11:45:15Z

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

Kevin-Mattheus-Moerman · 2023-08-09T12:43:09Z

@editorialbot accept

editorialbot · 2023-08-09T12:43:11Z

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

editorialbot · 2023-08-09T12:45:20Z

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: Kench
  given-names: Steve
  orcid: "https://orcid.org/0000-0002-7263-6724"
- family-names: Squires
  given-names: Isaac
  orcid: "https://orcid.org/0000-0003-1919-061X"
- family-names: Cooper
  given-names: Samuel
  orcid: "https://orcid.org/0000-0003-4055-6903"
contact:
- family-names: Cooper
  given-names: Samuel
  orcid: "https://orcid.org/0000-0003-4055-6903"
doi: 10.5281/zenodo.8177306
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Kench
    given-names: Steve
    orcid: "https://orcid.org/0000-0002-7263-6724"
  - family-names: Squires
    given-names: Isaac
    orcid: "https://orcid.org/0000-0003-1919-061X"
  - family-names: Cooper
    given-names: Samuel
    orcid: "https://orcid.org/0000-0003-4055-6903"
  date-published: 2023-08-09
  doi: 10.21105/joss.05358
  issn: 2475-9066
  issue: 88
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 5358
  title: "TauFactor 2: A GPU accelerated python tool for microstructural
    analysis"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.05358"
  volume: 8
title: "TauFactor 2: A GPU accelerated python tool for microstructural
  analysis"

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 · 2023-08-09T12:45:28Z

🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

editorialbot · 2023-08-09T12:45:29Z

🚨🚨🚨 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 👉 Creating pull request for 10.21105.joss.05358 joss-papers#4461
Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.05358
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

Kevin-Mattheus-Moerman · 2023-08-09T12:50:11Z

@stke9 congratulations on this JOSS publication!

Thanks for editing this one @zhubonan!

And a special thanks to the reviewers @alexsquires and @ma-sadeghi !

editorialbot · 2023-08-09T12:50:13Z

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

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</a>

reStructuredText:
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editorialbot added Makefile Python review TeX Track: 2 (BCM) Biomedical Engineering, Biosciences, Chemistry, and Materials waitlisted Submissions in the JOSS backlog due to reduced service mode. labels Apr 12, 2023

editorialbot assigned zhubonan Apr 12, 2023

editorialbot mentioned this issue Apr 12, 2023

[PRE REVIEW]: TauFactor 2: A GPU accelerated python tool for microstructural analysis #5306

Closed

xuanxu mentioned this issue Aug 3, 2023

Use frac instead of dfrac tldr-group/taufactor#86

Merged

editorialbot added the recommend-accept Papers recommended for acceptance in JOSS. label Aug 4, 2023

isaacsquires mentioned this issue Aug 9, 2023

Typo hotfix tldr-group/taufactor#87

Merged

editorialbot added accepted published Papers published in JOSS labels Aug 9, 2023

Kevin-Mattheus-Moerman closed this as completed Aug 9, 2023

adamltyson mentioned this issue Apr 29, 2024

[REVIEW]: Thresholdmann: A Web tool for interactively creating adaptive thresholds to segment MRI data. #6336

Closed

EFAcar mentioned this issue Sep 23, 2024

[REVIEW]: LocalCop: An R package for local likelihood inference for conditional copulas #6744

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editorialbot mentioned this issue Dec 2, 2024

[PRE REVIEW]: Pore2Chip: All-in-One Python Tool for Soil Microstructure Analysis and Micromodel Design #7546

Open

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

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

Comments

editorialbot commented Apr 12, 2023 • edited Loading

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Review checklist for @ma-sadeghi

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

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Review checklist for @alexsquires

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

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